From c8007d2f55c299257e92c305943231f6541b6182 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 11 Dec 2025 02:38:15 +0000 Subject: [PATCH 1/5] Initial plan From be529c8088989e80c3a30b6daacf015bc197d169 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 11 Dec 2025 02:42:36 +0000 Subject: [PATCH 2/5] Fix vocabulary generation script to use Python instead of vocab command Co-authored-by: rdhyee <153266+rdhyee@users.noreply.github.com> --- .../biology_sampledfeature_extension.md | 812 ++++++++ ...rthenv_material_extension_mineral_group.md | 193 ++ ...rthenv_material_extension_rock_sediment.md | 1836 +++++++++++++++++ .../earthenv_materialsampleobject_type.md | 1222 +++++++++++ .../earthenv_sampled_feature_role.md | 209 ++ .../opencontext_material_extension.md | 824 ++++++++ .../opencontext_materialsampleobjecttype.md | 203 ++ .../material_sample_object_type.qmd | 375 ++++ .../generated/vocabularies/material_type.qmd | 377 ++++ .../vocabularies/sampled_feature_type.qmd | 310 +++ scripts/generate_vocab_docs.sh | 16 +- 11 files changed, 6369 insertions(+), 8 deletions(-) create mode 100644 models/generated/extensions/biology_sampledfeature_extension.md create mode 100644 models/generated/extensions/earthenv_material_extension_mineral_group.md create mode 100644 models/generated/extensions/earthenv_material_extension_rock_sediment.md create mode 100644 models/generated/extensions/earthenv_materialsampleobject_type.md create mode 100644 models/generated/extensions/earthenv_sampled_feature_role.md create mode 100644 models/generated/extensions/opencontext_material_extension.md create mode 100644 models/generated/extensions/opencontext_materialsampleobjecttype.md create mode 100644 models/generated/vocabularies/material_sample_object_type.qmd create mode 100644 models/generated/vocabularies/material_type.qmd create mode 100644 models/generated/vocabularies/sampled_feature_type.qmd diff --git a/models/generated/extensions/biology_sampledfeature_extension.md b/models/generated/extensions/biology_sampledfeature_extension.md new file mode 100644 index 0000000..be954fc --- /dev/null +++ b/models/generated/extensions/biology_sampledfeature_extension.md @@ -0,0 +1,812 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "Biology Extension: Basic taxon classes for biological entity" +date: "2025-12-11T02:41:37.197064+00:00" +subtitle: | + This is a vocabulary to categorize sampled organisms (whole or part) according to taxonomic classes. Classes are based largely on taxonomy found in Wikipedia, particularly Whittaker's five kingdom system (1969) (https://en.wikipedia.org/wiki/Kingdom_(biology), https://doi.org/10.1126%2Fscience.163.3863.150). The intended use is in iSamples cross domain categorization of material samples, recognizing that there are multiple view for taxonomy and cladistics for the tree of life. This is a high level view intended for cross domain purposes, not expert analysis. Other extension vocabularies should be used for other taxonomic schemes +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_biology/main/vocabulary/biology_sampledfeature_extension.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_biology/main/vocabulary/biology_sampledfeature_extension.ttl) + + +Namespace: +[`https://w3id.org/isample/biology/biosampledfeature/biologicentityvocabulary`](https://w3id.org/isample/biology/biosampledfeature/biologicentityvocabulary) + +**History** + +* 2024-01-19 SMR add cross reference to GBIF taxonomy backbone where mapping was apparent. +* 2024-04-12 SMR. Import of GEOME records show that many samples are classified as Kingdom Chromista, but this is missing from this vocabulary extension (https://github.com/isamplesorg/vocabularies/issues/17). Hierarchy and classes reviewed; deprecate Protista and make it an alternate name in Eukaryotic microorganism class and update definition; add Chromista; update scope notes for Eukaryote. Harmonize better with GBIF tree of life: Make Mycetozoa subclass of Protozoa, not subclass of Amoebozoa, add Other Protozoa class for logical completeness. increment version to 1.1; these are not breaking changes, but addition of new class and hierarchy adjustments in protozoa are more than incremental. +* 2024-09-13 SMR remove version number from URI +* Based on draft DiSSCo specimen & collection classification, table 2, https://docs.google.com/document/d/19OPyOm9VF2qfI3M6RmJPvRfo8JlZ3tt0II05aGCyBHQ/ , with added classes to attempt a logical hierarchy. + +**Concepts** + +- [Biological entity](#biologicalentity) + - [Eukaryote](#eukaryote) + - [Algae](#algae) + - [Animalia](#animalia) + - [Arthropod](#arthropod) + - [Arachnid](#arachnid) + - [Crustaceans](#crustacea) + - [Insect](#hexapoda) + - [Myriapod](#myriapod) + - [Other arthropod ](#otherarthropod) + - [Mollusca](#mollusca) + - [Other invertebrate ](#otherinvertebrate) + - [Porifera](#porifera) + - [Vertebrate ](#vertebrate) + - [Amphibian](#amphibian) + - [Bird](#bird) + - [Fish](#fish) + - [Mammal](#mammal) + - [Reptile](#reptile) + - [Chromista](#chromista) + - [Eukaryotic microorganism](#eukaryoticmicroorganism) + - [Fungi](#fungi) + - [Macrofungi](#macrofungi) + - [Microfungi](#microfungi) + - [Plantae](#plantae) + - [Non-vascular plant](#nonvascularplant) + - [Other plant](#otherplant) + - [Vascular seed plant](#vascularseedplant) + - [Vascular spore plant](#vascularsportplant) + - [Protozoa](#protozoa) + - [Amoebozoa](#amoebozoa) + - [Mycetozoa](#mycetozoa) + - [Other Protozoa](#otherprotozoa) + - [Lichen](#lichen) + - [Plasmid](#plasmid) + - [Prokaryote](#prokaryote) + - [Archaea](#archaea) + - [Bacteria](#bacteria) + - [Virus](#virus) + - [Other Virus](#othervirus) + - [Phage](#phage) + +## Biological entity + +[]{#biologicalentity} + +Concept: [`biologicalentity`](https://w3id.org/isample/vocabulary/sampledfeature/biologicalentity) + +Sampled feature is an organism. Use for samples that represent some +species of organism as the proximate sampled feature for which the +focus is not the environment that the organism inhabits. + +### Eukaryote + +[]{#eukaryote} + +Concept: [`eukaryote`](https://w3id.org/isample/biology/biosampledfeature/eukaryote) + +Child of: + [`biologicalentity`](#biologicalentity) + +Organism whose cells have a nucleus. Includes all animals, plants, +fungi, and many unicellular organisms +(https://en.wikipedia.org/wiki/Eukaryote). Eucaryote membranes are +flexible, and contain cholesterol. The membrane, nucleus, and +structures are supported by cross-connecting protein filaments. Cells +are ~10 times larger in radius relative to prokaryotes. Cells have +several types of internal enclosed compartments. Cell walls, if +present, are made from cellulose or chitin, in contrast to +prokaryotes. Eukaryotes have novel modes of direct body movement and +swimming, based on sensors, and the mode of reproduction uses sexual +combination. Their DNA is linear but wound up into nucleosomes and +then chromosomes. (https://doi.org/10.1016/B978-044452115-6/50050-6, +table 7-2). Eukaryotes can be considered a chimera; a combination of +archaeal and bacterial features that result in the cellular complexity +and distinctive characteristics. +(https://doi.org/10.1016/j.tim.2021.11.003). + +#### Algae + +[]{#algae} + +Concept: [`algae`](https://w3id.org/isample/biology/biosampledfeature/algae) + +Child of: + [`eukaryote`](#eukaryote) + +Informal term for a large and diverse group of photosynthetic +eukaryotic organisms. Included organisms range from unicellular +microalgae, such as Chlorella, Prototheca and the diatoms, to +multicellular forms, such as the giant kelp, a large brown alga which +may grow up to 50 metres (160 ft) in length. Most are aquatic and +autotrophic (they generate food internally) and lack many of the +distinct cell and tissue types, such as stomata, xylem and phloem that +are found in land plants. Includes red algae (Rhodophycophyta), brown +algae (Phaeophycophyta), and green algae (Chlorophyta). +https://en.wikipedia.org/wiki/Algae + +#### Animalia + +[]{#animalia} + +Concept: [`animalia`](https://w3id.org/isample/biology/biosampledfeature/animalia) + +Child of: + [`eukaryote`](#eukaryote) + +Animals are distinguished from other eukaryotes based on several key +characteristics, including: 1) animals are multicellular organisms 2) +Animals are heterotrophic, they obtain their food by consuming other +organisms or organic matter; 3) Animals lack cell walls; 4) Many +animals have a nervous system; 5) Most animals reproduce sexually +(Chat GPT) + +See Also: + +* [](https://www.gbif.org/species/1) + +##### Arthropod + +[]{#arthropod} + +Concept: [`arthropod`](https://w3id.org/isample/biology/biosampledfeature/arthropod) + +Child of: + [`animalia`](#animalia) + +invertebrate animals with an exoskeleton, a segmented body, and paired +jointed appendages. Arthropods form the phylum Arthropoda. They are +distinguished by their jointed limbs and cuticle made of chitin, often +mineralised with calcium carbonate. The arthropod body plan consists +of segments, each with a pair of appendages. Arthropods are +bilaterally symmetrical and their body possesses an external skeleton. +(https://en.wikipedia.org/wiki/Arthropod) + +See Also: + +* [](https://www.gbif.org/species/54) + +###### Arachnid + +[]{#arachnid} + +Concept: [`arachnid`](https://w3id.org/isample/biology/biosampledfeature/arachnid) + +Child of: + [`arthropod`](#arthropod) + +a group of arthropods that share several key characteristics, +including two main body segments, four pairs of legs, lack of +antennae, simple eyes, and specialized feeding and defense structures +called chelicerae (ChatGPT) + +See Also: + +* [](https://en.wikipedia.org/wiki/Arachnid) +* [](https://www.gbif.org/species/367) + +###### Crustaceans + +[]{#crustacea} + +Concept: [`crustacea`](https://w3id.org/isample/biology/biosampledfeature/crustacea) + +Child of: + [`arthropod`](#arthropod) + +arthropod taxon which includes such animals as decapods, seed shrimp, +branchiopods, fish lice, krill, remipedes, isopods, barnacles, +copepods, amphipods and mantis shrimp. crustaceans have an +exoskeleton, which they moult to grow. They are distinguished from +other groups of arthropods, such as insects, myriapods and +chelicerates, by the possession of biramous (two-parted) limbs, and by +their larval forms, such as the nauplius stage of branchiopods and +copepods. (https://en.wikipedia.org/wiki/Crustacean) + +###### Insect + +[]{#hexapoda} + +Concept: [`hexapoda`](https://w3id.org/isample/biology/biosampledfeature/hexapoda) + +Child of: + [`arthropod`](#arthropod) + +Include all hexapoda here; Insects are a group of hexapod arthropods +characterized by having three main body segments (head, thorax, and +abdomen), six legs, and wings in many species. All other hexapod +arthropods, such as springtails and diplurans, are not classified as +insects, but they share the same body plan of three main body segments +and six legs. However, they lack wings and other features that are +unique to insects. Therefore, all insects are hexapods, but not all +hexapods are insects. (ChatGPT) + +See Also: + +* [](https://www.gbif.org/species/174780701) + +###### Myriapod + +[]{#myriapod} + +Concept: [`myriapod`](https://w3id.org/isample/biology/biosampledfeature/myriapod) + +Child of: + [`arthropod`](#arthropod) + +Arthropods such as millipedes and centipedes. +(https://en.wikipedia.org/wiki/Myriapoda). A group of arthropods that +have long, segmented body with numerous pairs of legs, simple eyes, +specialized mouthparts, and a primarily terrestrial habitat, which +distinguishes them from other arthropod groups such as insects and +crustaceans. (ChatGPT) + +###### Other arthropod + +[]{#otherarthropod} + +Concept: [`otherarthropod`](https://w3id.org/isample/biology/biosampledfeature/otherarthropod) + +Child of: + [`arthropod`](#arthropod) + +includes Chelicerata (horseshoe crabs, scorpions, and sea spiders), +Trilobitomorpha ( extinct trilobites), and Pentastomida (parasitic +arthropods that infect the respiratory systems of reptiles and +mammals). (ChatGPT) + +##### Mollusca + +[]{#mollusca} + +Concept: [`mollusca`](https://w3id.org/isample/biology/biosampledfeature/mollusca) + +Child of: + [`animalia`](#animalia) + +animals that have a soft body with a mantle, a radula (ribbon-like +structure covered in tiny teeth that is used to scrape food), a +muscular foot, an open circulatory system, and a visceral mass that +contains the internal organs, including the digestive, excretory, and +reproductive systems. (ChatGPT) + +See Also: + +* [](https://www.gbif.org/species/52) + +##### Other invertebrate + +[]{#otherinvertebrate} + +Concept: [`otherinvertebrate`](https://w3id.org/isample/biology/biosampledfeature/otherinvertebrate) + +Child of: + [`animalia`](#animalia) + +Includes Cnidaria (jellyfish, coral, anemones), Echinodermata +(starfish, sea urchins, sea cucumbers), Nematoda (roundworms), +Platyhelminthes (flatworms), Annelida (segmented worms), Ctenophora +(comb jellies), Brachiopoda (lamp shells), Bryozoa (moss animals), +Chaetognatha (arrow worms), Hemichordata (acorn worms), +Xenacoelomorpha (simple-bodied worms) (ChatGPT) + +##### Porifera + +[]{#porifera} + +Concept: [`porifera`](https://w3id.org/isample/biology/biosampledfeature/porifera) + +Child of: + [`animalia`](#animalia) + +multicellular animals that have bodies full of pores and channels +allowing water to circulate through them, consisting of jelly-like +mesohyl sandwiched between two thin layers of cells. +(https://en.wikipedia.org/wiki/Sponge) + +See Also: + +* [](https://www.gbif.org/species/105) + +##### Vertebrate + +[]{#vertebrate} + +Concept: [`vertebrate`](https://w3id.org/isample/biology/biosampledfeature/vertebrate) + +Child of: + [`animalia`](#animalia) + +Animals that have a vertebral column, a cranium, an endoskeleton, a +well-developed muscular system, and an advanced nervous system +(ChatGPT); + +###### Amphibian + +[]{#amphibian} + +Concept: [`amphibian`](https://w3id.org/isample/biology/biosampledfeature/amphibian) + +Child of: + [`vertebrate`](#vertebrate) + +Vertebrates that have a dual life cycle, semi-permeable skin, absence +of scales and claws, a three-chambered heart, and dependence on water +for reproduction and survival (ChatGPT) + +###### Bird + +[]{#bird} + +Concept: [`bird`](https://w3id.org/isample/biology/biosampledfeature/bird) + +Child of: + [`vertebrate`](#vertebrate) + +Vertebrates that have feathers, lightweight, hollow bones, a beak, an +efficient respiratory system, and are warm-blooded. (ChatGPT) + +###### Fish + +[]{#fish} + +Concept: [`fish`](https://w3id.org/isample/biology/biosampledfeature/fish) + +Child of: + [`vertebrate`](#vertebrate) + +Vertebrates that have gills, scales, fins, are cold-blooded, and +commonly have a swim bladder; includes jawless fish, cartilaginous +fish and bony fish. (ChatGPT) + +###### Mammal + +[]{#mammal} + +Concept: [`mammal`](https://w3id.org/isample/biology/biosampledfeature/mammal) + +Child of: + [`vertebrate`](#vertebrate) + +vertebrates that have mammary glands, hair or fur, three middle ear +bones, specialized teeth, and are warm-blooded. (ChatGPT) + +###### Reptile + +[]{#reptile} + +Concept: [`reptile`](https://w3id.org/isample/biology/biosampledfeature/reptile) + +Child of: + [`vertebrate`](#vertebrate) + +Vertebrates that have scaly skin and claws, amniotic eggs, are cold- +blooded, and are ectothermic (ChatGPT) + +#### Chromista + +[]{#chromista} + +Concept: [`chromista`](https://w3id.org/isample/biology/biosampledfeature/chromista) + +Child of: + [`eukaryote`](#eukaryote) + +Chromists are unified by a shared common ancestral body plan with (1) +a skeleton comprising cortical alveoli with subpellicular microtubules +and a microtubule bypassing band distinct from the three major +microtubule centriolar roots inherited from excavate protozoa, and (2) +chloroplasts of red algal origin inside the endomembrane system with +unique membrane topology and derlin-based periplastid protein import +machinery. Chromists are distinguished from Plantae because of more +complex chloroplast-associated membrane topology and rigid tubular +multipartite ciliary hairs. The kingdom includes highly divergent +cytoskeletons and trophic modes. Chromista comprise eight distinctive +phyla (Cavalier-Smith, 2018) and includes a majority of marine algae +and of heterotrophic protists, various human disease agents such as +malaria parasites, and agricultural pathogens like potato blight and +sugar beet rhizomania disease. They have a greater range of body plans +and lifestyles than the entire plant kingdom and more phyla than +kingdoms Fungi or Protozoa. + +See Also: + +* [](https://www.gbif.org/species/4) + +#### Eukaryotic microorganism + +[]{#eukaryoticmicroorganism} + +Concept: [`eukaryoticmicroorganism`](https://w3id.org/isample/biology/biosampledfeature/eukaryoticmicroorganism) + +Child of: + [`eukaryote`](#eukaryote) + +Unclassified Eukaryote single-cell organisms; might be microfungi, +microalgae, Protista or Chromista. + +See Also: + +* [](https://en.wikipedia.org/wiki/Protist) + +#### Fungi + +[]{#fungi} + +Concept: [`fungi`](https://w3id.org/isample/biology/biosampledfeature/fungi) + +Child of: + [`eukaryote`](#eukaryote) + +eukaryotic organisms that contain chitin in their cell walls, are +heterotrophs (they obtain their nutrients by absorbing organic +material from their environment, either as decomposers, parasites, or +symbionts) , lack chloroplasts, reproduce both sexually and asexually, +and can take on a variety of growth forms, including single-celled +yeasts, multicellular molds, and complex, specialized fruiting bodies. +(ChatGPT). Biologists use the term ‘fungus’ to include eukaryotic, +spore-bearing, achlorophyllous organisms that generally reproduce +sexually and asexually. They are usually made up of filamentous, +branched somatic structures which are typically surrounded by cell +walls containing chitin or cellulose, or both of these substances. +(https://plantlet.org/lower-fungi-higher-fungi/) + +See Also: + +* [](https://www.gbif.org/species/5) + +##### Macrofungi + +[]{#macrofungi} + +Concept: [`macrofungi`](https://w3id.org/isample/biology/biosampledfeature/macrofungi) + +Child of: + [`fungi`](#fungi) + +Macrofungi refers to all fungi that produce visible fruiting bodies. +These fungi are evolutionarily and ecologically very divergent. +Evolutionarily, they belong to two main phyla, Ascomycota and +Basidiomycota, and many of them have relatives that cannot form +visible fruiting +bodies.(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6106070/) + +##### Microfungi + +[]{#microfungi} + +Concept: [`microfungi`](https://w3id.org/isample/biology/biosampledfeature/microfungi) + +Child of: + [`fungi`](#fungi) + +Microfungi or micromycetes are fungi—eukaryotic organisms such as +molds, mildews and rusts, which have microscopic spore-producing +structures. They exhibit tube tip-growth and have cell walls composed +of chitin, a polymer of N-acetylglucosamine. Microfungi are a +paraphyletic group, distinguished from macrofungi only by the absence +of a large, multicellular fruiting body. Include moulds, yeasts. +(https://en.wikipedia.org/wiki/Microfungi) + +#### Plantae + +[]{#plantae} + +Concept: [`plantae`](https://w3id.org/isample/biology/biosampledfeature/plantae) + +Child of: + [`eukaryote`](#eukaryote) + +Plants are eukaryotes that have cell walls made of cellulose, +specialized organelles called chloroplasts, which contain chlorophyll +and other pigments that allow plants to perform photosynthesis and +produce their own food; a unique life cycle that involves alternating +between a haploid gametophyte stage and a diploid sporophyte stage; +specialized regions called apical meristems at the tips of their roots +and shoots, which allow for growth and the development of new tissues; +specialized structures for reproduction, including flowers, cones, and +spores, and most plants have specialized tissues called xylem and +phloem, which transport water, nutrients, and other substances +throughout the plant. (ChatGPT). Subdivision here follows Margulis and +Schwartz 2001. + +See Also: + +* [](https://www.gbif.org/species/6) + +##### Non-vascular plant + +[]{#nonvascularplant} + +Concept: [`nonvascularplant`](https://w3id.org/isample/biology/biosampledfeature/nonvascularplant) + +Child of: + [`plantae`](#plantae) + +Non-vascular plants that do not have specialized tissues for +transporting water and nutrients; includes mosses, Marchantiophyta +(liverworts), and Anthocerotophyta (hornworts). (ChatGPT) + +See Also: + +* [](https://www.gbif.org/species/35) + +##### Other plant + +[]{#otherplant} + +Concept: [`otherplant`](https://w3id.org/isample/biology/biosampledfeature/otherplant) + +Child of: + [`plantae`](#plantae) + +plants that do not fit in other plant sub class. Includes +Lycopodiophyta (clubmosses) and Equisetophyta (horsetails) + +##### Vascular seed plant + +[]{#vascularseedplant} + +Concept: [`vascularseedplant`](https://w3id.org/isample/biology/biosampledfeature/vascularseedplant) + +Child of: + [`plantae`](#plantae) + +Plant that produces seeds, hence the alternative name seed plant. +Spermatophytes are a subset of the embryophytes or land plants. They +include most familiar types of plants, including all flowers and most +trees, but exclude some other types of plants such as ferns, mosses, +algae. (https://en.wikipedia.org/wiki/Spermatophyte). Includes +Gymnosperms (naked-seed plants) and Angiosperms (flowering plants). + +##### Vascular spore plant + +[]{#vascularsportplant} + +Concept: [`vascularsportplant`](https://w3id.org/isample/biology/biosampledfeature/vascularsportplant) + +Child of: + [`plantae`](#plantae) + +a vascular plant (with xylem and phloem) that disperses spores; they +produce neither flowers nor seeds, Includes Ferns, horsetails (often +treated as ferns), and lycophytes (clubmosses, spikemosses, and +quillworts) + +#### Protozoa + +[]{#protozoa} + +Concept: [`protozoa`](https://w3id.org/isample/biology/biosampledfeature/protozoa) + +Child of: + [`eukaryote`](#eukaryote) + +A single-celled eukaryote, either free-living or parasitic, that feed +on organic matter such as other microorganisms or organic tissues and +debris (predominantly heterotrophic). Historically, protozoans were +regarded as 'one-celled animals', because they often possess animal- +like behaviours, such as motility and predation, and lack a cell wall, +as found in plants and many algae. +(https://en.wikipedia.org/wiki/Protozoa) + +See Also: + +* [](https://www.gbif.org/species/7) + +##### Amoebozoa + +[]{#amoebozoa} + +Concept: [`amoebozoa`](https://w3id.org/isample/biology/biosampledfeature/amoebozoa) + +Child of: + [`protozoa`](#protozoa) + +a diverse group of organisms that share certain characteristics, such +as the ability to move using pseudopodia, temporary extensions of the +cell membrane and cytoplasm that allow the cell to crawl or engulf +food particles, the lack of rigid cell walls, presence of +mitochondria, which are organelles that generate energy for the cell +through cellular respiration (chatGPT) + +See Also: + +* [](https://www.gbif.org/species/7509337) + +##### Mycetozoa + +[]{#mycetozoa} + +Concept: [`mycetozoa`](https://w3id.org/isample/biology/biosampledfeature/mycetozoa) + +Child of: + [`protozoa`](#protozoa) + +Mycetozoa includes the slime molds, which are a group of organisms +that have both amoeboid and fungal-like characteristics. The Mycetozoa +can be further subdivided into two groups: the plasmodial slime molds +and the cellular slime molds. Myxomycetes has most child orders; they +are class of slime molds. Myxomycetes have a complex life cycle +involving the formation of spore-bearing structures called fruiting +bodies, which is a key feature that distinguishes them from other +amoebae. All species pass through several, very different +morphologic phases, such as microscopic individual cells, slimy +amorphous organisms visible with the naked eye and conspicuously +shaped fruit bodies. Although they are monocellular, they can reach +immense widths and weights. +(https://en.wikipedia.org/wiki/Mycetozoa). (ChatGPT) + +See Also: + +* [](https://www.gbif.org/species/33) + +##### Other Protozoa + +[]{#otherprotozoa} + +Concept: [`otherprotozoa`](https://w3id.org/isample/biology/biosampledfeature/otherprotozoa) + +Child of: + [`protozoa`](#protozoa) + +Protozoa is not Amoebozoa or Mycetozoa. Includes phylum Euglenozoa +and Microsporidia prominently among others. + +### Lichen + +[]{#lichen} + +Concept: [`lichen`](https://w3id.org/isample/biology/biosampledfeature/lichen) + +Child of: + [`biologicalentity`](#biologicalentity) + +A composite organism that arises from algae or cyanobacteria living +among filaments of multiple fungi species in a mutualistic +relationship. (https://en.wikipedia.org/wiki/Lichen). Lichens are not +classified under a specific kingdom as they are a symbiotic +association between a fungus and either an alga or a cyanobacterium. +The fungal partner belongs to the kingdom Fungi, while the algal or +cyanobacterial partner belongs to either the kingdom Plantae or the +kingdom Bacteria, respectively. (ChatGPT) + +### Plasmid + +[]{#plasmid} + +Concept: [`plasmid`](https://w3id.org/isample/biology/biosampledfeature/plasmid) + +Child of: + [`biologicalentity`](#biologicalentity) + +A plasmid is a small, extrachromosomal DNA molecule within a cell that +is physically separated from chromosomal DNA and can replicate +independently. While chromosomes are large and contain all the +essential genetic information for living under normal conditions, +plasmids are usually very small and contain only additional genes that +may be useful in certain situations or conditions. +(https://en.wikipedia.org/wiki/Plasmid) + +### Prokaryote + +[]{#prokaryote} + +Concept: [`prokaryote`](https://w3id.org/isample/biology/biosampledfeature/prokaryote) + +Child of: + [`biologicalentity`](#biologicalentity) + +single-celled organisms that lack a nucleus and other membrane-bound +organelles. Unlike cells of animals and other eukaryotes, bacterial +cells do not contain a nucleus and rarely harbour membrane-bound +organelles. Molecular systematics showed prokaryotic life to consist +of two separate domains, originally called Eubacteria and +Archaebacteria, but now called Bacteria and Archaea that evolved +independently from an ancient common ancestor. Almost all prokaryotes +have a cell wall, a protective structure that allows them to survive +in extreme conditions, which is located outside of their plasma +membrane. Archaea and bacteria cannot reproduce sexually. + +#### Archaea + +[]{#archaea} + +Concept: [`archaea`](https://w3id.org/isample/biology/biosampledfeature/archaea) + +Child of: + [`prokaryote`](#prokaryote) + +archaeal cell walls are composed of polysaccharides (sugars). they +never have peptidoglycan in their cell walls, their cell membranes +contain lipids of unique composition (glycerol molecules are mirror +images of those found in other cells, and form ether linkages to +isoprenoid side chains), and their 16S ribosomal- RNA nucleotide +sequences are unlike those of bacteria. +(https://quizlet.com/234154298/archaea-and-bacteria-flash-cards/). +The common characteristics of Archaebacteria known to date are these: +(1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the +absence of peptidoglycan cell walls, with in many cases, replacement +by a largely proteinaceous coat; (3) the occurrence of ether linked +lipids built from phytanyl chains and (4) in all cases known so far, +their occurrence only in unusual habitats. +(https://pubmed.ncbi.nlm.nih.gov/691075/) + +See Also: + +* [](https://www.gbif.org/species/2) + +#### Bacteria + +[]{#bacteria} + +Concept: [`bacteria`](https://w3id.org/isample/biology/biosampledfeature/bacteria) + +Child of: + [`prokaryote`](#prokaryote) + +a large domain of prokaryotic microorganisms. Bacterial cells do not +contain a nucleus and rarely harbour membrane-bound organelles. The +bacterial cell is surrounded by a cell membrane, which is made +primarily of phospholipids. This membrane encloses the contents of the +cell and acts as a barrier to hold nutrients, proteins and other +essential components of the cytoplasm within the cell. Bacterial cell +walls are composed of peptidoglycan, a complex of protein and sugars, +while archaeal cell walls are composed of polysaccharides (sugars). +(https://en.wikipedia.org/wiki/Bacteria) + +See Also: + +* [](https://www.gbif.org/species/3) + +### Virus + +[]{#virus} + +Concept: [`virus`](https://w3id.org/isample/biology/biosampledfeature/virus) + +Child of: + [`biologicalentity`](#biologicalentity) + +A virus is a submicroscopic infectious agent that replicates only +inside the living cells of an organism. Realms are Adnaviria, +Duplodnaviria, Monodnaviria, Riboviria, Ribozyviria, Varidnaviria +(https://en.wikipedia.org/wiki/Virus). Viruses are not cells at all, +so they are neither prokaryotes nor eukaryotes. (https://bio.libretext +s.org/Bookshelves/Introductory_and_General_Biology/Book) + +See Also: + +* [](https://www.gbif.org/species/8) + +#### Other Virus + +[]{#othervirus} + +Concept: [`othervirus`](https://w3id.org/isample/biology/biosampledfeature/othervirus) + +Child of: + [`virus`](#virus) + +Virus that is not a member of order Caudovirales (e.g., bacteriophage +T4, lambda phage). + +#### Phage + +[]{#phage} + +Concept: [`phage`](https://w3id.org/isample/biology/biosampledfeature/phage) + +Child of: + [`virus`](#virus) + +A bacteriophage, also known informally as a phage, is a duplodnaviria +virus that infects and replicates within bacteria and archaea. +Bacteriophages are composed of proteins that encapsulate a DNA or RNA +genome, and may have structures that are either simple or elaborate. +Their genomes may encode as few as four genes (e.g. MS2) and as many +as hundreds of genes. Phages replicate within the bacterium following +the injection of their genome into its cytoplasm. +(https://en.wikipedia.org/wiki/Bacteriophage). Includes all virus in +order Caudovirales (e.g., bacteriophage T4, lambda phage). + + diff --git a/models/generated/extensions/earthenv_material_extension_mineral_group.md b/models/generated/extensions/earthenv_material_extension_mineral_group.md new file mode 100644 index 0000000..17da62a --- /dev/null +++ b/models/generated/extensions/earthenv_material_extension_mineral_group.md @@ -0,0 +1,193 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "Earth and Environmental Science extension - Mineral group vocabulary" +date: "2025-12-11T02:41:29.241788+00:00" +subtitle: | + Vocabulary to extend the mineral material type category with the top level mineral group categories. Uses the Nickel–Strunz mineral classes, which divide minerals into ten classes according to chemical composition and crystal structure. Nickel-Strunz group 10 is not included because that material would be mat:organiccompounds. Version 10 of the classification is modified from v 9 (Strunz and Nickel,2002) by Jim Ferraiolo and others, and now extended and maintained by mindat.org. Some scope notes from linked.data.gov.au. +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_material_extension_mineral_group.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_material_extension_mineral_group.ttl) + + +Namespace: +[`https://w3id.org/isample/earthenv/mingroup/mineralgroupvocabulary`](https://w3id.org/isample/earthenv/mingroup/mineralgroupvocabulary) + +**History** + +* 2024-09-13 SMR remove version number from URI + +**Concepts** + +- [mineral](#mineral) + - [Mineral-Borate](#boratemineral) + - [Mineral-Carbonate or Nitrate](#carbonatenitratemineral) + - [Mineral-Halide](#halidemineral) + - [Mineral-Native Element](#nativeelementmineral) + - [Mineral-Organic Compound](#organicmineral) + - [Mineral-Oxide](#oxidemineral) + - [Mineral-Phosphate, Arsenate, or Vanadate](#phosphatearsenatevanadatemineral) + - [Mineral-Silicate or Germanate](#silicategermanatemineral) + - [Mineral-Sulfate, Selenate, or Tellurate](#sulfateselenatetelluratemineral) + - [Mineral-Sulfide or Sulfosalt](#sulfidesulfosaltmineral) + +## mineral + +[]{#mineral} + +Concept: [`mineral`](https://w3id.org/isample/vocabulary/material/mineral) + +Material consists of a single mineral or mineraloid phase. . 'A +mineral is an element or chemical compound that is normally +crystalline and that has been formed as a result of geological +processes.' (Nickel, Ernest H. (1995), The definition of a mineral, +The Canadian Mineralogist. 33 (3): 689–90). Include mineraloids. ... A +material primarily composed of some substance that is naturally +occurring, solid and stable at room temperature, representable by a +chemical formula, usually abiogenic, and that has an ordered atomic +structure. (http://purl.obolibrary.org/obo/ENVO_01000256). Comment: +the identity of a mineral species is defined by a crystal structure +and a chemical composition that might include various specific +elemental substitutions in that structure. Mineraloid: A naturally +occurring mineral-like substance that does not demonstrate +crystallinity. Mineraloids possess chemical compositions that vary +beyond the generally accepted ranges for specific minerals. Examples: +obsidian, Opal. (https://en.wikipedia.org/wiki/Mineraloid) + +### Mineral-Borate + +[]{#boratemineral} + +Concept: [`boratemineral`](https://w3id.org/isample/earthenv/mingroup/boratemineral) + +Child of: + [`mineral`](#mineral) + +Minerals which contain a borate anion group. + +### Mineral-Carbonate or Nitrate + +[]{#carbonatenitratemineral} + +Concept: [`carbonatenitratemineral`](https://w3id.org/isample/earthenv/mingroup/carbonatenitratemineral) + +Child of: + [`mineral`](#mineral) + +Carbonate minerals are those minerals containing the carbonate ion + +### Mineral-Halide + +[]{#halidemineral} + +Concept: [`halidemineral`](https://w3id.org/isample/earthenv/mingroup/halidemineral) + +Child of: + [`mineral`](#mineral) + +Minerals with a dominant halide anion. + +### Mineral-Native Element + +[]{#nativeelementmineral} + +Concept: [`nativeelementmineral`](https://w3id.org/isample/earthenv/mingroup/nativeelementmineral) + +Child of: + [`mineral`](#mineral) + +Elements that occur in nature in uncombined form with a distinct +mineral structure. Includes metals and intermetallic alloys; +metalloids and nonmetals; carbides, silicides, nitrides, phosphides + +### Mineral-Organic Compound + +[]{#organicmineral} + +Concept: [`organicmineral`](https://w3id.org/isample/earthenv/mingroup/organicmineral) + +Child of: + [`mineral`](#mineral) + +Salts of organic acids, hydrocarbons, and miscellaneous organic +minerals formed as a result of geological processes. Includes +hydrocarbons, formates, acetates, oxalates, benzine salts, cyanates. +Chemical compounds in which one or more atoms of carbon are covalently +linked to atoms of other elements, most commonly hydrogen, oxygen, or +nitrogen (https://www.britannica.com/science/organic-compound). + +### Mineral-Oxide + +[]{#oxidemineral} + +Concept: [`oxidemineral`](https://w3id.org/isample/earthenv/mingroup/oxidemineral) + +Child of: + [`mineral`](#mineral) + +Includes class oxides, hydroxides, and arsenties. Oxides are minerals +in which the oxide anion is bonded to one or more metal alloys. The +hydroxide-bearing minerals are typically included in the oxide class. +Arsenite minerals are very rare oxygen-bearing arsenic minerals. + +### Mineral-Phosphate, Arsenate, or Vanadate + +[]{#phosphatearsenatevanadatemineral} + +Concept: [`phosphatearsenatevanadatemineral`](https://w3id.org/isample/earthenv/mingroup/phosphatearsenatevanadatemineral) + +Child of: + [`mineral`](#mineral) + +Phosphate minerals contain the phosphate anion along sometimes with +arsenate and vanadate substitutions, and chloride, fluoride, and +hydroxide anions that also fit into the crystal structure. Arsenate +minerals usually refer to the naturally occurring orthoarsenates. + +### Mineral-Silicate or Germanate + +[]{#silicategermanatemineral} + +Concept: [`silicategermanatemineral`](https://w3id.org/isample/earthenv/mingroup/silicategermanatemineral) + +Child of: + [`mineral`](#mineral) + +Rock-forming minerals made up of silicate groups + +### Mineral-Sulfate, Selenate, or Tellurate + +[]{#sulfateselenatetelluratemineral} + +Concept: [`sulfateselenatetelluratemineral`](https://w3id.org/isample/earthenv/mingroup/sulfateselenatetelluratemineral) + +Child of: + [`mineral`](#mineral) + +class of minerals that include the sulfate ion within their structure. + +### Mineral-Sulfide or Sulfosalt + +[]{#sulfidesulfosaltmineral} + +Concept: [`sulfidesulfosaltmineral`](https://w3id.org/isample/earthenv/mingroup/sulfidesulfosaltmineral) + +Child of: + [`mineral`](#mineral) + +Sulfide minerals are a class of minerals containing sulfide or +disulfide as the major anion. Sulfosalt minerals are those complex +sulfide minerals with the general formula: AmBnSp; where A represents +a metal such as copper, lead, silver, iron, and rarely mercury, zinc, +vanadium; B usually represents semi-metal such as arsenic, antimony, +bismuth, and rarely germanium, or metals like tin and rarely vanadium; +and S is sulfur or rarely selenium or/and tellurium (m, n, and p are +integer formula subscripts). Includes sulfides, selenides, tellurides; +arsenides, antimonides, bismuthides; sulfarsenites, sulfantimonites, +sulfbismuthites + + diff --git a/models/generated/extensions/earthenv_material_extension_rock_sediment.md b/models/generated/extensions/earthenv_material_extension_rock_sediment.md new file mode 100644 index 0000000..b515728 --- /dev/null +++ b/models/generated/extensions/earthenv_material_extension_rock_sediment.md @@ -0,0 +1,1836 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "Earth and Environmental Science extension - Rock and sediment materials vocabulary" +date: "2025-12-11T02:41:29.838564+00:00" +subtitle: | + Rock and sediment categories for iSamples materialType classification. Remove anthropogenic materials and classes for consolidated or non-consolidated material; remove leaf classes subjectively based on abundance of material type and number of subclasses. There are 83 'mat:rock' subclasses; these include some classes that are non-consolidated material (e.g. fault gouge) but these are not sediment and adding 'material' classes that are independent of consolidation seems like more overhead than needed. Note that a given material is likely to fit in more that one class; for example the sediment subclasses include compositional classes (e.g. carbonate, clastic) as well as grain size classes (gravel-size sediment). A calcareous ooze sample would be both 'mud-size sediment' and 'carbonate sediment'. Change owl:class to skos:concept, and rdfs:subClassOf to skos:broader. +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_material_extension_rock_sediment.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_material_extension_rock_sediment.ttl) + + +Namespace: +[`https://w3id.org/isample/earthenv/rocksediment/rocksedimentvocabulary`](https://w3id.org/isample/earthenv/rocksediment/rocksedimentvocabulary) + +**History** + +* 2024-01-06 SMR updates to validate with SHACL rules in isamples/vocab_tools repo; extension vocabulary in skos:inScheme isamples parent voabularty; properties on inherited classes from iSample parent. +* 2024-09-13 SMR remove version number from URI + +**Concepts** + +- [Rock](#rock) + - [aphanite](#aphanite) + - [breccia](#breccia) + - [fault related material](#fault_related_material) + - [cataclasite series](#cataclasite_series) + - [mylonitic rock](#mylonitic_rock) + - [breccia gouge series](#breccia_gouge_series) + - [fragmental igneous rock](#fragmental_igneous_rock) + - [pyroclastic rock](#pyroclastic_rock) + - [igneous rock](#igneous_rock) + - [acidic igneous rock](#acidic_igneous_rock) + - [dacite](#dacite) + - [granitoid](#granitoid) + - [alkali feldspar granite](#alkali_feldspar_granite) + - [granite](#granite) + - [granodiorite](#granodiorite) + - [tonalite](#tonalite) + - [quartz rich igneous rock](#quartz_rich_igneous_rock) + - [rhyolitoid](#rhyolitoid) + - [basic igneous rock](#basic_igneous_rock) + - [basalt](#basalt) + - [gabbroic rock](#gabbroic_rock) + - [doleritic rock](#doleritic_rock) + - [exotic composition igneous rock](#exotic_composition_igneous_rock) + - [fine grained igneous rock](#fine_grained_igneous_rock) + - [andesite](#andesite) + - [basalt](#basalt) + - [dacite](#dacite) + - [foiditoid](#foiditoid) + - [high magnesium fine grained igneous rock](#high_magnesium_fine_grained_igneous_rock) + - [phonolitoid](#phonolitoid) + - [rhyolitoid](#rhyolitoid) + - [tephritoid](#tephritoid) + - [trachytoid](#trachytoid) + - [fragmental igneous rock](#fragmental_igneous_rock) + - [pyroclastic rock](#pyroclastic_rock) + - [glass rich igneous rock](#glass_rich_igneous_rock) + - [hypabyssal intrusive rock](#hypabyssal_intrusive_rock) + - [intermediate composition igneous rock](#intermediate_composition_igneous_rock) + - [andesite](#andesite) + - [dioritoid](#dioritoid) + - [phaneritic igneous rock](#phaneritic_igneous_rock) + - [anorthositic rock](#anorthositic_rock) + - [aplite](#aplite) + - [dioritoid](#dioritoid) + - [foid dioritoid](#foid_dioritoid) + - [foid gabbroid](#foid_gabbroid) + - [foid syenitoid](#foid_syenitoid) + - [foidolite](#foidolite) + - [gabbroid](#gabbroid) + - [gabbroic rock](#gabbroic_rock) + - [monzogabbroic rock](#monzogabbroic_rock) + - [granitoid](#granitoid) + - [alkali feldspar granite](#alkali_feldspar_granite) + - [granite](#granite) + - [granodiorite](#granodiorite) + - [tonalite](#tonalite) + - [hornblendite](#hornblendite) + - [pegmatite](#pegmatite) + - [peridotite](#peridotite) + - [pyroxenite](#pyroxenite) + - [quartz rich igneous rock](#quartz_rich_igneous_rock) + - [syenitoid](#syenitoid) + - [plutonic rock](#plutonic_igneous_rock) + - [porphyry](#porphyry) + - [ultrabasic igneous rock](#ultrabasic_igneous_rock) + - [ultramafic igneous rock](#ultramafic_igneous_rock) + - [hornblendite](#hornblendite) + - [peridotite](#peridotite) + - [pyroxenite](#pyroxenite) + - [volcanic rock](#volcanic_rock) + - [impact generated material](#impact_generated_material) + - [massive sulphide](#massive_sulphide) + - [metamorphic rock](#metamorphic_rock) + - [metasomatic rock](#metasomatic_rock) + - [sedimentary rock](#sedimentary_rock) + - [carbonate sedimentary rock](#carbonate_sedimentary_rock) + - [clastic sedimentary rock](#clastic_sedimentary_rock) + - [diamictite](#diamictite) + - [generic conglomerate](#generic_conglomerate) + - [generic mudstone](#generic_mudstone) + - [generic sandstone](#generic_sandstone) + - [hybrid sedimentary rock](#hybrid_sedimentary_rock) + - [iron rich sedimentary rock](#iron_rich_sedimentary_rock) + - [non clastic siliceous sedimentary rock](#non_clastic_siliceous_sedimentary_rock) + - [organic rich sedimentary rock](#organic_rich_sedimentary_rock) + - [coal](#coal) + - [phosphorite](#phosphorite) + - [tuffit](#tuffite) + - [residual material](#residual_material) + +- [Sediment](#sediment) + - [biogenic sediment](#biogenic_sediment) + - [carbonate sediment](#carbonate_sediment) + - [chemical sedimentary material](#chemical_sedimentary_material) + - [clastic sediment](#clastic_sediment) + - [diamicton](#diamicton) + - [gravel size sediment](#gravel_size_sediment) + - [hybrid sediment](#hybrid_sediment) + - [iron rich sediment](#iron_rich_sediment) + - [mud size sediment](#mud_size_sediment) + - [non clastic siliceous sediment](#non_clastic_siliceous_sediment) + - [phosphate rich sediment](#phosphate_rich_sediment) + - [sand size sediment](#sand_size_sediment) + - [tephra](#tephra) + +## Rock + +[]{#rock} + +Concept: [`rock`](https://w3id.org/isample/vocabulary/material/rock) + +Consolidated aggregate of particles (grains) of rock, mineral +(including native elements), mineraloid, or solid organic material. +Includes mineral aggregates such as granite, shale, marble; natural +glass such as obsidian; organic material formed by geologic processes +such a coal; extraterrestrial material in meteorites; and crushed +rock fragments like drill cuttings from rock. (based on +http://resource.geosciml.org/classifier/cgi/lithology/rock, same as +http://purl.obolibrary.org/obo/ENVO_00001995) + +### aphanite + +[]{#aphanite} + +Concept: [`Aphanite`](https://w3id.org/isample/earthenv/rocksediment/Aphanite) + +Child of: + [`rock`](#rock) + +Rock that is too fine grained to categorize in more detail. + +### breccia + +[]{#breccia} + +Concept: [`Breccia`](https://w3id.org/isample/earthenv/rocksediment/Breccia) + +Child of: + [`rock`](#rock) + +Coarse-grained material composed of angular broken rock fragments; the +fragments typically have sharp edges and unworn corners. The fragments +may be held together by a mineral cement or in a fine-grained matrix, +and consolidated or nonconsolidated. Clasts may be of any composition +or origin. In sedimentary environments, breccia is used for material +that consists entirely of angular fragments, mostly derived from a +single source rock body, as in a rock avalanche deposit, and matrix is +interpreted to be the product of comminution of clasts during +transport. Diamictite or diamicton is used when the material reflects +mixing of rock from a variety of sources, some sub angular or +subrounded clasts may be present, and matrix is pre-existing fine +grained material that is not a direct product of the +brecciation/deposition process. + +### fault related material + +[]{#fault_related_material} + +Concept: [`Fault_Related_Material`](https://w3id.org/isample/earthenv/rocksediment/Fault_Related_Material) + +Child of: + [`rock`](#rock) + +Material formed as a result brittle faulting, composed of greater than +10 percent matrix; matrix is fine-grained material caused by tectonic +grainsize reduction. Includes cohesive (cataclasite series, mylonitic +rocks) and non-cohesive (breccia-gouge series) material. + +#### cataclasite series + +[]{#cataclasite_series} + +Concept: [`Cataclasite_Series`](https://w3id.org/isample/earthenv/rocksediment/Cataclasite_Series) + +Child of: + [`Fault_Related_Material`](#Fault_Related_Material) + +Fault-related rock that maintained primary cohesion during +deformation, with matrix comprising greater than 10 percent of rock +mass; matrix is fine-grained material formed through grain size +reduction by fracture as opposed to crystal plastic process that +operate in mylonitic rock. Includes cataclasite, protocataclasite and +ultracataclasite. + +#### mylonitic rock + +[]{#mylonitic_rock} + +Concept: [`Mylonitic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Mylonitic_Rock) + +Child of: + [`Fault_Related_Material`](#Fault_Related_Material) + +Metamorphic rock characterised by a foliation resulting from tectonic +grain size reduction, in which more than 10 percent of the rock volume +has undergone grain size reduction. Includes protomylonite, mylonite, +ultramylonite, and blastomylonite. + +#### breccia gouge series + +[]{#breccia_gouge_series} + +Concept: [`breccia_gouge_series`](https://w3id.org/isample/earthenv/rocksediment/breccia_gouge_series) + +Child of: + [`Fault_Related_Material`](#Fault_Related_Material) + +Fault-related material with features such as void spaces (filled or +unfilled), or unconsolidated matrix material between fragments, +indicating loss of cohesion during deformation. Includes fault-related +breccia and gouge. + +### fragmental igneous rock + +[]{#fragmental_igneous_rock} + +Concept: [`Fragmental_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Fragmental_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + [`rock`](#rock) + +Igneous rock in which greater than 75 percent of the rock consists of +fragments produced as a result of igneous rock-forming process. +Includes pyroclastic rocks, autobreccia associated with lava flows and +intrusive breccias. Excludes deposits reworked by epiclastic processes +(see Tuffite) + +#### pyroclastic rock + +[]{#pyroclastic_rock} + +Concept: [`Pyroclastic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Pyroclastic_Rock) + +Child of: + [`Fragmental_Igneous_Rock`](#Fragmental_Igneous_Rock) + +Fragmental igneous rock that consists of greater than 75 percent +fragments produced as a direct result of eruption or extrusion of +magma from within the earth onto its surface. Includes autobreccia +associated with lava flows and excludes deposits reworked by +epiclastic processes. + +### igneous rock + +[]{#igneous_rock} + +Concept: [`Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Igneous_Rock) + +Child of: + [`rock`](#rock) + +rock formed as a result of igneous processes, for example intrusion +and cooling of magma in the crust, or volcanic eruption. + +#### acidic igneous rock + +[]{#acidic_igneous_rock} + +Concept: [`Acidic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Acidic_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Igneous rock with more than 63 percent SiO2. + +##### dacite + +[]{#dacite} + +Concept: [`Dacite`](https://w3id.org/isample/earthenv/rocksediment/Dacite) + +Child of: + [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Fine grained or porphyritic crystalline rock that contains less than +90 percent mafic minerals, between 20 and 60 percent quartz in the +QAPF fraction, and has a plagioclase to total feldspar ratio greater +than 0.65. Includes rocks defined modally in QAPF fields 4 and 5 or +chemically in TAS Field O3. Typically composed of quartz and sodic +plagioclase with minor amounts of biotite and/or hornblende and/or +pyroxene; fine-grained equivalent of granodiorite and tonalite. + +##### granitoid + +[]{#granitoid} + +Concept: [`Granitoid`](https://w3id.org/isample/earthenv/rocksediment/Granitoid) + +Child of: + [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline igneous rock consisting of quartz, alkali +feldspar and/or plagioclase. Includes rocks defined modally in QAPF +fields 2, 3, 4 and 5 as alkali feldspar granite, granite, granodiorite +or tonalite. + +###### alkali feldspar granite + +[]{#alkali_feldspar_granite} + +Concept: [`Alkali_Feldspar_Granite`](https://w3id.org/isample/earthenv/rocksediment/Alkali_Feldspar_Granite) + +Child of: + [`Granitoid`](#Granitoid) + +Granitic rock that has a plagioclase to total feldspar ratio less than +0.1. QAPF field 2. + +###### granite + +[]{#granite} + +Concept: [`Granite`](https://w3id.org/isample/earthenv/rocksediment/Granite) + +Child of: + [`Granitoid`](#Granitoid) + +Phaneritic crystalline rock consisting of quartz, alkali feldspar and +plagioclase (typically sodic) in variable amounts, usually with +biotite and/or hornblende. Includes rocks defined modally in QAPF +Field 3. + +###### granodiorite + +[]{#granodiorite} + +Concept: [`Granodiorite`](https://w3id.org/isample/earthenv/rocksediment/Granodiorite) + +Child of: + [`Granitoid`](#Granitoid) + +Phaneritic crystalline rock consisting essentially of quartz, sodic +plagioclase and lesser amounts of alkali feldspar with minor +hornblende and biotite. Includes rocks defined modally in QAPF field +4. + +###### tonalite + +[]{#tonalite} + +Concept: [`Tonalite`](https://w3id.org/isample/earthenv/rocksediment/Tonalite) + +Child of: + [`Granitoid`](#Granitoid) + +Granitoid consisting of quartz and intermediate plagioclase, usually +with biotite and amphibole. Includes rocks defined modally in QAPF +field 5; ratio of plagioclase to total feldspar is greater than 0.9. + +##### quartz rich igneous rock + +[]{#quartz_rich_igneous_rock} + +Concept: [`Quartz_Rich_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Quartz_Rich_Igneous_Rock) + +Child of: + [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Occurrence of igneous rocks meeting this criteria seems to be +vanishingly rare, thus subdividing the category does not seem +warranted for the purposes of This vocabulary. Future usage of the +vocabulary may motivate including quatzolite and quartz-rich granitoid +in future revisions +Phaneritic crystalline igneous rock that contains less than 90 percent +mafic minerals and contains greater than 60 percent quartz in the QAPF +fraction. + +##### rhyolitoid + +[]{#rhyolitoid} + +Concept: [`Rhyolitoid`](https://w3id.org/isample/earthenv/rocksediment/Rhyolitoid) + +Child of: + [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Note that technical definition, based on modal mineralogy plotted in a +QAPF triangle may be applied qualitatively, based on phenocryst +mineralogy when ground mass mineralogy can not be determined +optically, or based on CIPW norm. Although TAS categories are defined +based on chemical analyses, the correspondence with the QAPF defined +categories is generally close enough that QAPF categories are commonly +used interchangeably with TAS categories. It is important to note the +basis for assignment of fine-grained igneous rocks to a specifice +lithology category. +fine_grained_igneous_rock consisting of quartz and alkali feldspar, +with minor plagioclase and biotite, in a microcrystalline, +cryptocrystalline or glassy groundmass. Flow texture is common. +Includes rocks defined modally in QAPF fields 2 and 3 or chemically in +TAS Field R as rhyolite. QAPF normative definition is based on modal +mineralogy thus: less than 90 percent mafic minerals, between 20 and +60 percent quartz in the QAPF fraction, and ratio of plagioclse to +total feldspar is less than 0.65. + +#### basic igneous rock + +[]{#basic_igneous_rock} + +Concept: [`Basic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Basic_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Igneous rock with between 45 and 52 percent SiO2. + +##### basalt + +[]{#basalt} + +Concept: [`Basalt`](https://w3id.org/isample/earthenv/rocksediment/Basalt) + +Child of: + [`Basic_Igneous_Rock`](#Basic_Igneous_Rock) + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Fine-grained or porphyritic igneous rock with less than 20 percent +quartz, and less than 10 percent feldspathoid minerals, in which the +ratio of plagioclase to total feldspar is greater 0.65. Typically +composed of calcic plagioclase and clinopyroxene; phenocrysts +typically include one or more of calcic plagioclase, clinopyroxene, +orthopyroxene, and olivine. Includes rocks defined modally in QAPF +fields 9 and 10 or chemically in TAS field B as basalt. Basalt and +andesite are distinguished chemically based on silica content, with +basalt defined to contain less than 52 weight percent silica. If +chemical data are not available, the color index is used to +distinguish the categories, with basalt defined to contain greater +than 35 percent mafic minerals by volume or greater than 40 percent +mafic minerals by weight. + +##### gabbroic rock + +[]{#gabbroic_rock} + +Concept: [`Gabbroic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Gabbroic_Rock) + +Child of: + [`Basic_Igneous_Rock`](#Basic_Igneous_Rock) + [`Gabbroid`](#Gabbroid) + +Gabbroid that has a plagioclase to total feldspar ratio greater than +0.9 in the QAPF fraction. Includes QAPF fields 10*, 10, and 10'. This +category includes the various categories defined in LeMaitre et al. +(2002) based on the mafic mineralogy, but apparently not subdivided +based on the quartz/feldspathoid content. + +#### doleritic rock + +[]{#doleritic_rock} + +Concept: [`Doleritic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Doleritic_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Dark colored gabbroic (basaltic) or dioritic (andesitic) rock +intermediate in grain size between basalt and gabbro and composed of +plagioclase, pyroxene and opaque minerals; often with ophitic texture. +Typically occurs as hypabyssal intrusions. Includes dolerite, +microdiorite, diabase and microgabbro. + +#### exotic composition igneous rock + +[]{#exotic_composition_igneous_rock} + +Concept: [`Exotic_Composition_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Exotic_Composition_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Rock with 'exotic' mineralogical, textural or field setting +characteristics; typically dark colored, with abundant phenocrysts. +Criteria include: presence of greater than 10 percent melilite or +leucite, or presence of kalsilite, or greater than 50 percent +carbonate minerals. Includes Carbonatite, Melilitic rock, Kalsilitic +rocks, Kimberlite, Lamproite, Leucitic rock and Lamprophyres. + +#### fine grained igneous rock + +[]{#fine_grained_igneous_rock} + +Concept: [`Fine_Grained_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Fine_Grained_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Need to make decision as to whether devitrified glass should be +considered glass or microcrystalline framework for purposes of +categorization +Igneous rock in which the framework of the rock consists of crystals +that are too small to determine mineralogy with the unaided eye; +framework may include up to 50 percent glass. A significant percentage +of the rock by volume may be phenocrysts. Includes rocks that are +generally called volcanic rocks. + +##### andesite + +[]{#andesite} + +Concept: [`Andesite`](https://w3id.org/isample/earthenv/rocksediment/Andesite) + +Child of: + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + [`Intermediate_Composition_Igneous_Rock`](#Intermediate_Composition_Igneous_Rock) + +Note the mela-andesite and leuco-basalt categories are not recommended +in this system. If chemical analytical data are available to constrain +the silica content, the basalt or andesite category should be used. +Fine-grained igneous rock with less than 20 percent quartz and less +than 10 percent feldspathoid minerals in the QAPF fraction, in which +the ratio of plagioclase to total feldspar is greater 0.65. Includes +rocks defined modally in QAPF fields 9 and 10 or chemically in TAS +field O2 as andesite. Basalt and andesite, which share the same QAPF +fields, are distinguished chemically based on silica content, with +basalt defined to contain less than 52 weight percent silica. If +chemical data are not available, the color index is used to +distinguish the categories, with basalt defined to contain greater +than 35 percent mafic minerals by volume or greater than 40 percent +mafic minerals by weight. Typically consists of plagioclase +(frequently zoned from labradorite to oligoclase), pyroxene, +hornblende and/or biotite. Fine grained equivalent of dioritic rock. + +##### basalt + +[]{#basalt} + +Concept: [`Basalt`](https://w3id.org/isample/earthenv/rocksediment/Basalt) + +Child of: + [`Basic_Igneous_Rock`](#Basic_Igneous_Rock) + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Fine-grained or porphyritic igneous rock with less than 20 percent +quartz, and less than 10 percent feldspathoid minerals, in which the +ratio of plagioclase to total feldspar is greater 0.65. Typically +composed of calcic plagioclase and clinopyroxene; phenocrysts +typically include one or more of calcic plagioclase, clinopyroxene, +orthopyroxene, and olivine. Includes rocks defined modally in QAPF +fields 9 and 10 or chemically in TAS field B as basalt. Basalt and +andesite are distinguished chemically based on silica content, with +basalt defined to contain less than 52 weight percent silica. If +chemical data are not available, the color index is used to +distinguish the categories, with basalt defined to contain greater +than 35 percent mafic minerals by volume or greater than 40 percent +mafic minerals by weight. + +##### dacite + +[]{#dacite} + +Concept: [`Dacite`](https://w3id.org/isample/earthenv/rocksediment/Dacite) + +Child of: + [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Fine grained or porphyritic crystalline rock that contains less than +90 percent mafic minerals, between 20 and 60 percent quartz in the +QAPF fraction, and has a plagioclase to total feldspar ratio greater +than 0.65. Includes rocks defined modally in QAPF fields 4 and 5 or +chemically in TAS Field O3. Typically composed of quartz and sodic +plagioclase with minor amounts of biotite and/or hornblende and/or +pyroxene; fine-grained equivalent of granodiorite and tonalite. + +##### foiditoid + +[]{#foiditoid} + +Concept: [`Foiditoid`](https://w3id.org/isample/earthenv/rocksediment/Foiditoid) + +Child of: + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Fine grained crystalline rock containing less than 90 percent mafic +minerals and more than 60 percent feldspathoid minerals in the QAPF +fraction. Includes rocks defined modally in QAPF field 15 or +chemically in TAS field F. + +##### high magnesium fine grained igneous rock + +[]{#high_magnesium_fine_grained_igneous_rock} + +Concept: [`High_Magnesium_Fine_Grained_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/High_Magnesium_Fine_Grained_Igneous_Rock) + +Child of: + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +fine-grained igneous rock that contains unusually high concentration +of MgO. For rocks that contain greater than 52 percent silica, MgO +must be greater than 8 percent. For rocks containing less than 52 +percent silica, MgO must be greater than 12 percent. + +##### phonolitoid + +[]{#phonolitoid} + +Concept: [`Phonolitoid`](https://w3id.org/isample/earthenv/rocksediment/Phonolitoid) + +Child of: + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Fine grained igneous rock than contains less than 90 percent mafic +minerals, between 10 and 60 percent feldspathoid mineral in the QAPF +fraction and has a plagioclase to total feldspar ratio less than 0.5. +Includes rocks defined modally in QAPF fields 11 and 12, and TAS field +Ph. + +##### rhyolitoid + +[]{#rhyolitoid} + +Concept: [`Rhyolitoid`](https://w3id.org/isample/earthenv/rocksediment/Rhyolitoid) + +Child of: + [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Note that technical definition, based on modal mineralogy plotted in a +QAPF triangle may be applied qualitatively, based on phenocryst +mineralogy when ground mass mineralogy can not be determined +optically, or based on CIPW norm. Although TAS categories are defined +based on chemical analyses, the correspondence with the QAPF defined +categories is generally close enough that QAPF categories are commonly +used interchangeably with TAS categories. It is important to note the +basis for assignment of fine-grained igneous rocks to a specifice +lithology category. +fine_grained_igneous_rock consisting of quartz and alkali feldspar, +with minor plagioclase and biotite, in a microcrystalline, +cryptocrystalline or glassy groundmass. Flow texture is common. +Includes rocks defined modally in QAPF fields 2 and 3 or chemically in +TAS Field R as rhyolite. QAPF normative definition is based on modal +mineralogy thus: less than 90 percent mafic minerals, between 20 and +60 percent quartz in the QAPF fraction, and ratio of plagioclse to +total feldspar is less than 0.65. + +##### tephritoid + +[]{#tephritoid} + +Concept: [`Tephritoid`](https://w3id.org/isample/earthenv/rocksediment/Tephritoid) + +Child of: + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Fine grained igneous rock than contains less than 90 percent mafic +minerals, between 10 and 60 percent feldspathoid mineral in the QAPF +fraction and has a plagioclase to total feldspar ratio greater than +0.5. Includes rocks classified in QAPF field 13 and 14 or chemically +in TAS field U1 as basanite or tephrite. + +##### trachytoid + +[]{#trachytoid} + +Concept: [`Trachytoid`](https://w3id.org/isample/earthenv/rocksediment/Trachytoid) + +Child of: + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + +Fine grained igneous rock than contains less than 90 percent mafic +minerals, less than 10 percent feldspathoid mineral and less than 20 +percent quartz in the QAPF fraction and has a plagioclase to total +feldspar ratio less than 0.65. Mafic minerals typically include +amphibole or mica; typically porphyritic. Includes rocks defined +modally in QAPF fields 6, 7 and 8 (with subdivisions) or chemically in +TAS Field T as trachyte or latite. + +#### fragmental igneous rock + +[]{#fragmental_igneous_rock} + +Concept: [`Fragmental_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Fragmental_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + [`rock`](#rock) + +Igneous rock in which greater than 75 percent of the rock consists of +fragments produced as a result of igneous rock-forming process. +Includes pyroclastic rocks, autobreccia associated with lava flows and +intrusive breccias. Excludes deposits reworked by epiclastic processes +(see Tuffite) + +##### pyroclastic rock + +[]{#pyroclastic_rock} + +Concept: [`Pyroclastic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Pyroclastic_Rock) + +Child of: + [`Fragmental_Igneous_Rock`](#Fragmental_Igneous_Rock) + +Fragmental igneous rock that consists of greater than 75 percent +fragments produced as a direct result of eruption or extrusion of +magma from within the earth onto its surface. Includes autobreccia +associated with lava flows and excludes deposits reworked by +epiclastic processes. + +#### glass rich igneous rock + +[]{#glass_rich_igneous_rock} + +Concept: [`Glass_Rich_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Glass_Rich_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Igneous rock that contains greater than 50 percent massive glass. + +#### hypabyssal intrusive rock + +[]{#hypabyssal_intrusive_rock} + +Concept: [`Hypabyssal_Intrusive_Rock`](https://w3id.org/isample/earthenv/rocksediment/Hypabyssal_Intrusive_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Igneous rocks formed by crystallisation close to the Earth's surface, +characterized by more rapid cooling than plutonic setting to produce +generally fine-grained intrusive igneous rock, commonly associated +with co-magmatic volcanic rocks. + +#### intermediate composition igneous rock + +[]{#intermediate_composition_igneous_rock} + +Concept: [`Intermediate_Composition_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Intermediate_Composition_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Igneous rock with between 52 and 63 percent SiO2. + +##### andesite + +[]{#andesite} + +Concept: [`Andesite`](https://w3id.org/isample/earthenv/rocksediment/Andesite) + +Child of: + [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) + [`Intermediate_Composition_Igneous_Rock`](#Intermediate_Composition_Igneous_Rock) + +Note the mela-andesite and leuco-basalt categories are not recommended +in this system. If chemical analytical data are available to constrain +the silica content, the basalt or andesite category should be used. +Fine-grained igneous rock with less than 20 percent quartz and less +than 10 percent feldspathoid minerals in the QAPF fraction, in which +the ratio of plagioclase to total feldspar is greater 0.65. Includes +rocks defined modally in QAPF fields 9 and 10 or chemically in TAS +field O2 as andesite. Basalt and andesite, which share the same QAPF +fields, are distinguished chemically based on silica content, with +basalt defined to contain less than 52 weight percent silica. If +chemical data are not available, the color index is used to +distinguish the categories, with basalt defined to contain greater +than 35 percent mafic minerals by volume or greater than 40 percent +mafic minerals by weight. Typically consists of plagioclase +(frequently zoned from labradorite to oligoclase), pyroxene, +hornblende and/or biotite. Fine grained equivalent of dioritic rock. + +##### dioritoid + +[]{#dioritoid} + +Concept: [`Dioritoid`](https://w3id.org/isample/earthenv/rocksediment/Dioritoid) + +Child of: + [`Intermediate_Composition_Igneous_Rock`](#Intermediate_Composition_Igneous_Rock) + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline igneous rock with M less than 90, consisting of +intermediate plagioclase, commonly with hornblende and often with +biotite or augite. Plagioclase to total feldspar ratio is greater that +0.65, and anorthite content of plagioclase is less than 50 percent. +Less than 10 percent feldspathoid mineral and less than 20 percent +quartz in the QAPF fraction. Includes rocks defined modally in QAPF +fields 9 and 10 (and their subdivisions). + +#### phaneritic igneous rock + +[]{#phaneritic_igneous_rock} + +Concept: [`Phaneritic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Phaneritic_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Igneous rock in which the framework of the rock consists of individual +crystals that can be discerned with the unaided eye. Bounding grain +size is on the order of 32 to 100 microns. Igneous rocks with 'exotic' +composition are excluded from this concept. + +##### anorthositic rock + +[]{#anorthositic_rock} + +Concept: [`Anorthositic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Anorthositic_Rock) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Leucocratic phaneritic crystalline igneous rock consisting essentially +of plagioclase, often with small amounts of pyroxene. By definition, +colour index M is less than 10, and plagiclase to total feldspar ratio +is greater than 0.9. Less than 20 percent quartz and less than 10 +percent feldspathoid in the QAPF fraction. QAPF field 10, 10*, and +10'. +Anorthositic rock term invented to label the combined QAPF fields 10, +10*, and 10', in order to construct hierarchy in this vocabulary. + +##### aplite + +[]{#aplite} + +Concept: [`Aplite`](https://w3id.org/isample/earthenv/rocksediment/Aplite) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Light coloured crystalline rock, characterized by a fine grained +allotriomorphic-granular (aplitic, saccharoidal or xenomorphic) +texture; typically granitic composition, consisting of quartz, alkali +feldspar and sodic plagioclase. + +##### dioritoid + +[]{#dioritoid} + +Concept: [`Dioritoid`](https://w3id.org/isample/earthenv/rocksediment/Dioritoid) + +Child of: + [`Intermediate_Composition_Igneous_Rock`](#Intermediate_Composition_Igneous_Rock) + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline igneous rock with M less than 90, consisting of +intermediate plagioclase, commonly with hornblende and often with +biotite or augite. Plagioclase to total feldspar ratio is greater that +0.65, and anorthite content of plagioclase is less than 50 percent. +Less than 10 percent feldspathoid mineral and less than 20 percent +quartz in the QAPF fraction. Includes rocks defined modally in QAPF +fields 9 and 10 (and their subdivisions). + +##### foid dioritoid + +[]{#foid_dioritoid} + +Concept: [`Foid_Dioritoid`](https://w3id.org/isample/earthenv/rocksediment/Foid_Dioritoid) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline igneous rock in which M is less than 90, the +plagioclase to total feldspar ratio is greater than 0.5, feldspathoid +minerals form 10-60 percent of the QAPF fraction, plagioclase has +anorthite content less than 50 percent. These rocks typically contain +large amounts of mafic minerals. Includes rocks defined modally in +QAPF fields 13 and 14. + +##### foid gabbroid + +[]{#foid_gabbroid} + +Concept: [`Foid_Gabbroid`](https://w3id.org/isample/earthenv/rocksediment/Foid_Gabbroid) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline igneous rock in which M is less than 90, the +plagioclase to total feldspar ratio is greater than 0.5, feldspathoids +form 10-60 percent of the QAPF fraction, and plagioclase has anorthite +content greater than 50 percent. These rocks typically contain large +amounts of mafic minerals. Includes rocks defined modally in QAPF +fields 13 and 14. + +##### foid syenitoid + +[]{#foid_syenitoid} + +Concept: [`Foid_Syenitoid`](https://w3id.org/isample/earthenv/rocksediment/Foid_Syenitoid) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline igneous rock with M less than 90, contains +between 10 and 60 percent feldspathoid mineral in the QAPF fraction, +and has a plagioclase to total feldspar ratio less than 0.5. Includes +QAPF fields 11 and 12. + +##### foidolite + +[]{#foidolite} + +Concept: [`Foidolite`](https://w3id.org/isample/earthenv/rocksediment/Foidolite) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline rock containing more than 60 percent +feldspathoid minerals in the QAPF fraction. Includes rocks defined +modally in QAPF field 15 + +##### gabbroid + +[]{#gabbroid} + +Concept: [`Gabbroid`](https://w3id.org/isample/earthenv/rocksediment/Gabbroid) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline igneous rock that contains less than 90 percent +mafic minerals, and up to 20 percent quartz or up to 10 percent +feldspathoid in the QAPF fraction. The ratio of plagioclase to total +feldspar is greater than 0.65, and anorthite content of the +plagioclase is greater than 50 percent. Includes rocks defined modally +in QAPF fields 9 and 10 and their subdivisions. + +###### gabbroic rock + +[]{#gabbroic_rock} + +Concept: [`Gabbroic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Gabbroic_Rock) + +Child of: + [`Basic_Igneous_Rock`](#Basic_Igneous_Rock) + [`Gabbroid`](#Gabbroid) + +Gabbroid that has a plagioclase to total feldspar ratio greater than +0.9 in the QAPF fraction. Includes QAPF fields 10*, 10, and 10'. This +category includes the various categories defined in LeMaitre et al. +(2002) based on the mafic mineralogy, but apparently not subdivided +based on the quartz/feldspathoid content. + +###### monzogabbroic rock + +[]{#monzogabbroic_rock} + +Concept: [`Monzogabbroic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Monzogabbroic_Rock) + +Child of: + [`Gabbroid`](#Gabbroid) + +Gabbroid with a plagioclase to total feldspar ratio between 0.65 and +0.9. QAPF field 9, 9 prime and 9 asterisk + +##### granitoid + +[]{#granitoid} + +Concept: [`Granitoid`](https://w3id.org/isample/earthenv/rocksediment/Granitoid) + +Child of: + [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline igneous rock consisting of quartz, alkali +feldspar and/or plagioclase. Includes rocks defined modally in QAPF +fields 2, 3, 4 and 5 as alkali feldspar granite, granite, granodiorite +or tonalite. + +###### alkali feldspar granite + +[]{#alkali_feldspar_granite} + +Concept: [`Alkali_Feldspar_Granite`](https://w3id.org/isample/earthenv/rocksediment/Alkali_Feldspar_Granite) + +Child of: + [`Granitoid`](#Granitoid) + +Granitic rock that has a plagioclase to total feldspar ratio less than +0.1. QAPF field 2. + +###### granite + +[]{#granite} + +Concept: [`Granite`](https://w3id.org/isample/earthenv/rocksediment/Granite) + +Child of: + [`Granitoid`](#Granitoid) + +Phaneritic crystalline rock consisting of quartz, alkali feldspar and +plagioclase (typically sodic) in variable amounts, usually with +biotite and/or hornblende. Includes rocks defined modally in QAPF +Field 3. + +###### granodiorite + +[]{#granodiorite} + +Concept: [`Granodiorite`](https://w3id.org/isample/earthenv/rocksediment/Granodiorite) + +Child of: + [`Granitoid`](#Granitoid) + +Phaneritic crystalline rock consisting essentially of quartz, sodic +plagioclase and lesser amounts of alkali feldspar with minor +hornblende and biotite. Includes rocks defined modally in QAPF field +4. + +###### tonalite + +[]{#tonalite} + +Concept: [`Tonalite`](https://w3id.org/isample/earthenv/rocksediment/Tonalite) + +Child of: + [`Granitoid`](#Granitoid) + +Granitoid consisting of quartz and intermediate plagioclase, usually +with biotite and amphibole. Includes rocks defined modally in QAPF +field 5; ratio of plagioclase to total feldspar is greater than 0.9. + +##### hornblendite + +[]{#hornblendite} + +Concept: [`Hornblendite`](https://w3id.org/isample/earthenv/rocksediment/Hornblendite) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) + +Ultramafic rock that consists of greater than 40 percent hornblende +plus pyroxene and has a hornblende to pyroxene ratio greater than 1. +Includes olivine hornblendite, olivine-pyroxene hornblendite, pyroxene +hornblendite, and hornblendite. + +##### pegmatite + +[]{#pegmatite} + +Concept: [`Pegmatite`](https://w3id.org/isample/earthenv/rocksediment/Pegmatite) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Exceptionally coarse grained crystalline rock with interlocking +crystals; most grains are 1cm or more diameter; composition is +generally that of granite, but the term may refer to the coarse +grained facies of any type of igneous rock;usually found as irregular +dikes, lenses, or veins associated with plutons or batholiths. + +##### peridotite + +[]{#peridotite} + +Concept: [`Peridotite`](https://w3id.org/isample/earthenv/rocksediment/Peridotite) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) + +Ultramafic rock consisting of more than 40 percent (by volume) olivine +with pyroxene and/or amphibole and little or no feldspar. commonly +altered to serpentinite. Includes rocks defined modally in the +ultramafic rock classification as dunite, harzburgite, lherzolite, +wehrlite, olivinite, pyroxene peridotite, pyroxene hornblende +peridotite or hornblende peridotite. + +##### pyroxenite + +[]{#pyroxenite} + +Concept: [`Pyroxenite`](https://w3id.org/isample/earthenv/rocksediment/Pyroxenite) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) + +Ultramafic phaneritic igneous rock composed almost entirely of one or +more pyroxenes and occasionally biotite, hornblende and olivine. +Includes rocks defined modally in the ultramafic rock classification +as olivine pyroxenite, olivine-hornblende pyroxenite, pyroxenite, +orthopyroxenite, clinopyroxenite and websterite. + +##### quartz rich igneous rock + +[]{#quartz_rich_igneous_rock} + +Concept: [`Quartz_Rich_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Quartz_Rich_Igneous_Rock) + +Child of: + [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Occurrence of igneous rocks meeting this criteria seems to be +vanishingly rare, thus subdividing the category does not seem +warranted for the purposes of This vocabulary. Future usage of the +vocabulary may motivate including quatzolite and quartz-rich granitoid +in future revisions +Phaneritic crystalline igneous rock that contains less than 90 percent +mafic minerals and contains greater than 60 percent quartz in the QAPF +fraction. + +##### syenitoid + +[]{#syenitoid} + +Concept: [`Syenitoid`](https://w3id.org/isample/earthenv/rocksediment/Syenitoid) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + +Phaneritic crystalline igneous rock with M less than 90, consisting +mainly of alkali feldspar and plagioclase; minor quartz or nepheline +may be present, along with pyroxene, amphibole or biotite. Ratio of +plagioclase to total feldspar is less than 0.65, quartz forms less +than 20 percent of QAPF fraction, and feldspathoid minerals form less +than 10 percent of QAPF fraction. Includes rocks classified in QAPF +fields 6, 7 and 8 and their subdivisions. + +#### plutonic rock + +[]{#plutonic_igneous_rock} + +Concept: [`Plutonic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Plutonic_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Instrusive igneous rock formed by crystallisation of magma far enough +below Earth surface that complete crystallization of magma bodies +forms holocrystalline medium to coarse grained igneous rock, wall +rocks generally do not include volcanic products related to the magma, +and some contact metamorphism is tyypically developed at intrusive +contacts. + +#### porphyry + +[]{#porphyry} + +Concept: [`Porphyry`](https://w3id.org/isample/earthenv/rocksediment/Porphyry) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Igneous rock that contains conspicuous phenocrysts in a finer grained +groundmass; groundmass itself may be phaneritic or fine-grained. + +#### ultrabasic igneous rock + +[]{#ultrabasic_igneous_rock} + +Concept: [`Ultrabasic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Ultrabasic_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Igneous rock with less than 45 percent SiO2. + +#### ultramafic igneous rock + +[]{#ultramafic_igneous_rock} + +Concept: [`Ultramafic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Ultramafic_Igneous_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Igneous rock that consists of greater than 90 percent mafic minerals. + +##### hornblendite + +[]{#hornblendite} + +Concept: [`Hornblendite`](https://w3id.org/isample/earthenv/rocksediment/Hornblendite) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) + +Ultramafic rock that consists of greater than 40 percent hornblende +plus pyroxene and has a hornblende to pyroxene ratio greater than 1. +Includes olivine hornblendite, olivine-pyroxene hornblendite, pyroxene +hornblendite, and hornblendite. + +##### peridotite + +[]{#peridotite} + +Concept: [`Peridotite`](https://w3id.org/isample/earthenv/rocksediment/Peridotite) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) + +Ultramafic rock consisting of more than 40 percent (by volume) olivine +with pyroxene and/or amphibole and little or no feldspar. commonly +altered to serpentinite. Includes rocks defined modally in the +ultramafic rock classification as dunite, harzburgite, lherzolite, +wehrlite, olivinite, pyroxene peridotite, pyroxene hornblende +peridotite or hornblende peridotite. + +##### pyroxenite + +[]{#pyroxenite} + +Concept: [`Pyroxenite`](https://w3id.org/isample/earthenv/rocksediment/Pyroxenite) + +Child of: + [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) + [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) + +Ultramafic phaneritic igneous rock composed almost entirely of one or +more pyroxenes and occasionally biotite, hornblende and olivine. +Includes rocks defined modally in the ultramafic rock classification +as olivine pyroxenite, olivine-hornblende pyroxenite, pyroxenite, +orthopyroxenite, clinopyroxenite and websterite. + +#### volcanic rock + +[]{#volcanic_rock} + +Concept: [`Volcanic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Volcanic_Rock) + +Child of: + [`Igneous_Rock`](#Igneous_Rock) + +Rock that exhibits direct evidence of extrusive igneous processes in +its genesis. + +### impact generated material + +[]{#impact_generated_material} + +Concept: [`Impact_Generated_Material`](https://w3id.org/isample/earthenv/rocksediment/Impact_Generated_Material) + +Child of: + [`rock`](#rock) + +Material that contains features indicative of shock metamorphism, such +as microscopic planar deformation features within grains or shatter +cones, interpreted to be the result of extraterrestrial bolide impact. +Includes breccias and melt rocks. + +### massive sulphide + +[]{#massive_sulphide} + +Concept: [`Massive_Sulphide`](https://w3id.org/isample/earthenv/rocksediment/Massive_Sulphide) + +Child of: + [`rock`](#rock) + +rock consisting of greater than 50% sulphide or sulfosalt minerals +formed by any processes. Includes hydrothermal and sedimentary +ehalative sulfide. + +### metamorphic rock + +[]{#metamorphic_rock} + +Concept: [`Metamorphic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Metamorphic_Rock) + +Child of: + [`rock`](#rock) + +Robertson (1999, Classification of metamorphic rocks: British +Geological Survey Research Report, RR 99–02) defines the boundary +between diagenesis and metamorphism in sedimentary rocks as follows: +“…the boundary between diagenesis and metamorphism is somewhat +arbitrary and strongly dependent on the lithologies involved. For +example changes take place in organic materials at lower temperatures +than in rocks dominated by silicate minerals. In mudrocks, a white +mica (illite) crystallinity value of less than 0.42 Delta 2 Theta +obtained by X-ray diffraction analysis, is used to define the onset of +metamorphism (Kisch, 1991). In this scheme, the first appearance of +glaucophane, lawsonite, paragonite, prehnite, pumpellyite or +stilpnomelane is taken to indicate the lower limit of metamorphism +(Frey and Kisch, 1987; Bucher and Frey, 1994; Frey and Robinson, +1998). Most workers agree that such mineral growth starts at 150 +/- +50° C in silicate rocks. Many lithologies may show no change in +mineralogy under these conditions and hence the recognition of the +onset of metamorphism will vary with bulk composition.” +Rock formed by solid-state mineralogical, chemical and/or structural +changes to a pre-existing rock, in response to marked changes in +temperature, pressure, shearing stress and chemical environment. + +### metasomatic rock + +[]{#metasomatic_rock} + +Concept: [`Metasomatic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Metasomatic_Rock) + +Child of: + [`rock`](#rock) + +SLTTm (2004) proposed the following criteria to distinguish +hydrothermally altered or metasomatic rock from igneous rock. "The +rock is classified as metamorphic if (1) the texture has been modified +such that it can no longer be considered igneous, (2) the bulk +composition of the rock is inconsistent with compositions that can be +derived purely from a magma and associated processes such as +assimilation and differentiation, or (3) minerals inconsistent with +magmatic crystallization are present." +Rock that has fabric and composition indicating open-system +mineralogical and chemical changes in response to interaction with a +fluid phase, typically water rich. + +### sedimentary rock + +[]{#sedimentary_rock} + +Concept: [`Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Sedimentary_Rock) + +Child of: + [`rock`](#rock) + +Rock formed by accumulation and cementation of solid fragmental +material deposited by air, water or ice, or as a result of other +natural agents, such as precipitation from solution, the accumulation +of organic material, or from biogenic processes, including secretion +by organisms. Includes epiclastic deposits. + +#### carbonate sedimentary rock + +[]{#carbonate_sedimentary_rock} + +Concept: [`Carbonate_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Carbonate_Sedimentary_Rock) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +Particularly for fine-grained sedimentary rocks, distinction of +'intrabasinal' versus 'clastic' genesis can be very interpretive. In +practice the use of clastic mudstone terminology as opposed to +carbonate mudstone terminology may be dermined by a priori knowledge +about the rock being categorized. If it is associated with other +clastic rocks, the clastic categories will be favored, if with +cabonate rocks, the carbonate categories will be favored. Carbonate +rock subcatgories are defined on two orthogonal dimensions--mineralogy +(calcitic vs. dolomitic vs non-carbonate impurities), and texture. The +texture categories used here are those of Dunham (1962), and involve +grain size (matrix vs. grains/allochems), fabric (matrix vs. grain +supported), and genesis (bound, frame, or fragmental). The textural +approach used for carbonate rocks is conceptually incompatible with +that used for clastic sedimentary rocks, which is solely grain size or +mineralogy based. This leads to problems in the vocabulary for rocks +of mixed siliclastic/carbonate mineralogy (grainstone vs. sandstone, +carbonate mudstone vs. carbonate rich mudstone, how to accomodate +marlstone...). +Sedimentary rock in which at least 50 percent of the primary and/or +recrystallized constituents are composed of one (or more) of the +carbonate minerals calcite, aragonite, magnesite or dolomite. + +#### clastic sedimentary rock + +[]{#clastic_sedimentary_rock} + +Concept: [`Clastic_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Clastic_Sedimentary_Rock) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +The conglomerate, sandstone, mudstone, and wackestone categories are +not defined as kinds of clastic sedimentary rocks because rocks +meeting their purely grainsize based definitions might also be iron- +rich, phosphatic, or carbonate. This is based on GeoSciML allowance to +assign rocks to more than one lithology category. For example to +categorize a rock as a clastic conglomerate requires assignment ot the +'clastic sedimentary rock' category and to the 'conglomerate' +category. Particularly for fine-grained sedimentary rocks, distinction +of 'intrabasinal' versus 'clastic' genesis can be very interpretive. +In practice the use of clastic mudstone terminology as opposed to +carbonate mudstone terminology may be dermined by a priori knowledge +about the rock being categorized. If it is associated with other +clastic rocks, the clastic categories will be favored, if with +cabonate rocks, the carbonate categories will be favored. +Sedimentary rock in which at least 50 percent of the constituent +particles were derived from erosion, weathering, or mass-wasting of +pre-existing earth materials, and transported to the place of +deposition by mechanical agents such as water, wind, ice and gravity. + +##### diamictite + +[]{#diamictite} + +Concept: [`Diamictite`](https://w3id.org/isample/earthenv/rocksediment/Diamictite) + +Child of: + [`Clastic_Sedimentary_Rock`](#Clastic_Sedimentary_Rock) + +Unsorted or poorly sorted, clastic sedimentary rock with a wide range +of particle sizes including a muddy matrix. Biogenic materials that +have such texture are excluded. Distinguished from conglomerate, +sandstone, mudstone based on polymodality and lack of structures +related to transport and deposition of sediment by moving air or +water. If more than 10 percent of the fine grained matrix is of +indeterminant clastic or diagenetic origin and the fabric is matrix +supported, may also be categorized as wacke. + +#### generic conglomerate + +[]{#generic_conglomerate} + +Concept: [`Generic_Conglomerate`](https://w3id.org/isample/earthenv/rocksediment/Generic_Conglomerate) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +Sedimentary rock composed of at least 30 percent rounded to subangular +fragments larger than 2 mm in diameter; typically contains finer +grained material in interstices between larger fragments. If more than +15 percent of the fine grained matrix is of indeterminant clastic or +diagenetic origin and the fabric is matrix supported, may also be +categorized as wackestone. If rock has unsorted or poorly sorted +texture with a wide range of particle sizes, may also be categorized +as diamictite. + +#### generic mudstone + +[]{#generic_mudstone} + +Concept: [`Generic_Mudstone`](https://w3id.org/isample/earthenv/rocksediment/Generic_Mudstone) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +Distinction of intrabasinal, diagenetic, or clastic genesis for very +fine-grained carbonate minerals is so interpretive that it is proposed +to not define the mudstone category based on intrabasinal vs +epiclastic distinction required for clastic sedimentary rock-carbonate +sedimentary rock categorization in this system. Schnurrenberger, D., +Russell, J. and Kelts, K., 2003, Classification of lacustrine +sediments based on sedimentary components: Journal of Paleolimnology, +v.29, p141-154. +Sedimentary rock consisting of less than 30 percent gravel-size (2 mm) +particles and with a mud to sand ratio greater than 1. Clasts may be +of any composition or origin. + +#### generic sandstone + +[]{#generic_sandstone} + +Concept: [`Generic_Sandstone`](https://w3id.org/isample/earthenv/rocksediment/Generic_Sandstone) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +Sedimentary rock in which less than 30 percent of particles are +greater than 2 mm in diameter (gravel) and the sand to mud ratio is at +least 1. + +#### hybrid sedimentary rock + +[]{#hybrid_sedimentary_rock} + +Concept: [`Hybrid_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Hybrid_Sedimentary_Rock) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +Sedimentary rock that does not fit any of the other +composition/genesis categories. Sedimentary rock consisting of three +or more components which form more than 5 percent but less than 50 +precent of the material. + +#### iron rich sedimentary rock + +[]{#iron_rich_sedimentary_rock} + +Concept: [`Iron_Rich_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Iron_Rich_Sedimentary_Rock) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +Sedimentary rock that consists of at least 50 percent iron-bearing +minerals (hematite, magnetite, limonite-group, siderite, iron- +sulfides), as determined by hand-lens or petrographic analysis. +Corresponds to a rock typically containing 15 percent iron by weight. + +#### non clastic siliceous sedimentary rock + +[]{#non_clastic_siliceous_sedimentary_rock} + +Concept: [`Non_Clastic_Siliceous_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Non_Clastic_Siliceous_Sedimentary_Rock) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +Definition updated to include chert, flint SMR 2020-09-21 +Sedimentary rock that consists of at least 50 percent silicate mineral +material, deposited directly by chemical or biological processes at +the depositional surface, in particles formed by chemical or +biological processes within the basin of deposition, or formed by +diagenetic processes. Includes chert and flint found in carbonate +rocks. + +#### organic rich sedimentary rock + +[]{#organic_rich_sedimentary_rock} + +Concept: [`Organic_Rich_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Organic_Rich_Sedimentary_Rock) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +Sapropelic coal, and asphaltite are not differentiated in This +vocabulary +Sedimentary rock with color, composition, texture and apparent density +indicating greater than 50 percent organic content by weight on a +moisture-free basis. + +##### coal +* `kohle` + +[]{#coal} + +Concept: [`Coal`](https://w3id.org/isample/earthenv/rocksediment/Coal) + +Child of: + [`Organic_Rich_Sedimentary_Rock`](#Organic_Rich_Sedimentary_Rock) + +A consolidated organic sedimentary material having less than 75% +moisture. This category includes low, medium, and high rank coals +according to International Classification of In-Seam Coal (United +Nations, 1998), thus including lignite. Sapropelic coal is not +distinguished in this category from humic coals. Formed from the +compaction or induration of variously altered plant remains similar to +those of peaty deposits. + +#### phosphorite + +[]{#phosphorite} + +Concept: [`Phosphorite`](https://w3id.org/isample/earthenv/rocksediment/Phosphorite) + +Child of: + [`Sedimentary_Rock`](#Sedimentary_Rock) + +Sedimentary rock in which at least 50 percent of the primary or +recrystallized constituents are phosphate minerals. Most commonly +occurs as a bedded primary or reworked secondary marine rock, composed +of microcrystalline carbonate fluorapatite in the form of lamina, +pellets, oolites and nodules, and skeletal, shell and bone fragments. + +### tuffit +* `tuffite` + +[]{#tuffite} + +Concept: [`Tuffite`](https://w3id.org/isample/earthenv/rocksediment/Tuffite) + +Child of: + [`rock`](#rock) + +In practice, it is likely that any rock for which there is suspicion +that it may consist of redeposited pyroclastic material, usually based +on sedimentary structures, irrespective of the presence or percentage +of clearly epiclastic particles, would be called a tuffite. 50 percent +cutoff with epiclastic rock is in contrast with LeMaitre et al., but +is used for consistentency with other sedimentary rock categories +following the pattern that the rock name reflects the predominant +constituent. +synonym: volcaniclastic rock +Rock consists of more than 50 percent particles of indeterminate +pyroclastic or epiclastic origin and less than 75 percent particles of +clearly pyroclastic origin. commonly the rock is laminated or exhibits +size grading. (based on LeMaitre et al. 2002; Murawski and Meyer +1998). + +### residual material + +[]{#residual_material} + +Concept: [`residual_material`](https://w3id.org/isample/earthenv/rocksediment/residual_material) + +Child of: + [`rock`](#rock) + +Material of composite origin resulting from weathering processes at +the Earth's surface, with genesis dominated by removal of chemical +constituents by aqueous leaching. Minor clastic, chemical, or organic +input may also contribute. Consolidation state is not inherent in +definition, but typically material is unconsolidated or weakly +consolidated. + + +## Sediment + +[]{#sediment} + +Concept: [`sediment`](https://w3id.org/isample/vocabulary/material/sediment) + +Solid granular material transported by wind, water, or gravity, not +modified by interaction with biosphere or atmosphere (to differentiate +from soil). Particles derived by erosion of pre-existing rock, from +shell or other body parts from organisms, precipitated chemically in +the surficial environment, or generated by explosive volcanic +activity. +(http://resource.geosciml.org/classifier/cgi/lithology/sediment). +Sediment is not consolidated, i.e. Particulate constituents of a +compound material do not adhere to each other strongly enough that the +aggregate can be considered a solid material in its own right. Similar +to http://purl.obolibrary.org/obo/ENVO_00002007 + +### biogenic sediment + +[]{#biogenic_sediment} + +Concept: [`Biogenic_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Biogenic_Sediment) + +Child of: + [`sediment`](#sediment) + +Corresponding biogenic sedimentary material and biogenic sedimentary +rock categories are not included based on the interpretation that +biogenic sedimentary rock will be in a different category, e.g. +carbonate sedimentary rock or organic rich sedimentary rock. +Sediment composed of greater than 50 percent material of biogenic +origin. Because the biogenic material may be skeletal remains that are +not organic, all biogenic sediment is not necessarily organic-rich. + +### carbonate sediment + +[]{#carbonate_sediment} + +Concept: [`Carbonate_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Carbonate_Sediment) + +Child of: + [`sediment`](#sediment) + +Sediment in which at least 50 percent of the primary and/or +recrystallized constituents are composed of one (or more) of the +carbonate minerals calcite, aragonite and dolomite, in particles of +intrabasinal origin. + +### chemical sedimentary material + +[]{#chemical_sedimentary_material} + +Concept: [`Chemical_Sedimentary_Material`](https://w3id.org/isample/earthenv/rocksediment/Chemical_Sedimentary_Material) + +Child of: + [`sediment`](#sediment) + +Sedimentary material that consists of at least 50 percent material +produced by inorganic chemical processes within the basin of +deposition. Includes inorganic siliceous, carbonate, evaporite, iron- +rich, and phosphatic sediment classes, as well as chemical sediments +associated with submarine hot springs ('black smokers'). Note that +these sediments might crystallize as a solid as they are deposited, +thus similar to rock.... + +### clastic sediment + +[]{#clastic_sediment} + +Concept: [`Clastic_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Clastic_Sediment) + +Child of: + [`sediment`](#sediment) + +Choice of 'clastic' is purposful. Other suggested labels for this +category include siliciclastic and terrigineous clastic. Siliciclastic +is considered too limiting because the category includes rocks that +consists clasts of carbonate minerals, e.g. epiclastic detritus eroded +from carbonate rock. Terrigineous clastic was considered and rejected +first because it is considered redundant, anything that is +terrigineous is clastic. Second, it is questionable if clastic +sediment derived by submarine processes (fragementation by gravity +sliding, faulting, or volcanic activity, with transport by sediment +gravity flow or submarine currents) is terrigineous, but it is clastic +and is meant to be included in this category. +Sediment in which at least 50 percent of the constituent particles +were derived from erosion, weathering, or mass-wasting of pre-existing +earth materials, and transported to the place of deposition by +mechanical agents such as water, wind, ice and gravity. + +#### diamicton + +[]{#diamicton} + +Concept: [`Diamicton`](https://w3id.org/isample/earthenv/rocksediment/Diamicton) + +Child of: + [`Clastic_Sediment`](#Clastic_Sediment) + +definition amplified to help distinguish diamicton, conglomerate and +wackestone in this version +Unsorted or poorly sorted, clastic sediment with a wide range of +particle sizes, including a muddy matrix. Biogenic materials that have +such texture are excluded. Distinguished from conglomerate, sandstone, +mudstone based on polymodality and lack of structures related to +transport and deposition of sediment by moving air or water. +Assignment to an other size class can be used in conjunction to +indicate the dominant grain size. + +### gravel size sediment + +[]{#gravel_size_sediment} + +Concept: [`Gravel_Size_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Gravel_Size_Sediment) + +Child of: + [`sediment`](#sediment) + +Sediment containing greater than 30 percent gravel-size particles +(greater than 2.0 mm diameter). Composition or gensis of clasts not +specified. + +### hybrid sediment + +[]{#hybrid_sediment} + +Concept: [`Hybrid_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Hybrid_Sediment) + +Child of: + [`sediment`](#sediment) + +Sediment that does not fit any of the other sediment +composition/genesis categories. Sediment consisting of three or more +components which form more than 5 percent but less than 50 precent of +the material. + +### iron rich sediment + +[]{#iron_rich_sediment} + +Concept: [`Iron_Rich_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Iron_Rich_Sediment) + +Child of: + [`sediment`](#sediment) + +Sediment that consists of at least 50 percent iron-bearing minerals +(hematite, magnetite, limonite-group, siderite, iron-sulfides), as +determined by hand-lens or petrographic analysis. Corresponds to a +rock typically containing 15 percent iron by weight. + +### mud size sediment + +[]{#mud_size_sediment} + +Concept: [`Mud_Size_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Mud_Size_Sediment) + +Child of: + [`sediment`](#sediment) + +Sediment consisting of less than 30 percent gravel-size (2 mm) +particles and with a mud-size to sand-size particle ratio greater than +1. Clasts may be of any composition or origin. BGS (Hallsworth and +Knox, 1999, p. 9) define the 'upper size limit of mud ... at 32 +micrometers (.032 mm)', but Wentworth scale and Krumbein scale put +boundary at .064 or .062 mm (inidistinguishable difference in +rocks...) BGS 'mud-grade sediment' or sedimentary rock definition is +'over 75% of the clasts smaller than .032 mm', which is narrower than +the definition here. + +### non clastic siliceous sediment + +[]{#non_clastic_siliceous_sediment} + +Concept: [`Non_Clastic_Siliceous_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Non_Clastic_Siliceous_Sediment) + +Child of: + [`sediment`](#sediment) + +Sediment that consists of at least 50 percent silicate mineral +material, deposited directly by chemical or biological processes at +the depositional surface, or in particles formed by chemical or +biological processes within the basin of deposition. + +### phosphate rich sediment + +[]{#phosphate_rich_sediment} + +Concept: [`Phosphate_Rich_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Phosphate_Rich_Sediment) + +Child of: + [`sediment`](#sediment) + +Sediment in which at least 50 percent of the primary and/or +recrystallized constituents are phosphate minerals. + +### sand size sediment + +[]{#sand_size_sediment} + +Concept: [`Sand_Size_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Sand_Size_Sediment) + +Child of: + [`sediment`](#sediment) + +Sediment in which less than 30 percent of particles are gravel +(greater than 2 mm in diameter) and the sand to mud ratio is at least +1. composition or genesis of clasts not specified. + +### tephra + +[]{#tephra} + +Concept: [`Tephra`](https://w3id.org/isample/earthenv/rocksediment/Tephra) + +Child of: + [`sediment`](#sediment) + +Unconsolidated pyroclastic material in which greater than 75 percent +of the fragments are deposited as a direct result of volcanic +processes and the deposit has not been reworked by epiclastic +processes. Includes ash, lapilli tephra, bomb tephra, block tephra and +unconsolidated agglomerate. + + diff --git a/models/generated/extensions/earthenv_materialsampleobject_type.md b/models/generated/extensions/earthenv_materialsampleobject_type.md new file mode 100644 index 0000000..f5eb1a4 --- /dev/null +++ b/models/generated/extensions/earthenv_materialsampleobject_type.md @@ -0,0 +1,1222 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "Earth and Environmental Science extension - Material sample type" +date: "2025-12-11T02:41:32.972715+00:00" +subtitle: | + This concept scheme contains skos concepts for categorizing kinds of Earth Material sample types, extending the iSamples Material Sample Object Type vocabulary. Defintions from SESAR, ODM2, wikipedia, ESS-DIVE, and other sources; sources are cited with each term. +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_materialsampleobject_type.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_materialsampleobject_type.ttl) + + +Namespace: +[`https://w3id.org/isample/earthenv/esmaterialsample/essampletype`](https://w3id.org/isample/earthenv/esmaterialsample/essampletype) + +**History** + +* 2023-07-07 SMR add solid material sample and broader relations from classes it subsumes. +* 2023-07-27 SMR modify base specimen type vocabulary, add 'Non biologic solid object' to replace 'solid material sample', change broader relations in this vocab to use that as parent class where appropriate. 'Solid material sample' is too closely linked to material type, created confusion. Intention is a specimen category for solid objects that are not biologic. Obviously there is some overlap with Research specimens. +* 2024-07-15 SMR fix import to base vocabulary on renamed material_sample_type vocabulary, change from specimentypevocabulary to materialsampleobjecttype/conceptscheme + +**Concepts** + +- [Analytical preparation](#analyticalpreparation) + - [Cell culture](#cellculture) + - [Dissolved chemical fraction](#dissolvedchemicalfraction) + - [Eluate](#eluate) + - [FIB lamella](#fiblamella) + - [Glass slide smear](#glassslidesmear) + - [Individual solid cube](#individualsolidcube) + - [Magnetic fraction](#magneticfraction) + - [Mechanical fraction](#mechanicalfraction) + - [Mineral separate](#mineralseparate) + - [Magnetic fraction](#magneticfraction) + - [Non-magnetic fraction](#nonmagneticfraction) + - [Sectioned specimen](#mountedsection) + - [Thick section](#thicksection) + - [Thin section](#thinsection) + - [Polished thin section](#polishedthinsection) + - [Ultra thin section](#ultrathinsection) + - [Non-magnetic fraction](#nonmagneticfraction) + - [Peel](#peel) + - [Prepared powder](#preparedpowder) + - [Prepared rock powder](#preparedrockpowder) + - [Pressed pellet](#pressedpellet) + - [Residual material](#residualmaterial) + - [Slab](#slab) + +- [Bundle biome aggregation](#bundlebiomeaggregation) + - [Cell culture](#cellculture) + +- [Fluid in container](#fluidincontainer) + - [Direct fluid sample](#directfluidsample) + - [Dissolved chemical fraction](#dissolvedchemicalfraction) + - [Eluate](#eluate) + - [Processed fluid sample](#processedfluidsample) + - [Filtrate](#filtrate) + +- [Generic aggregation](#genericaggregation) + - [Boxed core](#boxedcore) + - [Composite sample](#compositesample) + - [Chip Channel Sample](#chipchannelsample) + - [High Grade Sample](#highgradesample) + - [Site composite sample](#sitecompositesample) + - [Core catcher](#corecatcher) + - [Cuttings](#cuttings) + - [Dredge](#dredge) + - [Material captured in filter](#materialcapturedinfilter) + - [Mechanical fraction](#mechanicalfraction) + - [Mineral separate](#mineralseparate) + - [Magnetic fraction](#magneticfraction) + - [Non-magnetic fraction](#nonmagneticfraction) + - [Natural aggregate specimen](#naturalaggregate) + - [Prepared powder](#preparedpowder) + - [Prepared rock powder](#preparedrockpowder) + - [TEM grid](#temgrid) + - [Trawl](#trawl) + +- [Other solid object](#othersolidobject) + - [Dust wipe](#dustwipe) + - [Glass slide smear](#glassslidesmear) + - [Peel](#peel) + +- [Solid material sample](#solidmaterialsample) + - [Core](#core) + - [Core half round](#corehalfround) + - [Core piece](#corepiece) + - [Core quarter round](#corequarterround) + - [Core section](#coresection) + - [Core subpeice](#coresubpeice) + - [FIB lamella](#fiblamella) + - [Individual solid cube](#individualsolidcube) + - [Individual solid cylinder](#individualsolidcylinder) + - [Meteorite](#meteorite) + - [Mineral specimen](#mineralspecimen) + - [Sectioned specimen](#mountedsection) + - [Thick section](#thicksection) + - [Thin section](#thinsection) + - [Polished thin section](#polishedthinsection) + - [Ultra thin section](#ultrathinsection) + - [Pressed pellet](#pressedpellet) + - [Rock hand sample](#rockhandsample) + - [Slab](#slab) + - [U-channel sample](#uchannelsample) + - [Atom probe tip](#atomprobetip) + - [Chip](#chip) + - [Microtome slice](#microtomeslice) + - [Mounted specimen](#mountedspecimen) + - [Polished mounted specimen](#polishedmountedspecimen) + - [Particle](#particle) + +## Analytical preparation + +[]{#analyticalpreparation} + +Concept: [`analyticalpreparation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/analyticalpreparation) + +Specimen is a product of processing required for some observation +procedure, e.g. thin section, XRF bead, SEM stub, rock powder. If +identified separately, this should have a ‘parent’ link to the +original sample + +### Cell culture + +[]{#cellculture} + +Concept: [`cellculture`](https://w3id.org/isample/earthenv/esmaterialsample/cellculture) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`bundlebiomeaggregation`](#bundlebiomeaggregation) + +a collection of cells are grown under controlled conditions, generally +outside of their natural environment + +### Dissolved chemical fraction + +[]{#dissolvedchemicalfraction} + +Concept: [`dissolvedchemicalfraction`](https://w3id.org/isample/earthenv/esmaterialsample/dissolvedchemicalfraction) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`fluidincontainer`](#fluidincontainer) + +A fluid concentrating some constituent of interest from a parent +sample. The dissolved constituent is actually the sample material of +interest. + +#### Eluate + +[]{#eluate} + +Concept: [`eluate`](https://w3id.org/isample/earthenv/esmaterialsample/eluate) + +Child of: + [`dissolvedchemicalfraction`](#dissolvedchemicalfraction) + +The fluid product that contains the analyte of interest washed from a +chromatography column + +### FIB lamella + +[]{#fiblamella} + +Concept: [`fiblamella`](https://w3id.org/isample/earthenv/esmaterialsample/fiblamella) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +very thin sheet of solid material milled from a larger sample using a +focused ion beam. Used for TEM analysis. + +### Glass slide smear + +[]{#glassslidesmear} + +Concept: [`glassslidesmear`](https://w3id.org/isample/earthenv/esmaterialsample/glassslidesmear) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`othersolidobject`](#othersolidobject) + +sample from a cell culture (or other microparticulate suspension) +spread into a thin layer on a glass slide for optical investigation + +### Individual solid cube + +[]{#individualsolidcube} + +Concept: [`individualsolidcube`](https://w3id.org/isample/earthenv/esmaterialsample/individualsolidcube) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +A sample that is a prepared cube of material, intended as a sample of +that material. + +### Magnetic fraction + +[]{#magneticfraction} + +Concept: [`magneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/magneticfraction) + +Child of: + [`mineralseparate`](#mineralseparate) + [`analyticalpreparation`](#analyticalpreparation) + +a collection of particles separated from a crushed rock sample based +on their attraction to a magnet. + +### Mechanical fraction + +[]{#mechanicalfraction} + +Concept: [`mechanicalfraction`](https://w3id.org/isample/earthenv/esmaterialsample/mechanicalfraction) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`genericaggregation`](#genericaggregation) + +defined by sample preparation involving mechanical processing, e.g. +grain size, density, or grain shape separation. + +### Mineral separate + +[]{#mineralseparate} + +Concept: [`mineralseparate`](https://w3id.org/isample/earthenv/esmaterialsample/mineralseparate) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`genericaggregation`](#genericaggregation) + +an aggregation of particles of the same mineral extracted and +concentrated from a rock. + +#### Magnetic fraction + +[]{#magneticfraction} + +Concept: [`magneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/magneticfraction) + +Child of: + [`mineralseparate`](#mineralseparate) + [`analyticalpreparation`](#analyticalpreparation) + +a collection of particles separated from a crushed rock sample based +on their attraction to a magnet. + +#### Non-magnetic fraction + +[]{#nonmagneticfraction} + +Concept: [`nonmagneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/nonmagneticfraction) + +Child of: + [`mineralseparate`](#mineralseparate) + [`analyticalpreparation`](#analyticalpreparation) + +collection of particles from a crushed rock sample based on their lack +of attraction to a magnet + +### Sectioned specimen + +[]{#mountedsection} + +Concept: [`mountedsection`](https://w3id.org/isample/earthenv/esmaterialsample/mountedsection) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +a thin slice of a solid material that has been mounted on a glass +slide for study + +#### Thick section + +[]{#thicksection} + +Concept: [`thicksection`](https://w3id.org/isample/earthenv/esmaterialsample/thicksection) + +Child of: + [`mountedsection`](#mountedsection) + +Thick sections are like thin sections, but milled to a greater +thickness. Typcially polished on one or both sides and used for fluid +or melt inclusion studies, Raman analyses, and infrared spectroscopy +analyses, and SEM or electron microprobe. The standard thickness for a +fluid inclusion thick section is 50 micrometers, but thick sections +can be made at any thickness. Thick sections can be attached to a +glass slide, or can be prepared so that they can be removed from their +mount as a stand-alone slice of rock. + +#### Thin section + +[]{#thinsection} + +Concept: [`thinsection`](https://w3id.org/isample/earthenv/esmaterialsample/thinsection) + +Child of: + [`mountedsection`](#mountedsection) + +thin sliver of rock cut from a sample with a diamond saw and ground +optically flat, and then mounted on a glass slide and ground smooth +using progressively finer abrasive grit until the sample is 30 microns +thick. + +##### Polished thin section + +[]{#polishedthinsection} + +Concept: [`polishedthinsection`](https://w3id.org/isample/earthenv/esmaterialsample/polishedthinsection) + +Child of: + [`thinsection`](#thinsection) + +a thin section that has its free surface polished until perfectly +planar and free of pits and scratches. Used for reflected light +petrography and for electron microprobe or SEM investigation. + +#### Ultra thin section + +[]{#ultrathinsection} + +Concept: [`ultrathinsection`](https://w3id.org/isample/earthenv/esmaterialsample/ultrathinsection) + +Child of: + [`mountedsection`](#mountedsection) + +An ordinary thin section that is attached to the glass slide using a +soluble cement such as Canada balsam (soluble in ethanol) to allow +both sides to be worked on. The section is polished on both sides +using a fine diamond paste until it has a thickness in the range of +2-12 microns. This technique has been used to study the microstructure +of very fine-grained carbonate rocks, and also in the preparation of +mineral and rock specimens for transmission electron microscopy. + +### Non-magnetic fraction + +[]{#nonmagneticfraction} + +Concept: [`nonmagneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/nonmagneticfraction) + +Child of: + [`mineralseparate`](#mineralseparate) + [`analyticalpreparation`](#analyticalpreparation) + +collection of particles from a crushed rock sample based on their lack +of attraction to a magnet + +### Peel + +[]{#peel} + +Concept: [`peel`](https://w3id.org/isample/earthenv/esmaterialsample/peel) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`othersolidobject`](#othersolidobject) + +Acetate peels are made by polishing a planar surface on a sample, +etching it with acid to give it some relief, and then chemically +melting a piece of acetate onto that surface. The acetate is then +pulled off for examination under a microscope. The acetate preserves a +fingerprint of the internal structure of the sample surface. Used in +paleontology to study complex fossils, e.g. bryozoan. + +### Prepared powder + +[]{#preparedpowder} + +Concept: [`preparedpowder`](https://w3id.org/isample/earthenv/esmaterialsample/preparedpowder) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`genericaggregation`](#genericaggregation) + +distinguish from particulate in that particulate is sampled as a +micron-size aggregate, whereas this material is ground to a powder for +subsequent analysis; it is a powder as a function of some preparation +process (e.g. chemical precipitation) + +#### Prepared rock powder + +[]{#preparedrockpowder} + +Concept: [`preparedrockpowder`](https://w3id.org/isample/earthenv/esmaterialsample/preparedrockpowder) + +Child of: + [`preparedpowder`](#preparedpowder) + +a powder manufactured by pulverizing a rock. + +### Pressed pellet + +[]{#pressedpellet} + +Concept: [`pressedpellet`](https://w3id.org/isample/earthenv/esmaterialsample/pressedpellet) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +a sample prepared by grinding a parent sample to a fine powder, mixing +it with a binder, and pressing the mixture into a die at a pressure of +between 15 and 35 tons to produce a solid disc for subsequent +analysis, typically by X-Ray fluorescence. + +### Residual material + +[]{#residualmaterial} + +Concept: [`residualmaterial`](https://w3id.org/isample/earthenv/esmaterialsample/residualmaterial) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + +Sample is material remaining after processing to extract some other +components of interest from the sample. + +### Slab + +[]{#slab} + +Concept: [`slab`](https://w3id.org/isample/earthenv/esmaterialsample/slab) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +a relatively planar rock sample,cut from a large sample to produce a +tabular peice of rock with the irregular outline of the original +sample on the diameter where the cut was mate. + + +## Bundle biome aggregation + +[]{#bundlebiomeaggregation} + +Concept: [`bundlebiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/bundlebiomeaggregation) + +An aggregation of whole organisms representative of some biome + +### Cell culture + +[]{#cellculture} + +Concept: [`cellculture`](https://w3id.org/isample/earthenv/esmaterialsample/cellculture) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`bundlebiomeaggregation`](#bundlebiomeaggregation) + +a collection of cells are grown under controlled conditions, generally +outside of their natural environment + + +## Fluid in container + +[]{#fluidincontainer} + +Concept: [`fluidincontainer`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/fluidincontainer) + +Specimen is a container whose contents are liquid, gas, or mixed +dominantly fluid phases that is the actual sample material. Fluid +might include minor solid particles. Container typically human made, +but also includes natural fluid container, e.g. fluid inclusion in a +mineral grain. Includes colloids, foams, gels, suspensions. The +sample is the fluid substance; fluid samples collected to analyze the +contained biome should be considered 'Biome Aggregation' + +### Direct fluid sample + +[]{#directfluidsample} + +Concept: [`directfluidsample`](https://w3id.org/isample/earthenv/esmaterialsample/directfluidsample) + +Child of: + [`fluidincontainer`](#fluidincontainer) + +a fluid collected from the sampled feature (e.g. water body, +hydrothermal vent, atmosphere...) with no processing. (e.g. +filtration, addition of preservatives). + +### Dissolved chemical fraction + +[]{#dissolvedchemicalfraction} + +Concept: [`dissolvedchemicalfraction`](https://w3id.org/isample/earthenv/esmaterialsample/dissolvedchemicalfraction) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`fluidincontainer`](#fluidincontainer) + +A fluid concentrating some constituent of interest from a parent +sample. The dissolved constituent is actually the sample material of +interest. + +#### Eluate + +[]{#eluate} + +Concept: [`eluate`](https://w3id.org/isample/earthenv/esmaterialsample/eluate) + +Child of: + [`dissolvedchemicalfraction`](#dissolvedchemicalfraction) + +The fluid product that contains the analyte of interest washed from a +chromatography column + +### Processed fluid sample + +[]{#processedfluidsample} + +Concept: [`processedfluidsample`](https://w3id.org/isample/earthenv/esmaterialsample/processedfluidsample) + +Child of: + [`fluidincontainer`](#fluidincontainer) + +fluid sample that has been processed in some way during or after +collection, e.g. by filtering, addition of preservatives. + +#### Filtrate + +[]{#filtrate} + +Concept: [`filtrate`](https://w3id.org/isample/earthenv/esmaterialsample/filtrate) + +Child of: + [`processedfluidsample`](#processedfluidsample) + +A sample that has gone through a filtration process to separate solids +from fluids (liquids or gases), using a filter medium through which +only the fluid can pass. Must be associated with a filter size. + + +## Generic aggregation + +[]{#genericaggregation} + +Concept: [`genericaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/genericaggregation) + +An aggregate specimen that is not biogenic or composed of +anthropogenic material fragments. Examples: loose soil or sediment +(e.g. in a bag), rock chips, particulate filtrate or precipitate; rock +powders. + +### Boxed core + +[]{#boxedcore} + +Concept: [`boxedcore`](https://w3id.org/isample/earthenv/esmaterialsample/boxedcore) + +Child of: + [`genericaggregation`](#genericaggregation) + +A collection of core peices that are stored in an individual box. +Typically the box will contain core peices from the same core. + +### Composite sample + +[]{#compositesample} + +Concept: [`compositesample`](https://w3id.org/isample/earthenv/esmaterialsample/compositesample) + +Child of: + [`genericaggregation`](#genericaggregation) + +a sample composed of multiple peices, representative of some material, +or representative of some site. The peices do not all originate from +the same object. + +#### Chip Channel Sample + +[]{#chipchannelsample} + +Concept: [`chipchannelsample`](https://w3id.org/isample/earthenv/esmaterialsample/chipchannelsample) + +Child of: + [`compositesample`](#compositesample) + +small chips of rock collected over a specified interval, with the +objective to obtain a representative sample for that interval. Most of +the time chip channel samples are collected in succession along a +sample line which is laid out in advance using a tape. The freshest +material possible is sampled, preferably chipping directly from +bedrock. Sample intervals are set at a specified width, usually +ranging from 30cm to 7m. Due to the method of sampling, chip channel +samples tend to be rather large (up to 20 pounds for a five foot +interval) + +#### High Grade Sample + +[]{#highgradesample} + +Concept: [`highgradesample`](https://w3id.org/isample/earthenv/esmaterialsample/highgradesample) + +Child of: + [`compositesample`](#compositesample) + +in mineral exploration, selective pieces of the most highly +mineralized material from a mineralize site, intentionally excluding +less mineralized material. A high grade sample might be collected to +indicate what the best possible values are, or to provide material for +certain types of trace element analyses. + +#### Site composite sample + +[]{#sitecompositesample} + +Concept: [`sitecompositesample`](https://w3id.org/isample/earthenv/esmaterialsample/sitecompositesample) + +Child of: + [`compositesample`](#compositesample) + +an aggregation of peices of uniform material collected over some area +(generally greater than 2.5m across). These are the ideal +'representative' samples used in mineral exploration. A composite +sample might be collected to determine the background values of trace +elements in a particular type of rock, or to determine if ore grade +mineralization is present over a large area. + +### Core catcher + +[]{#corecatcher} + +Concept: [`corecatcher`](https://w3id.org/isample/earthenv/esmaterialsample/corecatcher) + +Child of: + [`genericaggregation`](#genericaggregation) + +material recovered from the core catcher of a sedimentary core and +which is treated as a separate section from the core. The core catcher +is a device at the bottom of the core barrel that prevents the core +from sliding out while the barrel is retrieved from the hole. +(http://publications.iodp.org/proceedings/323/102/102_.htm) + +### Cuttings + +[]{#cuttings} + +Concept: [`cuttings`](https://w3id.org/isample/earthenv/esmaterialsample/cuttings) + +Child of: + [`genericaggregation`](#genericaggregation) + +unconsolidated Earth material produced by the grinding action of a +drill bit during drilling of a borehole. + +### Dredge + +[]{#dredge} + +Concept: [`dredge`](https://w3id.org/isample/earthenv/esmaterialsample/dredge) + +Child of: + [`genericaggregation`](#genericaggregation) + +an aggregation of material sampled by dragging a collection bucket +(dredge) across the bottom of a water body + +### Material captured in filter + +[]{#materialcapturedinfilter} + +Concept: [`materialcapturedinfilter`](https://w3id.org/isample/earthenv/esmaterialsample/materialcapturedinfilter) + +Child of: + [`genericaggregation`](#genericaggregation) + +A material sample captured in filter, for example from a water sample +that was filtered. Must be associated with filter size field. + +### Mechanical fraction + +[]{#mechanicalfraction} + +Concept: [`mechanicalfraction`](https://w3id.org/isample/earthenv/esmaterialsample/mechanicalfraction) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`genericaggregation`](#genericaggregation) + +defined by sample preparation involving mechanical processing, e.g. +grain size, density, or grain shape separation. + +### Mineral separate + +[]{#mineralseparate} + +Concept: [`mineralseparate`](https://w3id.org/isample/earthenv/esmaterialsample/mineralseparate) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`genericaggregation`](#genericaggregation) + +an aggregation of particles of the same mineral extracted and +concentrated from a rock. + +#### Magnetic fraction + +[]{#magneticfraction} + +Concept: [`magneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/magneticfraction) + +Child of: + [`mineralseparate`](#mineralseparate) + [`analyticalpreparation`](#analyticalpreparation) + +a collection of particles separated from a crushed rock sample based +on their attraction to a magnet. + +#### Non-magnetic fraction + +[]{#nonmagneticfraction} + +Concept: [`nonmagneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/nonmagneticfraction) + +Child of: + [`mineralseparate`](#mineralseparate) + [`analyticalpreparation`](#analyticalpreparation) + +collection of particles from a crushed rock sample based on their lack +of attraction to a magnet + +### Natural aggregate specimen + +[]{#naturalaggregate} + +Concept: [`naturalaggregate`](https://w3id.org/isample/earthenv/esmaterialsample/naturalaggregate) + +Child of: + [`genericaggregation`](#genericaggregation) + +E.g beach sand, soil, river sediment, scoop of regolith. +Specimen is aggregate of non-consolidated material formed by natural +processes. Particles have not been intentionally modified from the +sampled feature. + +### Prepared powder + +[]{#preparedpowder} + +Concept: [`preparedpowder`](https://w3id.org/isample/earthenv/esmaterialsample/preparedpowder) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`genericaggregation`](#genericaggregation) + +distinguish from particulate in that particulate is sampled as a +micron-size aggregate, whereas this material is ground to a powder for +subsequent analysis; it is a powder as a function of some preparation +process (e.g. chemical precipitation) + +#### Prepared rock powder + +[]{#preparedrockpowder} + +Concept: [`preparedrockpowder`](https://w3id.org/isample/earthenv/esmaterialsample/preparedrockpowder) + +Child of: + [`preparedpowder`](#preparedpowder) + +a powder manufactured by pulverizing a rock. + +### TEM grid + +[]{#temgrid} + +Concept: [`temgrid`](https://w3id.org/isample/earthenv/esmaterialsample/temgrid) + +Child of: + [`genericaggregation`](#genericaggregation) + +FIB sections and microtome slices set onto a small grid for handling, +transport, and analysis using a transmission electron microscope +(TEM). The grid itself can be given a single sample identifier +(similar to how there are multiple grains in a grain mount). The +linkage from the individual samples in the grid to their parent +sample(s) should be documented + +### Trawl + +[]{#trawl} + +Concept: [`trawl`](https://w3id.org/isample/earthenv/esmaterialsample/trawl) + +Child of: + [`genericaggregation`](#genericaggregation) + +an aggregation of biogenic or non-biogenic material extracted from a +water body + + +## Other solid object + +[]{#othersolidobject} + +Concept: [`othersolidobject`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/othersolidobject) + +Single piece of material not one of the other types. + +### Dust wipe + +[]{#dustwipe} + +Concept: [`dustwipe`](https://w3id.org/isample/earthenv/esmaterialsample/dustwipe) + +Child of: + [`othersolidobject`](#othersolidobject) + +a pre-weighed and packaged paper towel (wipe) used to wipe over a +surface to collect particulates from the surface + +### Glass slide smear + +[]{#glassslidesmear} + +Concept: [`glassslidesmear`](https://w3id.org/isample/earthenv/esmaterialsample/glassslidesmear) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`othersolidobject`](#othersolidobject) + +sample from a cell culture (or other microparticulate suspension) +spread into a thin layer on a glass slide for optical investigation + +### Peel + +[]{#peel} + +Concept: [`peel`](https://w3id.org/isample/earthenv/esmaterialsample/peel) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`othersolidobject`](#othersolidobject) + +Acetate peels are made by polishing a planar surface on a sample, +etching it with acid to give it some relief, and then chemically +melting a piece of acetate onto that surface. The acetate is then +pulled off for examination under a microscope. The acetate preserves a +fingerprint of the internal structure of the sample surface. Used in +paleontology to study complex fossils, e.g. bryozoan. + + +## Solid material sample + +[]{#solidmaterialsample} + +Concept: [`solidmaterialsample`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/solidmaterialsample) + + +### Core + +[]{#core} + +Concept: [`core`](https://w3id.org/isample/earthenv/esmaterialsample/core) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +Cylinder of rock or sediment extracted from within the earth, and +representing the entire sample extracted during a single borehole +drilling event. Typically using some rotary drilling technology. In +many cases the core is extracted in segments that are 'core sections'. +A core from a single borehole is rarely a continous unbroken object; +commonly parts of the core will break up during drilling or +extraction, leaving gaps or sections that are granular material. Cores +are normally composed of consolidated ('solid') material, but in some +cases loosely consolidated material might be recovered, and considered +sediment or tephra. To be called 'core' the material must be +sufficiently consolidated to maintain a cylindrical shape. A core +hasPart (hasChild) 'Core section' + +### Core half round + +[]{#corehalfround} + +Concept: [`corehalfround`](https://w3id.org/isample/earthenv/esmaterialsample/corehalfround) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +Half-cylindrical peice of consolidated material produced by along-axis +split of a core whole round along a selected diameter . Has childOf +relation to core section or core, core section, or Core peice from +which is was split + +### Core piece + +[]{#corepiece} + +Concept: [`corepiece`](https://w3id.org/isample/earthenv/esmaterialsample/corepiece) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +A cylindrical peice of consolidated earth material extracted as a +single solid object between breaks in recovery of core from a +borehole. has parent core section + +### Core quarter round + +[]{#corequarterround} + +Concept: [`corequarterround`](https://w3id.org/isample/earthenv/esmaterialsample/corequarterround) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +a partial cylindrical peice of consolidated material created by along- +axis split of a core half round. Has Parent core half round + +### Core section + +[]{#coresection} + +Concept: [`coresection`](https://w3id.org/isample/earthenv/esmaterialsample/coresection) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +Segment of a core representing some interval along the well bore. +Child of Core + +### Core subpeice + +[]{#coresubpeice} + +Concept: [`coresubpeice`](https://w3id.org/isample/earthenv/esmaterialsample/coresubpeice) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +A peice of consolidated material broken from a core peice. has Parent +core peice or core section + +### FIB lamella + +[]{#fiblamella} + +Concept: [`fiblamella`](https://w3id.org/isample/earthenv/esmaterialsample/fiblamella) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +very thin sheet of solid material milled from a larger sample using a +focused ion beam. Used for TEM analysis. + +### Individual solid cube + +[]{#individualsolidcube} + +Concept: [`individualsolidcube`](https://w3id.org/isample/earthenv/esmaterialsample/individualsolidcube) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +A sample that is a prepared cube of material, intended as a sample of +that material. + +### Individual solid cylinder + +[]{#individualsolidcylinder} + +Concept: [`individualsolidcylinder`](https://w3id.org/isample/earthenv/esmaterialsample/individualsolidcylinder) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +A cylindrical peice of consolidated material not obtained by +subsurface drilling. Cores drilled for paleomagnetic analysis are a +common example. Tree ring cores are another... + +### Meteorite + +[]{#meteorite} + +Concept: [`meteorite`](https://w3id.org/isample/earthenv/esmaterialsample/meteorite) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +A meteorite is a solid object that originates in interplanetary space +and survives passage through an atmosphere to reach the surface of a +planet or moon. + +### Mineral specimen + +[]{#mineralspecimen} + +Concept: [`mineralspecimen`](https://w3id.org/isample/earthenv/esmaterialsample/mineralspecimen) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +a solid object consisting of one particular mineral, or several +minerals intended to be representative of one or more of the mineral +species. + +### Sectioned specimen + +[]{#mountedsection} + +Concept: [`mountedsection`](https://w3id.org/isample/earthenv/esmaterialsample/mountedsection) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +a thin slice of a solid material that has been mounted on a glass +slide for study + +#### Thick section + +[]{#thicksection} + +Concept: [`thicksection`](https://w3id.org/isample/earthenv/esmaterialsample/thicksection) + +Child of: + [`mountedsection`](#mountedsection) + +Thick sections are like thin sections, but milled to a greater +thickness. Typcially polished on one or both sides and used for fluid +or melt inclusion studies, Raman analyses, and infrared spectroscopy +analyses, and SEM or electron microprobe. The standard thickness for a +fluid inclusion thick section is 50 micrometers, but thick sections +can be made at any thickness. Thick sections can be attached to a +glass slide, or can be prepared so that they can be removed from their +mount as a stand-alone slice of rock. + +#### Thin section + +[]{#thinsection} + +Concept: [`thinsection`](https://w3id.org/isample/earthenv/esmaterialsample/thinsection) + +Child of: + [`mountedsection`](#mountedsection) + +thin sliver of rock cut from a sample with a diamond saw and ground +optically flat, and then mounted on a glass slide and ground smooth +using progressively finer abrasive grit until the sample is 30 microns +thick. + +##### Polished thin section + +[]{#polishedthinsection} + +Concept: [`polishedthinsection`](https://w3id.org/isample/earthenv/esmaterialsample/polishedthinsection) + +Child of: + [`thinsection`](#thinsection) + +a thin section that has its free surface polished until perfectly +planar and free of pits and scratches. Used for reflected light +petrography and for electron microprobe or SEM investigation. + +#### Ultra thin section + +[]{#ultrathinsection} + +Concept: [`ultrathinsection`](https://w3id.org/isample/earthenv/esmaterialsample/ultrathinsection) + +Child of: + [`mountedsection`](#mountedsection) + +An ordinary thin section that is attached to the glass slide using a +soluble cement such as Canada balsam (soluble in ethanol) to allow +both sides to be worked on. The section is polished on both sides +using a fine diamond paste until it has a thickness in the range of +2-12 microns. This technique has been used to study the microstructure +of very fine-grained carbonate rocks, and also in the preparation of +mineral and rock specimens for transmission electron microscopy. + +### Pressed pellet + +[]{#pressedpellet} + +Concept: [`pressedpellet`](https://w3id.org/isample/earthenv/esmaterialsample/pressedpellet) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +a sample prepared by grinding a parent sample to a fine powder, mixing +it with a binder, and pressing the mixture into a die at a pressure of +between 15 and 35 tons to produce a solid disc for subsequent +analysis, typically by X-Ray fluorescence. + +### Rock hand sample + +[]{#rockhandsample} + +Concept: [`rockhandsample`](https://w3id.org/isample/earthenv/esmaterialsample/rockhandsample) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +individual peice of rock broken from an outcrop or larger peice of +rock. + +### Slab + +[]{#slab} + +Concept: [`slab`](https://w3id.org/isample/earthenv/esmaterialsample/slab) + +Child of: + [`analyticalpreparation`](#analyticalpreparation) + [`solidmaterialsample`](#solidmaterialsample) + +a relatively planar rock sample,cut from a large sample to produce a +tabular peice of rock with the irregular outline of the original +sample on the diameter where the cut was mate. + +### U-channel sample + +[]{#uchannelsample} + +Concept: [`uchannelsample`](https://w3id.org/isample/earthenv/esmaterialsample/uchannelsample) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +a rectangular prism of loosely consolidated sediment extracted from a +core segment. has parent core piece or core segment + +### Atom probe tip + +[]{#atomprobetip} + +Concept: [`atomprobetip`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/atomprobetip) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +needle-shaped sample milled out of a larger sample with a focused ion +beam (FIB). + +### Chip + +[]{#chip} + +Concept: [`chip`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/chip) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +Individual solid object intentionally broken off a larger solid object +sample. A Chip must have a documented parent sample. + +### Microtome slice + +[]{#microtomeslice} + +Concept: [`microtomeslice`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/microtomeslice) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +Typically from TEM analysis. Slices are commonly deposited in a grid +contain with multiple slices and the grid will be given a single +sample name, not the individual slices within it. The provenance of +the slice from paticle to mounted specimen to slice should be +carefully documented +A very thin slice cut from a mounted specimen using a mocrotome or +ultramicrotome. + +### Mounted specimen + +[]{#mountedspecimen} + +Concept: [`mountedspecimen`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/mountedspecimen) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +one or more solid objects embedded in a stabilizing matrix, typically +epoxy, metal, or paraffin to allow slicing through the mounted +object(s). + +#### Polished mounted specimen + +[]{#polishedmountedspecimen} + +Concept: [`polishedmountedspecimen`](https://w3id.org/isample/earthenv/esmaterialsample/polishedmountedspecimen) + +Child of: + [`mountedspecimen`](#mountedspecimen) + +Mounted specimen with polished surface exposing mounted material for +analysis + +### Particle + +[]{#particle} + +Concept: [`particle`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/particle) + +Child of: + [`solidmaterialsample`](#solidmaterialsample) + +Can also used for small peices broken from a 'Rock hand sample'. +OSIRIS-Rex definition specifies 'competent individual geologic sample +of any size'. 'Competent' interpreted to be equivalent to 'solid', or +'consolidated'. The definition here is broader in that it includes +materials of any origin, but narrower in that it is restricted to +small objects. +A small individual solid object that is not one of the other sample +types. + + diff --git a/models/generated/extensions/earthenv_sampled_feature_role.md b/models/generated/extensions/earthenv_sampled_feature_role.md new file mode 100644 index 0000000..f69b786 --- /dev/null +++ b/models/generated/extensions/earthenv_sampled_feature_role.md @@ -0,0 +1,209 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "Earth and Environmental Science extension - Sampled feature role" +date: "2025-12-11T02:41:32.323627+00:00" +subtitle: | + Terms to categorize the relation of a sampled feature to its context. In the Earth Science realm this is typically relation of sampled feature to a containing rock body or rock body part. +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_sampled_feature_role.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_sampled_feature_role.ttl) + + +Namespace: +[`https://w3id.org/isample/earthenv/essampledfeatrole/sfrolevocabulary`](https://w3id.org/isample/earthenv/essampledfeatrole/sfrolevocabulary) + +**History** + +* 2023-11-17 SMR generate to account for sample classifications in SESAR +* 2024-09-13 SMR remove version number from URI + +**Concepts** + +- [Sampled feature part](#sampledfeaturepart) + - [inclusion](#inclusion) + - [clast](#clast) + - [cognate inclusion](#cognateinclusion) + - [fluid inclusion](#fluidinclusion) + - [melt inclusion](#meltinclusion) + - [mineral inclusion](#mineralinclusion) + - [xenolith](#xenolith) + - [individual constituent](#individualconstituent) + - [cement](#cement) + - [groundmass](#groundmass) + - [phenocryst](#phenocryst) + - [porphyroblast](#porphyroblast) + - [rock body](#rockbody) + +## Sampled feature part + +[]{#sampledfeaturepart} + +Concept: [`sampledfeaturepart`](https://w3id.org/isample/earthenv/essampledfeatrole/sampledfeaturepart) + +A sampled feature that is part of a larger sampled feature; Could be +improper part (e.g. the whole larger feature) + +### inclusion + +[]{#inclusion} + +Concept: [`inclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/inclusion) + +Child of: + [`sampledfeaturepart`](#sampledfeaturepart) + +sampled feature is an object contained within a larger body of +material. + +#### clast + +[]{#clast} + +Concept: [`clast`](https://w3id.org/isample/earthenv/essampledfeatrole/clast) + +Child of: + [`inclusion`](#inclusion) + +A clast is a fragment of rock or mineral derived from some pre- +existing rock or generated by intrabasinal processes that is a part of +a sediment + +#### cognate inclusion + +[]{#cognateinclusion} + +Concept: [`cognateinclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/cognateinclusion) + +Child of: + [`inclusion`](#inclusion) + +An inclusion in an igneous rock that is interpreted to be genetically +related to the enclosing rock. + +#### fluid inclusion + +[]{#fluidinclusion} + +Concept: [`fluidinclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/fluidinclusion) + +Child of: + [`inclusion`](#inclusion) + +an inclusion that is an opening in a mineral grain containing fluid +(liquid or gas). + +#### melt inclusion + +[]{#meltinclusion} + +Concept: [`meltinclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/meltinclusion) + +Child of: + [`inclusion`](#inclusion) + +An inclusion in a mineral grain in an igneous rock that is interpreted +to consist of trapped magma from which the igneous rock was formed. + +#### mineral inclusion + +[]{#mineralinclusion} + +Concept: [`mineralinclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/mineralinclusion) + +Child of: + [`inclusion`](#inclusion) + +An inclusion of a mineral phase contained inside a grain of another +mineral. + +#### xenolith + +[]{#xenolith} + +Concept: [`xenolith`](https://w3id.org/isample/earthenv/essampledfeatrole/xenolith) + +Child of: + [`inclusion`](#inclusion) + +An inclusion that is a fragment of pre-existing material that is +contained in an igneous rock and unrelated to the magma that formed +the rock. + +### individual constituent + +[]{#individualconstituent} + +Concept: [`individualconstituent`](https://w3id.org/isample/earthenv/essampledfeatrole/individualconstituent) + +Child of: + [`sampledfeaturepart`](#sampledfeaturepart) + +sampled feature is a single particle or collection of particles that +share some characteristic, within or extracted from a larger sample. + +#### cement + +[]{#cement} + +Concept: [`cement`](https://w3id.org/isample/earthenv/essampledfeatrole/cement) + +Child of: + [`individualconstituent`](#individualconstituent) + +sampled feature is material that binds constituent particles together +in a sedimentary rock. + +#### groundmass + +[]{#groundmass} + +Concept: [`groundmass`](https://w3id.org/isample/earthenv/essampledfeatrole/groundmass) + +Child of: + [`individualconstituent`](#individualconstituent) + +sampled feature is fine-grained to aphanitic material that is +interstitial to larger crystals or particles in a sample. + +#### phenocryst + +[]{#phenocryst} + +Concept: [`phenocryst`](https://w3id.org/isample/earthenv/essampledfeatrole/phenocryst) + +Child of: + [`individualconstituent`](#individualconstituent) + +Sampled feature is a crystal that is significantly larger than +surrounding crystals in an igneous rock. + +#### porphyroblast + +[]{#porphyroblast} + +Concept: [`porphyroblast`](https://w3id.org/isample/earthenv/essampledfeatrole/porphyroblast) + +Child of: + [`individualconstituent`](#individualconstituent) + +Sampled feature is a crystal that is significantly larger than +surrounding crystals in a metamorphic rock. + +### rock body + +[]{#rockbody} + +Concept: [`rockbody`](https://w3id.org/isample/earthenv/essampledfeatrole/rockbody) + +Child of: + [`sampledfeaturepart`](#sampledfeaturepart) + +sampled feature is representative of a rock body, i.e. it represents +the whole of the sampled body. + + diff --git a/models/generated/extensions/opencontext_material_extension.md b/models/generated/extensions/opencontext_material_extension.md new file mode 100644 index 0000000..e1a2ae6 --- /dev/null +++ b/models/generated/extensions/opencontext_material_extension.md @@ -0,0 +1,824 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "OpenContext material type extension draft" +date: "2025-12-11T02:41:34.992752+00:00" +subtitle: | + vocabulary of materials typical of archeological samples +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/opencontext_material_extension.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/opencontext_material_extension.ttl) + + +Namespace: +[`https://w3id.org/isample/opencontext/material/oc_materialsvocab`](https://w3id.org/isample/opencontext/material/oc_materialsvocab) + +**History** + +* 2024-09-13 SMR remove version number from URI + +**Concepts** + +- [anthropogenic metal](#anthropogenicmetal) + - [brass](#brass) + - [bronze](#bronze) + - [copper](#copper) + - [gold](#gold) + - [iron](#iron) + - [lead](#lead) + - [pewter](#pewter) + +- [biogenic non-organic material](#biogenicnonorganicmaterial) + - [amber](#amber) + - [bone](#bone) + - [charcoal](#charcoal) + - [coal](#coal) + - [shell](#shell) + +- [mineral](#mineral) + - [hematite](#hematite) + - [kaolin](#kaolin) + - [mica](#mica) + - [quartz](#quartz) + +- [organic material](#organicmaterial) + - [organic animal material](#organicanimalmaterial) + - [hair](#hair) + - [leather](#leather) + - [organic plant material](#organicplantmaterial) + - [plant fiber](#plantfiber) + - [wood](#wood) + +- [other anthropogenic material](#otheranthropogenicmaterial) + - [anthropogenic organic material](#anthropogenicorganicmaterial) + - [plastic (material)](#plastic) + - [ceramic clay](#ceramicclay) + - [brick clay](#brickclay) + - [bucchero](#bucchero) + - [faience](#faience) + - [porcelain](#porcelain) + - [terracotta](#terracotta) + - [terra sigilata](#terrasigilata) + - [fiber material](#fibermaterial) + - [glass](#glass) + - [paper](#paper) + - [plaster or mortar](#plasterormortar) + - [rubber](#rubber) + +- [particulate material](#particulate) + - [cinder](#cinder) + +- [rock](#rock) + - [basalt](#basalt) + - [chert](#chert) + - [flint](#flint) + - [cinder](#cinder) + - [coal](#coal) + - [dolomite](#dolomite) + - [gabbro](#gabbro) + - [greywacke](#greywacke) + - [limestone](#limestone) + - [marble](#marble) + - [obsidian](#obsidian) + - [pumice](#pumice) + - [slate](#slate) + - [travertine](#travertine) + +## anthropogenic metal + +[]{#anthropogenicmetal} + +Concept: [`anthropogenicmetal`](https://w3id.org/isample/vocabulary/material/anthropogenicmetal) + +Specimen is dominantly composed of metal that has been produced or +used by humans; subclass of anthropogenic material. Samples of +naturally occuring metallic material (e.g. native copper, gold +nuggets) should be considered mineral material. Metallic material is +material that when polished or fractured, shows a lustrous appearance, +and conducts electricity and heat relatively well. Metals are +typically malleable (they can be hammered into thin sheets) or ductile +(can be drawn into wires). The boundaries between metals, nonmetals, +and metalloids fluctuate slightly due to a lack of universally +accepted definitions of the categories involved. +(https://en.wikipedia.org/wiki/Metal). c.f. +http://purl.obolibrary.org/obo/ENVO_01001069 + +### brass + +[]{#brass} + +Concept: [`brass`](https://w3id.org/isample/opencontext/material/brass) + +Child of: + [`anthropogenicmetal`](#anthropogenicmetal) + +alloy of copper (Cu) and zinc (Zn) + +### bronze + +[]{#bronze} + +Concept: [`bronze`](https://w3id.org/isample/opencontext/material/bronze) + +Child of: + [`anthropogenicmetal`](#anthropogenicmetal) + +alloy consisting primarily of copper with subordinate tin; often +includes other metals + +### copper + +[]{#copper} + +Concept: [`copper`](https://w3id.org/isample/opencontext/material/copper) + +Child of: + [`anthropogenicmetal`](#anthropogenicmetal) + +copper metal, includes copper-rich alloys not identifiable as brass or +bronze. + +### gold + +[]{#gold} + +Concept: [`gold`](https://w3id.org/isample/opencontext/material/gold) + +Child of: + [`anthropogenicmetal`](#anthropogenicmetal) + +a chemical element with atomic number 79; a dense, soft metal that is +easily malleable and ductile. It has a melting point of 1064 degrees +Celsius and a boiling point of 2,807 degrees Celsius. (ChatGPT) + +### iron + +[]{#iron} + +Concept: [`iron`](https://w3id.org/isample/opencontext/material/iron) + +Child of: + [`anthropogenicmetal`](#anthropogenicmetal) + +Iron or iron-rich alloy +missing + +### lead + +[]{#lead} + +Concept: [`lead`](https://w3id.org/isample/opencontext/material/lead) + +Child of: + [`anthropogenicmetal`](#anthropogenicmetal) + +lead or lead-rich alloy + +### pewter + +[]{#pewter} + +Concept: [`pewter`](https://w3id.org/isample/opencontext/material/pewter) + +Child of: + [`anthropogenicmetal`](#anthropogenicmetal) + +alloy consisting of mostly tin, with antimony, minor copper or +bismuth, and sometimes silver. + + +## biogenic non-organic material + +[]{#biogenicnonorganicmaterial} + +Concept: [`biogenicnonorganicmaterial`](https://w3id.org/isample/vocabulary/material/biogenicnonorganicmaterial) + +Material produced by an organism but not composed of 'very large +molecules of biological origin.' E.g. bone, tooth, shell, coral +skeleton, + +### amber + +[]{#amber} + +Concept: [`amber`](https://w3id.org/isample/opencontext/material/amber) + +Child of: + [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) + +missing + +### bone + +[]{#bone} + +Concept: [`bone`](https://w3id.org/isample/opencontext/material/bone) + +Child of: + [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) + +missing + +### charcoal + +[]{#charcoal} + +Concept: [`charcoal`](https://w3id.org/isample/opencontext/material/charcoal) + +Child of: + [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) + +missing + +### coal + +[]{#coal} + +Concept: [`coal`](https://w3id.org/isample/opencontext/material/coal) + +Child of: + [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) + [`rock`](#rock) + +missing + +### shell + +[]{#shell} + +Concept: [`shell`](https://w3id.org/isample/opencontext/material/shell) + +Child of: + [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) + +Hard outer covering of invertebrate creatures, composed of calcareous +or chitinous material (http://vocab.getty.edu/page/aat/300011829) + + +## mineral + +[]{#mineral} + +Concept: [`mineral`](https://w3id.org/isample/vocabulary/material/mineral) + +Material consists of a single mineral or mineraloid phase. . 'A +mineral is an element or chemical compound that is normally +crystalline and that has been formed as a result of geological +processes.' (Nickel, Ernest H. (1995), The definition of a mineral, +The Canadian Mineralogist. 33 (3): 689–90). Include mineraloids. ... A +material primarily composed of some substance that is naturally +occurring, solid and stable at room temperature, representable by a +chemical formula, usually abiogenic, and that has an ordered atomic +structure. (http://purl.obolibrary.org/obo/ENVO_01000256). Comment: +the identity of a mineral species is defined by a crystal structure +and a chemical composition that might include various specific +elemental substitutions in that structure. Mineraloid: A naturally +occurring mineral-like substance that does not demonstrate +crystallinity. Mineraloids possess chemical compositions that vary +beyond the generally accepted ranges for specific minerals. Examples: +obsidian, Opal. (https://en.wikipedia.org/wiki/Mineraloid) + +### hematite + +[]{#hematite} + +Concept: [`hematite`](https://w3id.org/isample/opencontext/material/hematite) + +Child of: + [`mineral`](#mineral) + +missing + +### kaolin + +[]{#kaolin} + +Concept: [`kaolin`](https://w3id.org/isample/opencontext/material/kaolin) + +Child of: + [`mineral`](#mineral) + +missing + +### mica + +[]{#mica} + +Concept: [`mica`](https://w3id.org/isample/opencontext/material/mica) + +Child of: + [`mineral`](#mineral) + +missing + +### quartz + +[]{#quartz} + +Concept: [`quartz`](https://w3id.org/isample/opencontext/material/quartz) + +Child of: + [`mineral`](#mineral) + +missing + + +## organic material + +[]{#organicmaterial} + +Concept: [`organicmaterial`](https://w3id.org/isample/vocabulary/material/organicmaterial) + +Environmental material derived from living organisms and composed +primarily of one or more very large molecules of biological origin. +Examples: body (animal or plant), body part, fecal matter, seeds, +wood, tissue, biological fluids, biological waste, algal material, +biofilm, necromass, plankton. source: +http://purl.obolibrary.org/obo/ENVO_01000155 + +### organic animal material + +[]{#organicanimalmaterial} + +Concept: [`organicanimalmaterial`](https://w3id.org/isample/opencontext/material/organicanimalmaterial) + +Child of: + [`organicmaterial`](#organicmaterial) + +Material that is (or was) a constituent of an animal organisms, +composed primarily of one or more very large molecules of biological +origin. + +#### hair + +[]{#hair} + +Concept: [`hair`](https://w3id.org/isample/opencontext/material/hair) + +Child of: + [`organicanimalmaterial`](#organicanimalmaterial) + +Material comprising the cylindrical filaments that grow from follicles +embedded in the skin of mammals. Hair is a column of overlapping, +fused cells that are composed of the protein keratin; hair is composed +of three parts: the innermost column is the medula, the surrounding +live cells (the cortex) contain pigment, and the outermost dead +transparent cells are the cuticular scales. The portion of the hair +outside of the skin is called the shaft. Fine, closely spaced hair +that covers most of an animal's body is called fur. Dense, soft, +curled hair is called wool. Coarse, stiff hairs are called bristles, +spines, or quills. Horsehair and cattle hair have been used for +brushes, plaster binders, haircloth, and upholstery stuffing. Rabbit +hair, often called rabbit fur, has been used to make felt hats. +(http://vocab.getty.edu/page/aat/300011814) + +#### leather + +[]{#leather} + +Concept: [`leather`](https://w3id.org/isample/opencontext/material/leather) + +Child of: + [`organicanimalmaterial`](#organicanimalmaterial) + +The skin or hide of an animal that has been tanned to render it +resistant to putrefication and relatively soft and flexible when dry. +(http://vocab.getty.edu/page/aat/300011845) + +### organic plant material + +[]{#organicplantmaterial} + +Concept: [`organicplantmaterial`](https://w3id.org/isample/opencontext/material/organicplantmaterial) + +Child of: + [`organicmaterial`](#organicmaterial) + +missing + +#### plant fiber + +[]{#plantfiber} + +Concept: [`plantfiber`](https://w3id.org/isample/opencontext/material/plantfiber) + +Child of: + [`organicplantmaterial`](#organicplantmaterial) + +missing + +#### wood + +[]{#wood} + +Concept: [`wood`](https://w3id.org/isample/opencontext/material/wood) + +Child of: + [`organicplantmaterial`](#organicplantmaterial) + +missing + + +## other anthropogenic material + +[]{#otheranthropogenicmaterial} + +Concept: [`otheranthropogenicmaterial`](https://w3id.org/isample/vocabulary/material/otheranthropogenicmaterial) + +Non-metallic material produced by human activity. Organic products of +agricultural activity are both anthropogenic and organic. Include lab +preparations like XRF pellet and rock powders. Examples: ceramics, +concrete, slag, (anthropogenic) glass, mine tailing, plaster, waste. + +### anthropogenic organic material + +[]{#anthropogenicorganicmaterial} + +Concept: [`anthropogenicorganicmaterial`](https://w3id.org/isample/opencontext/material/anthropogenicorganicmaterial) + +Child of: + [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) + +Organic material manufactured by humans + +#### plastic (material) + +[]{#plastic} + +Concept: [`plastic`](https://w3id.org/isample/opencontext/material/plastic) + +Child of: + [`anthropogenicorganicmaterial`](#anthropogenicorganicmaterial) + +Synthetic or semi-synthetic material that uses organic polymers as a +main ingredient. + +### ceramic clay + +[]{#ceramicclay} + +Concept: [`ceramicclay`](https://w3id.org/isample/opencontext/material/ceramicclay) + +Child of: + [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) + +Any of the various hard, brittle, heat-resistant and corrosion- +resistant materials made by shaping and then firing an inorganic, +nonmetallic material, such as clay, at a high temperature. Common +examples are earthenware, porcelain, and brick. +(https://en.wikipedia.org/wiki/Ceramic) + +#### brick clay + +[]{#brickclay} + +Concept: [`brickclay`](https://w3id.org/isample/opencontext/material/brickclay) + +Child of: + [`ceramicclay`](#ceramicclay) + +dried or low-fired clay-rich material used to make blocks for +construction + +#### bucchero + +[]{#bucchero} + +Concept: [`bucchero`](https://w3id.org/isample/opencontext/material/bucchero) + +Child of: + [`ceramicclay`](#ceramicclay) + +ceramic with black fabric and glossy, black surface achieved through +reduction firing + +#### faience + +[]{#faience} + +Concept: [`faience`](https://w3id.org/isample/opencontext/material/faience) + +Child of: + [`ceramicclay`](#ceramicclay) + +fine white-glazed ceramic (tin oxide based glaze) + +#### porcelain + +[]{#porcelain} + +Concept: [`porcelain`](https://w3id.org/isample/opencontext/material/porcelain) + +Child of: + [`ceramicclay`](#ceramicclay) + +Kaolin rich high-fired ceramic; In China, it includes any such ware +that is highly fired enough to produce a ringing sound when struck. In +Europe, it is limited to hard-fired ceramic that is translucent. +(https://vocab.getty.edu/aat/scopeNote/45436) + +#### terracotta + +[]{#terracotta} + +Concept: [`terracotta`](https://w3id.org/isample/opencontext/material/terracotta) + +Child of: + [`ceramicclay`](#ceramicclay) + +clay-based unglazed or glazed, porous ceramic + +#### terra sigilata + +[]{#terrasigilata} + +Concept: [`terrasigilata`](https://w3id.org/isample/opencontext/material/terrasigilata) + +Child of: + [`ceramicclay`](#ceramicclay) + +Fine red Ancient Roman pottery with glossy surface slips + +### fiber material + +[]{#fibermaterial} + +Concept: [`fibermaterial`](https://w3id.org/isample/opencontext/material/fibermaterial) + +Child of: + [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) + +material composed of fibers twisted or woved togther. Fibers might be +plant material or Anthropogenic Organic material. + +### glass + +[]{#glass} + +Concept: [`glass`](https://w3id.org/isample/opencontext/material/glass) + +Child of: + [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) + +A non-crystalline, often transparent amorphous solid, most often +formed by rapid cooling (quenching) of the molten silca rich material. +(https://en.wikipedia.org/wiki/Glass) + +### paper + +[]{#paper} + +Concept: [`paper`](https://w3id.org/isample/opencontext/material/paper) + +Child of: + [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) + +thin matted or felted sheets or webs of fiber formed and dried on a +fine screen from a pulpy water suspension. The fibers may be animal, +such as hair, silk or wool, or mineral, such as asbestos, or +synthetic. However most paper is made from cellulosic plant fiber, +such as from wood pulp, grass, cotton, linen, and straw. +(http://vocab.getty.edu/page/aat/300014109) + +### plaster or mortar + +[]{#plasterormortar} + +Concept: [`plasterormortar`](https://w3id.org/isample/opencontext/material/plasterormortar) + +Child of: + [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) + +Plaster is a pasty material that hardens on drying and is used for +coating walls, ceilings, and partitions. Mortar is a similar pasty +material used for cementing bricks or block together or coating walls +in building construction. + +### rubber + +[]{#rubber} + +Concept: [`rubber`](https://w3id.org/isample/opencontext/material/rubber) + +Child of: + [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) + +An elastomer, synthesized from petroleum byproducts or from latex +harvested from the rubber tree (Hevea brasiliensis). + + +## particulate material + +[]{#particulate} + +Concept: [`particulate`](https://w3id.org/isample/vocabulary/material/particulate) + +Material consists of microscopic particulate material derived by +precipitation, filtering, or settling from suspension in a fluid, e.g. +filtrate from water, deposition from atmosphere, astro material +particles. Might include mineral, organic, or biological material. +ENVO definition (ENVO_01000060) has "composed of microscopic portions +of solid or liquid material suspended in another environmental +material.", refine here to define as the solid particles, distinct +from a material in which they are suspended. A material that includes +solid or liquid particles suspended in another material would be a +dispersed_media in this scheme, not defined in ENVO. Human +manufactured particulates (e.g. rock powder) should be categorized as +'anthropogenic material' as well as 'Particulate' + +### cinder + +[]{#cinder} + +Concept: [`cinder`](https://w3id.org/isample/opencontext/material/cinder) + +Child of: + [`particulate`](#particulate) + [`rock`](#rock) + +The incombustible residue of something burnt. +(http://vocab.getty.edu/page/aat/300011788) +missing + + +## rock + +[]{#rock} + +Concept: [`rock`](https://w3id.org/isample/vocabulary/material/rock) + +Consolidated aggregate of particles (grains) of rock, mineral +(including native elements), mineraloid, or solid organic material. +Includes mineral aggregates such as granite, shale, marble; natural +glass such as obsidian; organic material formed by geologic processes +such a coal; extraterrestrial material in meteorites; and crushed +rock fragments like drill cuttings from rock. (based on +http://resource.geosciml.org/classifier/cgi/lithology/rock, same as +http://purl.obolibrary.org/obo/ENVO_00001995) + +### basalt + +[]{#basalt} + +Concept: [`basalt`](https://w3id.org/isample/opencontext/material/basalt) + +Child of: + [`rock`](#rock) + +missing + +### chert + +[]{#chert} + +Concept: [`chert`](https://w3id.org/isample/opencontext/material/chert) + +Child of: + [`rock`](#rock) + +missing + +#### flint + +[]{#flint} + +Concept: [`flint`](https://w3id.org/isample/opencontext/material/flint) + +Child of: + [`chert`](#chert) + +missing + +### cinder + +[]{#cinder} + +Concept: [`cinder`](https://w3id.org/isample/opencontext/material/cinder) + +Child of: + [`particulate`](#particulate) + [`rock`](#rock) + +The incombustible residue of something burnt. +(http://vocab.getty.edu/page/aat/300011788) +missing + +### coal + +[]{#coal} + +Concept: [`coal`](https://w3id.org/isample/opencontext/material/coal) + +Child of: + [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) + [`rock`](#rock) + +missing + +### dolomite + +[]{#dolomite} + +Concept: [`dolomite`](https://w3id.org/isample/opencontext/material/dolomite) + +Child of: + [`rock`](#rock) + +missing + +### gabbro + +[]{#gabbro} + +Concept: [`gabbro`](https://w3id.org/isample/opencontext/material/gabbro) + +Child of: + [`rock`](#rock) + +missing + +### greywacke + +[]{#greywacke} + +Concept: [`greywacke`](https://w3id.org/isample/opencontext/material/greywacke) + +Child of: + [`rock`](#rock) + +missing + +### limestone + +[]{#limestone} + +Concept: [`limestone`](https://w3id.org/isample/opencontext/material/limestone) + +Child of: + [`rock`](#rock) + +missing + +### marble + +[]{#marble} + +Concept: [`marble`](https://w3id.org/isample/opencontext/material/marble) + +Child of: + [`rock`](#rock) + +missing + +### obsidian + +[]{#obsidian} + +Concept: [`obsidian`](https://w3id.org/isample/opencontext/material/obsidian) + +Child of: + [`rock`](#rock) + +missing + +### pumice + +[]{#pumice} + +Concept: [`pumice`](https://w3id.org/isample/opencontext/material/pumice) + +Child of: + [`rock`](#rock) + +missing + +### slate + +[]{#slate} + +Concept: [`slate`](https://w3id.org/isample/opencontext/material/slate) + +Child of: + [`rock`](#rock) + +missing + +### travertine + +[]{#travertine} + +Concept: [`travertine`](https://w3id.org/isample/opencontext/material/travertine) + +Child of: + [`rock`](#rock) + +A limestone consisting of a massive usually layered calcium carbonate +(such as aragonite or calcite) formed by deposition from spring +waters, especially from hot springs. +(https://www.mindat.org/min-39057.html) + + diff --git a/models/generated/extensions/opencontext_materialsampleobjecttype.md b/models/generated/extensions/opencontext_materialsampleobjecttype.md new file mode 100644 index 0000000..cb0b3c6 --- /dev/null +++ b/models/generated/extensions/opencontext_materialsampleobjecttype.md @@ -0,0 +1,203 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "Open Context vocabulary extension for material sample object type" +date: "2025-12-11T02:41:36.548073+00:00" +subtitle: | + categories for kinds of sample objects specific to archaeological studies + Vocabulary created based on summary of 'type' values found in OpenContext sample descriptions. This is a bottom-up vocabulary intended as a first draft and demonstration of a material sample type extension for the Open Context community in the iSamples context. Most of the categories are subclasses of msot:Artifact, except for 'bone object' which is a msot:OrganismPart. +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/opencontext_materialsampleobjecttype.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/opencontext_materialsampleobjecttype.ttl) + + +Namespace: +[`https://w3id.org/isample/opencontext/materialsampleobjecttype/oc_msotvocab`](https://w3id.org/isample/opencontext/materialsampleobjecttype/oc_msotvocab) + +**History** + +* 2024-09-13 SMR remove version number from URI + +**Concepts** + +- [Artifact](#artifact) + - [Architectural element](#architecturalelement) + - [Clothing](#clothing) + - [Coin](#coin) + - [Container object](#containerobject) + - [Domestic item](#domesticitem) + - [Ornament](#ornament) + - [Photograph](#photograph) + - [Pot sherd](#sherd) + - [Tile](#tile) + - [Utility item](#utilityitem) + - [Weapon](#weapon) + +- [Organism part](#organismpart) + - [Bone object](#peiceofbone) + +## Artifact + +[]{#artifact} + +Concept: [`artifact`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/artifact) + +An object made (manufactured, shaped, modified) by a human being, or +precursor hominid. Include a set of pieces belonging originally to a +single object and treated as a single specimen. + +### Architectural element + +[]{#architecturalelement} + +Concept: [`architecturalelement`](https://w3id.org/isample/opencontext/materialsampleobjecttype/architecturalelement) + +Child of: + [`artifact`](#artifact) + +Artifact that was part of a building. + +### Clothing + +[]{#clothing} + +Concept: [`clothing`](https://w3id.org/isample/opencontext/materialsampleobjecttype/clothing) + +Child of: + [`artifact`](#artifact) + +Item intended to be worn to cover the (human) body + +### Coin + +[]{#coin} + +Concept: [`coin`](https://w3id.org/isample/opencontext/materialsampleobjecttype/coin) + +Child of: + [`artifact`](#artifact) + +peice of metal issued by some authority and recognized as money. + +### Container object + +[]{#containerobject} + +Concept: [`containerobject`](https://w3id.org/isample/opencontext/materialsampleobjecttype/containerobject) + +Child of: + [`artifact`](#artifact) + +Item designed to contain some fluid, granular material, or other items +for preservation, transportation or display. + +### Domestic item + +[]{#domesticitem} + +Concept: [`domesticitem`](https://w3id.org/isample/opencontext/materialsampleobjecttype/domesticitem) + +Child of: + [`artifact`](#artifact) + +item intended for household use. + +### Ornament + +[]{#ornament} + +Concept: [`ornament`](https://w3id.org/isample/opencontext/materialsampleobjecttype/ornament) + +Child of: + [`artifact`](#artifact) + +item intended for decoration. + +### Photograph + +[]{#photograph} + +Concept: [`photograph`](https://w3id.org/isample/opencontext/materialsampleobjecttype/photograph) + +Child of: + [`artifact`](#artifact) + +image produced by the action of light on a chemically sensitive +surface, preserved on paper, glass or other physical substrate. + +### Pot sherd + +[]{#sherd} + +Concept: [`sherd`](https://w3id.org/isample/opencontext/materialsampleobjecttype/sherd) + +Child of: + [`artifact`](#artifact) + +fragment of pottery + +### Tile + +[]{#tile} + +Concept: [`tile`](https://w3id.org/isample/opencontext/materialsampleobjecttype/tile) + +Child of: + [`artifact`](#artifact) + +flat or curved piece of fired clay, stone, or concrete used especially +for roofs, floors, or walls and often for ornamental work + +### Utility item + +[]{#utilityitem} + +Concept: [`utilityitem`](https://w3id.org/isample/opencontext/materialsampleobjecttype/utilityitem) + +Child of: + [`artifact`](#artifact) + +Item intended for use in manufacture, construction, agriculture or +other work activity. + +### Weapon + +[]{#weapon} + +Concept: [`weapon`](https://w3id.org/isample/opencontext/materialsampleobjecttype/weapon) + +Child of: + [`artifact`](#artifact) + +Item for use in combat, hunting, or self defense + + +## Organism part + +[]{#organismpart} + +Concept: [`organismpart`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismpart) + +Part of an organism, e.g. a tissue sample, plant leaf, flower, bird +feather. Include internal parts not composed of organic material (e.g. +teeth, bone), and hard body parts that are not shed (hoof, horn, tusk, +claw). Hair is tricky, include here for now. Does not necessarily +imply existance of parent sample. Not fossilized; generally includes +organism parts native to deposits of Holocene to Recent age. + +### Bone object + +[]{#peiceofbone} + +Concept: [`peiceofbone`](https://w3id.org/isample/opencontext/materialsampleobjecttype/peiceofbone) + +Child of: + [`organismpart`](#organismpart) + +Sample is an individual bone or part of a bone from an animal. + + diff --git a/models/generated/vocabularies/material_sample_object_type.qmd b/models/generated/vocabularies/material_sample_object_type.qmd new file mode 100644 index 0000000..28a2eb7 --- /dev/null +++ b/models/generated/vocabularies/material_sample_object_type.qmd @@ -0,0 +1,375 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "iSamples Material Sample Object Type Vocabulary" +date: "2025-12-11T02:41:28.407856+00:00" +subtitle: | + Broad categories to specify the kind of physical thing identified as the ‘sample’. +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/material_sample_object_type.ttl`](https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/material_sample_object_type.ttl) + + +Namespace: +[`https://w3id.org/isample/vocabulary/materialsampleobjecttype/conceptscheme`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/conceptscheme) + +**History** + +* 2022-01-07 SMR Change base URI to https://w3id.org/isample/vocabulary/, setting up resolution using w3id. Make the conceptScheme and ontology. Add Dublin core imports. +* 2022-03-11 SMR change definitions from rdfs:comment to skos:definition. Minor fixes in definitions. Add skos matches to URIs from other vocabularies. +* 2022-09-30 SMR per https://github.com/isamplesorg/metadata/issues/109, change specimen to sample in vocabulary names and labels. Add 'Slurry biome aggregation' and 'Bundle biome aggregation' (github issue 110). Rename 'liquid or gas' sample type to 'fluid in container' (github issue 108). +* 2023-07-27 SMR modify base specimen type vocabulary, add 'Non biologic solid object' change broader relations in this vocab to use that as parent class where appropriate. Intention is a specimen category for solid objects that are not biologic; this subsumes 'Fossil' and 'Artifact', but excludes living organism, their parts and products. Obviously there is some overlap with Research specimens. +* 2023-11-06 SMR add missing inScheme on Non-biologic solid object and solid materal specimen. Update version number in URI to 1.0 +* 2024-04-19 SMR update language to always use 'material sample' instead of specimen or physical specimen, including in text, labels, and in the URI tokens. Edit defintions to improve clarity. +* 2024-09-13 remove version numbers from URI + +**Concepts** + +- [Material sample](#materialsample) + - [Any aggregation material sample](#anyaggregation) + - [Anthropogenic aggregation](#anthropogenicaggregation) + - [Biome aggregation sample](#biomeaggregation) + - [Bundle biome aggregation](#bundlebiomeaggregation) + - [Slurry biome aggregation](#slurrybiomeaggregation) + - [Aggregation](#genericaggregation) + - [Biological material sample](#biologicalmaterialsample) + - [Biome aggregation sample](#biomeaggregation) + - [Bundle biome aggregation](#bundlebiomeaggregation) + - [Slurry biome aggregation](#slurrybiomeaggregation) + - [Organism part](#organismpart) + - [Organism product](#organismproduct) + - [Whole organism material sample](#wholeorganism) + - [Fluid in container](#fluidincontainer) + - [Non biologic solid object](#nonbiologicsolidobject) + - [Artifact](#artifact) + - [Fossil](#fossil) + - [Other solid object](#othersolidobject) + - [Solid material sample](#solidmaterialsample) + - [Research product](#researchproduct) + - [Analytical preparation](#analyticalpreparation) + - [Experiment product](#experimentalproduct) + +## Material sample + +[]{#materialsample} + +Concept: [`materialsample`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/materialsample) + +A material entity that represents an entity of interest in whole or in +part (http://rs.tdwg.org/dwc/terms/MaterialSample). Top concept in +material sample object type hierarchy. Represents any material sample +object. + +### Any aggregation material sample + +[]{#anyaggregation} + +Concept: [`anyaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/anyaggregation) + +Child of: + [`materialsample`](#materialsample) + +Sample consists of a bunch of material fragments, not related to the +same object (e.g. not a bunch of broken pot sherds that might be +reassembled), but taken together representative of the sampled +feature. Examples: loose soil, sediment, crushed rock, particulate, +bunches of unrelated pot sherd, human production waste, filtrates and +residues. The sample requires some kind of container to keep it +together. Cores of loosely consolidated material are considered 'Solid +material specimen' when preserved such that the internal parts have +spatial relationships (e.g. upper part, lower part, sedimentary +structures). + +#### Anthropogenic aggregation + +[]{#anthropogenicaggregation} + +Concept: [`anthropogenicaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/anthropogenicaggregation) + +Child of: + [`anyaggregation`](#anyaggregation) + +An aggregate material sample consisting of fragments of material +produced by human activity, not described individually, and generally +not all originating from the same object. Includes pottery in an +excavation unit that gets an aggregate description, production waste, +production raw-materials, or other residues (broken bits of plaster +from a destroyed wall), synthetic powders. + +#### Biome aggregation sample + +[]{#biomeaggregation} + +Concept: [`biomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/biomeaggregation) + +Child of: + [`anyaggregation`](#anyaggregation) + [`biologicalmaterialsample`](#biologicalmaterialsample) + +Material sample that is an aggregation of whole or fragmentary parts +of multiple organisms, microscopic or megascopic, representative of +some sampled feature. + +##### Bundle biome aggregation + +[]{#bundlebiomeaggregation} + +Concept: [`bundlebiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/bundlebiomeaggregation) + +Child of: + [`biomeaggregation`](#biomeaggregation) + +Material sample that is an aggregation of whole organisms +representative of some biome. + +##### Slurry biome aggregation + +[]{#slurrybiomeaggregation} + +Concept: [`slurrybiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/slurrybiomeaggregation) + +Child of: + [`biomeaggregation`](#biomeaggregation) + +Material sample that consists of mixed organic and inorganic material, +including whole organisms and organism fragments. + +#### Aggregation + +[]{#genericaggregation} + +Concept: [`genericaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/genericaggregation) + +Child of: + [`anyaggregation`](#anyaggregation) + +An aggregate material sample that is not biogenic or composed of +anthropogenic material fragments. Examples: loose soil or sediment +(e.g. in a bag), rock chips, particulate filtrate or precipitate; rock +powders. + +### Biological material sample + +[]{#biologicalmaterialsample} + +Concept: [`biologicalmaterialsample`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/biologicalmaterialsample) + +Child of: + [`materialsample`](#materialsample) + +Material sample representative of one or more living organisms from a +particular biome context, megascopic or microscopic + +#### Biome aggregation sample + +[]{#biomeaggregation} + +Concept: [`biomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/biomeaggregation) + +Child of: + [`anyaggregation`](#anyaggregation) + [`biologicalmaterialsample`](#biologicalmaterialsample) + +Material sample that is an aggregation of whole or fragmentary parts +of multiple organisms, microscopic or megascopic, representative of +some sampled feature. + +##### Bundle biome aggregation + +[]{#bundlebiomeaggregation} + +Concept: [`bundlebiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/bundlebiomeaggregation) + +Child of: + [`biomeaggregation`](#biomeaggregation) + +Material sample that is an aggregation of whole organisms +representative of some biome. + +##### Slurry biome aggregation + +[]{#slurrybiomeaggregation} + +Concept: [`slurrybiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/slurrybiomeaggregation) + +Child of: + [`biomeaggregation`](#biomeaggregation) + +Material sample that consists of mixed organic and inorganic material, +including whole organisms and organism fragments. + +#### Organism part + +[]{#organismpart} + +Concept: [`organismpart`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismpart) + +Child of: + [`biologicalmaterialsample`](#biologicalmaterialsample) + +Material sample that is part of an organism, e.g. a tissue sample, +plant leaf, flower, bird feather. Include internal parts not composed +of organic material (e.g. teeth, bone), and hard body parts that are +not shed (hoof, horn, tusk, claw). Hair is tricky, include here for +now. Does not necessarily imply existance of parent sample. Not +fossilized; generally includes organism parts native to deposits of +Holocene to Recent age. + +#### Organism product + +[]{#organismproduct} + +Concept: [`organismproduct`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismproduct) + +Child of: + [`biologicalmaterialsample`](#biologicalmaterialsample) + +Material sample is a thing produced by some organism, generally not +composed of organic material or including biological tissue, e.g. +Shell, antler, egg shell, coral skeleton (organic tissue not +included), fecal matter, cocoon, web. Consider internal parts not +composed of organic material (e.g. teeth, bone) and hard body parts +that are not shed (hoof, horn, tusk) to be organism parts. + +#### Whole organism material sample + +[]{#wholeorganism} + +Concept: [`wholeorganism`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/wholeorganism) + +Child of: + [`biologicalmaterialsample`](#biologicalmaterialsample) + +Material sample consists of the bodies of one or more entire organisms +of the same species, from any kingdom. + +### Fluid in container + +[]{#fluidincontainer} + +Concept: [`fluidincontainer`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/fluidincontainer) + +Child of: + [`materialsample`](#materialsample) + +Material sample is a liquid, gas, or mixed dominantly fluid phase +material that is necessarily inside some container. Fluids might +include minor solid particles. The container is typically human made, +but also includes natural fluid containers, e.g. a fluid inclusion in +a mineral grain. Fluids might be colloids, foams, gels, or +suspensions. The sample is the fluid substance; fluid samples +collected to analyze the contained biome should be considered 'Biome +aggregation sample' + +### Non biologic solid object + +[]{#nonbiologicsolidobject} + +Concept: [`nonbiologicsolidobject`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/nonbiologicsolidobject) + +Child of: + [`materialsample`](#materialsample) + +Individual solid object, the substance of which is not formed directly +by or part of a living organism + +#### Artifact + +[]{#artifact} + +Concept: [`artifact`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/artifact) + +Child of: + [`nonbiologicsolidobject`](#nonbiologicsolidobject) + +An object made (manufactured, shaped, modified) by a human being, or +precursor hominid. Include a set of pieces belonging originally to a +single object and treated as a single sample. + +#### Fossil + +[]{#fossil} + +Concept: [`fossil`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/fossil) + +Child of: + [`nonbiologicsolidobject`](#nonbiologicsolidobject) + +Material sample is the remains or trace of one or more organisms +preserved in rock; includes whole body, body parts (usually bone or +shell), and trace fossils. An organism or organism part becomes a +fossil when it has undergone some fossilization process that entails +physical and chemical changes akin to diagenesis in a sedimentary +rock. Includes trace fossils, which are manifestations of biologic +activity preserved in a rock body (typically sedimentary), without +included preserved body parts. + +#### Other solid object + +[]{#othersolidobject} + +Concept: [`othersolidobject`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/othersolidobject) + +Child of: + [`nonbiologicsolidobject`](#nonbiologicsolidobject) + +A non-biologic solid object that is not one of the other types. + +#### Solid material sample + +[]{#solidmaterialsample} + +Concept: [`solidmaterialsample`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/solidmaterialsample) + +Child of: + [`nonbiologicsolidobject`](#nonbiologicsolidobject) + +Individual solid object, not formed directly by or part of a living +organism, that is intended to be representative of some material. + +### Research product + +[]{#researchproduct} + +Concept: [`researchproduct`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/researchproduct) + +Child of: + [`materialsample`](#materialsample) + +Material sample is a product of some research workflow, e.g. a thin +section, an XRF pellet, a grain mount, SEM stub, synthetic rock or +mineral ... In general there should be a link to a parent material +sample from which this was derived. Might be aggregation (e.g. a +synthetic material powder) or a solid object. + +#### Analytical preparation + +[]{#analyticalpreparation} + +Concept: [`analyticalpreparation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/analyticalpreparation) + +Child of: + [`researchproduct`](#researchproduct) + +Material sample is a product of processing required for some +observation procedure, e.g. thin section, XRF bead, SEM stub, rock +powder. If identified separately, this should have a ‘parent’ link to +the original sample + +#### Experiment product + +[]{#experimentalproduct} + +Concept: [`experimentalproduct`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/experimentalproduct) + +Child of: + [`researchproduct`](#researchproduct) + +Material sample that is the product of an experimental procedure (e.g. +synthetic material) + + diff --git a/models/generated/vocabularies/material_type.qmd b/models/generated/vocabularies/material_type.qmd new file mode 100644 index 0000000..964fda3 --- /dev/null +++ b/models/generated/vocabularies/material_type.qmd @@ -0,0 +1,377 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "iSamples Materials Vocabulary" +date: "2025-12-11T02:41:26.834919+00:00" +subtitle: | + High level vocabulary to specify the kind of material that constitutes a physical sample +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/material_type.ttl`](https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/material_type.ttl) + + +Namespace: +[`https://w3id.org/isample/vocabulary/material/materialsvocabulary`](https://w3id.org/isample/vocabulary/material/materialsvocabulary) + +**History** + +* 2022-01-05 SMR version 0.9, change base uri to https://w3id.org/isample/vocabulary/material/0.9/ for testing with ESIP COR and w3id uri resolution +* 2022-03-11 SMR change definitions from rdfs:comment to skos:definition. Minor fixes to some definitions. Add skos matches to URIs from other vocabularies; 2023-11-05 version 1.0, in preparation for release. +* 2024-08-14 SMR, various updates since 2023-12: change seeAlso to closeMatch for Rock mapping to http://resource.geosciml.org/classifier/cgi/lithology/rock; minor edits to align with manuscript about the metadata schema; update vocabularies to use 'material sample' instead of 'specimen'; update schema.org namespace to http://; add provider and codeRepository in conceptScheme metadata; minor typo fixes and definition edits. +* 2024-09-13 remove version numbers from URI + +**Concepts** + +- [Material ](#material) + - [Anthropogenic material](#anyanthropogenicmaterial) + - [Anthropogenic metal material ](#anthropogenicmetal) + - [Other anthropogenic material](#otheranthropogenicmaterial) + - [Any ice](#anyice) + - [Frozen water](#waterice) + - [Biogenic non-organic material](#biogenicnonorganicmaterial) + - [Dispersed media](#dispersedmedia) + - [Natural Solid Material](#earthmaterial) + - [Mineral ](#mineral) + - [Mixed soil sediment or rock](#mixedsoilsedimentrock) + - [Particulate](#particulate) + - [Rock or sediment](#rockorsediment) + - [Rock](#rock) + - [Sediment](#sediment) + - [Soil](#soil) + - [Fluid material](#fluid) + - [Gaseous material](#gas) + - [Liquid water](#liquidwater) + - [Non-aqueous liquid material ](#nonaqueousliquid) + - [Organic material](#organicmaterial) + +## Material + +[]{#material} + +Concept: [`material`](https://w3id.org/isample/vocabulary/material/material) + +Top Concept in iSamples Material Category scheme + +### Anthropogenic material + +[]{#anyanthropogenicmaterial} + +Concept: [`anyanthropogenicmaterial`](https://w3id.org/isample/vocabulary/material/anyanthropogenicmaterial) + +Child of: + [`material`](#material) + +Material produced by human activity. + +#### Anthropogenic metal material + +[]{#anthropogenicmetal} + +Concept: [`anthropogenicmetal`](https://w3id.org/isample/vocabulary/material/anthropogenicmetal) + +Child of: + [`anyanthropogenicmaterial`](#anyanthropogenicmaterial) + +Metal that has been produced or used by humans. Samples of naturally +occurring metallic material (e.g. native copper, gold nuggets) should +be considered mineral material. Metallic material is material that +when polished or fractured, shows a lustrous appearance, and conducts +electricity and heat relatively well. Metals are typically malleable +(they can be hammered into thin sheets) or ductile (can be drawn into +wires). The boundaries between metals, nonmetals, and metalloids +fluctuate slightly due to a lack of universally accepted definitions +of the categories involved. (https://en.wikipedia.org/wiki/Metal, c.f. +http://purl.obolibrary.org/obo/ENVO_01001069) + +#### Other anthropogenic material + +[]{#otheranthropogenicmaterial} + +Concept: [`otheranthropogenicmaterial`](https://w3id.org/isample/vocabulary/material/otheranthropogenicmaterial) + +Child of: + [`anyanthropogenicmaterial`](#anyanthropogenicmaterial) + +Non-metallic material produced by human activity. Organic products of +agricultural activity are both anthropogenic and organic. Include lab +preparations like XRF pellet and rock powders. Examples: ceramics, +concrete, slag, (anthropogenic) glass, mine tailing, plaster, waste. + +### Any ice + +[]{#anyice} + +Concept: [`anyice`](https://w3id.org/isample/vocabulary/material/anyice) + +Child of: + [`material`](#material) + +a material that is in a solid state under the temperature and pressure +conditions of the preserved sample, but is a liquid or gas at Standard +Temperature and Pressure (STP). + +#### Frozen water + +[]{#waterice} + +Concept: [`waterice`](https://w3id.org/isample/vocabulary/material/waterice) + +Child of: + [`anyice`](#anyice) + +Water that is in a solid state. + +### Biogenic non-organic material + +[]{#biogenicnonorganicmaterial} + +Concept: [`biogenicnonorganicmaterial`](https://w3id.org/isample/vocabulary/material/biogenicnonorganicmaterial) + +Child of: + [`material`](#material) + +Material produced by an organism but not composed of 'very large +molecules of biological origin.' E.g. bone, tooth, shell, coral +skeleton, + +### Dispersed media + +[]{#dispersedmedia} + +Concept: [`dispersedmedia`](https://w3id.org/isample/vocabulary/material/dispersedmedia) + +Child of: + [`material`](#material) + +Material that contains discrete elements of some material dispersed in +a continuous fluid medium. The dispersed component can be a gas, a +liquid or a solid (based on +https://en.wikipedia.org/wiki/Dispersed_media). Does not include +mixtures of granular material like soil, sediment, particulate, or +solids that would be considered rock material. + +### Natural Solid Material + +[]{#earthmaterial} + +Concept: [`earthmaterial`](https://w3id.org/isample/vocabulary/material/earthmaterial) + +Child of: + [`material`](#material) + +A naturally occurring solid material that is not anthropogenic, +biogenic, or ice. + +#### Mineral + +[]{#mineral} + +Concept: [`mineral`](https://w3id.org/isample/vocabulary/material/mineral) + +Child of: + [`earthmaterial`](#earthmaterial) + +Material consists of a single mineral or mineraloid phase. 'A mineral +is an element or chemical compound that is normally crystalline and +that has been formed as a result of geological processes.' (Nickel, +Ernest H. (1995), The definition of a mineral, The Canadian +Mineralogist. 33 (3): 689–90). Include mineraloids. ... A material +primarily composed of some substance that is naturally occurring, +solid and stable at room temperature, representable by a chemical +formula, usually abiogenic, and that has an ordered atomic structure. +(http://purl.obolibrary.org/obo/ENVO_01000256). The identity of a +mineral species is defined by a crystal structure and a chemical +composition that might include various specific elemental +substitutions in that structure. Mineraloid: A naturally occurring +mineral-like substance that does not demonstrate crystallinity. +Mineraloids possess chemical compositions that vary beyond the +generally accepted ranges for specific minerals. Examples: obsidian, +Opal. (https://en.wikipedia.org/wiki/Mineraloid) + +#### Mixed soil sediment or rock + +[]{#mixedsoilsedimentrock} + +Concept: [`mixedsoilsedimentrock`](https://w3id.org/isample/vocabulary/material/mixedsoilsedimentrock) + +Child of: + [`earthmaterial`](#earthmaterial) + +Material is mixed aggregation of fragments of undifferentiated soil, +sediment or rock origin. e.g. cuttings from some boreholes (rock +fragments and caved soil or sediment). + +#### Particulate + +[]{#particulate} + +Concept: [`particulate`](https://w3id.org/isample/vocabulary/material/particulate) + +Child of: + [`earthmaterial`](#earthmaterial) + +Material consists of microscopic particulate material derived by +precipitation, filtering, or settling from suspension in a fluid, e.g. +filtrate from water, deposition from atmosphere, astro material +particles. Might include mineral, organic, or biological material. +ENVO definition (ENVO_01000060) has "composed of microscopic portions +of solid or liquid material suspended in another environmental +material." Refine here to define as the solid particles, distinct from +a material in which they are suspended. A material that includes solid +or liquid particles suspended in another material would be a +dispersed_media in this scheme, not defined in ENVO. Human +manufactured particulates (e.g. rock powder) should be categorized as +'Anthropogenic material' as well as 'Particulate' + +#### Rock or sediment + +[]{#rockorsediment} + +Concept: [`rockorsediment`](https://w3id.org/isample/vocabulary/material/rockorsediment) + +Child of: + [`earthmaterial`](#earthmaterial) + +Material is rock or sediment. For example core from boreholes that +likely penetrate sediment near the surface and rock at greater depth, +with descriptions that do not clearly distinguish non-consolidated +sediment from rock. + +##### Rock + +[]{#rock} + +Concept: [`rock`](https://w3id.org/isample/vocabulary/material/rock) + +Child of: + [`rockorsediment`](#rockorsediment) + +Consolidated aggregate of particles (grains) of rock, mineral +(including native elements), mineraloid, or solid organic material. +Includes mineral aggregates such as granite, shale, marble; natural +glass such as obsidian; organic material formed by geologic processes +such a coal; extraterrestrial material in meteorites; and crushed +rock fragments like drill cuttings from rock. (based on +http://resource.geosciml.org/classifier/cgi/lithology/rock, same as +http://purl.obolibrary.org/obo/ENVO_00001995) + +##### Sediment + +[]{#sediment} + +Concept: [`sediment`](https://w3id.org/isample/vocabulary/material/sediment) + +Child of: + [`rockorsediment`](#rockorsediment) + +Solid granular material transported by wind, water, or gravity, not +modified by interaction with biosphere or atmosphere (to differentiate +from soil). Particles might be derived by erosion of pre-existing +rock, from shell or other body parts from organisms, precipitated +chemically in the surficial environment, or generated by explosive +volcanic activity. +(http://resource.geosciml.org/classifier/cgi/lithology/sediment). +Sediment is not consolidated, i.e. the particulate constituents do not +adhere to each other strongly enough that the aggregate can be +considered a solid material in its own right. Similar to +http://purl.obolibrary.org/obo/ENVO_00002007 + +#### Soil + +[]{#soil} + +Concept: [`soil`](https://w3id.org/isample/vocabulary/material/soil) + +Child of: + [`earthmaterial`](#earthmaterial) + +Mixed granular mineral and organic matter modified by interaction +between earth material, biosphere, and atmosphere, consisting of +varying proportions of sand, silt, and clay, organic material such as +humus, gases, liquids, and a broad range of resident micro- and +macroorganisms. (https://en.wikipedia.org/wiki/Soil) Soil consists of +horizons near the Earth's surface that, in contrast to the underlying +parent material, have been altered by the interactions of climate, +relief, and living organisms over time. (http://www.nrcs.usda.gov/wps/ +portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280) +(http://purl.obolibrary.org/obo/ENVO_00001998) + +See Also: + +* [](http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280) + +### Fluid material + +[]{#fluid} + +Concept: [`fluid`](https://w3id.org/isample/vocabulary/material/fluid) + +Child of: + [`material`](#material) + +Substance that continually deforms (flows) under an applied shear +stress, or external force. Fluids are a phase of matter and include +liquids, gases and plasmas. They are substances with zero or small +shear modulus, and flow at a perceptible rate under any shear force +applied to them. (https://en.wikipedia.org/wiki/Fluid) + +#### Gaseous material + +[]{#gas} + +Concept: [`gas`](https://w3id.org/isample/vocabulary/material/gas) + +Child of: + [`fluid`](#fluid) + +Material composed of one or more chemical entities that has neither +independent shape nor volume but tends to expand indefinitely +(http://purl.obolibrary.org/obo/ENVO_01000797). Infer that the sample +is curated in some kind of container. + +#### Liquid water + +[]{#liquidwater} + +Concept: [`liquidwater`](https://w3id.org/isample/vocabulary/material/liquidwater) + +Child of: + [`fluid`](#fluid) + +A material primarily composed of dihydrogen oxide in its liquid form; +infer that the sample is curated in some kind of container. + +#### Non-aqueous liquid material + +[]{#nonaqueousliquid} + +Concept: [`nonaqueousliquid`](https://w3id.org/isample/vocabulary/material/nonaqueousliquid) + +Child of: + [`fluid`](#fluid) + +Liquid composed dominantly of material other than water. Includes +liquids that do not fit in any other category. E.g. alcohol, +petroleum. + +### Organic material + +[]{#organicmaterial} + +Concept: [`organicmaterial`](https://w3id.org/isample/vocabulary/material/organicmaterial) + +Child of: + [`material`](#material) + +Material derived from living organisms and composed primarily of one +or more very large molecules of biological origin. Examples: body +(animal or plant), body part, fecal matter, seeds, wood, tissue, +biological fluids, biological waste, algal material, biofilm, +necromass, plankton. source: +http://purl.obolibrary.org/obo/ENVO_01000155 + + diff --git a/models/generated/vocabularies/sampled_feature_type.qmd b/models/generated/vocabularies/sampled_feature_type.qmd new file mode 100644 index 0000000..da28979 --- /dev/null +++ b/models/generated/vocabularies/sampled_feature_type.qmd @@ -0,0 +1,310 @@ +--- +comment: | + WARNING: This file is generated. Any edits will be lost! +title: "Sampled Feature Type vocabulary" +date: "2025-12-11T02:41:27.623699+00:00" +subtitle: | + Categories to specify the broad context that a sample is intended to represent. +execute: + echo: false +categories: ["vocabulary"] +--- + +Source: +[`https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/sampled_feature_type.ttl`](https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/sampled_feature_type.ttl) + + +Namespace: +[`https://w3id.org/isample/vocabulary/sampledfeature/sampledfeaturevocabulary`](https://w3id.org/isample/vocabulary/sampledfeature/sampledfeaturevocabulary) + +**History** + +* 2021-07-09 Remove Marine biome, Subaerial terrestrial environment, Subaqueous terrestrial environment per github issue https://github.com/isamplesorg/metadata/issues/41. Make Experiment setting and Laboratory or curatorial environment subclasses of Active human occupation site. +* 2021-12-10 SMR add missing skos:inScheme statements +* 2022-01-07 SMR change to https://w3id.org/isample/ uri base, make the ConceptScheme an ontology as well. For uploading to ESIP COR and w3id resolution redirect set up. Add some mappings to other ontologies using seeAlso, closeMatch, narrowMatch. +* 2022-03-11 SMR change definitions from rdfs:comment to skos:definition. Minor fixes in definitions. Add skos matches to URIs from other vocabularies. Fix typo in glacierenvrionment URI (changed the URI to glacierenvironment) +* 2022-09-07 SMR update some of the skos mappings to other vocabularies; remove references to other vocabularies as NamedIndividual. Remove rocksample class, it was not linked in hierarchy and inconsistent with design. +* 2022-09-30 add biological entity as sampled feature, per issue https://github.com/isamplesorg/metadata/issues/107. This update was lost at some point and added back in 2022-12-09. +* 2023-11-05 SMR update version to 1.0, prep for release +* 2024-04-19 SMR update definitions to remove use of 'specimen'. Edit some definitions for better clarity +* 2024-09-13 remove version numbers from URI + +**Concepts** + +- [Any sampled feature](#anysampledfeature) + - [Anthropogenic environment](#anthropogenicenvironment) + - [Active human occupation site](#activehumanoccupationsite) + - [Experiment setting](#experimentsetting) + - [Laboratory or curatorial environment](#laboratorycuratorialenvironment) + - [Site of past human activities](#pasthumanoccupationsite) + - [Biological entity](#biologicalentity) + - [Earth environment](#earthenvironment) + - [Atmosphere](#atmosphere) + - [Earth interior](#earthinterior) + - [Earth surface](#earthsurface) + - [Lake river or stream bottom](#lakeriverstreambottom) + - [Marine water body bottom](#marinewaterbodybottom) + - [Subaerial surface environment](#subaerialsurfaceenvironment) + - [Glacier environment](#glacierenvironment) + - [Subsurface fluid reservoir](#subsurfacefluidreservoir) + - [Water body](#waterbody) + - [Marine environment](#marinewaterbody) + - [Terrestrial water body](#terrestrialwaterbody) + - [Extraterrestrial environment](#extraterrestrialenvironment) + +## Any sampled feature + +[]{#anysampledfeature} + +Concept: [`anysampledfeature`](https://w3id.org/isample/vocabulary/sampledfeature/anysampledfeature) + +Any thing that can be sampled. Top concept in sampled feature type +vocabulary. + +### Anthropogenic environment + +[]{#anthropogenicenvironment} + +Concept: [`anthropogenicenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/anthropogenicenvironment) + +Child of: + [`anysampledfeature`](#anysampledfeature) + +Sampled feature is produced by or related to human activity past or +present. + +#### Active human occupation site + +[]{#activehumanoccupationsite} + +Concept: [`activehumanoccupationsite`](https://w3id.org/isample/vocabulary/sampledfeature/activehumanoccupationsite) + +Child of: + [`anthropogenicenvironment`](#anthropogenicenvironment) + +sampled feature is a site at which there are ongoing human activities + +##### Experiment setting + +[]{#experimentsetting} + +Concept: [`experimentsetting`](https://w3id.org/isample/vocabulary/sampledfeature/experimentsetting) + +Child of: + [`activehumanoccupationsite`](#activehumanoccupationsite) + +Sampled feature is an experimental set up that produced the sample; +the sample is the product of the experiment. + +##### Laboratory or curatorial environment + +[]{#laboratorycuratorialenvironment} + +Concept: [`laboratorycuratorialenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/laboratorycuratorialenvironment) + +Child of: + [`activehumanoccupationsite`](#activehumanoccupationsite) + +Sampled feature is a laboratory or other research site, collected with +intention of characterizing the environment in which data are +collected or other research conducted, that might affect results or +safety; e.g. lab blank measurements. + +#### Site of past human activities + +[]{#pasthumanoccupationsite} + +Concept: [`pasthumanoccupationsite`](https://w3id.org/isample/vocabulary/sampledfeature/pasthumanoccupationsite) + +Child of: + [`anthropogenicenvironment`](#anthropogenicenvironment) + +sampled feature is a place where humans have been and left evidence of +their activity. Includes prehistoric and paleo hominid sites + +### Biological entity + +[]{#biologicalentity} + +Concept: [`biologicalentity`](https://w3id.org/isample/vocabulary/sampledfeature/biologicalentity) + +Child of: + [`anysampledfeature`](#anysampledfeature) + +Sampled feature is an organism. Use for samples that represent some +species of organism as the proximate sampled feature, not the +environment that the organism inhabits. + +### Earth environment + +[]{#earthenvironment} + +Concept: [`earthenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/earthenvironment) + +Child of: + [`anysampledfeature`](#anysampledfeature) + +Sampled feature is the natural Earth environment + +See Also: + +* [](http://purl.bioontology.org/ontology/MESH/D004777) +* [](http://semanticscience.org/resource/SIO_000955) + +#### Atmosphere + +[]{#atmosphere} + +Concept: [`atmosphere`](https://w3id.org/isample/vocabulary/sampledfeature/atmosphere) + +Child of: + [`earthenvironment`](#earthenvironment) + +Sampled feature is the Earth's atmosphere + +See Also: + +* [obo:ENVO_01000267](http://purl.obolibrary.org/obo/ENVO_01000267) +* [obo:RBO_00000018](http://purl.obolibrary.org/obo/RBO_00000018) + +#### Earth interior + +[]{#earthinterior} + +Concept: [`earthinterior`](https://w3id.org/isample/vocabulary/sampledfeature/earthinterior) + +Child of: + [`earthenvironment`](#earthenvironment) + +Sampled feature is solid material from within the Earth + +#### Earth surface + +[]{#earthsurface} + +Concept: [`earthsurface`](https://w3id.org/isample/vocabulary/sampledfeature/earthsurface) + +Child of: + [`earthenvironment`](#earthenvironment) + +Sampled feature is the interface between solid earth and hydrosphere +or atmosphere. Includes samples representing things collected on the +surface, in the uppermost part of the material below the surface, or +air or water directly at the contact with the Earth surface. + +##### Lake river or stream bottom + +[]{#lakeriverstreambottom} + +Concept: [`lakeriverstreambottom`](https://w3id.org/isample/vocabulary/sampledfeature/lakeriverstreambottom) + +Child of: + [`earthsurface`](#earthsurface) + +Sampled feature is the interface between the solid Earth interface and +a lake or flowing water body. + +##### Marine water body bottom + +[]{#marinewaterbodybottom} + +Concept: [`marinewaterbodybottom`](https://w3id.org/isample/vocabulary/sampledfeature/marinewaterbodybottom) + +Child of: + [`earthsurface`](#earthsurface) + +Sampled feature is the interface between the solid Earth and a marine +or brackish water body. Includes benthic boundary layer: the bottom +layer of water and the uppermost layer of sediment directly influenced +by the overlying water. + +##### Subaerial surface environment + +[]{#subaerialsurfaceenvironment} + +Concept: [`subaerialsurfaceenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/subaerialsurfaceenvironment) + +Child of: + [`earthsurface`](#earthsurface) + +sampled feature is the interface between solid Earth and atmosphere. +Sample is collected on the surface, or immediately below surface (zone +of bioturbation). Include soil and recently deposited subaerial +sediment at the surface. + +#### Glacier environment + +[]{#glacierenvironment} + +Concept: [`glacierenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/glacierenvironment) + +Child of: + [`earthenvironment`](#earthenvironment) + +Sampled feature is a glacier, ice sheet, ice shelf, iceberg, or rock +or water directly under or on top of such ice. + +#### Subsurface fluid reservoir + +[]{#subsurfacefluidreservoir} + +Concept: [`subsurfacefluidreservoir`](https://w3id.org/isample/vocabulary/sampledfeature/subsurfacefluidreservoir) + +Child of: + [`earthenvironment`](#earthenvironment) + +Sampled feature is fluid that resides in fractures, intergranular +porosity or other open space in the solid earth. + +#### Water body + +[]{#waterbody} + +Concept: [`waterbody`](https://w3id.org/isample/vocabulary/sampledfeature/waterbody) + +Child of: + [`earthenvironment`](#earthenvironment) + +Sampled feature is the Earth's hydrosphere. + +##### Marine environment + +[]{#marinewaterbody} + +Concept: [`marinewaterbody`](https://w3id.org/isample/vocabulary/sampledfeature/marinewaterbody) + +Child of: + [`waterbody`](#waterbody) + +Sampled feature is the marine hydrosphere. + +See Also: + +* [obo:ENVO_01000686](http://purl.obolibrary.org/obo/ENVO_01000686) + +##### Terrestrial water body + +[]{#terrestrialwaterbody} + +Concept: [`terrestrialwaterbody`](https://w3id.org/isample/vocabulary/sampledfeature/terrestrialwaterbody) + +Child of: + [`waterbody`](#waterbody) + +Sampled feature is terrestrial hydrosphere-- lake, other standing +water, or a flowing water body (river, stream..). Include saline water +in terrestrial evaporite environments. + +### Extraterrestrial environment + +[]{#extraterrestrialenvironment} + +Concept: [`extraterrestrialenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/extraterrestrialenvironment) + +Child of: + [`anysampledfeature`](#anysampledfeature) + +Sampled feature is the environment outside of solid earth, +hydrosphere, or atmosphere. + + diff --git a/scripts/generate_vocab_docs.sh b/scripts/generate_vocab_docs.sh index 20d9b22..b93ca72 100755 --- a/scripts/generate_vocab_docs.sh +++ b/scripts/generate_vocab_docs.sh @@ -16,8 +16,8 @@ mkdir -p "${DEST_FOLDER}" for src in ${SOURCES[@]}; do fname="${src%%.*}.qmd" echo "Generating ${fname}..." -# python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" - vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" + python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" +# vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" done # @@ -35,8 +35,8 @@ mkdir -p "${DEST_FOLDER}" for src in ${SOURCES[@]}; do fname="${src%%.*}.md" echo "Generating ${fname}..." -# python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" - vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" + python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" +# vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" done SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/" @@ -46,8 +46,8 @@ mkdir -p "${DEST_FOLDER}" for src in ${SOURCES[@]}; do fname="${src%%.*}.md" echo "Generating ${fname}..." -# python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" - vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" + python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" +# vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" done SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_biology/main/vocabulary/" @@ -57,8 +57,8 @@ mkdir -p "${DEST_FOLDER}" for src in ${SOURCES[@]}; do fname="${src%%.*}.md" echo "Generating ${fname}..." -# python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" - vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" + python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" +# vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" done echo "Done." From e74522a7da1a949249161db60b51562c85271264 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 11 Dec 2025 02:43:11 +0000 Subject: [PATCH 3/5] Update vocabulary links in models/index.qmd to point to generated files Co-authored-by: rdhyee <153266+rdhyee@users.noreply.github.com> --- models/index.qmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/models/index.qmd b/models/index.qmd index dc17d94..5663f73 100644 --- a/models/index.qmd +++ b/models/index.qmd @@ -37,10 +37,10 @@ The iSamples taxonomies are used to characterize three fundamental concepts pert Three taxonomies are currently defined : -[Material Sample (specimen) Type Vocabulary](https://isamplesorg.github.io/metadata/vocabularies/specimentype.html) +[Material Sample (specimen) Type Vocabulary](generated/vocabularies/material_sample_object_type.qmd) -[Materials Vocabulary](https://isamplesorg.github.io/metadata/vocabularies/materialtype.html) +[Materials Vocabulary](generated/vocabularies/material_type.qmd) -[Sampled Feature (context) Type vocabulary](https://isamplesorg.github.io/metadata/vocabularies/sampledfeature.html) +[Sampled Feature (context) Type vocabulary](generated/vocabularies/sampled_feature_type.qmd) From 5794976d0dcc8a29d67c29f7d61bb2278894a55a Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 11 Dec 2025 02:44:45 +0000 Subject: [PATCH 4/5] Fix vocabulary links to point to .html files instead of .qmd sources Co-authored-by: rdhyee <153266+rdhyee@users.noreply.github.com> --- models/index.qmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/models/index.qmd b/models/index.qmd index 5663f73..dcbae0d 100644 --- a/models/index.qmd +++ b/models/index.qmd @@ -37,10 +37,10 @@ The iSamples taxonomies are used to characterize three fundamental concepts pert Three taxonomies are currently defined : -[Material Sample (specimen) Type Vocabulary](generated/vocabularies/material_sample_object_type.qmd) +[Material Sample (specimen) Type Vocabulary](generated/vocabularies/material_sample_object_type.html) -[Materials Vocabulary](generated/vocabularies/material_type.qmd) +[Materials Vocabulary](generated/vocabularies/material_type.html) -[Sampled Feature (context) Type vocabulary](generated/vocabularies/sampled_feature_type.qmd) +[Sampled Feature (context) Type vocabulary](generated/vocabularies/sampled_feature_type.html) From 27701f749830381da59b847487e21d61d88bb7d0 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 11 Dec 2025 06:36:24 +0000 Subject: [PATCH 5/5] Remove generated files from git, update .gitignore, and clean up script Co-authored-by: rdhyee <153266+rdhyee@users.noreply.github.com> --- .gitignore | 7 + .../biology_sampledfeature_extension.md | 812 -------- ...rthenv_material_extension_mineral_group.md | 193 -- ...rthenv_material_extension_rock_sediment.md | 1836 ----------------- .../earthenv_materialsampleobject_type.md | 1222 ----------- .../earthenv_sampled_feature_role.md | 209 -- .../opencontext_material_extension.md | 824 -------- .../opencontext_materialsampleobjecttype.md | 203 -- models/generated/extensions/readme.md | 2 +- .../material_sample_object_type.qmd | 375 ---- .../generated/vocabularies/material_type.qmd | 377 ---- .../vocabularies/sampled_feature_type.qmd | 310 --- scripts/generate_vocab_docs.sh | 5 - 13 files changed, 8 insertions(+), 6367 deletions(-) delete mode 100644 models/generated/extensions/biology_sampledfeature_extension.md delete mode 100644 models/generated/extensions/earthenv_material_extension_mineral_group.md delete mode 100644 models/generated/extensions/earthenv_material_extension_rock_sediment.md delete mode 100644 models/generated/extensions/earthenv_materialsampleobject_type.md delete mode 100644 models/generated/extensions/earthenv_sampled_feature_role.md delete mode 100644 models/generated/extensions/opencontext_material_extension.md delete mode 100644 models/generated/extensions/opencontext_materialsampleobjecttype.md delete mode 100644 models/generated/vocabularies/material_sample_object_type.qmd delete mode 100644 models/generated/vocabularies/material_type.qmd delete mode 100644 models/generated/vocabularies/sampled_feature_type.qmd diff --git a/.gitignore b/.gitignore index 7d61b28..40f2d5c 100644 --- a/.gitignore +++ b/.gitignore @@ -3,6 +3,13 @@ uv.lock plantuml-images docs +# Generated vocabulary documentation (but keep readme.md files) +models/generated/vocabularies/*.qmd +models/generated/vocabularies/*.md +!models/generated/vocabularies/readme.md +models/generated/extensions/*.md +!models/generated/extensions/readme.md + # Large data files *.parquet diff --git a/models/generated/extensions/biology_sampledfeature_extension.md b/models/generated/extensions/biology_sampledfeature_extension.md deleted file mode 100644 index be954fc..0000000 --- a/models/generated/extensions/biology_sampledfeature_extension.md +++ /dev/null @@ -1,812 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "Biology Extension: Basic taxon classes for biological entity" -date: "2025-12-11T02:41:37.197064+00:00" -subtitle: | - This is a vocabulary to categorize sampled organisms (whole or part) according to taxonomic classes. Classes are based largely on taxonomy found in Wikipedia, particularly Whittaker's five kingdom system (1969) (https://en.wikipedia.org/wiki/Kingdom_(biology), https://doi.org/10.1126%2Fscience.163.3863.150). The intended use is in iSamples cross domain categorization of material samples, recognizing that there are multiple view for taxonomy and cladistics for the tree of life. This is a high level view intended for cross domain purposes, not expert analysis. Other extension vocabularies should be used for other taxonomic schemes -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_biology/main/vocabulary/biology_sampledfeature_extension.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_biology/main/vocabulary/biology_sampledfeature_extension.ttl) - - -Namespace: -[`https://w3id.org/isample/biology/biosampledfeature/biologicentityvocabulary`](https://w3id.org/isample/biology/biosampledfeature/biologicentityvocabulary) - -**History** - -* 2024-01-19 SMR add cross reference to GBIF taxonomy backbone where mapping was apparent. -* 2024-04-12 SMR. Import of GEOME records show that many samples are classified as Kingdom Chromista, but this is missing from this vocabulary extension (https://github.com/isamplesorg/vocabularies/issues/17). Hierarchy and classes reviewed; deprecate Protista and make it an alternate name in Eukaryotic microorganism class and update definition; add Chromista; update scope notes for Eukaryote. Harmonize better with GBIF tree of life: Make Mycetozoa subclass of Protozoa, not subclass of Amoebozoa, add Other Protozoa class for logical completeness. increment version to 1.1; these are not breaking changes, but addition of new class and hierarchy adjustments in protozoa are more than incremental. -* 2024-09-13 SMR remove version number from URI -* Based on draft DiSSCo specimen & collection classification, table 2, https://docs.google.com/document/d/19OPyOm9VF2qfI3M6RmJPvRfo8JlZ3tt0II05aGCyBHQ/ , with added classes to attempt a logical hierarchy. - -**Concepts** - -- [Biological entity](#biologicalentity) - - [Eukaryote](#eukaryote) - - [Algae](#algae) - - [Animalia](#animalia) - - [Arthropod](#arthropod) - - [Arachnid](#arachnid) - - [Crustaceans](#crustacea) - - [Insect](#hexapoda) - - [Myriapod](#myriapod) - - [Other arthropod ](#otherarthropod) - - [Mollusca](#mollusca) - - [Other invertebrate ](#otherinvertebrate) - - [Porifera](#porifera) - - [Vertebrate ](#vertebrate) - - [Amphibian](#amphibian) - - [Bird](#bird) - - [Fish](#fish) - - [Mammal](#mammal) - - [Reptile](#reptile) - - [Chromista](#chromista) - - [Eukaryotic microorganism](#eukaryoticmicroorganism) - - [Fungi](#fungi) - - [Macrofungi](#macrofungi) - - [Microfungi](#microfungi) - - [Plantae](#plantae) - - [Non-vascular plant](#nonvascularplant) - - [Other plant](#otherplant) - - [Vascular seed plant](#vascularseedplant) - - [Vascular spore plant](#vascularsportplant) - - [Protozoa](#protozoa) - - [Amoebozoa](#amoebozoa) - - [Mycetozoa](#mycetozoa) - - [Other Protozoa](#otherprotozoa) - - [Lichen](#lichen) - - [Plasmid](#plasmid) - - [Prokaryote](#prokaryote) - - [Archaea](#archaea) - - [Bacteria](#bacteria) - - [Virus](#virus) - - [Other Virus](#othervirus) - - [Phage](#phage) - -## Biological entity - -[]{#biologicalentity} - -Concept: [`biologicalentity`](https://w3id.org/isample/vocabulary/sampledfeature/biologicalentity) - -Sampled feature is an organism. Use for samples that represent some -species of organism as the proximate sampled feature for which the -focus is not the environment that the organism inhabits. - -### Eukaryote - -[]{#eukaryote} - -Concept: [`eukaryote`](https://w3id.org/isample/biology/biosampledfeature/eukaryote) - -Child of: - [`biologicalentity`](#biologicalentity) - -Organism whose cells have a nucleus. Includes all animals, plants, -fungi, and many unicellular organisms -(https://en.wikipedia.org/wiki/Eukaryote). Eucaryote membranes are -flexible, and contain cholesterol. The membrane, nucleus, and -structures are supported by cross-connecting protein filaments. Cells -are ~10 times larger in radius relative to prokaryotes. Cells have -several types of internal enclosed compartments. Cell walls, if -present, are made from cellulose or chitin, in contrast to -prokaryotes. Eukaryotes have novel modes of direct body movement and -swimming, based on sensors, and the mode of reproduction uses sexual -combination. Their DNA is linear but wound up into nucleosomes and -then chromosomes. (https://doi.org/10.1016/B978-044452115-6/50050-6, -table 7-2). Eukaryotes can be considered a chimera; a combination of -archaeal and bacterial features that result in the cellular complexity -and distinctive characteristics. -(https://doi.org/10.1016/j.tim.2021.11.003). - -#### Algae - -[]{#algae} - -Concept: [`algae`](https://w3id.org/isample/biology/biosampledfeature/algae) - -Child of: - [`eukaryote`](#eukaryote) - -Informal term for a large and diverse group of photosynthetic -eukaryotic organisms. Included organisms range from unicellular -microalgae, such as Chlorella, Prototheca and the diatoms, to -multicellular forms, such as the giant kelp, a large brown alga which -may grow up to 50 metres (160 ft) in length. Most are aquatic and -autotrophic (they generate food internally) and lack many of the -distinct cell and tissue types, such as stomata, xylem and phloem that -are found in land plants. Includes red algae (Rhodophycophyta), brown -algae (Phaeophycophyta), and green algae (Chlorophyta). -https://en.wikipedia.org/wiki/Algae - -#### Animalia - -[]{#animalia} - -Concept: [`animalia`](https://w3id.org/isample/biology/biosampledfeature/animalia) - -Child of: - [`eukaryote`](#eukaryote) - -Animals are distinguished from other eukaryotes based on several key -characteristics, including: 1) animals are multicellular organisms 2) -Animals are heterotrophic, they obtain their food by consuming other -organisms or organic matter; 3) Animals lack cell walls; 4) Many -animals have a nervous system; 5) Most animals reproduce sexually -(Chat GPT) - -See Also: - -* [](https://www.gbif.org/species/1) - -##### Arthropod - -[]{#arthropod} - -Concept: [`arthropod`](https://w3id.org/isample/biology/biosampledfeature/arthropod) - -Child of: - [`animalia`](#animalia) - -invertebrate animals with an exoskeleton, a segmented body, and paired -jointed appendages. Arthropods form the phylum Arthropoda. They are -distinguished by their jointed limbs and cuticle made of chitin, often -mineralised with calcium carbonate. The arthropod body plan consists -of segments, each with a pair of appendages. Arthropods are -bilaterally symmetrical and their body possesses an external skeleton. -(https://en.wikipedia.org/wiki/Arthropod) - -See Also: - -* [](https://www.gbif.org/species/54) - -###### Arachnid - -[]{#arachnid} - -Concept: [`arachnid`](https://w3id.org/isample/biology/biosampledfeature/arachnid) - -Child of: - [`arthropod`](#arthropod) - -a group of arthropods that share several key characteristics, -including two main body segments, four pairs of legs, lack of -antennae, simple eyes, and specialized feeding and defense structures -called chelicerae (ChatGPT) - -See Also: - -* [](https://en.wikipedia.org/wiki/Arachnid) -* [](https://www.gbif.org/species/367) - -###### Crustaceans - -[]{#crustacea} - -Concept: [`crustacea`](https://w3id.org/isample/biology/biosampledfeature/crustacea) - -Child of: - [`arthropod`](#arthropod) - -arthropod taxon which includes such animals as decapods, seed shrimp, -branchiopods, fish lice, krill, remipedes, isopods, barnacles, -copepods, amphipods and mantis shrimp. crustaceans have an -exoskeleton, which they moult to grow. They are distinguished from -other groups of arthropods, such as insects, myriapods and -chelicerates, by the possession of biramous (two-parted) limbs, and by -their larval forms, such as the nauplius stage of branchiopods and -copepods. (https://en.wikipedia.org/wiki/Crustacean) - -###### Insect - -[]{#hexapoda} - -Concept: [`hexapoda`](https://w3id.org/isample/biology/biosampledfeature/hexapoda) - -Child of: - [`arthropod`](#arthropod) - -Include all hexapoda here; Insects are a group of hexapod arthropods -characterized by having three main body segments (head, thorax, and -abdomen), six legs, and wings in many species. All other hexapod -arthropods, such as springtails and diplurans, are not classified as -insects, but they share the same body plan of three main body segments -and six legs. However, they lack wings and other features that are -unique to insects. Therefore, all insects are hexapods, but not all -hexapods are insects. (ChatGPT) - -See Also: - -* [](https://www.gbif.org/species/174780701) - -###### Myriapod - -[]{#myriapod} - -Concept: [`myriapod`](https://w3id.org/isample/biology/biosampledfeature/myriapod) - -Child of: - [`arthropod`](#arthropod) - -Arthropods such as millipedes and centipedes. -(https://en.wikipedia.org/wiki/Myriapoda). A group of arthropods that -have long, segmented body with numerous pairs of legs, simple eyes, -specialized mouthparts, and a primarily terrestrial habitat, which -distinguishes them from other arthropod groups such as insects and -crustaceans. (ChatGPT) - -###### Other arthropod - -[]{#otherarthropod} - -Concept: [`otherarthropod`](https://w3id.org/isample/biology/biosampledfeature/otherarthropod) - -Child of: - [`arthropod`](#arthropod) - -includes Chelicerata (horseshoe crabs, scorpions, and sea spiders), -Trilobitomorpha ( extinct trilobites), and Pentastomida (parasitic -arthropods that infect the respiratory systems of reptiles and -mammals). (ChatGPT) - -##### Mollusca - -[]{#mollusca} - -Concept: [`mollusca`](https://w3id.org/isample/biology/biosampledfeature/mollusca) - -Child of: - [`animalia`](#animalia) - -animals that have a soft body with a mantle, a radula (ribbon-like -structure covered in tiny teeth that is used to scrape food), a -muscular foot, an open circulatory system, and a visceral mass that -contains the internal organs, including the digestive, excretory, and -reproductive systems. (ChatGPT) - -See Also: - -* [](https://www.gbif.org/species/52) - -##### Other invertebrate - -[]{#otherinvertebrate} - -Concept: [`otherinvertebrate`](https://w3id.org/isample/biology/biosampledfeature/otherinvertebrate) - -Child of: - [`animalia`](#animalia) - -Includes Cnidaria (jellyfish, coral, anemones), Echinodermata -(starfish, sea urchins, sea cucumbers), Nematoda (roundworms), -Platyhelminthes (flatworms), Annelida (segmented worms), Ctenophora -(comb jellies), Brachiopoda (lamp shells), Bryozoa (moss animals), -Chaetognatha (arrow worms), Hemichordata (acorn worms), -Xenacoelomorpha (simple-bodied worms) (ChatGPT) - -##### Porifera - -[]{#porifera} - -Concept: [`porifera`](https://w3id.org/isample/biology/biosampledfeature/porifera) - -Child of: - [`animalia`](#animalia) - -multicellular animals that have bodies full of pores and channels -allowing water to circulate through them, consisting of jelly-like -mesohyl sandwiched between two thin layers of cells. -(https://en.wikipedia.org/wiki/Sponge) - -See Also: - -* [](https://www.gbif.org/species/105) - -##### Vertebrate - -[]{#vertebrate} - -Concept: [`vertebrate`](https://w3id.org/isample/biology/biosampledfeature/vertebrate) - -Child of: - [`animalia`](#animalia) - -Animals that have a vertebral column, a cranium, an endoskeleton, a -well-developed muscular system, and an advanced nervous system -(ChatGPT); - -###### Amphibian - -[]{#amphibian} - -Concept: [`amphibian`](https://w3id.org/isample/biology/biosampledfeature/amphibian) - -Child of: - [`vertebrate`](#vertebrate) - -Vertebrates that have a dual life cycle, semi-permeable skin, absence -of scales and claws, a three-chambered heart, and dependence on water -for reproduction and survival (ChatGPT) - -###### Bird - -[]{#bird} - -Concept: [`bird`](https://w3id.org/isample/biology/biosampledfeature/bird) - -Child of: - [`vertebrate`](#vertebrate) - -Vertebrates that have feathers, lightweight, hollow bones, a beak, an -efficient respiratory system, and are warm-blooded. (ChatGPT) - -###### Fish - -[]{#fish} - -Concept: [`fish`](https://w3id.org/isample/biology/biosampledfeature/fish) - -Child of: - [`vertebrate`](#vertebrate) - -Vertebrates that have gills, scales, fins, are cold-blooded, and -commonly have a swim bladder; includes jawless fish, cartilaginous -fish and bony fish. (ChatGPT) - -###### Mammal - -[]{#mammal} - -Concept: [`mammal`](https://w3id.org/isample/biology/biosampledfeature/mammal) - -Child of: - [`vertebrate`](#vertebrate) - -vertebrates that have mammary glands, hair or fur, three middle ear -bones, specialized teeth, and are warm-blooded. (ChatGPT) - -###### Reptile - -[]{#reptile} - -Concept: [`reptile`](https://w3id.org/isample/biology/biosampledfeature/reptile) - -Child of: - [`vertebrate`](#vertebrate) - -Vertebrates that have scaly skin and claws, amniotic eggs, are cold- -blooded, and are ectothermic (ChatGPT) - -#### Chromista - -[]{#chromista} - -Concept: [`chromista`](https://w3id.org/isample/biology/biosampledfeature/chromista) - -Child of: - [`eukaryote`](#eukaryote) - -Chromists are unified by a shared common ancestral body plan with (1) -a skeleton comprising cortical alveoli with subpellicular microtubules -and a microtubule bypassing band distinct from the three major -microtubule centriolar roots inherited from excavate protozoa, and (2) -chloroplasts of red algal origin inside the endomembrane system with -unique membrane topology and derlin-based periplastid protein import -machinery. Chromists are distinguished from Plantae because of more -complex chloroplast-associated membrane topology and rigid tubular -multipartite ciliary hairs. The kingdom includes highly divergent -cytoskeletons and trophic modes. Chromista comprise eight distinctive -phyla (Cavalier-Smith, 2018) and includes a majority of marine algae -and of heterotrophic protists, various human disease agents such as -malaria parasites, and agricultural pathogens like potato blight and -sugar beet rhizomania disease. They have a greater range of body plans -and lifestyles than the entire plant kingdom and more phyla than -kingdoms Fungi or Protozoa. - -See Also: - -* [](https://www.gbif.org/species/4) - -#### Eukaryotic microorganism - -[]{#eukaryoticmicroorganism} - -Concept: [`eukaryoticmicroorganism`](https://w3id.org/isample/biology/biosampledfeature/eukaryoticmicroorganism) - -Child of: - [`eukaryote`](#eukaryote) - -Unclassified Eukaryote single-cell organisms; might be microfungi, -microalgae, Protista or Chromista. - -See Also: - -* [](https://en.wikipedia.org/wiki/Protist) - -#### Fungi - -[]{#fungi} - -Concept: [`fungi`](https://w3id.org/isample/biology/biosampledfeature/fungi) - -Child of: - [`eukaryote`](#eukaryote) - -eukaryotic organisms that contain chitin in their cell walls, are -heterotrophs (they obtain their nutrients by absorbing organic -material from their environment, either as decomposers, parasites, or -symbionts) , lack chloroplasts, reproduce both sexually and asexually, -and can take on a variety of growth forms, including single-celled -yeasts, multicellular molds, and complex, specialized fruiting bodies. -(ChatGPT). Biologists use the term ‘fungus’ to include eukaryotic, -spore-bearing, achlorophyllous organisms that generally reproduce -sexually and asexually. They are usually made up of filamentous, -branched somatic structures which are typically surrounded by cell -walls containing chitin or cellulose, or both of these substances. -(https://plantlet.org/lower-fungi-higher-fungi/) - -See Also: - -* [](https://www.gbif.org/species/5) - -##### Macrofungi - -[]{#macrofungi} - -Concept: [`macrofungi`](https://w3id.org/isample/biology/biosampledfeature/macrofungi) - -Child of: - [`fungi`](#fungi) - -Macrofungi refers to all fungi that produce visible fruiting bodies. -These fungi are evolutionarily and ecologically very divergent. -Evolutionarily, they belong to two main phyla, Ascomycota and -Basidiomycota, and many of them have relatives that cannot form -visible fruiting -bodies.(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6106070/) - -##### Microfungi - -[]{#microfungi} - -Concept: [`microfungi`](https://w3id.org/isample/biology/biosampledfeature/microfungi) - -Child of: - [`fungi`](#fungi) - -Microfungi or micromycetes are fungi—eukaryotic organisms such as -molds, mildews and rusts, which have microscopic spore-producing -structures. They exhibit tube tip-growth and have cell walls composed -of chitin, a polymer of N-acetylglucosamine. Microfungi are a -paraphyletic group, distinguished from macrofungi only by the absence -of a large, multicellular fruiting body. Include moulds, yeasts. -(https://en.wikipedia.org/wiki/Microfungi) - -#### Plantae - -[]{#plantae} - -Concept: [`plantae`](https://w3id.org/isample/biology/biosampledfeature/plantae) - -Child of: - [`eukaryote`](#eukaryote) - -Plants are eukaryotes that have cell walls made of cellulose, -specialized organelles called chloroplasts, which contain chlorophyll -and other pigments that allow plants to perform photosynthesis and -produce their own food; a unique life cycle that involves alternating -between a haploid gametophyte stage and a diploid sporophyte stage; -specialized regions called apical meristems at the tips of their roots -and shoots, which allow for growth and the development of new tissues; -specialized structures for reproduction, including flowers, cones, and -spores, and most plants have specialized tissues called xylem and -phloem, which transport water, nutrients, and other substances -throughout the plant. (ChatGPT). Subdivision here follows Margulis and -Schwartz 2001. - -See Also: - -* [](https://www.gbif.org/species/6) - -##### Non-vascular plant - -[]{#nonvascularplant} - -Concept: [`nonvascularplant`](https://w3id.org/isample/biology/biosampledfeature/nonvascularplant) - -Child of: - [`plantae`](#plantae) - -Non-vascular plants that do not have specialized tissues for -transporting water and nutrients; includes mosses, Marchantiophyta -(liverworts), and Anthocerotophyta (hornworts). (ChatGPT) - -See Also: - -* [](https://www.gbif.org/species/35) - -##### Other plant - -[]{#otherplant} - -Concept: [`otherplant`](https://w3id.org/isample/biology/biosampledfeature/otherplant) - -Child of: - [`plantae`](#plantae) - -plants that do not fit in other plant sub class. Includes -Lycopodiophyta (clubmosses) and Equisetophyta (horsetails) - -##### Vascular seed plant - -[]{#vascularseedplant} - -Concept: [`vascularseedplant`](https://w3id.org/isample/biology/biosampledfeature/vascularseedplant) - -Child of: - [`plantae`](#plantae) - -Plant that produces seeds, hence the alternative name seed plant. -Spermatophytes are a subset of the embryophytes or land plants. They -include most familiar types of plants, including all flowers and most -trees, but exclude some other types of plants such as ferns, mosses, -algae. (https://en.wikipedia.org/wiki/Spermatophyte). Includes -Gymnosperms (naked-seed plants) and Angiosperms (flowering plants). - -##### Vascular spore plant - -[]{#vascularsportplant} - -Concept: [`vascularsportplant`](https://w3id.org/isample/biology/biosampledfeature/vascularsportplant) - -Child of: - [`plantae`](#plantae) - -a vascular plant (with xylem and phloem) that disperses spores; they -produce neither flowers nor seeds, Includes Ferns, horsetails (often -treated as ferns), and lycophytes (clubmosses, spikemosses, and -quillworts) - -#### Protozoa - -[]{#protozoa} - -Concept: [`protozoa`](https://w3id.org/isample/biology/biosampledfeature/protozoa) - -Child of: - [`eukaryote`](#eukaryote) - -A single-celled eukaryote, either free-living or parasitic, that feed -on organic matter such as other microorganisms or organic tissues and -debris (predominantly heterotrophic). Historically, protozoans were -regarded as 'one-celled animals', because they often possess animal- -like behaviours, such as motility and predation, and lack a cell wall, -as found in plants and many algae. -(https://en.wikipedia.org/wiki/Protozoa) - -See Also: - -* [](https://www.gbif.org/species/7) - -##### Amoebozoa - -[]{#amoebozoa} - -Concept: [`amoebozoa`](https://w3id.org/isample/biology/biosampledfeature/amoebozoa) - -Child of: - [`protozoa`](#protozoa) - -a diverse group of organisms that share certain characteristics, such -as the ability to move using pseudopodia, temporary extensions of the -cell membrane and cytoplasm that allow the cell to crawl or engulf -food particles, the lack of rigid cell walls, presence of -mitochondria, which are organelles that generate energy for the cell -through cellular respiration (chatGPT) - -See Also: - -* [](https://www.gbif.org/species/7509337) - -##### Mycetozoa - -[]{#mycetozoa} - -Concept: [`mycetozoa`](https://w3id.org/isample/biology/biosampledfeature/mycetozoa) - -Child of: - [`protozoa`](#protozoa) - -Mycetozoa includes the slime molds, which are a group of organisms -that have both amoeboid and fungal-like characteristics. The Mycetozoa -can be further subdivided into two groups: the plasmodial slime molds -and the cellular slime molds. Myxomycetes has most child orders; they -are class of slime molds. Myxomycetes have a complex life cycle -involving the formation of spore-bearing structures called fruiting -bodies, which is a key feature that distinguishes them from other -amoebae. All species pass through several, very different -morphologic phases, such as microscopic individual cells, slimy -amorphous organisms visible with the naked eye and conspicuously -shaped fruit bodies. Although they are monocellular, they can reach -immense widths and weights. -(https://en.wikipedia.org/wiki/Mycetozoa). (ChatGPT) - -See Also: - -* [](https://www.gbif.org/species/33) - -##### Other Protozoa - -[]{#otherprotozoa} - -Concept: [`otherprotozoa`](https://w3id.org/isample/biology/biosampledfeature/otherprotozoa) - -Child of: - [`protozoa`](#protozoa) - -Protozoa is not Amoebozoa or Mycetozoa. Includes phylum Euglenozoa -and Microsporidia prominently among others. - -### Lichen - -[]{#lichen} - -Concept: [`lichen`](https://w3id.org/isample/biology/biosampledfeature/lichen) - -Child of: - [`biologicalentity`](#biologicalentity) - -A composite organism that arises from algae or cyanobacteria living -among filaments of multiple fungi species in a mutualistic -relationship. (https://en.wikipedia.org/wiki/Lichen). Lichens are not -classified under a specific kingdom as they are a symbiotic -association between a fungus and either an alga or a cyanobacterium. -The fungal partner belongs to the kingdom Fungi, while the algal or -cyanobacterial partner belongs to either the kingdom Plantae or the -kingdom Bacteria, respectively. (ChatGPT) - -### Plasmid - -[]{#plasmid} - -Concept: [`plasmid`](https://w3id.org/isample/biology/biosampledfeature/plasmid) - -Child of: - [`biologicalentity`](#biologicalentity) - -A plasmid is a small, extrachromosomal DNA molecule within a cell that -is physically separated from chromosomal DNA and can replicate -independently. While chromosomes are large and contain all the -essential genetic information for living under normal conditions, -plasmids are usually very small and contain only additional genes that -may be useful in certain situations or conditions. -(https://en.wikipedia.org/wiki/Plasmid) - -### Prokaryote - -[]{#prokaryote} - -Concept: [`prokaryote`](https://w3id.org/isample/biology/biosampledfeature/prokaryote) - -Child of: - [`biologicalentity`](#biologicalentity) - -single-celled organisms that lack a nucleus and other membrane-bound -organelles. Unlike cells of animals and other eukaryotes, bacterial -cells do not contain a nucleus and rarely harbour membrane-bound -organelles. Molecular systematics showed prokaryotic life to consist -of two separate domains, originally called Eubacteria and -Archaebacteria, but now called Bacteria and Archaea that evolved -independently from an ancient common ancestor. Almost all prokaryotes -have a cell wall, a protective structure that allows them to survive -in extreme conditions, which is located outside of their plasma -membrane. Archaea and bacteria cannot reproduce sexually. - -#### Archaea - -[]{#archaea} - -Concept: [`archaea`](https://w3id.org/isample/biology/biosampledfeature/archaea) - -Child of: - [`prokaryote`](#prokaryote) - -archaeal cell walls are composed of polysaccharides (sugars). they -never have peptidoglycan in their cell walls, their cell membranes -contain lipids of unique composition (glycerol molecules are mirror -images of those found in other cells, and form ether linkages to -isoprenoid side chains), and their 16S ribosomal- RNA nucleotide -sequences are unlike those of bacteria. -(https://quizlet.com/234154298/archaea-and-bacteria-flash-cards/). -The common characteristics of Archaebacteria known to date are these: -(1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the -absence of peptidoglycan cell walls, with in many cases, replacement -by a largely proteinaceous coat; (3) the occurrence of ether linked -lipids built from phytanyl chains and (4) in all cases known so far, -their occurrence only in unusual habitats. -(https://pubmed.ncbi.nlm.nih.gov/691075/) - -See Also: - -* [](https://www.gbif.org/species/2) - -#### Bacteria - -[]{#bacteria} - -Concept: [`bacteria`](https://w3id.org/isample/biology/biosampledfeature/bacteria) - -Child of: - [`prokaryote`](#prokaryote) - -a large domain of prokaryotic microorganisms. Bacterial cells do not -contain a nucleus and rarely harbour membrane-bound organelles. The -bacterial cell is surrounded by a cell membrane, which is made -primarily of phospholipids. This membrane encloses the contents of the -cell and acts as a barrier to hold nutrients, proteins and other -essential components of the cytoplasm within the cell. Bacterial cell -walls are composed of peptidoglycan, a complex of protein and sugars, -while archaeal cell walls are composed of polysaccharides (sugars). -(https://en.wikipedia.org/wiki/Bacteria) - -See Also: - -* [](https://www.gbif.org/species/3) - -### Virus - -[]{#virus} - -Concept: [`virus`](https://w3id.org/isample/biology/biosampledfeature/virus) - -Child of: - [`biologicalentity`](#biologicalentity) - -A virus is a submicroscopic infectious agent that replicates only -inside the living cells of an organism. Realms are Adnaviria, -Duplodnaviria, Monodnaviria, Riboviria, Ribozyviria, Varidnaviria -(https://en.wikipedia.org/wiki/Virus). Viruses are not cells at all, -so they are neither prokaryotes nor eukaryotes. (https://bio.libretext -s.org/Bookshelves/Introductory_and_General_Biology/Book) - -See Also: - -* [](https://www.gbif.org/species/8) - -#### Other Virus - -[]{#othervirus} - -Concept: [`othervirus`](https://w3id.org/isample/biology/biosampledfeature/othervirus) - -Child of: - [`virus`](#virus) - -Virus that is not a member of order Caudovirales (e.g., bacteriophage -T4, lambda phage). - -#### Phage - -[]{#phage} - -Concept: [`phage`](https://w3id.org/isample/biology/biosampledfeature/phage) - -Child of: - [`virus`](#virus) - -A bacteriophage, also known informally as a phage, is a duplodnaviria -virus that infects and replicates within bacteria and archaea. -Bacteriophages are composed of proteins that encapsulate a DNA or RNA -genome, and may have structures that are either simple or elaborate. -Their genomes may encode as few as four genes (e.g. MS2) and as many -as hundreds of genes. Phages replicate within the bacterium following -the injection of their genome into its cytoplasm. -(https://en.wikipedia.org/wiki/Bacteriophage). Includes all virus in -order Caudovirales (e.g., bacteriophage T4, lambda phage). - - diff --git a/models/generated/extensions/earthenv_material_extension_mineral_group.md b/models/generated/extensions/earthenv_material_extension_mineral_group.md deleted file mode 100644 index 17da62a..0000000 --- a/models/generated/extensions/earthenv_material_extension_mineral_group.md +++ /dev/null @@ -1,193 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "Earth and Environmental Science extension - Mineral group vocabulary" -date: "2025-12-11T02:41:29.241788+00:00" -subtitle: | - Vocabulary to extend the mineral material type category with the top level mineral group categories. Uses the Nickel–Strunz mineral classes, which divide minerals into ten classes according to chemical composition and crystal structure. Nickel-Strunz group 10 is not included because that material would be mat:organiccompounds. Version 10 of the classification is modified from v 9 (Strunz and Nickel,2002) by Jim Ferraiolo and others, and now extended and maintained by mindat.org. Some scope notes from linked.data.gov.au. -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_material_extension_mineral_group.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_material_extension_mineral_group.ttl) - - -Namespace: -[`https://w3id.org/isample/earthenv/mingroup/mineralgroupvocabulary`](https://w3id.org/isample/earthenv/mingroup/mineralgroupvocabulary) - -**History** - -* 2024-09-13 SMR remove version number from URI - -**Concepts** - -- [mineral](#mineral) - - [Mineral-Borate](#boratemineral) - - [Mineral-Carbonate or Nitrate](#carbonatenitratemineral) - - [Mineral-Halide](#halidemineral) - - [Mineral-Native Element](#nativeelementmineral) - - [Mineral-Organic Compound](#organicmineral) - - [Mineral-Oxide](#oxidemineral) - - [Mineral-Phosphate, Arsenate, or Vanadate](#phosphatearsenatevanadatemineral) - - [Mineral-Silicate or Germanate](#silicategermanatemineral) - - [Mineral-Sulfate, Selenate, or Tellurate](#sulfateselenatetelluratemineral) - - [Mineral-Sulfide or Sulfosalt](#sulfidesulfosaltmineral) - -## mineral - -[]{#mineral} - -Concept: [`mineral`](https://w3id.org/isample/vocabulary/material/mineral) - -Material consists of a single mineral or mineraloid phase. . 'A -mineral is an element or chemical compound that is normally -crystalline and that has been formed as a result of geological -processes.' (Nickel, Ernest H. (1995), The definition of a mineral, -The Canadian Mineralogist. 33 (3): 689–90). Include mineraloids. ... A -material primarily composed of some substance that is naturally -occurring, solid and stable at room temperature, representable by a -chemical formula, usually abiogenic, and that has an ordered atomic -structure. (http://purl.obolibrary.org/obo/ENVO_01000256). Comment: -the identity of a mineral species is defined by a crystal structure -and a chemical composition that might include various specific -elemental substitutions in that structure. Mineraloid: A naturally -occurring mineral-like substance that does not demonstrate -crystallinity. Mineraloids possess chemical compositions that vary -beyond the generally accepted ranges for specific minerals. Examples: -obsidian, Opal. (https://en.wikipedia.org/wiki/Mineraloid) - -### Mineral-Borate - -[]{#boratemineral} - -Concept: [`boratemineral`](https://w3id.org/isample/earthenv/mingroup/boratemineral) - -Child of: - [`mineral`](#mineral) - -Minerals which contain a borate anion group. - -### Mineral-Carbonate or Nitrate - -[]{#carbonatenitratemineral} - -Concept: [`carbonatenitratemineral`](https://w3id.org/isample/earthenv/mingroup/carbonatenitratemineral) - -Child of: - [`mineral`](#mineral) - -Carbonate minerals are those minerals containing the carbonate ion - -### Mineral-Halide - -[]{#halidemineral} - -Concept: [`halidemineral`](https://w3id.org/isample/earthenv/mingroup/halidemineral) - -Child of: - [`mineral`](#mineral) - -Minerals with a dominant halide anion. - -### Mineral-Native Element - -[]{#nativeelementmineral} - -Concept: [`nativeelementmineral`](https://w3id.org/isample/earthenv/mingroup/nativeelementmineral) - -Child of: - [`mineral`](#mineral) - -Elements that occur in nature in uncombined form with a distinct -mineral structure. Includes metals and intermetallic alloys; -metalloids and nonmetals; carbides, silicides, nitrides, phosphides - -### Mineral-Organic Compound - -[]{#organicmineral} - -Concept: [`organicmineral`](https://w3id.org/isample/earthenv/mingroup/organicmineral) - -Child of: - [`mineral`](#mineral) - -Salts of organic acids, hydrocarbons, and miscellaneous organic -minerals formed as a result of geological processes. Includes -hydrocarbons, formates, acetates, oxalates, benzine salts, cyanates. -Chemical compounds in which one or more atoms of carbon are covalently -linked to atoms of other elements, most commonly hydrogen, oxygen, or -nitrogen (https://www.britannica.com/science/organic-compound). - -### Mineral-Oxide - -[]{#oxidemineral} - -Concept: [`oxidemineral`](https://w3id.org/isample/earthenv/mingroup/oxidemineral) - -Child of: - [`mineral`](#mineral) - -Includes class oxides, hydroxides, and arsenties. Oxides are minerals -in which the oxide anion is bonded to one or more metal alloys. The -hydroxide-bearing minerals are typically included in the oxide class. -Arsenite minerals are very rare oxygen-bearing arsenic minerals. - -### Mineral-Phosphate, Arsenate, or Vanadate - -[]{#phosphatearsenatevanadatemineral} - -Concept: [`phosphatearsenatevanadatemineral`](https://w3id.org/isample/earthenv/mingroup/phosphatearsenatevanadatemineral) - -Child of: - [`mineral`](#mineral) - -Phosphate minerals contain the phosphate anion along sometimes with -arsenate and vanadate substitutions, and chloride, fluoride, and -hydroxide anions that also fit into the crystal structure. Arsenate -minerals usually refer to the naturally occurring orthoarsenates. - -### Mineral-Silicate or Germanate - -[]{#silicategermanatemineral} - -Concept: [`silicategermanatemineral`](https://w3id.org/isample/earthenv/mingroup/silicategermanatemineral) - -Child of: - [`mineral`](#mineral) - -Rock-forming minerals made up of silicate groups - -### Mineral-Sulfate, Selenate, or Tellurate - -[]{#sulfateselenatetelluratemineral} - -Concept: [`sulfateselenatetelluratemineral`](https://w3id.org/isample/earthenv/mingroup/sulfateselenatetelluratemineral) - -Child of: - [`mineral`](#mineral) - -class of minerals that include the sulfate ion within their structure. - -### Mineral-Sulfide or Sulfosalt - -[]{#sulfidesulfosaltmineral} - -Concept: [`sulfidesulfosaltmineral`](https://w3id.org/isample/earthenv/mingroup/sulfidesulfosaltmineral) - -Child of: - [`mineral`](#mineral) - -Sulfide minerals are a class of minerals containing sulfide or -disulfide as the major anion. Sulfosalt minerals are those complex -sulfide minerals with the general formula: AmBnSp; where A represents -a metal such as copper, lead, silver, iron, and rarely mercury, zinc, -vanadium; B usually represents semi-metal such as arsenic, antimony, -bismuth, and rarely germanium, or metals like tin and rarely vanadium; -and S is sulfur or rarely selenium or/and tellurium (m, n, and p are -integer formula subscripts). Includes sulfides, selenides, tellurides; -arsenides, antimonides, bismuthides; sulfarsenites, sulfantimonites, -sulfbismuthites - - diff --git a/models/generated/extensions/earthenv_material_extension_rock_sediment.md b/models/generated/extensions/earthenv_material_extension_rock_sediment.md deleted file mode 100644 index b515728..0000000 --- a/models/generated/extensions/earthenv_material_extension_rock_sediment.md +++ /dev/null @@ -1,1836 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "Earth and Environmental Science extension - Rock and sediment materials vocabulary" -date: "2025-12-11T02:41:29.838564+00:00" -subtitle: | - Rock and sediment categories for iSamples materialType classification. Remove anthropogenic materials and classes for consolidated or non-consolidated material; remove leaf classes subjectively based on abundance of material type and number of subclasses. There are 83 'mat:rock' subclasses; these include some classes that are non-consolidated material (e.g. fault gouge) but these are not sediment and adding 'material' classes that are independent of consolidation seems like more overhead than needed. Note that a given material is likely to fit in more that one class; for example the sediment subclasses include compositional classes (e.g. carbonate, clastic) as well as grain size classes (gravel-size sediment). A calcareous ooze sample would be both 'mud-size sediment' and 'carbonate sediment'. Change owl:class to skos:concept, and rdfs:subClassOf to skos:broader. -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_material_extension_rock_sediment.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_material_extension_rock_sediment.ttl) - - -Namespace: -[`https://w3id.org/isample/earthenv/rocksediment/rocksedimentvocabulary`](https://w3id.org/isample/earthenv/rocksediment/rocksedimentvocabulary) - -**History** - -* 2024-01-06 SMR updates to validate with SHACL rules in isamples/vocab_tools repo; extension vocabulary in skos:inScheme isamples parent voabularty; properties on inherited classes from iSample parent. -* 2024-09-13 SMR remove version number from URI - -**Concepts** - -- [Rock](#rock) - - [aphanite](#aphanite) - - [breccia](#breccia) - - [fault related material](#fault_related_material) - - [cataclasite series](#cataclasite_series) - - [mylonitic rock](#mylonitic_rock) - - [breccia gouge series](#breccia_gouge_series) - - [fragmental igneous rock](#fragmental_igneous_rock) - - [pyroclastic rock](#pyroclastic_rock) - - [igneous rock](#igneous_rock) - - [acidic igneous rock](#acidic_igneous_rock) - - [dacite](#dacite) - - [granitoid](#granitoid) - - [alkali feldspar granite](#alkali_feldspar_granite) - - [granite](#granite) - - [granodiorite](#granodiorite) - - [tonalite](#tonalite) - - [quartz rich igneous rock](#quartz_rich_igneous_rock) - - [rhyolitoid](#rhyolitoid) - - [basic igneous rock](#basic_igneous_rock) - - [basalt](#basalt) - - [gabbroic rock](#gabbroic_rock) - - [doleritic rock](#doleritic_rock) - - [exotic composition igneous rock](#exotic_composition_igneous_rock) - - [fine grained igneous rock](#fine_grained_igneous_rock) - - [andesite](#andesite) - - [basalt](#basalt) - - [dacite](#dacite) - - [foiditoid](#foiditoid) - - [high magnesium fine grained igneous rock](#high_magnesium_fine_grained_igneous_rock) - - [phonolitoid](#phonolitoid) - - [rhyolitoid](#rhyolitoid) - - [tephritoid](#tephritoid) - - [trachytoid](#trachytoid) - - [fragmental igneous rock](#fragmental_igneous_rock) - - [pyroclastic rock](#pyroclastic_rock) - - [glass rich igneous rock](#glass_rich_igneous_rock) - - [hypabyssal intrusive rock](#hypabyssal_intrusive_rock) - - [intermediate composition igneous rock](#intermediate_composition_igneous_rock) - - [andesite](#andesite) - - [dioritoid](#dioritoid) - - [phaneritic igneous rock](#phaneritic_igneous_rock) - - [anorthositic rock](#anorthositic_rock) - - [aplite](#aplite) - - [dioritoid](#dioritoid) - - [foid dioritoid](#foid_dioritoid) - - [foid gabbroid](#foid_gabbroid) - - [foid syenitoid](#foid_syenitoid) - - [foidolite](#foidolite) - - [gabbroid](#gabbroid) - - [gabbroic rock](#gabbroic_rock) - - [monzogabbroic rock](#monzogabbroic_rock) - - [granitoid](#granitoid) - - [alkali feldspar granite](#alkali_feldspar_granite) - - [granite](#granite) - - [granodiorite](#granodiorite) - - [tonalite](#tonalite) - - [hornblendite](#hornblendite) - - [pegmatite](#pegmatite) - - [peridotite](#peridotite) - - [pyroxenite](#pyroxenite) - - [quartz rich igneous rock](#quartz_rich_igneous_rock) - - [syenitoid](#syenitoid) - - [plutonic rock](#plutonic_igneous_rock) - - [porphyry](#porphyry) - - [ultrabasic igneous rock](#ultrabasic_igneous_rock) - - [ultramafic igneous rock](#ultramafic_igneous_rock) - - [hornblendite](#hornblendite) - - [peridotite](#peridotite) - - [pyroxenite](#pyroxenite) - - [volcanic rock](#volcanic_rock) - - [impact generated material](#impact_generated_material) - - [massive sulphide](#massive_sulphide) - - [metamorphic rock](#metamorphic_rock) - - [metasomatic rock](#metasomatic_rock) - - [sedimentary rock](#sedimentary_rock) - - [carbonate sedimentary rock](#carbonate_sedimentary_rock) - - [clastic sedimentary rock](#clastic_sedimentary_rock) - - [diamictite](#diamictite) - - [generic conglomerate](#generic_conglomerate) - - [generic mudstone](#generic_mudstone) - - [generic sandstone](#generic_sandstone) - - [hybrid sedimentary rock](#hybrid_sedimentary_rock) - - [iron rich sedimentary rock](#iron_rich_sedimentary_rock) - - [non clastic siliceous sedimentary rock](#non_clastic_siliceous_sedimentary_rock) - - [organic rich sedimentary rock](#organic_rich_sedimentary_rock) - - [coal](#coal) - - [phosphorite](#phosphorite) - - [tuffit](#tuffite) - - [residual material](#residual_material) - -- [Sediment](#sediment) - - [biogenic sediment](#biogenic_sediment) - - [carbonate sediment](#carbonate_sediment) - - [chemical sedimentary material](#chemical_sedimentary_material) - - [clastic sediment](#clastic_sediment) - - [diamicton](#diamicton) - - [gravel size sediment](#gravel_size_sediment) - - [hybrid sediment](#hybrid_sediment) - - [iron rich sediment](#iron_rich_sediment) - - [mud size sediment](#mud_size_sediment) - - [non clastic siliceous sediment](#non_clastic_siliceous_sediment) - - [phosphate rich sediment](#phosphate_rich_sediment) - - [sand size sediment](#sand_size_sediment) - - [tephra](#tephra) - -## Rock - -[]{#rock} - -Concept: [`rock`](https://w3id.org/isample/vocabulary/material/rock) - -Consolidated aggregate of particles (grains) of rock, mineral -(including native elements), mineraloid, or solid organic material. -Includes mineral aggregates such as granite, shale, marble; natural -glass such as obsidian; organic material formed by geologic processes -such a coal; extraterrestrial material in meteorites; and crushed -rock fragments like drill cuttings from rock. (based on -http://resource.geosciml.org/classifier/cgi/lithology/rock, same as -http://purl.obolibrary.org/obo/ENVO_00001995) - -### aphanite - -[]{#aphanite} - -Concept: [`Aphanite`](https://w3id.org/isample/earthenv/rocksediment/Aphanite) - -Child of: - [`rock`](#rock) - -Rock that is too fine grained to categorize in more detail. - -### breccia - -[]{#breccia} - -Concept: [`Breccia`](https://w3id.org/isample/earthenv/rocksediment/Breccia) - -Child of: - [`rock`](#rock) - -Coarse-grained material composed of angular broken rock fragments; the -fragments typically have sharp edges and unworn corners. The fragments -may be held together by a mineral cement or in a fine-grained matrix, -and consolidated or nonconsolidated. Clasts may be of any composition -or origin. In sedimentary environments, breccia is used for material -that consists entirely of angular fragments, mostly derived from a -single source rock body, as in a rock avalanche deposit, and matrix is -interpreted to be the product of comminution of clasts during -transport. Diamictite or diamicton is used when the material reflects -mixing of rock from a variety of sources, some sub angular or -subrounded clasts may be present, and matrix is pre-existing fine -grained material that is not a direct product of the -brecciation/deposition process. - -### fault related material - -[]{#fault_related_material} - -Concept: [`Fault_Related_Material`](https://w3id.org/isample/earthenv/rocksediment/Fault_Related_Material) - -Child of: - [`rock`](#rock) - -Material formed as a result brittle faulting, composed of greater than -10 percent matrix; matrix is fine-grained material caused by tectonic -grainsize reduction. Includes cohesive (cataclasite series, mylonitic -rocks) and non-cohesive (breccia-gouge series) material. - -#### cataclasite series - -[]{#cataclasite_series} - -Concept: [`Cataclasite_Series`](https://w3id.org/isample/earthenv/rocksediment/Cataclasite_Series) - -Child of: - [`Fault_Related_Material`](#Fault_Related_Material) - -Fault-related rock that maintained primary cohesion during -deformation, with matrix comprising greater than 10 percent of rock -mass; matrix is fine-grained material formed through grain size -reduction by fracture as opposed to crystal plastic process that -operate in mylonitic rock. Includes cataclasite, protocataclasite and -ultracataclasite. - -#### mylonitic rock - -[]{#mylonitic_rock} - -Concept: [`Mylonitic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Mylonitic_Rock) - -Child of: - [`Fault_Related_Material`](#Fault_Related_Material) - -Metamorphic rock characterised by a foliation resulting from tectonic -grain size reduction, in which more than 10 percent of the rock volume -has undergone grain size reduction. Includes protomylonite, mylonite, -ultramylonite, and blastomylonite. - -#### breccia gouge series - -[]{#breccia_gouge_series} - -Concept: [`breccia_gouge_series`](https://w3id.org/isample/earthenv/rocksediment/breccia_gouge_series) - -Child of: - [`Fault_Related_Material`](#Fault_Related_Material) - -Fault-related material with features such as void spaces (filled or -unfilled), or unconsolidated matrix material between fragments, -indicating loss of cohesion during deformation. Includes fault-related -breccia and gouge. - -### fragmental igneous rock - -[]{#fragmental_igneous_rock} - -Concept: [`Fragmental_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Fragmental_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - [`rock`](#rock) - -Igneous rock in which greater than 75 percent of the rock consists of -fragments produced as a result of igneous rock-forming process. -Includes pyroclastic rocks, autobreccia associated with lava flows and -intrusive breccias. Excludes deposits reworked by epiclastic processes -(see Tuffite) - -#### pyroclastic rock - -[]{#pyroclastic_rock} - -Concept: [`Pyroclastic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Pyroclastic_Rock) - -Child of: - [`Fragmental_Igneous_Rock`](#Fragmental_Igneous_Rock) - -Fragmental igneous rock that consists of greater than 75 percent -fragments produced as a direct result of eruption or extrusion of -magma from within the earth onto its surface. Includes autobreccia -associated with lava flows and excludes deposits reworked by -epiclastic processes. - -### igneous rock - -[]{#igneous_rock} - -Concept: [`Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Igneous_Rock) - -Child of: - [`rock`](#rock) - -rock formed as a result of igneous processes, for example intrusion -and cooling of magma in the crust, or volcanic eruption. - -#### acidic igneous rock - -[]{#acidic_igneous_rock} - -Concept: [`Acidic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Acidic_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Igneous rock with more than 63 percent SiO2. - -##### dacite - -[]{#dacite} - -Concept: [`Dacite`](https://w3id.org/isample/earthenv/rocksediment/Dacite) - -Child of: - [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Fine grained or porphyritic crystalline rock that contains less than -90 percent mafic minerals, between 20 and 60 percent quartz in the -QAPF fraction, and has a plagioclase to total feldspar ratio greater -than 0.65. Includes rocks defined modally in QAPF fields 4 and 5 or -chemically in TAS Field O3. Typically composed of quartz and sodic -plagioclase with minor amounts of biotite and/or hornblende and/or -pyroxene; fine-grained equivalent of granodiorite and tonalite. - -##### granitoid - -[]{#granitoid} - -Concept: [`Granitoid`](https://w3id.org/isample/earthenv/rocksediment/Granitoid) - -Child of: - [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline igneous rock consisting of quartz, alkali -feldspar and/or plagioclase. Includes rocks defined modally in QAPF -fields 2, 3, 4 and 5 as alkali feldspar granite, granite, granodiorite -or tonalite. - -###### alkali feldspar granite - -[]{#alkali_feldspar_granite} - -Concept: [`Alkali_Feldspar_Granite`](https://w3id.org/isample/earthenv/rocksediment/Alkali_Feldspar_Granite) - -Child of: - [`Granitoid`](#Granitoid) - -Granitic rock that has a plagioclase to total feldspar ratio less than -0.1. QAPF field 2. - -###### granite - -[]{#granite} - -Concept: [`Granite`](https://w3id.org/isample/earthenv/rocksediment/Granite) - -Child of: - [`Granitoid`](#Granitoid) - -Phaneritic crystalline rock consisting of quartz, alkali feldspar and -plagioclase (typically sodic) in variable amounts, usually with -biotite and/or hornblende. Includes rocks defined modally in QAPF -Field 3. - -###### granodiorite - -[]{#granodiorite} - -Concept: [`Granodiorite`](https://w3id.org/isample/earthenv/rocksediment/Granodiorite) - -Child of: - [`Granitoid`](#Granitoid) - -Phaneritic crystalline rock consisting essentially of quartz, sodic -plagioclase and lesser amounts of alkali feldspar with minor -hornblende and biotite. Includes rocks defined modally in QAPF field -4. - -###### tonalite - -[]{#tonalite} - -Concept: [`Tonalite`](https://w3id.org/isample/earthenv/rocksediment/Tonalite) - -Child of: - [`Granitoid`](#Granitoid) - -Granitoid consisting of quartz and intermediate plagioclase, usually -with biotite and amphibole. Includes rocks defined modally in QAPF -field 5; ratio of plagioclase to total feldspar is greater than 0.9. - -##### quartz rich igneous rock - -[]{#quartz_rich_igneous_rock} - -Concept: [`Quartz_Rich_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Quartz_Rich_Igneous_Rock) - -Child of: - [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Occurrence of igneous rocks meeting this criteria seems to be -vanishingly rare, thus subdividing the category does not seem -warranted for the purposes of This vocabulary. Future usage of the -vocabulary may motivate including quatzolite and quartz-rich granitoid -in future revisions -Phaneritic crystalline igneous rock that contains less than 90 percent -mafic minerals and contains greater than 60 percent quartz in the QAPF -fraction. - -##### rhyolitoid - -[]{#rhyolitoid} - -Concept: [`Rhyolitoid`](https://w3id.org/isample/earthenv/rocksediment/Rhyolitoid) - -Child of: - [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Note that technical definition, based on modal mineralogy plotted in a -QAPF triangle may be applied qualitatively, based on phenocryst -mineralogy when ground mass mineralogy can not be determined -optically, or based on CIPW norm. Although TAS categories are defined -based on chemical analyses, the correspondence with the QAPF defined -categories is generally close enough that QAPF categories are commonly -used interchangeably with TAS categories. It is important to note the -basis for assignment of fine-grained igneous rocks to a specifice -lithology category. -fine_grained_igneous_rock consisting of quartz and alkali feldspar, -with minor plagioclase and biotite, in a microcrystalline, -cryptocrystalline or glassy groundmass. Flow texture is common. -Includes rocks defined modally in QAPF fields 2 and 3 or chemically in -TAS Field R as rhyolite. QAPF normative definition is based on modal -mineralogy thus: less than 90 percent mafic minerals, between 20 and -60 percent quartz in the QAPF fraction, and ratio of plagioclse to -total feldspar is less than 0.65. - -#### basic igneous rock - -[]{#basic_igneous_rock} - -Concept: [`Basic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Basic_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Igneous rock with between 45 and 52 percent SiO2. - -##### basalt - -[]{#basalt} - -Concept: [`Basalt`](https://w3id.org/isample/earthenv/rocksediment/Basalt) - -Child of: - [`Basic_Igneous_Rock`](#Basic_Igneous_Rock) - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Fine-grained or porphyritic igneous rock with less than 20 percent -quartz, and less than 10 percent feldspathoid minerals, in which the -ratio of plagioclase to total feldspar is greater 0.65. Typically -composed of calcic plagioclase and clinopyroxene; phenocrysts -typically include one or more of calcic plagioclase, clinopyroxene, -orthopyroxene, and olivine. Includes rocks defined modally in QAPF -fields 9 and 10 or chemically in TAS field B as basalt. Basalt and -andesite are distinguished chemically based on silica content, with -basalt defined to contain less than 52 weight percent silica. If -chemical data are not available, the color index is used to -distinguish the categories, with basalt defined to contain greater -than 35 percent mafic minerals by volume or greater than 40 percent -mafic minerals by weight. - -##### gabbroic rock - -[]{#gabbroic_rock} - -Concept: [`Gabbroic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Gabbroic_Rock) - -Child of: - [`Basic_Igneous_Rock`](#Basic_Igneous_Rock) - [`Gabbroid`](#Gabbroid) - -Gabbroid that has a plagioclase to total feldspar ratio greater than -0.9 in the QAPF fraction. Includes QAPF fields 10*, 10, and 10'. This -category includes the various categories defined in LeMaitre et al. -(2002) based on the mafic mineralogy, but apparently not subdivided -based on the quartz/feldspathoid content. - -#### doleritic rock - -[]{#doleritic_rock} - -Concept: [`Doleritic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Doleritic_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Dark colored gabbroic (basaltic) or dioritic (andesitic) rock -intermediate in grain size between basalt and gabbro and composed of -plagioclase, pyroxene and opaque minerals; often with ophitic texture. -Typically occurs as hypabyssal intrusions. Includes dolerite, -microdiorite, diabase and microgabbro. - -#### exotic composition igneous rock - -[]{#exotic_composition_igneous_rock} - -Concept: [`Exotic_Composition_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Exotic_Composition_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Rock with 'exotic' mineralogical, textural or field setting -characteristics; typically dark colored, with abundant phenocrysts. -Criteria include: presence of greater than 10 percent melilite or -leucite, or presence of kalsilite, or greater than 50 percent -carbonate minerals. Includes Carbonatite, Melilitic rock, Kalsilitic -rocks, Kimberlite, Lamproite, Leucitic rock and Lamprophyres. - -#### fine grained igneous rock - -[]{#fine_grained_igneous_rock} - -Concept: [`Fine_Grained_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Fine_Grained_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Need to make decision as to whether devitrified glass should be -considered glass or microcrystalline framework for purposes of -categorization -Igneous rock in which the framework of the rock consists of crystals -that are too small to determine mineralogy with the unaided eye; -framework may include up to 50 percent glass. A significant percentage -of the rock by volume may be phenocrysts. Includes rocks that are -generally called volcanic rocks. - -##### andesite - -[]{#andesite} - -Concept: [`Andesite`](https://w3id.org/isample/earthenv/rocksediment/Andesite) - -Child of: - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - [`Intermediate_Composition_Igneous_Rock`](#Intermediate_Composition_Igneous_Rock) - -Note the mela-andesite and leuco-basalt categories are not recommended -in this system. If chemical analytical data are available to constrain -the silica content, the basalt or andesite category should be used. -Fine-grained igneous rock with less than 20 percent quartz and less -than 10 percent feldspathoid minerals in the QAPF fraction, in which -the ratio of plagioclase to total feldspar is greater 0.65. Includes -rocks defined modally in QAPF fields 9 and 10 or chemically in TAS -field O2 as andesite. Basalt and andesite, which share the same QAPF -fields, are distinguished chemically based on silica content, with -basalt defined to contain less than 52 weight percent silica. If -chemical data are not available, the color index is used to -distinguish the categories, with basalt defined to contain greater -than 35 percent mafic minerals by volume or greater than 40 percent -mafic minerals by weight. Typically consists of plagioclase -(frequently zoned from labradorite to oligoclase), pyroxene, -hornblende and/or biotite. Fine grained equivalent of dioritic rock. - -##### basalt - -[]{#basalt} - -Concept: [`Basalt`](https://w3id.org/isample/earthenv/rocksediment/Basalt) - -Child of: - [`Basic_Igneous_Rock`](#Basic_Igneous_Rock) - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Fine-grained or porphyritic igneous rock with less than 20 percent -quartz, and less than 10 percent feldspathoid minerals, in which the -ratio of plagioclase to total feldspar is greater 0.65. Typically -composed of calcic plagioclase and clinopyroxene; phenocrysts -typically include one or more of calcic plagioclase, clinopyroxene, -orthopyroxene, and olivine. Includes rocks defined modally in QAPF -fields 9 and 10 or chemically in TAS field B as basalt. Basalt and -andesite are distinguished chemically based on silica content, with -basalt defined to contain less than 52 weight percent silica. If -chemical data are not available, the color index is used to -distinguish the categories, with basalt defined to contain greater -than 35 percent mafic minerals by volume or greater than 40 percent -mafic minerals by weight. - -##### dacite - -[]{#dacite} - -Concept: [`Dacite`](https://w3id.org/isample/earthenv/rocksediment/Dacite) - -Child of: - [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Fine grained or porphyritic crystalline rock that contains less than -90 percent mafic minerals, between 20 and 60 percent quartz in the -QAPF fraction, and has a plagioclase to total feldspar ratio greater -than 0.65. Includes rocks defined modally in QAPF fields 4 and 5 or -chemically in TAS Field O3. Typically composed of quartz and sodic -plagioclase with minor amounts of biotite and/or hornblende and/or -pyroxene; fine-grained equivalent of granodiorite and tonalite. - -##### foiditoid - -[]{#foiditoid} - -Concept: [`Foiditoid`](https://w3id.org/isample/earthenv/rocksediment/Foiditoid) - -Child of: - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Fine grained crystalline rock containing less than 90 percent mafic -minerals and more than 60 percent feldspathoid minerals in the QAPF -fraction. Includes rocks defined modally in QAPF field 15 or -chemically in TAS field F. - -##### high magnesium fine grained igneous rock - -[]{#high_magnesium_fine_grained_igneous_rock} - -Concept: [`High_Magnesium_Fine_Grained_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/High_Magnesium_Fine_Grained_Igneous_Rock) - -Child of: - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -fine-grained igneous rock that contains unusually high concentration -of MgO. For rocks that contain greater than 52 percent silica, MgO -must be greater than 8 percent. For rocks containing less than 52 -percent silica, MgO must be greater than 12 percent. - -##### phonolitoid - -[]{#phonolitoid} - -Concept: [`Phonolitoid`](https://w3id.org/isample/earthenv/rocksediment/Phonolitoid) - -Child of: - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Fine grained igneous rock than contains less than 90 percent mafic -minerals, between 10 and 60 percent feldspathoid mineral in the QAPF -fraction and has a plagioclase to total feldspar ratio less than 0.5. -Includes rocks defined modally in QAPF fields 11 and 12, and TAS field -Ph. - -##### rhyolitoid - -[]{#rhyolitoid} - -Concept: [`Rhyolitoid`](https://w3id.org/isample/earthenv/rocksediment/Rhyolitoid) - -Child of: - [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Note that technical definition, based on modal mineralogy plotted in a -QAPF triangle may be applied qualitatively, based on phenocryst -mineralogy when ground mass mineralogy can not be determined -optically, or based on CIPW norm. Although TAS categories are defined -based on chemical analyses, the correspondence with the QAPF defined -categories is generally close enough that QAPF categories are commonly -used interchangeably with TAS categories. It is important to note the -basis for assignment of fine-grained igneous rocks to a specifice -lithology category. -fine_grained_igneous_rock consisting of quartz and alkali feldspar, -with minor plagioclase and biotite, in a microcrystalline, -cryptocrystalline or glassy groundmass. Flow texture is common. -Includes rocks defined modally in QAPF fields 2 and 3 or chemically in -TAS Field R as rhyolite. QAPF normative definition is based on modal -mineralogy thus: less than 90 percent mafic minerals, between 20 and -60 percent quartz in the QAPF fraction, and ratio of plagioclse to -total feldspar is less than 0.65. - -##### tephritoid - -[]{#tephritoid} - -Concept: [`Tephritoid`](https://w3id.org/isample/earthenv/rocksediment/Tephritoid) - -Child of: - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Fine grained igneous rock than contains less than 90 percent mafic -minerals, between 10 and 60 percent feldspathoid mineral in the QAPF -fraction and has a plagioclase to total feldspar ratio greater than -0.5. Includes rocks classified in QAPF field 13 and 14 or chemically -in TAS field U1 as basanite or tephrite. - -##### trachytoid - -[]{#trachytoid} - -Concept: [`Trachytoid`](https://w3id.org/isample/earthenv/rocksediment/Trachytoid) - -Child of: - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - -Fine grained igneous rock than contains less than 90 percent mafic -minerals, less than 10 percent feldspathoid mineral and less than 20 -percent quartz in the QAPF fraction and has a plagioclase to total -feldspar ratio less than 0.65. Mafic minerals typically include -amphibole or mica; typically porphyritic. Includes rocks defined -modally in QAPF fields 6, 7 and 8 (with subdivisions) or chemically in -TAS Field T as trachyte or latite. - -#### fragmental igneous rock - -[]{#fragmental_igneous_rock} - -Concept: [`Fragmental_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Fragmental_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - [`rock`](#rock) - -Igneous rock in which greater than 75 percent of the rock consists of -fragments produced as a result of igneous rock-forming process. -Includes pyroclastic rocks, autobreccia associated with lava flows and -intrusive breccias. Excludes deposits reworked by epiclastic processes -(see Tuffite) - -##### pyroclastic rock - -[]{#pyroclastic_rock} - -Concept: [`Pyroclastic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Pyroclastic_Rock) - -Child of: - [`Fragmental_Igneous_Rock`](#Fragmental_Igneous_Rock) - -Fragmental igneous rock that consists of greater than 75 percent -fragments produced as a direct result of eruption or extrusion of -magma from within the earth onto its surface. Includes autobreccia -associated with lava flows and excludes deposits reworked by -epiclastic processes. - -#### glass rich igneous rock - -[]{#glass_rich_igneous_rock} - -Concept: [`Glass_Rich_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Glass_Rich_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Igneous rock that contains greater than 50 percent massive glass. - -#### hypabyssal intrusive rock - -[]{#hypabyssal_intrusive_rock} - -Concept: [`Hypabyssal_Intrusive_Rock`](https://w3id.org/isample/earthenv/rocksediment/Hypabyssal_Intrusive_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Igneous rocks formed by crystallisation close to the Earth's surface, -characterized by more rapid cooling than plutonic setting to produce -generally fine-grained intrusive igneous rock, commonly associated -with co-magmatic volcanic rocks. - -#### intermediate composition igneous rock - -[]{#intermediate_composition_igneous_rock} - -Concept: [`Intermediate_Composition_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Intermediate_Composition_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Igneous rock with between 52 and 63 percent SiO2. - -##### andesite - -[]{#andesite} - -Concept: [`Andesite`](https://w3id.org/isample/earthenv/rocksediment/Andesite) - -Child of: - [`Fine_Grained_Igneous_Rock`](#Fine_Grained_Igneous_Rock) - [`Intermediate_Composition_Igneous_Rock`](#Intermediate_Composition_Igneous_Rock) - -Note the mela-andesite and leuco-basalt categories are not recommended -in this system. If chemical analytical data are available to constrain -the silica content, the basalt or andesite category should be used. -Fine-grained igneous rock with less than 20 percent quartz and less -than 10 percent feldspathoid minerals in the QAPF fraction, in which -the ratio of plagioclase to total feldspar is greater 0.65. Includes -rocks defined modally in QAPF fields 9 and 10 or chemically in TAS -field O2 as andesite. Basalt and andesite, which share the same QAPF -fields, are distinguished chemically based on silica content, with -basalt defined to contain less than 52 weight percent silica. If -chemical data are not available, the color index is used to -distinguish the categories, with basalt defined to contain greater -than 35 percent mafic minerals by volume or greater than 40 percent -mafic minerals by weight. Typically consists of plagioclase -(frequently zoned from labradorite to oligoclase), pyroxene, -hornblende and/or biotite. Fine grained equivalent of dioritic rock. - -##### dioritoid - -[]{#dioritoid} - -Concept: [`Dioritoid`](https://w3id.org/isample/earthenv/rocksediment/Dioritoid) - -Child of: - [`Intermediate_Composition_Igneous_Rock`](#Intermediate_Composition_Igneous_Rock) - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline igneous rock with M less than 90, consisting of -intermediate plagioclase, commonly with hornblende and often with -biotite or augite. Plagioclase to total feldspar ratio is greater that -0.65, and anorthite content of plagioclase is less than 50 percent. -Less than 10 percent feldspathoid mineral and less than 20 percent -quartz in the QAPF fraction. Includes rocks defined modally in QAPF -fields 9 and 10 (and their subdivisions). - -#### phaneritic igneous rock - -[]{#phaneritic_igneous_rock} - -Concept: [`Phaneritic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Phaneritic_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Igneous rock in which the framework of the rock consists of individual -crystals that can be discerned with the unaided eye. Bounding grain -size is on the order of 32 to 100 microns. Igneous rocks with 'exotic' -composition are excluded from this concept. - -##### anorthositic rock - -[]{#anorthositic_rock} - -Concept: [`Anorthositic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Anorthositic_Rock) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Leucocratic phaneritic crystalline igneous rock consisting essentially -of plagioclase, often with small amounts of pyroxene. By definition, -colour index M is less than 10, and plagiclase to total feldspar ratio -is greater than 0.9. Less than 20 percent quartz and less than 10 -percent feldspathoid in the QAPF fraction. QAPF field 10, 10*, and -10'. -Anorthositic rock term invented to label the combined QAPF fields 10, -10*, and 10', in order to construct hierarchy in this vocabulary. - -##### aplite - -[]{#aplite} - -Concept: [`Aplite`](https://w3id.org/isample/earthenv/rocksediment/Aplite) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Light coloured crystalline rock, characterized by a fine grained -allotriomorphic-granular (aplitic, saccharoidal or xenomorphic) -texture; typically granitic composition, consisting of quartz, alkali -feldspar and sodic plagioclase. - -##### dioritoid - -[]{#dioritoid} - -Concept: [`Dioritoid`](https://w3id.org/isample/earthenv/rocksediment/Dioritoid) - -Child of: - [`Intermediate_Composition_Igneous_Rock`](#Intermediate_Composition_Igneous_Rock) - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline igneous rock with M less than 90, consisting of -intermediate plagioclase, commonly with hornblende and often with -biotite or augite. Plagioclase to total feldspar ratio is greater that -0.65, and anorthite content of plagioclase is less than 50 percent. -Less than 10 percent feldspathoid mineral and less than 20 percent -quartz in the QAPF fraction. Includes rocks defined modally in QAPF -fields 9 and 10 (and their subdivisions). - -##### foid dioritoid - -[]{#foid_dioritoid} - -Concept: [`Foid_Dioritoid`](https://w3id.org/isample/earthenv/rocksediment/Foid_Dioritoid) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline igneous rock in which M is less than 90, the -plagioclase to total feldspar ratio is greater than 0.5, feldspathoid -minerals form 10-60 percent of the QAPF fraction, plagioclase has -anorthite content less than 50 percent. These rocks typically contain -large amounts of mafic minerals. Includes rocks defined modally in -QAPF fields 13 and 14. - -##### foid gabbroid - -[]{#foid_gabbroid} - -Concept: [`Foid_Gabbroid`](https://w3id.org/isample/earthenv/rocksediment/Foid_Gabbroid) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline igneous rock in which M is less than 90, the -plagioclase to total feldspar ratio is greater than 0.5, feldspathoids -form 10-60 percent of the QAPF fraction, and plagioclase has anorthite -content greater than 50 percent. These rocks typically contain large -amounts of mafic minerals. Includes rocks defined modally in QAPF -fields 13 and 14. - -##### foid syenitoid - -[]{#foid_syenitoid} - -Concept: [`Foid_Syenitoid`](https://w3id.org/isample/earthenv/rocksediment/Foid_Syenitoid) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline igneous rock with M less than 90, contains -between 10 and 60 percent feldspathoid mineral in the QAPF fraction, -and has a plagioclase to total feldspar ratio less than 0.5. Includes -QAPF fields 11 and 12. - -##### foidolite - -[]{#foidolite} - -Concept: [`Foidolite`](https://w3id.org/isample/earthenv/rocksediment/Foidolite) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline rock containing more than 60 percent -feldspathoid minerals in the QAPF fraction. Includes rocks defined -modally in QAPF field 15 - -##### gabbroid - -[]{#gabbroid} - -Concept: [`Gabbroid`](https://w3id.org/isample/earthenv/rocksediment/Gabbroid) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline igneous rock that contains less than 90 percent -mafic minerals, and up to 20 percent quartz or up to 10 percent -feldspathoid in the QAPF fraction. The ratio of plagioclase to total -feldspar is greater than 0.65, and anorthite content of the -plagioclase is greater than 50 percent. Includes rocks defined modally -in QAPF fields 9 and 10 and their subdivisions. - -###### gabbroic rock - -[]{#gabbroic_rock} - -Concept: [`Gabbroic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Gabbroic_Rock) - -Child of: - [`Basic_Igneous_Rock`](#Basic_Igneous_Rock) - [`Gabbroid`](#Gabbroid) - -Gabbroid that has a plagioclase to total feldspar ratio greater than -0.9 in the QAPF fraction. Includes QAPF fields 10*, 10, and 10'. This -category includes the various categories defined in LeMaitre et al. -(2002) based on the mafic mineralogy, but apparently not subdivided -based on the quartz/feldspathoid content. - -###### monzogabbroic rock - -[]{#monzogabbroic_rock} - -Concept: [`Monzogabbroic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Monzogabbroic_Rock) - -Child of: - [`Gabbroid`](#Gabbroid) - -Gabbroid with a plagioclase to total feldspar ratio between 0.65 and -0.9. QAPF field 9, 9 prime and 9 asterisk - -##### granitoid - -[]{#granitoid} - -Concept: [`Granitoid`](https://w3id.org/isample/earthenv/rocksediment/Granitoid) - -Child of: - [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline igneous rock consisting of quartz, alkali -feldspar and/or plagioclase. Includes rocks defined modally in QAPF -fields 2, 3, 4 and 5 as alkali feldspar granite, granite, granodiorite -or tonalite. - -###### alkali feldspar granite - -[]{#alkali_feldspar_granite} - -Concept: [`Alkali_Feldspar_Granite`](https://w3id.org/isample/earthenv/rocksediment/Alkali_Feldspar_Granite) - -Child of: - [`Granitoid`](#Granitoid) - -Granitic rock that has a plagioclase to total feldspar ratio less than -0.1. QAPF field 2. - -###### granite - -[]{#granite} - -Concept: [`Granite`](https://w3id.org/isample/earthenv/rocksediment/Granite) - -Child of: - [`Granitoid`](#Granitoid) - -Phaneritic crystalline rock consisting of quartz, alkali feldspar and -plagioclase (typically sodic) in variable amounts, usually with -biotite and/or hornblende. Includes rocks defined modally in QAPF -Field 3. - -###### granodiorite - -[]{#granodiorite} - -Concept: [`Granodiorite`](https://w3id.org/isample/earthenv/rocksediment/Granodiorite) - -Child of: - [`Granitoid`](#Granitoid) - -Phaneritic crystalline rock consisting essentially of quartz, sodic -plagioclase and lesser amounts of alkali feldspar with minor -hornblende and biotite. Includes rocks defined modally in QAPF field -4. - -###### tonalite - -[]{#tonalite} - -Concept: [`Tonalite`](https://w3id.org/isample/earthenv/rocksediment/Tonalite) - -Child of: - [`Granitoid`](#Granitoid) - -Granitoid consisting of quartz and intermediate plagioclase, usually -with biotite and amphibole. Includes rocks defined modally in QAPF -field 5; ratio of plagioclase to total feldspar is greater than 0.9. - -##### hornblendite - -[]{#hornblendite} - -Concept: [`Hornblendite`](https://w3id.org/isample/earthenv/rocksediment/Hornblendite) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) - -Ultramafic rock that consists of greater than 40 percent hornblende -plus pyroxene and has a hornblende to pyroxene ratio greater than 1. -Includes olivine hornblendite, olivine-pyroxene hornblendite, pyroxene -hornblendite, and hornblendite. - -##### pegmatite - -[]{#pegmatite} - -Concept: [`Pegmatite`](https://w3id.org/isample/earthenv/rocksediment/Pegmatite) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Exceptionally coarse grained crystalline rock with interlocking -crystals; most grains are 1cm or more diameter; composition is -generally that of granite, but the term may refer to the coarse -grained facies of any type of igneous rock;usually found as irregular -dikes, lenses, or veins associated with plutons or batholiths. - -##### peridotite - -[]{#peridotite} - -Concept: [`Peridotite`](https://w3id.org/isample/earthenv/rocksediment/Peridotite) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) - -Ultramafic rock consisting of more than 40 percent (by volume) olivine -with pyroxene and/or amphibole and little or no feldspar. commonly -altered to serpentinite. Includes rocks defined modally in the -ultramafic rock classification as dunite, harzburgite, lherzolite, -wehrlite, olivinite, pyroxene peridotite, pyroxene hornblende -peridotite or hornblende peridotite. - -##### pyroxenite - -[]{#pyroxenite} - -Concept: [`Pyroxenite`](https://w3id.org/isample/earthenv/rocksediment/Pyroxenite) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) - -Ultramafic phaneritic igneous rock composed almost entirely of one or -more pyroxenes and occasionally biotite, hornblende and olivine. -Includes rocks defined modally in the ultramafic rock classification -as olivine pyroxenite, olivine-hornblende pyroxenite, pyroxenite, -orthopyroxenite, clinopyroxenite and websterite. - -##### quartz rich igneous rock - -[]{#quartz_rich_igneous_rock} - -Concept: [`Quartz_Rich_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Quartz_Rich_Igneous_Rock) - -Child of: - [`Acidic_Igneous_Rock`](#Acidic_Igneous_Rock) - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Occurrence of igneous rocks meeting this criteria seems to be -vanishingly rare, thus subdividing the category does not seem -warranted for the purposes of This vocabulary. Future usage of the -vocabulary may motivate including quatzolite and quartz-rich granitoid -in future revisions -Phaneritic crystalline igneous rock that contains less than 90 percent -mafic minerals and contains greater than 60 percent quartz in the QAPF -fraction. - -##### syenitoid - -[]{#syenitoid} - -Concept: [`Syenitoid`](https://w3id.org/isample/earthenv/rocksediment/Syenitoid) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - -Phaneritic crystalline igneous rock with M less than 90, consisting -mainly of alkali feldspar and plagioclase; minor quartz or nepheline -may be present, along with pyroxene, amphibole or biotite. Ratio of -plagioclase to total feldspar is less than 0.65, quartz forms less -than 20 percent of QAPF fraction, and feldspathoid minerals form less -than 10 percent of QAPF fraction. Includes rocks classified in QAPF -fields 6, 7 and 8 and their subdivisions. - -#### plutonic rock - -[]{#plutonic_igneous_rock} - -Concept: [`Plutonic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Plutonic_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Instrusive igneous rock formed by crystallisation of magma far enough -below Earth surface that complete crystallization of magma bodies -forms holocrystalline medium to coarse grained igneous rock, wall -rocks generally do not include volcanic products related to the magma, -and some contact metamorphism is tyypically developed at intrusive -contacts. - -#### porphyry - -[]{#porphyry} - -Concept: [`Porphyry`](https://w3id.org/isample/earthenv/rocksediment/Porphyry) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Igneous rock that contains conspicuous phenocrysts in a finer grained -groundmass; groundmass itself may be phaneritic or fine-grained. - -#### ultrabasic igneous rock - -[]{#ultrabasic_igneous_rock} - -Concept: [`Ultrabasic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Ultrabasic_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Igneous rock with less than 45 percent SiO2. - -#### ultramafic igneous rock - -[]{#ultramafic_igneous_rock} - -Concept: [`Ultramafic_Igneous_Rock`](https://w3id.org/isample/earthenv/rocksediment/Ultramafic_Igneous_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Igneous rock that consists of greater than 90 percent mafic minerals. - -##### hornblendite - -[]{#hornblendite} - -Concept: [`Hornblendite`](https://w3id.org/isample/earthenv/rocksediment/Hornblendite) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) - -Ultramafic rock that consists of greater than 40 percent hornblende -plus pyroxene and has a hornblende to pyroxene ratio greater than 1. -Includes olivine hornblendite, olivine-pyroxene hornblendite, pyroxene -hornblendite, and hornblendite. - -##### peridotite - -[]{#peridotite} - -Concept: [`Peridotite`](https://w3id.org/isample/earthenv/rocksediment/Peridotite) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) - -Ultramafic rock consisting of more than 40 percent (by volume) olivine -with pyroxene and/or amphibole and little or no feldspar. commonly -altered to serpentinite. Includes rocks defined modally in the -ultramafic rock classification as dunite, harzburgite, lherzolite, -wehrlite, olivinite, pyroxene peridotite, pyroxene hornblende -peridotite or hornblende peridotite. - -##### pyroxenite - -[]{#pyroxenite} - -Concept: [`Pyroxenite`](https://w3id.org/isample/earthenv/rocksediment/Pyroxenite) - -Child of: - [`Phaneritic_Igneous_Rock`](#Phaneritic_Igneous_Rock) - [`Ultramafic_Igneous_Rock`](#Ultramafic_Igneous_Rock) - -Ultramafic phaneritic igneous rock composed almost entirely of one or -more pyroxenes and occasionally biotite, hornblende and olivine. -Includes rocks defined modally in the ultramafic rock classification -as olivine pyroxenite, olivine-hornblende pyroxenite, pyroxenite, -orthopyroxenite, clinopyroxenite and websterite. - -#### volcanic rock - -[]{#volcanic_rock} - -Concept: [`Volcanic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Volcanic_Rock) - -Child of: - [`Igneous_Rock`](#Igneous_Rock) - -Rock that exhibits direct evidence of extrusive igneous processes in -its genesis. - -### impact generated material - -[]{#impact_generated_material} - -Concept: [`Impact_Generated_Material`](https://w3id.org/isample/earthenv/rocksediment/Impact_Generated_Material) - -Child of: - [`rock`](#rock) - -Material that contains features indicative of shock metamorphism, such -as microscopic planar deformation features within grains or shatter -cones, interpreted to be the result of extraterrestrial bolide impact. -Includes breccias and melt rocks. - -### massive sulphide - -[]{#massive_sulphide} - -Concept: [`Massive_Sulphide`](https://w3id.org/isample/earthenv/rocksediment/Massive_Sulphide) - -Child of: - [`rock`](#rock) - -rock consisting of greater than 50% sulphide or sulfosalt minerals -formed by any processes. Includes hydrothermal and sedimentary -ehalative sulfide. - -### metamorphic rock - -[]{#metamorphic_rock} - -Concept: [`Metamorphic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Metamorphic_Rock) - -Child of: - [`rock`](#rock) - -Robertson (1999, Classification of metamorphic rocks: British -Geological Survey Research Report, RR 99–02) defines the boundary -between diagenesis and metamorphism in sedimentary rocks as follows: -“…the boundary between diagenesis and metamorphism is somewhat -arbitrary and strongly dependent on the lithologies involved. For -example changes take place in organic materials at lower temperatures -than in rocks dominated by silicate minerals. In mudrocks, a white -mica (illite) crystallinity value of less than 0.42 Delta 2 Theta -obtained by X-ray diffraction analysis, is used to define the onset of -metamorphism (Kisch, 1991). In this scheme, the first appearance of -glaucophane, lawsonite, paragonite, prehnite, pumpellyite or -stilpnomelane is taken to indicate the lower limit of metamorphism -(Frey and Kisch, 1987; Bucher and Frey, 1994; Frey and Robinson, -1998). Most workers agree that such mineral growth starts at 150 +/- -50° C in silicate rocks. Many lithologies may show no change in -mineralogy under these conditions and hence the recognition of the -onset of metamorphism will vary with bulk composition.” -Rock formed by solid-state mineralogical, chemical and/or structural -changes to a pre-existing rock, in response to marked changes in -temperature, pressure, shearing stress and chemical environment. - -### metasomatic rock - -[]{#metasomatic_rock} - -Concept: [`Metasomatic_Rock`](https://w3id.org/isample/earthenv/rocksediment/Metasomatic_Rock) - -Child of: - [`rock`](#rock) - -SLTTm (2004) proposed the following criteria to distinguish -hydrothermally altered or metasomatic rock from igneous rock. "The -rock is classified as metamorphic if (1) the texture has been modified -such that it can no longer be considered igneous, (2) the bulk -composition of the rock is inconsistent with compositions that can be -derived purely from a magma and associated processes such as -assimilation and differentiation, or (3) minerals inconsistent with -magmatic crystallization are present." -Rock that has fabric and composition indicating open-system -mineralogical and chemical changes in response to interaction with a -fluid phase, typically water rich. - -### sedimentary rock - -[]{#sedimentary_rock} - -Concept: [`Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Sedimentary_Rock) - -Child of: - [`rock`](#rock) - -Rock formed by accumulation and cementation of solid fragmental -material deposited by air, water or ice, or as a result of other -natural agents, such as precipitation from solution, the accumulation -of organic material, or from biogenic processes, including secretion -by organisms. Includes epiclastic deposits. - -#### carbonate sedimentary rock - -[]{#carbonate_sedimentary_rock} - -Concept: [`Carbonate_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Carbonate_Sedimentary_Rock) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -Particularly for fine-grained sedimentary rocks, distinction of -'intrabasinal' versus 'clastic' genesis can be very interpretive. In -practice the use of clastic mudstone terminology as opposed to -carbonate mudstone terminology may be dermined by a priori knowledge -about the rock being categorized. If it is associated with other -clastic rocks, the clastic categories will be favored, if with -cabonate rocks, the carbonate categories will be favored. Carbonate -rock subcatgories are defined on two orthogonal dimensions--mineralogy -(calcitic vs. dolomitic vs non-carbonate impurities), and texture. The -texture categories used here are those of Dunham (1962), and involve -grain size (matrix vs. grains/allochems), fabric (matrix vs. grain -supported), and genesis (bound, frame, or fragmental). The textural -approach used for carbonate rocks is conceptually incompatible with -that used for clastic sedimentary rocks, which is solely grain size or -mineralogy based. This leads to problems in the vocabulary for rocks -of mixed siliclastic/carbonate mineralogy (grainstone vs. sandstone, -carbonate mudstone vs. carbonate rich mudstone, how to accomodate -marlstone...). -Sedimentary rock in which at least 50 percent of the primary and/or -recrystallized constituents are composed of one (or more) of the -carbonate minerals calcite, aragonite, magnesite or dolomite. - -#### clastic sedimentary rock - -[]{#clastic_sedimentary_rock} - -Concept: [`Clastic_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Clastic_Sedimentary_Rock) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -The conglomerate, sandstone, mudstone, and wackestone categories are -not defined as kinds of clastic sedimentary rocks because rocks -meeting their purely grainsize based definitions might also be iron- -rich, phosphatic, or carbonate. This is based on GeoSciML allowance to -assign rocks to more than one lithology category. For example to -categorize a rock as a clastic conglomerate requires assignment ot the -'clastic sedimentary rock' category and to the 'conglomerate' -category. Particularly for fine-grained sedimentary rocks, distinction -of 'intrabasinal' versus 'clastic' genesis can be very interpretive. -In practice the use of clastic mudstone terminology as opposed to -carbonate mudstone terminology may be dermined by a priori knowledge -about the rock being categorized. If it is associated with other -clastic rocks, the clastic categories will be favored, if with -cabonate rocks, the carbonate categories will be favored. -Sedimentary rock in which at least 50 percent of the constituent -particles were derived from erosion, weathering, or mass-wasting of -pre-existing earth materials, and transported to the place of -deposition by mechanical agents such as water, wind, ice and gravity. - -##### diamictite - -[]{#diamictite} - -Concept: [`Diamictite`](https://w3id.org/isample/earthenv/rocksediment/Diamictite) - -Child of: - [`Clastic_Sedimentary_Rock`](#Clastic_Sedimentary_Rock) - -Unsorted or poorly sorted, clastic sedimentary rock with a wide range -of particle sizes including a muddy matrix. Biogenic materials that -have such texture are excluded. Distinguished from conglomerate, -sandstone, mudstone based on polymodality and lack of structures -related to transport and deposition of sediment by moving air or -water. If more than 10 percent of the fine grained matrix is of -indeterminant clastic or diagenetic origin and the fabric is matrix -supported, may also be categorized as wacke. - -#### generic conglomerate - -[]{#generic_conglomerate} - -Concept: [`Generic_Conglomerate`](https://w3id.org/isample/earthenv/rocksediment/Generic_Conglomerate) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -Sedimentary rock composed of at least 30 percent rounded to subangular -fragments larger than 2 mm in diameter; typically contains finer -grained material in interstices between larger fragments. If more than -15 percent of the fine grained matrix is of indeterminant clastic or -diagenetic origin and the fabric is matrix supported, may also be -categorized as wackestone. If rock has unsorted or poorly sorted -texture with a wide range of particle sizes, may also be categorized -as diamictite. - -#### generic mudstone - -[]{#generic_mudstone} - -Concept: [`Generic_Mudstone`](https://w3id.org/isample/earthenv/rocksediment/Generic_Mudstone) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -Distinction of intrabasinal, diagenetic, or clastic genesis for very -fine-grained carbonate minerals is so interpretive that it is proposed -to not define the mudstone category based on intrabasinal vs -epiclastic distinction required for clastic sedimentary rock-carbonate -sedimentary rock categorization in this system. Schnurrenberger, D., -Russell, J. and Kelts, K., 2003, Classification of lacustrine -sediments based on sedimentary components: Journal of Paleolimnology, -v.29, p141-154. -Sedimentary rock consisting of less than 30 percent gravel-size (2 mm) -particles and with a mud to sand ratio greater than 1. Clasts may be -of any composition or origin. - -#### generic sandstone - -[]{#generic_sandstone} - -Concept: [`Generic_Sandstone`](https://w3id.org/isample/earthenv/rocksediment/Generic_Sandstone) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -Sedimentary rock in which less than 30 percent of particles are -greater than 2 mm in diameter (gravel) and the sand to mud ratio is at -least 1. - -#### hybrid sedimentary rock - -[]{#hybrid_sedimentary_rock} - -Concept: [`Hybrid_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Hybrid_Sedimentary_Rock) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -Sedimentary rock that does not fit any of the other -composition/genesis categories. Sedimentary rock consisting of three -or more components which form more than 5 percent but less than 50 -precent of the material. - -#### iron rich sedimentary rock - -[]{#iron_rich_sedimentary_rock} - -Concept: [`Iron_Rich_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Iron_Rich_Sedimentary_Rock) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -Sedimentary rock that consists of at least 50 percent iron-bearing -minerals (hematite, magnetite, limonite-group, siderite, iron- -sulfides), as determined by hand-lens or petrographic analysis. -Corresponds to a rock typically containing 15 percent iron by weight. - -#### non clastic siliceous sedimentary rock - -[]{#non_clastic_siliceous_sedimentary_rock} - -Concept: [`Non_Clastic_Siliceous_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Non_Clastic_Siliceous_Sedimentary_Rock) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -Definition updated to include chert, flint SMR 2020-09-21 -Sedimentary rock that consists of at least 50 percent silicate mineral -material, deposited directly by chemical or biological processes at -the depositional surface, in particles formed by chemical or -biological processes within the basin of deposition, or formed by -diagenetic processes. Includes chert and flint found in carbonate -rocks. - -#### organic rich sedimentary rock - -[]{#organic_rich_sedimentary_rock} - -Concept: [`Organic_Rich_Sedimentary_Rock`](https://w3id.org/isample/earthenv/rocksediment/Organic_Rich_Sedimentary_Rock) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -Sapropelic coal, and asphaltite are not differentiated in This -vocabulary -Sedimentary rock with color, composition, texture and apparent density -indicating greater than 50 percent organic content by weight on a -moisture-free basis. - -##### coal -* `kohle` - -[]{#coal} - -Concept: [`Coal`](https://w3id.org/isample/earthenv/rocksediment/Coal) - -Child of: - [`Organic_Rich_Sedimentary_Rock`](#Organic_Rich_Sedimentary_Rock) - -A consolidated organic sedimentary material having less than 75% -moisture. This category includes low, medium, and high rank coals -according to International Classification of In-Seam Coal (United -Nations, 1998), thus including lignite. Sapropelic coal is not -distinguished in this category from humic coals. Formed from the -compaction or induration of variously altered plant remains similar to -those of peaty deposits. - -#### phosphorite - -[]{#phosphorite} - -Concept: [`Phosphorite`](https://w3id.org/isample/earthenv/rocksediment/Phosphorite) - -Child of: - [`Sedimentary_Rock`](#Sedimentary_Rock) - -Sedimentary rock in which at least 50 percent of the primary or -recrystallized constituents are phosphate minerals. Most commonly -occurs as a bedded primary or reworked secondary marine rock, composed -of microcrystalline carbonate fluorapatite in the form of lamina, -pellets, oolites and nodules, and skeletal, shell and bone fragments. - -### tuffit -* `tuffite` - -[]{#tuffite} - -Concept: [`Tuffite`](https://w3id.org/isample/earthenv/rocksediment/Tuffite) - -Child of: - [`rock`](#rock) - -In practice, it is likely that any rock for which there is suspicion -that it may consist of redeposited pyroclastic material, usually based -on sedimentary structures, irrespective of the presence or percentage -of clearly epiclastic particles, would be called a tuffite. 50 percent -cutoff with epiclastic rock is in contrast with LeMaitre et al., but -is used for consistentency with other sedimentary rock categories -following the pattern that the rock name reflects the predominant -constituent. -synonym: volcaniclastic rock -Rock consists of more than 50 percent particles of indeterminate -pyroclastic or epiclastic origin and less than 75 percent particles of -clearly pyroclastic origin. commonly the rock is laminated or exhibits -size grading. (based on LeMaitre et al. 2002; Murawski and Meyer -1998). - -### residual material - -[]{#residual_material} - -Concept: [`residual_material`](https://w3id.org/isample/earthenv/rocksediment/residual_material) - -Child of: - [`rock`](#rock) - -Material of composite origin resulting from weathering processes at -the Earth's surface, with genesis dominated by removal of chemical -constituents by aqueous leaching. Minor clastic, chemical, or organic -input may also contribute. Consolidation state is not inherent in -definition, but typically material is unconsolidated or weakly -consolidated. - - -## Sediment - -[]{#sediment} - -Concept: [`sediment`](https://w3id.org/isample/vocabulary/material/sediment) - -Solid granular material transported by wind, water, or gravity, not -modified by interaction with biosphere or atmosphere (to differentiate -from soil). Particles derived by erosion of pre-existing rock, from -shell or other body parts from organisms, precipitated chemically in -the surficial environment, or generated by explosive volcanic -activity. -(http://resource.geosciml.org/classifier/cgi/lithology/sediment). -Sediment is not consolidated, i.e. Particulate constituents of a -compound material do not adhere to each other strongly enough that the -aggregate can be considered a solid material in its own right. Similar -to http://purl.obolibrary.org/obo/ENVO_00002007 - -### biogenic sediment - -[]{#biogenic_sediment} - -Concept: [`Biogenic_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Biogenic_Sediment) - -Child of: - [`sediment`](#sediment) - -Corresponding biogenic sedimentary material and biogenic sedimentary -rock categories are not included based on the interpretation that -biogenic sedimentary rock will be in a different category, e.g. -carbonate sedimentary rock or organic rich sedimentary rock. -Sediment composed of greater than 50 percent material of biogenic -origin. Because the biogenic material may be skeletal remains that are -not organic, all biogenic sediment is not necessarily organic-rich. - -### carbonate sediment - -[]{#carbonate_sediment} - -Concept: [`Carbonate_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Carbonate_Sediment) - -Child of: - [`sediment`](#sediment) - -Sediment in which at least 50 percent of the primary and/or -recrystallized constituents are composed of one (or more) of the -carbonate minerals calcite, aragonite and dolomite, in particles of -intrabasinal origin. - -### chemical sedimentary material - -[]{#chemical_sedimentary_material} - -Concept: [`Chemical_Sedimentary_Material`](https://w3id.org/isample/earthenv/rocksediment/Chemical_Sedimentary_Material) - -Child of: - [`sediment`](#sediment) - -Sedimentary material that consists of at least 50 percent material -produced by inorganic chemical processes within the basin of -deposition. Includes inorganic siliceous, carbonate, evaporite, iron- -rich, and phosphatic sediment classes, as well as chemical sediments -associated with submarine hot springs ('black smokers'). Note that -these sediments might crystallize as a solid as they are deposited, -thus similar to rock.... - -### clastic sediment - -[]{#clastic_sediment} - -Concept: [`Clastic_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Clastic_Sediment) - -Child of: - [`sediment`](#sediment) - -Choice of 'clastic' is purposful. Other suggested labels for this -category include siliciclastic and terrigineous clastic. Siliciclastic -is considered too limiting because the category includes rocks that -consists clasts of carbonate minerals, e.g. epiclastic detritus eroded -from carbonate rock. Terrigineous clastic was considered and rejected -first because it is considered redundant, anything that is -terrigineous is clastic. Second, it is questionable if clastic -sediment derived by submarine processes (fragementation by gravity -sliding, faulting, or volcanic activity, with transport by sediment -gravity flow or submarine currents) is terrigineous, but it is clastic -and is meant to be included in this category. -Sediment in which at least 50 percent of the constituent particles -were derived from erosion, weathering, or mass-wasting of pre-existing -earth materials, and transported to the place of deposition by -mechanical agents such as water, wind, ice and gravity. - -#### diamicton - -[]{#diamicton} - -Concept: [`Diamicton`](https://w3id.org/isample/earthenv/rocksediment/Diamicton) - -Child of: - [`Clastic_Sediment`](#Clastic_Sediment) - -definition amplified to help distinguish diamicton, conglomerate and -wackestone in this version -Unsorted or poorly sorted, clastic sediment with a wide range of -particle sizes, including a muddy matrix. Biogenic materials that have -such texture are excluded. Distinguished from conglomerate, sandstone, -mudstone based on polymodality and lack of structures related to -transport and deposition of sediment by moving air or water. -Assignment to an other size class can be used in conjunction to -indicate the dominant grain size. - -### gravel size sediment - -[]{#gravel_size_sediment} - -Concept: [`Gravel_Size_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Gravel_Size_Sediment) - -Child of: - [`sediment`](#sediment) - -Sediment containing greater than 30 percent gravel-size particles -(greater than 2.0 mm diameter). Composition or gensis of clasts not -specified. - -### hybrid sediment - -[]{#hybrid_sediment} - -Concept: [`Hybrid_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Hybrid_Sediment) - -Child of: - [`sediment`](#sediment) - -Sediment that does not fit any of the other sediment -composition/genesis categories. Sediment consisting of three or more -components which form more than 5 percent but less than 50 precent of -the material. - -### iron rich sediment - -[]{#iron_rich_sediment} - -Concept: [`Iron_Rich_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Iron_Rich_Sediment) - -Child of: - [`sediment`](#sediment) - -Sediment that consists of at least 50 percent iron-bearing minerals -(hematite, magnetite, limonite-group, siderite, iron-sulfides), as -determined by hand-lens or petrographic analysis. Corresponds to a -rock typically containing 15 percent iron by weight. - -### mud size sediment - -[]{#mud_size_sediment} - -Concept: [`Mud_Size_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Mud_Size_Sediment) - -Child of: - [`sediment`](#sediment) - -Sediment consisting of less than 30 percent gravel-size (2 mm) -particles and with a mud-size to sand-size particle ratio greater than -1. Clasts may be of any composition or origin. BGS (Hallsworth and -Knox, 1999, p. 9) define the 'upper size limit of mud ... at 32 -micrometers (.032 mm)', but Wentworth scale and Krumbein scale put -boundary at .064 or .062 mm (inidistinguishable difference in -rocks...) BGS 'mud-grade sediment' or sedimentary rock definition is -'over 75% of the clasts smaller than .032 mm', which is narrower than -the definition here. - -### non clastic siliceous sediment - -[]{#non_clastic_siliceous_sediment} - -Concept: [`Non_Clastic_Siliceous_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Non_Clastic_Siliceous_Sediment) - -Child of: - [`sediment`](#sediment) - -Sediment that consists of at least 50 percent silicate mineral -material, deposited directly by chemical or biological processes at -the depositional surface, or in particles formed by chemical or -biological processes within the basin of deposition. - -### phosphate rich sediment - -[]{#phosphate_rich_sediment} - -Concept: [`Phosphate_Rich_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Phosphate_Rich_Sediment) - -Child of: - [`sediment`](#sediment) - -Sediment in which at least 50 percent of the primary and/or -recrystallized constituents are phosphate minerals. - -### sand size sediment - -[]{#sand_size_sediment} - -Concept: [`Sand_Size_Sediment`](https://w3id.org/isample/earthenv/rocksediment/Sand_Size_Sediment) - -Child of: - [`sediment`](#sediment) - -Sediment in which less than 30 percent of particles are gravel -(greater than 2 mm in diameter) and the sand to mud ratio is at least -1. composition or genesis of clasts not specified. - -### tephra - -[]{#tephra} - -Concept: [`Tephra`](https://w3id.org/isample/earthenv/rocksediment/Tephra) - -Child of: - [`sediment`](#sediment) - -Unconsolidated pyroclastic material in which greater than 75 percent -of the fragments are deposited as a direct result of volcanic -processes and the deposit has not been reworked by epiclastic -processes. Includes ash, lapilli tephra, bomb tephra, block tephra and -unconsolidated agglomerate. - - diff --git a/models/generated/extensions/earthenv_materialsampleobject_type.md b/models/generated/extensions/earthenv_materialsampleobject_type.md deleted file mode 100644 index f5eb1a4..0000000 --- a/models/generated/extensions/earthenv_materialsampleobject_type.md +++ /dev/null @@ -1,1222 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "Earth and Environmental Science extension - Material sample type" -date: "2025-12-11T02:41:32.972715+00:00" -subtitle: | - This concept scheme contains skos concepts for categorizing kinds of Earth Material sample types, extending the iSamples Material Sample Object Type vocabulary. Defintions from SESAR, ODM2, wikipedia, ESS-DIVE, and other sources; sources are cited with each term. -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_materialsampleobject_type.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_materialsampleobject_type.ttl) - - -Namespace: -[`https://w3id.org/isample/earthenv/esmaterialsample/essampletype`](https://w3id.org/isample/earthenv/esmaterialsample/essampletype) - -**History** - -* 2023-07-07 SMR add solid material sample and broader relations from classes it subsumes. -* 2023-07-27 SMR modify base specimen type vocabulary, add 'Non biologic solid object' to replace 'solid material sample', change broader relations in this vocab to use that as parent class where appropriate. 'Solid material sample' is too closely linked to material type, created confusion. Intention is a specimen category for solid objects that are not biologic. Obviously there is some overlap with Research specimens. -* 2024-07-15 SMR fix import to base vocabulary on renamed material_sample_type vocabulary, change from specimentypevocabulary to materialsampleobjecttype/conceptscheme - -**Concepts** - -- [Analytical preparation](#analyticalpreparation) - - [Cell culture](#cellculture) - - [Dissolved chemical fraction](#dissolvedchemicalfraction) - - [Eluate](#eluate) - - [FIB lamella](#fiblamella) - - [Glass slide smear](#glassslidesmear) - - [Individual solid cube](#individualsolidcube) - - [Magnetic fraction](#magneticfraction) - - [Mechanical fraction](#mechanicalfraction) - - [Mineral separate](#mineralseparate) - - [Magnetic fraction](#magneticfraction) - - [Non-magnetic fraction](#nonmagneticfraction) - - [Sectioned specimen](#mountedsection) - - [Thick section](#thicksection) - - [Thin section](#thinsection) - - [Polished thin section](#polishedthinsection) - - [Ultra thin section](#ultrathinsection) - - [Non-magnetic fraction](#nonmagneticfraction) - - [Peel](#peel) - - [Prepared powder](#preparedpowder) - - [Prepared rock powder](#preparedrockpowder) - - [Pressed pellet](#pressedpellet) - - [Residual material](#residualmaterial) - - [Slab](#slab) - -- [Bundle biome aggregation](#bundlebiomeaggregation) - - [Cell culture](#cellculture) - -- [Fluid in container](#fluidincontainer) - - [Direct fluid sample](#directfluidsample) - - [Dissolved chemical fraction](#dissolvedchemicalfraction) - - [Eluate](#eluate) - - [Processed fluid sample](#processedfluidsample) - - [Filtrate](#filtrate) - -- [Generic aggregation](#genericaggregation) - - [Boxed core](#boxedcore) - - [Composite sample](#compositesample) - - [Chip Channel Sample](#chipchannelsample) - - [High Grade Sample](#highgradesample) - - [Site composite sample](#sitecompositesample) - - [Core catcher](#corecatcher) - - [Cuttings](#cuttings) - - [Dredge](#dredge) - - [Material captured in filter](#materialcapturedinfilter) - - [Mechanical fraction](#mechanicalfraction) - - [Mineral separate](#mineralseparate) - - [Magnetic fraction](#magneticfraction) - - [Non-magnetic fraction](#nonmagneticfraction) - - [Natural aggregate specimen](#naturalaggregate) - - [Prepared powder](#preparedpowder) - - [Prepared rock powder](#preparedrockpowder) - - [TEM grid](#temgrid) - - [Trawl](#trawl) - -- [Other solid object](#othersolidobject) - - [Dust wipe](#dustwipe) - - [Glass slide smear](#glassslidesmear) - - [Peel](#peel) - -- [Solid material sample](#solidmaterialsample) - - [Core](#core) - - [Core half round](#corehalfround) - - [Core piece](#corepiece) - - [Core quarter round](#corequarterround) - - [Core section](#coresection) - - [Core subpeice](#coresubpeice) - - [FIB lamella](#fiblamella) - - [Individual solid cube](#individualsolidcube) - - [Individual solid cylinder](#individualsolidcylinder) - - [Meteorite](#meteorite) - - [Mineral specimen](#mineralspecimen) - - [Sectioned specimen](#mountedsection) - - [Thick section](#thicksection) - - [Thin section](#thinsection) - - [Polished thin section](#polishedthinsection) - - [Ultra thin section](#ultrathinsection) - - [Pressed pellet](#pressedpellet) - - [Rock hand sample](#rockhandsample) - - [Slab](#slab) - - [U-channel sample](#uchannelsample) - - [Atom probe tip](#atomprobetip) - - [Chip](#chip) - - [Microtome slice](#microtomeslice) - - [Mounted specimen](#mountedspecimen) - - [Polished mounted specimen](#polishedmountedspecimen) - - [Particle](#particle) - -## Analytical preparation - -[]{#analyticalpreparation} - -Concept: [`analyticalpreparation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/analyticalpreparation) - -Specimen is a product of processing required for some observation -procedure, e.g. thin section, XRF bead, SEM stub, rock powder. If -identified separately, this should have a ‘parent’ link to the -original sample - -### Cell culture - -[]{#cellculture} - -Concept: [`cellculture`](https://w3id.org/isample/earthenv/esmaterialsample/cellculture) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`bundlebiomeaggregation`](#bundlebiomeaggregation) - -a collection of cells are grown under controlled conditions, generally -outside of their natural environment - -### Dissolved chemical fraction - -[]{#dissolvedchemicalfraction} - -Concept: [`dissolvedchemicalfraction`](https://w3id.org/isample/earthenv/esmaterialsample/dissolvedchemicalfraction) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`fluidincontainer`](#fluidincontainer) - -A fluid concentrating some constituent of interest from a parent -sample. The dissolved constituent is actually the sample material of -interest. - -#### Eluate - -[]{#eluate} - -Concept: [`eluate`](https://w3id.org/isample/earthenv/esmaterialsample/eluate) - -Child of: - [`dissolvedchemicalfraction`](#dissolvedchemicalfraction) - -The fluid product that contains the analyte of interest washed from a -chromatography column - -### FIB lamella - -[]{#fiblamella} - -Concept: [`fiblamella`](https://w3id.org/isample/earthenv/esmaterialsample/fiblamella) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -very thin sheet of solid material milled from a larger sample using a -focused ion beam. Used for TEM analysis. - -### Glass slide smear - -[]{#glassslidesmear} - -Concept: [`glassslidesmear`](https://w3id.org/isample/earthenv/esmaterialsample/glassslidesmear) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`othersolidobject`](#othersolidobject) - -sample from a cell culture (or other microparticulate suspension) -spread into a thin layer on a glass slide for optical investigation - -### Individual solid cube - -[]{#individualsolidcube} - -Concept: [`individualsolidcube`](https://w3id.org/isample/earthenv/esmaterialsample/individualsolidcube) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -A sample that is a prepared cube of material, intended as a sample of -that material. - -### Magnetic fraction - -[]{#magneticfraction} - -Concept: [`magneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/magneticfraction) - -Child of: - [`mineralseparate`](#mineralseparate) - [`analyticalpreparation`](#analyticalpreparation) - -a collection of particles separated from a crushed rock sample based -on their attraction to a magnet. - -### Mechanical fraction - -[]{#mechanicalfraction} - -Concept: [`mechanicalfraction`](https://w3id.org/isample/earthenv/esmaterialsample/mechanicalfraction) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`genericaggregation`](#genericaggregation) - -defined by sample preparation involving mechanical processing, e.g. -grain size, density, or grain shape separation. - -### Mineral separate - -[]{#mineralseparate} - -Concept: [`mineralseparate`](https://w3id.org/isample/earthenv/esmaterialsample/mineralseparate) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`genericaggregation`](#genericaggregation) - -an aggregation of particles of the same mineral extracted and -concentrated from a rock. - -#### Magnetic fraction - -[]{#magneticfraction} - -Concept: [`magneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/magneticfraction) - -Child of: - [`mineralseparate`](#mineralseparate) - [`analyticalpreparation`](#analyticalpreparation) - -a collection of particles separated from a crushed rock sample based -on their attraction to a magnet. - -#### Non-magnetic fraction - -[]{#nonmagneticfraction} - -Concept: [`nonmagneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/nonmagneticfraction) - -Child of: - [`mineralseparate`](#mineralseparate) - [`analyticalpreparation`](#analyticalpreparation) - -collection of particles from a crushed rock sample based on their lack -of attraction to a magnet - -### Sectioned specimen - -[]{#mountedsection} - -Concept: [`mountedsection`](https://w3id.org/isample/earthenv/esmaterialsample/mountedsection) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -a thin slice of a solid material that has been mounted on a glass -slide for study - -#### Thick section - -[]{#thicksection} - -Concept: [`thicksection`](https://w3id.org/isample/earthenv/esmaterialsample/thicksection) - -Child of: - [`mountedsection`](#mountedsection) - -Thick sections are like thin sections, but milled to a greater -thickness. Typcially polished on one or both sides and used for fluid -or melt inclusion studies, Raman analyses, and infrared spectroscopy -analyses, and SEM or electron microprobe. The standard thickness for a -fluid inclusion thick section is 50 micrometers, but thick sections -can be made at any thickness. Thick sections can be attached to a -glass slide, or can be prepared so that they can be removed from their -mount as a stand-alone slice of rock. - -#### Thin section - -[]{#thinsection} - -Concept: [`thinsection`](https://w3id.org/isample/earthenv/esmaterialsample/thinsection) - -Child of: - [`mountedsection`](#mountedsection) - -thin sliver of rock cut from a sample with a diamond saw and ground -optically flat, and then mounted on a glass slide and ground smooth -using progressively finer abrasive grit until the sample is 30 microns -thick. - -##### Polished thin section - -[]{#polishedthinsection} - -Concept: [`polishedthinsection`](https://w3id.org/isample/earthenv/esmaterialsample/polishedthinsection) - -Child of: - [`thinsection`](#thinsection) - -a thin section that has its free surface polished until perfectly -planar and free of pits and scratches. Used for reflected light -petrography and for electron microprobe or SEM investigation. - -#### Ultra thin section - -[]{#ultrathinsection} - -Concept: [`ultrathinsection`](https://w3id.org/isample/earthenv/esmaterialsample/ultrathinsection) - -Child of: - [`mountedsection`](#mountedsection) - -An ordinary thin section that is attached to the glass slide using a -soluble cement such as Canada balsam (soluble in ethanol) to allow -both sides to be worked on. The section is polished on both sides -using a fine diamond paste until it has a thickness in the range of -2-12 microns. This technique has been used to study the microstructure -of very fine-grained carbonate rocks, and also in the preparation of -mineral and rock specimens for transmission electron microscopy. - -### Non-magnetic fraction - -[]{#nonmagneticfraction} - -Concept: [`nonmagneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/nonmagneticfraction) - -Child of: - [`mineralseparate`](#mineralseparate) - [`analyticalpreparation`](#analyticalpreparation) - -collection of particles from a crushed rock sample based on their lack -of attraction to a magnet - -### Peel - -[]{#peel} - -Concept: [`peel`](https://w3id.org/isample/earthenv/esmaterialsample/peel) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`othersolidobject`](#othersolidobject) - -Acetate peels are made by polishing a planar surface on a sample, -etching it with acid to give it some relief, and then chemically -melting a piece of acetate onto that surface. The acetate is then -pulled off for examination under a microscope. The acetate preserves a -fingerprint of the internal structure of the sample surface. Used in -paleontology to study complex fossils, e.g. bryozoan. - -### Prepared powder - -[]{#preparedpowder} - -Concept: [`preparedpowder`](https://w3id.org/isample/earthenv/esmaterialsample/preparedpowder) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`genericaggregation`](#genericaggregation) - -distinguish from particulate in that particulate is sampled as a -micron-size aggregate, whereas this material is ground to a powder for -subsequent analysis; it is a powder as a function of some preparation -process (e.g. chemical precipitation) - -#### Prepared rock powder - -[]{#preparedrockpowder} - -Concept: [`preparedrockpowder`](https://w3id.org/isample/earthenv/esmaterialsample/preparedrockpowder) - -Child of: - [`preparedpowder`](#preparedpowder) - -a powder manufactured by pulverizing a rock. - -### Pressed pellet - -[]{#pressedpellet} - -Concept: [`pressedpellet`](https://w3id.org/isample/earthenv/esmaterialsample/pressedpellet) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -a sample prepared by grinding a parent sample to a fine powder, mixing -it with a binder, and pressing the mixture into a die at a pressure of -between 15 and 35 tons to produce a solid disc for subsequent -analysis, typically by X-Ray fluorescence. - -### Residual material - -[]{#residualmaterial} - -Concept: [`residualmaterial`](https://w3id.org/isample/earthenv/esmaterialsample/residualmaterial) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - -Sample is material remaining after processing to extract some other -components of interest from the sample. - -### Slab - -[]{#slab} - -Concept: [`slab`](https://w3id.org/isample/earthenv/esmaterialsample/slab) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -a relatively planar rock sample,cut from a large sample to produce a -tabular peice of rock with the irregular outline of the original -sample on the diameter where the cut was mate. - - -## Bundle biome aggregation - -[]{#bundlebiomeaggregation} - -Concept: [`bundlebiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/bundlebiomeaggregation) - -An aggregation of whole organisms representative of some biome - -### Cell culture - -[]{#cellculture} - -Concept: [`cellculture`](https://w3id.org/isample/earthenv/esmaterialsample/cellculture) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`bundlebiomeaggregation`](#bundlebiomeaggregation) - -a collection of cells are grown under controlled conditions, generally -outside of their natural environment - - -## Fluid in container - -[]{#fluidincontainer} - -Concept: [`fluidincontainer`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/fluidincontainer) - -Specimen is a container whose contents are liquid, gas, or mixed -dominantly fluid phases that is the actual sample material. Fluid -might include minor solid particles. Container typically human made, -but also includes natural fluid container, e.g. fluid inclusion in a -mineral grain. Includes colloids, foams, gels, suspensions. The -sample is the fluid substance; fluid samples collected to analyze the -contained biome should be considered 'Biome Aggregation' - -### Direct fluid sample - -[]{#directfluidsample} - -Concept: [`directfluidsample`](https://w3id.org/isample/earthenv/esmaterialsample/directfluidsample) - -Child of: - [`fluidincontainer`](#fluidincontainer) - -a fluid collected from the sampled feature (e.g. water body, -hydrothermal vent, atmosphere...) with no processing. (e.g. -filtration, addition of preservatives). - -### Dissolved chemical fraction - -[]{#dissolvedchemicalfraction} - -Concept: [`dissolvedchemicalfraction`](https://w3id.org/isample/earthenv/esmaterialsample/dissolvedchemicalfraction) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`fluidincontainer`](#fluidincontainer) - -A fluid concentrating some constituent of interest from a parent -sample. The dissolved constituent is actually the sample material of -interest. - -#### Eluate - -[]{#eluate} - -Concept: [`eluate`](https://w3id.org/isample/earthenv/esmaterialsample/eluate) - -Child of: - [`dissolvedchemicalfraction`](#dissolvedchemicalfraction) - -The fluid product that contains the analyte of interest washed from a -chromatography column - -### Processed fluid sample - -[]{#processedfluidsample} - -Concept: [`processedfluidsample`](https://w3id.org/isample/earthenv/esmaterialsample/processedfluidsample) - -Child of: - [`fluidincontainer`](#fluidincontainer) - -fluid sample that has been processed in some way during or after -collection, e.g. by filtering, addition of preservatives. - -#### Filtrate - -[]{#filtrate} - -Concept: [`filtrate`](https://w3id.org/isample/earthenv/esmaterialsample/filtrate) - -Child of: - [`processedfluidsample`](#processedfluidsample) - -A sample that has gone through a filtration process to separate solids -from fluids (liquids or gases), using a filter medium through which -only the fluid can pass. Must be associated with a filter size. - - -## Generic aggregation - -[]{#genericaggregation} - -Concept: [`genericaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/genericaggregation) - -An aggregate specimen that is not biogenic or composed of -anthropogenic material fragments. Examples: loose soil or sediment -(e.g. in a bag), rock chips, particulate filtrate or precipitate; rock -powders. - -### Boxed core - -[]{#boxedcore} - -Concept: [`boxedcore`](https://w3id.org/isample/earthenv/esmaterialsample/boxedcore) - -Child of: - [`genericaggregation`](#genericaggregation) - -A collection of core peices that are stored in an individual box. -Typically the box will contain core peices from the same core. - -### Composite sample - -[]{#compositesample} - -Concept: [`compositesample`](https://w3id.org/isample/earthenv/esmaterialsample/compositesample) - -Child of: - [`genericaggregation`](#genericaggregation) - -a sample composed of multiple peices, representative of some material, -or representative of some site. The peices do not all originate from -the same object. - -#### Chip Channel Sample - -[]{#chipchannelsample} - -Concept: [`chipchannelsample`](https://w3id.org/isample/earthenv/esmaterialsample/chipchannelsample) - -Child of: - [`compositesample`](#compositesample) - -small chips of rock collected over a specified interval, with the -objective to obtain a representative sample for that interval. Most of -the time chip channel samples are collected in succession along a -sample line which is laid out in advance using a tape. The freshest -material possible is sampled, preferably chipping directly from -bedrock. Sample intervals are set at a specified width, usually -ranging from 30cm to 7m. Due to the method of sampling, chip channel -samples tend to be rather large (up to 20 pounds for a five foot -interval) - -#### High Grade Sample - -[]{#highgradesample} - -Concept: [`highgradesample`](https://w3id.org/isample/earthenv/esmaterialsample/highgradesample) - -Child of: - [`compositesample`](#compositesample) - -in mineral exploration, selective pieces of the most highly -mineralized material from a mineralize site, intentionally excluding -less mineralized material. A high grade sample might be collected to -indicate what the best possible values are, or to provide material for -certain types of trace element analyses. - -#### Site composite sample - -[]{#sitecompositesample} - -Concept: [`sitecompositesample`](https://w3id.org/isample/earthenv/esmaterialsample/sitecompositesample) - -Child of: - [`compositesample`](#compositesample) - -an aggregation of peices of uniform material collected over some area -(generally greater than 2.5m across). These are the ideal -'representative' samples used in mineral exploration. A composite -sample might be collected to determine the background values of trace -elements in a particular type of rock, or to determine if ore grade -mineralization is present over a large area. - -### Core catcher - -[]{#corecatcher} - -Concept: [`corecatcher`](https://w3id.org/isample/earthenv/esmaterialsample/corecatcher) - -Child of: - [`genericaggregation`](#genericaggregation) - -material recovered from the core catcher of a sedimentary core and -which is treated as a separate section from the core. The core catcher -is a device at the bottom of the core barrel that prevents the core -from sliding out while the barrel is retrieved from the hole. -(http://publications.iodp.org/proceedings/323/102/102_.htm) - -### Cuttings - -[]{#cuttings} - -Concept: [`cuttings`](https://w3id.org/isample/earthenv/esmaterialsample/cuttings) - -Child of: - [`genericaggregation`](#genericaggregation) - -unconsolidated Earth material produced by the grinding action of a -drill bit during drilling of a borehole. - -### Dredge - -[]{#dredge} - -Concept: [`dredge`](https://w3id.org/isample/earthenv/esmaterialsample/dredge) - -Child of: - [`genericaggregation`](#genericaggregation) - -an aggregation of material sampled by dragging a collection bucket -(dredge) across the bottom of a water body - -### Material captured in filter - -[]{#materialcapturedinfilter} - -Concept: [`materialcapturedinfilter`](https://w3id.org/isample/earthenv/esmaterialsample/materialcapturedinfilter) - -Child of: - [`genericaggregation`](#genericaggregation) - -A material sample captured in filter, for example from a water sample -that was filtered. Must be associated with filter size field. - -### Mechanical fraction - -[]{#mechanicalfraction} - -Concept: [`mechanicalfraction`](https://w3id.org/isample/earthenv/esmaterialsample/mechanicalfraction) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`genericaggregation`](#genericaggregation) - -defined by sample preparation involving mechanical processing, e.g. -grain size, density, or grain shape separation. - -### Mineral separate - -[]{#mineralseparate} - -Concept: [`mineralseparate`](https://w3id.org/isample/earthenv/esmaterialsample/mineralseparate) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`genericaggregation`](#genericaggregation) - -an aggregation of particles of the same mineral extracted and -concentrated from a rock. - -#### Magnetic fraction - -[]{#magneticfraction} - -Concept: [`magneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/magneticfraction) - -Child of: - [`mineralseparate`](#mineralseparate) - [`analyticalpreparation`](#analyticalpreparation) - -a collection of particles separated from a crushed rock sample based -on their attraction to a magnet. - -#### Non-magnetic fraction - -[]{#nonmagneticfraction} - -Concept: [`nonmagneticfraction`](https://w3id.org/isample/earthenv/esmaterialsample/nonmagneticfraction) - -Child of: - [`mineralseparate`](#mineralseparate) - [`analyticalpreparation`](#analyticalpreparation) - -collection of particles from a crushed rock sample based on their lack -of attraction to a magnet - -### Natural aggregate specimen - -[]{#naturalaggregate} - -Concept: [`naturalaggregate`](https://w3id.org/isample/earthenv/esmaterialsample/naturalaggregate) - -Child of: - [`genericaggregation`](#genericaggregation) - -E.g beach sand, soil, river sediment, scoop of regolith. -Specimen is aggregate of non-consolidated material formed by natural -processes. Particles have not been intentionally modified from the -sampled feature. - -### Prepared powder - -[]{#preparedpowder} - -Concept: [`preparedpowder`](https://w3id.org/isample/earthenv/esmaterialsample/preparedpowder) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`genericaggregation`](#genericaggregation) - -distinguish from particulate in that particulate is sampled as a -micron-size aggregate, whereas this material is ground to a powder for -subsequent analysis; it is a powder as a function of some preparation -process (e.g. chemical precipitation) - -#### Prepared rock powder - -[]{#preparedrockpowder} - -Concept: [`preparedrockpowder`](https://w3id.org/isample/earthenv/esmaterialsample/preparedrockpowder) - -Child of: - [`preparedpowder`](#preparedpowder) - -a powder manufactured by pulverizing a rock. - -### TEM grid - -[]{#temgrid} - -Concept: [`temgrid`](https://w3id.org/isample/earthenv/esmaterialsample/temgrid) - -Child of: - [`genericaggregation`](#genericaggregation) - -FIB sections and microtome slices set onto a small grid for handling, -transport, and analysis using a transmission electron microscope -(TEM). The grid itself can be given a single sample identifier -(similar to how there are multiple grains in a grain mount). The -linkage from the individual samples in the grid to their parent -sample(s) should be documented - -### Trawl - -[]{#trawl} - -Concept: [`trawl`](https://w3id.org/isample/earthenv/esmaterialsample/trawl) - -Child of: - [`genericaggregation`](#genericaggregation) - -an aggregation of biogenic or non-biogenic material extracted from a -water body - - -## Other solid object - -[]{#othersolidobject} - -Concept: [`othersolidobject`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/othersolidobject) - -Single piece of material not one of the other types. - -### Dust wipe - -[]{#dustwipe} - -Concept: [`dustwipe`](https://w3id.org/isample/earthenv/esmaterialsample/dustwipe) - -Child of: - [`othersolidobject`](#othersolidobject) - -a pre-weighed and packaged paper towel (wipe) used to wipe over a -surface to collect particulates from the surface - -### Glass slide smear - -[]{#glassslidesmear} - -Concept: [`glassslidesmear`](https://w3id.org/isample/earthenv/esmaterialsample/glassslidesmear) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`othersolidobject`](#othersolidobject) - -sample from a cell culture (or other microparticulate suspension) -spread into a thin layer on a glass slide for optical investigation - -### Peel - -[]{#peel} - -Concept: [`peel`](https://w3id.org/isample/earthenv/esmaterialsample/peel) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`othersolidobject`](#othersolidobject) - -Acetate peels are made by polishing a planar surface on a sample, -etching it with acid to give it some relief, and then chemically -melting a piece of acetate onto that surface. The acetate is then -pulled off for examination under a microscope. The acetate preserves a -fingerprint of the internal structure of the sample surface. Used in -paleontology to study complex fossils, e.g. bryozoan. - - -## Solid material sample - -[]{#solidmaterialsample} - -Concept: [`solidmaterialsample`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/solidmaterialsample) - - -### Core - -[]{#core} - -Concept: [`core`](https://w3id.org/isample/earthenv/esmaterialsample/core) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -Cylinder of rock or sediment extracted from within the earth, and -representing the entire sample extracted during a single borehole -drilling event. Typically using some rotary drilling technology. In -many cases the core is extracted in segments that are 'core sections'. -A core from a single borehole is rarely a continous unbroken object; -commonly parts of the core will break up during drilling or -extraction, leaving gaps or sections that are granular material. Cores -are normally composed of consolidated ('solid') material, but in some -cases loosely consolidated material might be recovered, and considered -sediment or tephra. To be called 'core' the material must be -sufficiently consolidated to maintain a cylindrical shape. A core -hasPart (hasChild) 'Core section' - -### Core half round - -[]{#corehalfround} - -Concept: [`corehalfround`](https://w3id.org/isample/earthenv/esmaterialsample/corehalfround) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -Half-cylindrical peice of consolidated material produced by along-axis -split of a core whole round along a selected diameter . Has childOf -relation to core section or core, core section, or Core peice from -which is was split - -### Core piece - -[]{#corepiece} - -Concept: [`corepiece`](https://w3id.org/isample/earthenv/esmaterialsample/corepiece) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -A cylindrical peice of consolidated earth material extracted as a -single solid object between breaks in recovery of core from a -borehole. has parent core section - -### Core quarter round - -[]{#corequarterround} - -Concept: [`corequarterround`](https://w3id.org/isample/earthenv/esmaterialsample/corequarterround) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -a partial cylindrical peice of consolidated material created by along- -axis split of a core half round. Has Parent core half round - -### Core section - -[]{#coresection} - -Concept: [`coresection`](https://w3id.org/isample/earthenv/esmaterialsample/coresection) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -Segment of a core representing some interval along the well bore. -Child of Core - -### Core subpeice - -[]{#coresubpeice} - -Concept: [`coresubpeice`](https://w3id.org/isample/earthenv/esmaterialsample/coresubpeice) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -A peice of consolidated material broken from a core peice. has Parent -core peice or core section - -### FIB lamella - -[]{#fiblamella} - -Concept: [`fiblamella`](https://w3id.org/isample/earthenv/esmaterialsample/fiblamella) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -very thin sheet of solid material milled from a larger sample using a -focused ion beam. Used for TEM analysis. - -### Individual solid cube - -[]{#individualsolidcube} - -Concept: [`individualsolidcube`](https://w3id.org/isample/earthenv/esmaterialsample/individualsolidcube) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -A sample that is a prepared cube of material, intended as a sample of -that material. - -### Individual solid cylinder - -[]{#individualsolidcylinder} - -Concept: [`individualsolidcylinder`](https://w3id.org/isample/earthenv/esmaterialsample/individualsolidcylinder) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -A cylindrical peice of consolidated material not obtained by -subsurface drilling. Cores drilled for paleomagnetic analysis are a -common example. Tree ring cores are another... - -### Meteorite - -[]{#meteorite} - -Concept: [`meteorite`](https://w3id.org/isample/earthenv/esmaterialsample/meteorite) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -A meteorite is a solid object that originates in interplanetary space -and survives passage through an atmosphere to reach the surface of a -planet or moon. - -### Mineral specimen - -[]{#mineralspecimen} - -Concept: [`mineralspecimen`](https://w3id.org/isample/earthenv/esmaterialsample/mineralspecimen) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -a solid object consisting of one particular mineral, or several -minerals intended to be representative of one or more of the mineral -species. - -### Sectioned specimen - -[]{#mountedsection} - -Concept: [`mountedsection`](https://w3id.org/isample/earthenv/esmaterialsample/mountedsection) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -a thin slice of a solid material that has been mounted on a glass -slide for study - -#### Thick section - -[]{#thicksection} - -Concept: [`thicksection`](https://w3id.org/isample/earthenv/esmaterialsample/thicksection) - -Child of: - [`mountedsection`](#mountedsection) - -Thick sections are like thin sections, but milled to a greater -thickness. Typcially polished on one or both sides and used for fluid -or melt inclusion studies, Raman analyses, and infrared spectroscopy -analyses, and SEM or electron microprobe. The standard thickness for a -fluid inclusion thick section is 50 micrometers, but thick sections -can be made at any thickness. Thick sections can be attached to a -glass slide, or can be prepared so that they can be removed from their -mount as a stand-alone slice of rock. - -#### Thin section - -[]{#thinsection} - -Concept: [`thinsection`](https://w3id.org/isample/earthenv/esmaterialsample/thinsection) - -Child of: - [`mountedsection`](#mountedsection) - -thin sliver of rock cut from a sample with a diamond saw and ground -optically flat, and then mounted on a glass slide and ground smooth -using progressively finer abrasive grit until the sample is 30 microns -thick. - -##### Polished thin section - -[]{#polishedthinsection} - -Concept: [`polishedthinsection`](https://w3id.org/isample/earthenv/esmaterialsample/polishedthinsection) - -Child of: - [`thinsection`](#thinsection) - -a thin section that has its free surface polished until perfectly -planar and free of pits and scratches. Used for reflected light -petrography and for electron microprobe or SEM investigation. - -#### Ultra thin section - -[]{#ultrathinsection} - -Concept: [`ultrathinsection`](https://w3id.org/isample/earthenv/esmaterialsample/ultrathinsection) - -Child of: - [`mountedsection`](#mountedsection) - -An ordinary thin section that is attached to the glass slide using a -soluble cement such as Canada balsam (soluble in ethanol) to allow -both sides to be worked on. The section is polished on both sides -using a fine diamond paste until it has a thickness in the range of -2-12 microns. This technique has been used to study the microstructure -of very fine-grained carbonate rocks, and also in the preparation of -mineral and rock specimens for transmission electron microscopy. - -### Pressed pellet - -[]{#pressedpellet} - -Concept: [`pressedpellet`](https://w3id.org/isample/earthenv/esmaterialsample/pressedpellet) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -a sample prepared by grinding a parent sample to a fine powder, mixing -it with a binder, and pressing the mixture into a die at a pressure of -between 15 and 35 tons to produce a solid disc for subsequent -analysis, typically by X-Ray fluorescence. - -### Rock hand sample - -[]{#rockhandsample} - -Concept: [`rockhandsample`](https://w3id.org/isample/earthenv/esmaterialsample/rockhandsample) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -individual peice of rock broken from an outcrop or larger peice of -rock. - -### Slab - -[]{#slab} - -Concept: [`slab`](https://w3id.org/isample/earthenv/esmaterialsample/slab) - -Child of: - [`analyticalpreparation`](#analyticalpreparation) - [`solidmaterialsample`](#solidmaterialsample) - -a relatively planar rock sample,cut from a large sample to produce a -tabular peice of rock with the irregular outline of the original -sample on the diameter where the cut was mate. - -### U-channel sample - -[]{#uchannelsample} - -Concept: [`uchannelsample`](https://w3id.org/isample/earthenv/esmaterialsample/uchannelsample) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -a rectangular prism of loosely consolidated sediment extracted from a -core segment. has parent core piece or core segment - -### Atom probe tip - -[]{#atomprobetip} - -Concept: [`atomprobetip`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/atomprobetip) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -needle-shaped sample milled out of a larger sample with a focused ion -beam (FIB). - -### Chip - -[]{#chip} - -Concept: [`chip`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/chip) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -Individual solid object intentionally broken off a larger solid object -sample. A Chip must have a documented parent sample. - -### Microtome slice - -[]{#microtomeslice} - -Concept: [`microtomeslice`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/microtomeslice) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -Typically from TEM analysis. Slices are commonly deposited in a grid -contain with multiple slices and the grid will be given a single -sample name, not the individual slices within it. The provenance of -the slice from paticle to mounted specimen to slice should be -carefully documented -A very thin slice cut from a mounted specimen using a mocrotome or -ultramicrotome. - -### Mounted specimen - -[]{#mountedspecimen} - -Concept: [`mountedspecimen`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/mountedspecimen) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -one or more solid objects embedded in a stabilizing matrix, typically -epoxy, metal, or paraffin to allow slicing through the mounted -object(s). - -#### Polished mounted specimen - -[]{#polishedmountedspecimen} - -Concept: [`polishedmountedspecimen`](https://w3id.org/isample/earthenv/esmaterialsample/polishedmountedspecimen) - -Child of: - [`mountedspecimen`](#mountedspecimen) - -Mounted specimen with polished surface exposing mounted material for -analysis - -### Particle - -[]{#particle} - -Concept: [`particle`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/particle) - -Child of: - [`solidmaterialsample`](#solidmaterialsample) - -Can also used for small peices broken from a 'Rock hand sample'. -OSIRIS-Rex definition specifies 'competent individual geologic sample -of any size'. 'Competent' interpreted to be equivalent to 'solid', or -'consolidated'. The definition here is broader in that it includes -materials of any origin, but narrower in that it is restricted to -small objects. -A small individual solid object that is not one of the other sample -types. - - diff --git a/models/generated/extensions/earthenv_sampled_feature_role.md b/models/generated/extensions/earthenv_sampled_feature_role.md deleted file mode 100644 index f69b786..0000000 --- a/models/generated/extensions/earthenv_sampled_feature_role.md +++ /dev/null @@ -1,209 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "Earth and Environmental Science extension - Sampled feature role" -date: "2025-12-11T02:41:32.323627+00:00" -subtitle: | - Terms to categorize the relation of a sampled feature to its context. In the Earth Science realm this is typically relation of sampled feature to a containing rock body or rock body part. -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_sampled_feature_role.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_earth_science/main/vocabulary/earthenv_sampled_feature_role.ttl) - - -Namespace: -[`https://w3id.org/isample/earthenv/essampledfeatrole/sfrolevocabulary`](https://w3id.org/isample/earthenv/essampledfeatrole/sfrolevocabulary) - -**History** - -* 2023-11-17 SMR generate to account for sample classifications in SESAR -* 2024-09-13 SMR remove version number from URI - -**Concepts** - -- [Sampled feature part](#sampledfeaturepart) - - [inclusion](#inclusion) - - [clast](#clast) - - [cognate inclusion](#cognateinclusion) - - [fluid inclusion](#fluidinclusion) - - [melt inclusion](#meltinclusion) - - [mineral inclusion](#mineralinclusion) - - [xenolith](#xenolith) - - [individual constituent](#individualconstituent) - - [cement](#cement) - - [groundmass](#groundmass) - - [phenocryst](#phenocryst) - - [porphyroblast](#porphyroblast) - - [rock body](#rockbody) - -## Sampled feature part - -[]{#sampledfeaturepart} - -Concept: [`sampledfeaturepart`](https://w3id.org/isample/earthenv/essampledfeatrole/sampledfeaturepart) - -A sampled feature that is part of a larger sampled feature; Could be -improper part (e.g. the whole larger feature) - -### inclusion - -[]{#inclusion} - -Concept: [`inclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/inclusion) - -Child of: - [`sampledfeaturepart`](#sampledfeaturepart) - -sampled feature is an object contained within a larger body of -material. - -#### clast - -[]{#clast} - -Concept: [`clast`](https://w3id.org/isample/earthenv/essampledfeatrole/clast) - -Child of: - [`inclusion`](#inclusion) - -A clast is a fragment of rock or mineral derived from some pre- -existing rock or generated by intrabasinal processes that is a part of -a sediment - -#### cognate inclusion - -[]{#cognateinclusion} - -Concept: [`cognateinclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/cognateinclusion) - -Child of: - [`inclusion`](#inclusion) - -An inclusion in an igneous rock that is interpreted to be genetically -related to the enclosing rock. - -#### fluid inclusion - -[]{#fluidinclusion} - -Concept: [`fluidinclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/fluidinclusion) - -Child of: - [`inclusion`](#inclusion) - -an inclusion that is an opening in a mineral grain containing fluid -(liquid or gas). - -#### melt inclusion - -[]{#meltinclusion} - -Concept: [`meltinclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/meltinclusion) - -Child of: - [`inclusion`](#inclusion) - -An inclusion in a mineral grain in an igneous rock that is interpreted -to consist of trapped magma from which the igneous rock was formed. - -#### mineral inclusion - -[]{#mineralinclusion} - -Concept: [`mineralinclusion`](https://w3id.org/isample/earthenv/essampledfeatrole/mineralinclusion) - -Child of: - [`inclusion`](#inclusion) - -An inclusion of a mineral phase contained inside a grain of another -mineral. - -#### xenolith - -[]{#xenolith} - -Concept: [`xenolith`](https://w3id.org/isample/earthenv/essampledfeatrole/xenolith) - -Child of: - [`inclusion`](#inclusion) - -An inclusion that is a fragment of pre-existing material that is -contained in an igneous rock and unrelated to the magma that formed -the rock. - -### individual constituent - -[]{#individualconstituent} - -Concept: [`individualconstituent`](https://w3id.org/isample/earthenv/essampledfeatrole/individualconstituent) - -Child of: - [`sampledfeaturepart`](#sampledfeaturepart) - -sampled feature is a single particle or collection of particles that -share some characteristic, within or extracted from a larger sample. - -#### cement - -[]{#cement} - -Concept: [`cement`](https://w3id.org/isample/earthenv/essampledfeatrole/cement) - -Child of: - [`individualconstituent`](#individualconstituent) - -sampled feature is material that binds constituent particles together -in a sedimentary rock. - -#### groundmass - -[]{#groundmass} - -Concept: [`groundmass`](https://w3id.org/isample/earthenv/essampledfeatrole/groundmass) - -Child of: - [`individualconstituent`](#individualconstituent) - -sampled feature is fine-grained to aphanitic material that is -interstitial to larger crystals or particles in a sample. - -#### phenocryst - -[]{#phenocryst} - -Concept: [`phenocryst`](https://w3id.org/isample/earthenv/essampledfeatrole/phenocryst) - -Child of: - [`individualconstituent`](#individualconstituent) - -Sampled feature is a crystal that is significantly larger than -surrounding crystals in an igneous rock. - -#### porphyroblast - -[]{#porphyroblast} - -Concept: [`porphyroblast`](https://w3id.org/isample/earthenv/essampledfeatrole/porphyroblast) - -Child of: - [`individualconstituent`](#individualconstituent) - -Sampled feature is a crystal that is significantly larger than -surrounding crystals in a metamorphic rock. - -### rock body - -[]{#rockbody} - -Concept: [`rockbody`](https://w3id.org/isample/earthenv/essampledfeatrole/rockbody) - -Child of: - [`sampledfeaturepart`](#sampledfeaturepart) - -sampled feature is representative of a rock body, i.e. it represents -the whole of the sampled body. - - diff --git a/models/generated/extensions/opencontext_material_extension.md b/models/generated/extensions/opencontext_material_extension.md deleted file mode 100644 index e1a2ae6..0000000 --- a/models/generated/extensions/opencontext_material_extension.md +++ /dev/null @@ -1,824 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "OpenContext material type extension draft" -date: "2025-12-11T02:41:34.992752+00:00" -subtitle: | - vocabulary of materials typical of archeological samples -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/opencontext_material_extension.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/opencontext_material_extension.ttl) - - -Namespace: -[`https://w3id.org/isample/opencontext/material/oc_materialsvocab`](https://w3id.org/isample/opencontext/material/oc_materialsvocab) - -**History** - -* 2024-09-13 SMR remove version number from URI - -**Concepts** - -- [anthropogenic metal](#anthropogenicmetal) - - [brass](#brass) - - [bronze](#bronze) - - [copper](#copper) - - [gold](#gold) - - [iron](#iron) - - [lead](#lead) - - [pewter](#pewter) - -- [biogenic non-organic material](#biogenicnonorganicmaterial) - - [amber](#amber) - - [bone](#bone) - - [charcoal](#charcoal) - - [coal](#coal) - - [shell](#shell) - -- [mineral](#mineral) - - [hematite](#hematite) - - [kaolin](#kaolin) - - [mica](#mica) - - [quartz](#quartz) - -- [organic material](#organicmaterial) - - [organic animal material](#organicanimalmaterial) - - [hair](#hair) - - [leather](#leather) - - [organic plant material](#organicplantmaterial) - - [plant fiber](#plantfiber) - - [wood](#wood) - -- [other anthropogenic material](#otheranthropogenicmaterial) - - [anthropogenic organic material](#anthropogenicorganicmaterial) - - [plastic (material)](#plastic) - - [ceramic clay](#ceramicclay) - - [brick clay](#brickclay) - - [bucchero](#bucchero) - - [faience](#faience) - - [porcelain](#porcelain) - - [terracotta](#terracotta) - - [terra sigilata](#terrasigilata) - - [fiber material](#fibermaterial) - - [glass](#glass) - - [paper](#paper) - - [plaster or mortar](#plasterormortar) - - [rubber](#rubber) - -- [particulate material](#particulate) - - [cinder](#cinder) - -- [rock](#rock) - - [basalt](#basalt) - - [chert](#chert) - - [flint](#flint) - - [cinder](#cinder) - - [coal](#coal) - - [dolomite](#dolomite) - - [gabbro](#gabbro) - - [greywacke](#greywacke) - - [limestone](#limestone) - - [marble](#marble) - - [obsidian](#obsidian) - - [pumice](#pumice) - - [slate](#slate) - - [travertine](#travertine) - -## anthropogenic metal - -[]{#anthropogenicmetal} - -Concept: [`anthropogenicmetal`](https://w3id.org/isample/vocabulary/material/anthropogenicmetal) - -Specimen is dominantly composed of metal that has been produced or -used by humans; subclass of anthropogenic material. Samples of -naturally occuring metallic material (e.g. native copper, gold -nuggets) should be considered mineral material. Metallic material is -material that when polished or fractured, shows a lustrous appearance, -and conducts electricity and heat relatively well. Metals are -typically malleable (they can be hammered into thin sheets) or ductile -(can be drawn into wires). The boundaries between metals, nonmetals, -and metalloids fluctuate slightly due to a lack of universally -accepted definitions of the categories involved. -(https://en.wikipedia.org/wiki/Metal). c.f. -http://purl.obolibrary.org/obo/ENVO_01001069 - -### brass - -[]{#brass} - -Concept: [`brass`](https://w3id.org/isample/opencontext/material/brass) - -Child of: - [`anthropogenicmetal`](#anthropogenicmetal) - -alloy of copper (Cu) and zinc (Zn) - -### bronze - -[]{#bronze} - -Concept: [`bronze`](https://w3id.org/isample/opencontext/material/bronze) - -Child of: - [`anthropogenicmetal`](#anthropogenicmetal) - -alloy consisting primarily of copper with subordinate tin; often -includes other metals - -### copper - -[]{#copper} - -Concept: [`copper`](https://w3id.org/isample/opencontext/material/copper) - -Child of: - [`anthropogenicmetal`](#anthropogenicmetal) - -copper metal, includes copper-rich alloys not identifiable as brass or -bronze. - -### gold - -[]{#gold} - -Concept: [`gold`](https://w3id.org/isample/opencontext/material/gold) - -Child of: - [`anthropogenicmetal`](#anthropogenicmetal) - -a chemical element with atomic number 79; a dense, soft metal that is -easily malleable and ductile. It has a melting point of 1064 degrees -Celsius and a boiling point of 2,807 degrees Celsius. (ChatGPT) - -### iron - -[]{#iron} - -Concept: [`iron`](https://w3id.org/isample/opencontext/material/iron) - -Child of: - [`anthropogenicmetal`](#anthropogenicmetal) - -Iron or iron-rich alloy -missing - -### lead - -[]{#lead} - -Concept: [`lead`](https://w3id.org/isample/opencontext/material/lead) - -Child of: - [`anthropogenicmetal`](#anthropogenicmetal) - -lead or lead-rich alloy - -### pewter - -[]{#pewter} - -Concept: [`pewter`](https://w3id.org/isample/opencontext/material/pewter) - -Child of: - [`anthropogenicmetal`](#anthropogenicmetal) - -alloy consisting of mostly tin, with antimony, minor copper or -bismuth, and sometimes silver. - - -## biogenic non-organic material - -[]{#biogenicnonorganicmaterial} - -Concept: [`biogenicnonorganicmaterial`](https://w3id.org/isample/vocabulary/material/biogenicnonorganicmaterial) - -Material produced by an organism but not composed of 'very large -molecules of biological origin.' E.g. bone, tooth, shell, coral -skeleton, - -### amber - -[]{#amber} - -Concept: [`amber`](https://w3id.org/isample/opencontext/material/amber) - -Child of: - [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) - -missing - -### bone - -[]{#bone} - -Concept: [`bone`](https://w3id.org/isample/opencontext/material/bone) - -Child of: - [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) - -missing - -### charcoal - -[]{#charcoal} - -Concept: [`charcoal`](https://w3id.org/isample/opencontext/material/charcoal) - -Child of: - [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) - -missing - -### coal - -[]{#coal} - -Concept: [`coal`](https://w3id.org/isample/opencontext/material/coal) - -Child of: - [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) - [`rock`](#rock) - -missing - -### shell - -[]{#shell} - -Concept: [`shell`](https://w3id.org/isample/opencontext/material/shell) - -Child of: - [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) - -Hard outer covering of invertebrate creatures, composed of calcareous -or chitinous material (http://vocab.getty.edu/page/aat/300011829) - - -## mineral - -[]{#mineral} - -Concept: [`mineral`](https://w3id.org/isample/vocabulary/material/mineral) - -Material consists of a single mineral or mineraloid phase. . 'A -mineral is an element or chemical compound that is normally -crystalline and that has been formed as a result of geological -processes.' (Nickel, Ernest H. (1995), The definition of a mineral, -The Canadian Mineralogist. 33 (3): 689–90). Include mineraloids. ... A -material primarily composed of some substance that is naturally -occurring, solid and stable at room temperature, representable by a -chemical formula, usually abiogenic, and that has an ordered atomic -structure. (http://purl.obolibrary.org/obo/ENVO_01000256). Comment: -the identity of a mineral species is defined by a crystal structure -and a chemical composition that might include various specific -elemental substitutions in that structure. Mineraloid: A naturally -occurring mineral-like substance that does not demonstrate -crystallinity. Mineraloids possess chemical compositions that vary -beyond the generally accepted ranges for specific minerals. Examples: -obsidian, Opal. (https://en.wikipedia.org/wiki/Mineraloid) - -### hematite - -[]{#hematite} - -Concept: [`hematite`](https://w3id.org/isample/opencontext/material/hematite) - -Child of: - [`mineral`](#mineral) - -missing - -### kaolin - -[]{#kaolin} - -Concept: [`kaolin`](https://w3id.org/isample/opencontext/material/kaolin) - -Child of: - [`mineral`](#mineral) - -missing - -### mica - -[]{#mica} - -Concept: [`mica`](https://w3id.org/isample/opencontext/material/mica) - -Child of: - [`mineral`](#mineral) - -missing - -### quartz - -[]{#quartz} - -Concept: [`quartz`](https://w3id.org/isample/opencontext/material/quartz) - -Child of: - [`mineral`](#mineral) - -missing - - -## organic material - -[]{#organicmaterial} - -Concept: [`organicmaterial`](https://w3id.org/isample/vocabulary/material/organicmaterial) - -Environmental material derived from living organisms and composed -primarily of one or more very large molecules of biological origin. -Examples: body (animal or plant), body part, fecal matter, seeds, -wood, tissue, biological fluids, biological waste, algal material, -biofilm, necromass, plankton. source: -http://purl.obolibrary.org/obo/ENVO_01000155 - -### organic animal material - -[]{#organicanimalmaterial} - -Concept: [`organicanimalmaterial`](https://w3id.org/isample/opencontext/material/organicanimalmaterial) - -Child of: - [`organicmaterial`](#organicmaterial) - -Material that is (or was) a constituent of an animal organisms, -composed primarily of one or more very large molecules of biological -origin. - -#### hair - -[]{#hair} - -Concept: [`hair`](https://w3id.org/isample/opencontext/material/hair) - -Child of: - [`organicanimalmaterial`](#organicanimalmaterial) - -Material comprising the cylindrical filaments that grow from follicles -embedded in the skin of mammals. Hair is a column of overlapping, -fused cells that are composed of the protein keratin; hair is composed -of three parts: the innermost column is the medula, the surrounding -live cells (the cortex) contain pigment, and the outermost dead -transparent cells are the cuticular scales. The portion of the hair -outside of the skin is called the shaft. Fine, closely spaced hair -that covers most of an animal's body is called fur. Dense, soft, -curled hair is called wool. Coarse, stiff hairs are called bristles, -spines, or quills. Horsehair and cattle hair have been used for -brushes, plaster binders, haircloth, and upholstery stuffing. Rabbit -hair, often called rabbit fur, has been used to make felt hats. -(http://vocab.getty.edu/page/aat/300011814) - -#### leather - -[]{#leather} - -Concept: [`leather`](https://w3id.org/isample/opencontext/material/leather) - -Child of: - [`organicanimalmaterial`](#organicanimalmaterial) - -The skin or hide of an animal that has been tanned to render it -resistant to putrefication and relatively soft and flexible when dry. -(http://vocab.getty.edu/page/aat/300011845) - -### organic plant material - -[]{#organicplantmaterial} - -Concept: [`organicplantmaterial`](https://w3id.org/isample/opencontext/material/organicplantmaterial) - -Child of: - [`organicmaterial`](#organicmaterial) - -missing - -#### plant fiber - -[]{#plantfiber} - -Concept: [`plantfiber`](https://w3id.org/isample/opencontext/material/plantfiber) - -Child of: - [`organicplantmaterial`](#organicplantmaterial) - -missing - -#### wood - -[]{#wood} - -Concept: [`wood`](https://w3id.org/isample/opencontext/material/wood) - -Child of: - [`organicplantmaterial`](#organicplantmaterial) - -missing - - -## other anthropogenic material - -[]{#otheranthropogenicmaterial} - -Concept: [`otheranthropogenicmaterial`](https://w3id.org/isample/vocabulary/material/otheranthropogenicmaterial) - -Non-metallic material produced by human activity. Organic products of -agricultural activity are both anthropogenic and organic. Include lab -preparations like XRF pellet and rock powders. Examples: ceramics, -concrete, slag, (anthropogenic) glass, mine tailing, plaster, waste. - -### anthropogenic organic material - -[]{#anthropogenicorganicmaterial} - -Concept: [`anthropogenicorganicmaterial`](https://w3id.org/isample/opencontext/material/anthropogenicorganicmaterial) - -Child of: - [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) - -Organic material manufactured by humans - -#### plastic (material) - -[]{#plastic} - -Concept: [`plastic`](https://w3id.org/isample/opencontext/material/plastic) - -Child of: - [`anthropogenicorganicmaterial`](#anthropogenicorganicmaterial) - -Synthetic or semi-synthetic material that uses organic polymers as a -main ingredient. - -### ceramic clay - -[]{#ceramicclay} - -Concept: [`ceramicclay`](https://w3id.org/isample/opencontext/material/ceramicclay) - -Child of: - [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) - -Any of the various hard, brittle, heat-resistant and corrosion- -resistant materials made by shaping and then firing an inorganic, -nonmetallic material, such as clay, at a high temperature. Common -examples are earthenware, porcelain, and brick. -(https://en.wikipedia.org/wiki/Ceramic) - -#### brick clay - -[]{#brickclay} - -Concept: [`brickclay`](https://w3id.org/isample/opencontext/material/brickclay) - -Child of: - [`ceramicclay`](#ceramicclay) - -dried or low-fired clay-rich material used to make blocks for -construction - -#### bucchero - -[]{#bucchero} - -Concept: [`bucchero`](https://w3id.org/isample/opencontext/material/bucchero) - -Child of: - [`ceramicclay`](#ceramicclay) - -ceramic with black fabric and glossy, black surface achieved through -reduction firing - -#### faience - -[]{#faience} - -Concept: [`faience`](https://w3id.org/isample/opencontext/material/faience) - -Child of: - [`ceramicclay`](#ceramicclay) - -fine white-glazed ceramic (tin oxide based glaze) - -#### porcelain - -[]{#porcelain} - -Concept: [`porcelain`](https://w3id.org/isample/opencontext/material/porcelain) - -Child of: - [`ceramicclay`](#ceramicclay) - -Kaolin rich high-fired ceramic; In China, it includes any such ware -that is highly fired enough to produce a ringing sound when struck. In -Europe, it is limited to hard-fired ceramic that is translucent. -(https://vocab.getty.edu/aat/scopeNote/45436) - -#### terracotta - -[]{#terracotta} - -Concept: [`terracotta`](https://w3id.org/isample/opencontext/material/terracotta) - -Child of: - [`ceramicclay`](#ceramicclay) - -clay-based unglazed or glazed, porous ceramic - -#### terra sigilata - -[]{#terrasigilata} - -Concept: [`terrasigilata`](https://w3id.org/isample/opencontext/material/terrasigilata) - -Child of: - [`ceramicclay`](#ceramicclay) - -Fine red Ancient Roman pottery with glossy surface slips - -### fiber material - -[]{#fibermaterial} - -Concept: [`fibermaterial`](https://w3id.org/isample/opencontext/material/fibermaterial) - -Child of: - [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) - -material composed of fibers twisted or woved togther. Fibers might be -plant material or Anthropogenic Organic material. - -### glass - -[]{#glass} - -Concept: [`glass`](https://w3id.org/isample/opencontext/material/glass) - -Child of: - [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) - -A non-crystalline, often transparent amorphous solid, most often -formed by rapid cooling (quenching) of the molten silca rich material. -(https://en.wikipedia.org/wiki/Glass) - -### paper - -[]{#paper} - -Concept: [`paper`](https://w3id.org/isample/opencontext/material/paper) - -Child of: - [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) - -thin matted or felted sheets or webs of fiber formed and dried on a -fine screen from a pulpy water suspension. The fibers may be animal, -such as hair, silk or wool, or mineral, such as asbestos, or -synthetic. However most paper is made from cellulosic plant fiber, -such as from wood pulp, grass, cotton, linen, and straw. -(http://vocab.getty.edu/page/aat/300014109) - -### plaster or mortar - -[]{#plasterormortar} - -Concept: [`plasterormortar`](https://w3id.org/isample/opencontext/material/plasterormortar) - -Child of: - [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) - -Plaster is a pasty material that hardens on drying and is used for -coating walls, ceilings, and partitions. Mortar is a similar pasty -material used for cementing bricks or block together or coating walls -in building construction. - -### rubber - -[]{#rubber} - -Concept: [`rubber`](https://w3id.org/isample/opencontext/material/rubber) - -Child of: - [`otheranthropogenicmaterial`](#otheranthropogenicmaterial) - -An elastomer, synthesized from petroleum byproducts or from latex -harvested from the rubber tree (Hevea brasiliensis). - - -## particulate material - -[]{#particulate} - -Concept: [`particulate`](https://w3id.org/isample/vocabulary/material/particulate) - -Material consists of microscopic particulate material derived by -precipitation, filtering, or settling from suspension in a fluid, e.g. -filtrate from water, deposition from atmosphere, astro material -particles. Might include mineral, organic, or biological material. -ENVO definition (ENVO_01000060) has "composed of microscopic portions -of solid or liquid material suspended in another environmental -material.", refine here to define as the solid particles, distinct -from a material in which they are suspended. A material that includes -solid or liquid particles suspended in another material would be a -dispersed_media in this scheme, not defined in ENVO. Human -manufactured particulates (e.g. rock powder) should be categorized as -'anthropogenic material' as well as 'Particulate' - -### cinder - -[]{#cinder} - -Concept: [`cinder`](https://w3id.org/isample/opencontext/material/cinder) - -Child of: - [`particulate`](#particulate) - [`rock`](#rock) - -The incombustible residue of something burnt. -(http://vocab.getty.edu/page/aat/300011788) -missing - - -## rock - -[]{#rock} - -Concept: [`rock`](https://w3id.org/isample/vocabulary/material/rock) - -Consolidated aggregate of particles (grains) of rock, mineral -(including native elements), mineraloid, or solid organic material. -Includes mineral aggregates such as granite, shale, marble; natural -glass such as obsidian; organic material formed by geologic processes -such a coal; extraterrestrial material in meteorites; and crushed -rock fragments like drill cuttings from rock. (based on -http://resource.geosciml.org/classifier/cgi/lithology/rock, same as -http://purl.obolibrary.org/obo/ENVO_00001995) - -### basalt - -[]{#basalt} - -Concept: [`basalt`](https://w3id.org/isample/opencontext/material/basalt) - -Child of: - [`rock`](#rock) - -missing - -### chert - -[]{#chert} - -Concept: [`chert`](https://w3id.org/isample/opencontext/material/chert) - -Child of: - [`rock`](#rock) - -missing - -#### flint - -[]{#flint} - -Concept: [`flint`](https://w3id.org/isample/opencontext/material/flint) - -Child of: - [`chert`](#chert) - -missing - -### cinder - -[]{#cinder} - -Concept: [`cinder`](https://w3id.org/isample/opencontext/material/cinder) - -Child of: - [`particulate`](#particulate) - [`rock`](#rock) - -The incombustible residue of something burnt. -(http://vocab.getty.edu/page/aat/300011788) -missing - -### coal - -[]{#coal} - -Concept: [`coal`](https://w3id.org/isample/opencontext/material/coal) - -Child of: - [`biogenicnonorganicmaterial`](#biogenicnonorganicmaterial) - [`rock`](#rock) - -missing - -### dolomite - -[]{#dolomite} - -Concept: [`dolomite`](https://w3id.org/isample/opencontext/material/dolomite) - -Child of: - [`rock`](#rock) - -missing - -### gabbro - -[]{#gabbro} - -Concept: [`gabbro`](https://w3id.org/isample/opencontext/material/gabbro) - -Child of: - [`rock`](#rock) - -missing - -### greywacke - -[]{#greywacke} - -Concept: [`greywacke`](https://w3id.org/isample/opencontext/material/greywacke) - -Child of: - [`rock`](#rock) - -missing - -### limestone - -[]{#limestone} - -Concept: [`limestone`](https://w3id.org/isample/opencontext/material/limestone) - -Child of: - [`rock`](#rock) - -missing - -### marble - -[]{#marble} - -Concept: [`marble`](https://w3id.org/isample/opencontext/material/marble) - -Child of: - [`rock`](#rock) - -missing - -### obsidian - -[]{#obsidian} - -Concept: [`obsidian`](https://w3id.org/isample/opencontext/material/obsidian) - -Child of: - [`rock`](#rock) - -missing - -### pumice - -[]{#pumice} - -Concept: [`pumice`](https://w3id.org/isample/opencontext/material/pumice) - -Child of: - [`rock`](#rock) - -missing - -### slate - -[]{#slate} - -Concept: [`slate`](https://w3id.org/isample/opencontext/material/slate) - -Child of: - [`rock`](#rock) - -missing - -### travertine - -[]{#travertine} - -Concept: [`travertine`](https://w3id.org/isample/opencontext/material/travertine) - -Child of: - [`rock`](#rock) - -A limestone consisting of a massive usually layered calcium carbonate -(such as aragonite or calcite) formed by deposition from spring -waters, especially from hot springs. -(https://www.mindat.org/min-39057.html) - - diff --git a/models/generated/extensions/opencontext_materialsampleobjecttype.md b/models/generated/extensions/opencontext_materialsampleobjecttype.md deleted file mode 100644 index cb0b3c6..0000000 --- a/models/generated/extensions/opencontext_materialsampleobjecttype.md +++ /dev/null @@ -1,203 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "Open Context vocabulary extension for material sample object type" -date: "2025-12-11T02:41:36.548073+00:00" -subtitle: | - categories for kinds of sample objects specific to archaeological studies - Vocabulary created based on summary of 'type' values found in OpenContext sample descriptions. This is a bottom-up vocabulary intended as a first draft and demonstration of a material sample type extension for the Open Context community in the iSamples context. Most of the categories are subclasses of msot:Artifact, except for 'bone object' which is a msot:OrganismPart. -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/opencontext_materialsampleobjecttype.ttl`](https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/opencontext_materialsampleobjecttype.ttl) - - -Namespace: -[`https://w3id.org/isample/opencontext/materialsampleobjecttype/oc_msotvocab`](https://w3id.org/isample/opencontext/materialsampleobjecttype/oc_msotvocab) - -**History** - -* 2024-09-13 SMR remove version number from URI - -**Concepts** - -- [Artifact](#artifact) - - [Architectural element](#architecturalelement) - - [Clothing](#clothing) - - [Coin](#coin) - - [Container object](#containerobject) - - [Domestic item](#domesticitem) - - [Ornament](#ornament) - - [Photograph](#photograph) - - [Pot sherd](#sherd) - - [Tile](#tile) - - [Utility item](#utilityitem) - - [Weapon](#weapon) - -- [Organism part](#organismpart) - - [Bone object](#peiceofbone) - -## Artifact - -[]{#artifact} - -Concept: [`artifact`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/artifact) - -An object made (manufactured, shaped, modified) by a human being, or -precursor hominid. Include a set of pieces belonging originally to a -single object and treated as a single specimen. - -### Architectural element - -[]{#architecturalelement} - -Concept: [`architecturalelement`](https://w3id.org/isample/opencontext/materialsampleobjecttype/architecturalelement) - -Child of: - [`artifact`](#artifact) - -Artifact that was part of a building. - -### Clothing - -[]{#clothing} - -Concept: [`clothing`](https://w3id.org/isample/opencontext/materialsampleobjecttype/clothing) - -Child of: - [`artifact`](#artifact) - -Item intended to be worn to cover the (human) body - -### Coin - -[]{#coin} - -Concept: [`coin`](https://w3id.org/isample/opencontext/materialsampleobjecttype/coin) - -Child of: - [`artifact`](#artifact) - -peice of metal issued by some authority and recognized as money. - -### Container object - -[]{#containerobject} - -Concept: [`containerobject`](https://w3id.org/isample/opencontext/materialsampleobjecttype/containerobject) - -Child of: - [`artifact`](#artifact) - -Item designed to contain some fluid, granular material, or other items -for preservation, transportation or display. - -### Domestic item - -[]{#domesticitem} - -Concept: [`domesticitem`](https://w3id.org/isample/opencontext/materialsampleobjecttype/domesticitem) - -Child of: - [`artifact`](#artifact) - -item intended for household use. - -### Ornament - -[]{#ornament} - -Concept: [`ornament`](https://w3id.org/isample/opencontext/materialsampleobjecttype/ornament) - -Child of: - [`artifact`](#artifact) - -item intended for decoration. - -### Photograph - -[]{#photograph} - -Concept: [`photograph`](https://w3id.org/isample/opencontext/materialsampleobjecttype/photograph) - -Child of: - [`artifact`](#artifact) - -image produced by the action of light on a chemically sensitive -surface, preserved on paper, glass or other physical substrate. - -### Pot sherd - -[]{#sherd} - -Concept: [`sherd`](https://w3id.org/isample/opencontext/materialsampleobjecttype/sherd) - -Child of: - [`artifact`](#artifact) - -fragment of pottery - -### Tile - -[]{#tile} - -Concept: [`tile`](https://w3id.org/isample/opencontext/materialsampleobjecttype/tile) - -Child of: - [`artifact`](#artifact) - -flat or curved piece of fired clay, stone, or concrete used especially -for roofs, floors, or walls and often for ornamental work - -### Utility item - -[]{#utilityitem} - -Concept: [`utilityitem`](https://w3id.org/isample/opencontext/materialsampleobjecttype/utilityitem) - -Child of: - [`artifact`](#artifact) - -Item intended for use in manufacture, construction, agriculture or -other work activity. - -### Weapon - -[]{#weapon} - -Concept: [`weapon`](https://w3id.org/isample/opencontext/materialsampleobjecttype/weapon) - -Child of: - [`artifact`](#artifact) - -Item for use in combat, hunting, or self defense - - -## Organism part - -[]{#organismpart} - -Concept: [`organismpart`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismpart) - -Part of an organism, e.g. a tissue sample, plant leaf, flower, bird -feather. Include internal parts not composed of organic material (e.g. -teeth, bone), and hard body parts that are not shed (hoof, horn, tusk, -claw). Hair is tricky, include here for now. Does not necessarily -imply existance of parent sample. Not fossilized; generally includes -organism parts native to deposits of Holocene to Recent age. - -### Bone object - -[]{#peiceofbone} - -Concept: [`peiceofbone`](https://w3id.org/isample/opencontext/materialsampleobjecttype/peiceofbone) - -Child of: - [`organismpart`](#organismpart) - -Sample is an individual bone or part of a bone from an animal. - - diff --git a/models/generated/extensions/readme.md b/models/generated/extensions/readme.md index 37a8299..7c77b9f 100644 --- a/models/generated/extensions/readme.md +++ b/models/generated/extensions/readme.md @@ -1 +1 @@ -this folder contains markdown output for extension vocabularies \ No newline at end of file +this folder contains markdown output for extension vocabularies diff --git a/models/generated/vocabularies/material_sample_object_type.qmd b/models/generated/vocabularies/material_sample_object_type.qmd deleted file mode 100644 index 28a2eb7..0000000 --- a/models/generated/vocabularies/material_sample_object_type.qmd +++ /dev/null @@ -1,375 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "iSamples Material Sample Object Type Vocabulary" -date: "2025-12-11T02:41:28.407856+00:00" -subtitle: | - Broad categories to specify the kind of physical thing identified as the ‘sample’. -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/material_sample_object_type.ttl`](https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/material_sample_object_type.ttl) - - -Namespace: -[`https://w3id.org/isample/vocabulary/materialsampleobjecttype/conceptscheme`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/conceptscheme) - -**History** - -* 2022-01-07 SMR Change base URI to https://w3id.org/isample/vocabulary/, setting up resolution using w3id. Make the conceptScheme and ontology. Add Dublin core imports. -* 2022-03-11 SMR change definitions from rdfs:comment to skos:definition. Minor fixes in definitions. Add skos matches to URIs from other vocabularies. -* 2022-09-30 SMR per https://github.com/isamplesorg/metadata/issues/109, change specimen to sample in vocabulary names and labels. Add 'Slurry biome aggregation' and 'Bundle biome aggregation' (github issue 110). Rename 'liquid or gas' sample type to 'fluid in container' (github issue 108). -* 2023-07-27 SMR modify base specimen type vocabulary, add 'Non biologic solid object' change broader relations in this vocab to use that as parent class where appropriate. Intention is a specimen category for solid objects that are not biologic; this subsumes 'Fossil' and 'Artifact', but excludes living organism, their parts and products. Obviously there is some overlap with Research specimens. -* 2023-11-06 SMR add missing inScheme on Non-biologic solid object and solid materal specimen. Update version number in URI to 1.0 -* 2024-04-19 SMR update language to always use 'material sample' instead of specimen or physical specimen, including in text, labels, and in the URI tokens. Edit defintions to improve clarity. -* 2024-09-13 remove version numbers from URI - -**Concepts** - -- [Material sample](#materialsample) - - [Any aggregation material sample](#anyaggregation) - - [Anthropogenic aggregation](#anthropogenicaggregation) - - [Biome aggregation sample](#biomeaggregation) - - [Bundle biome aggregation](#bundlebiomeaggregation) - - [Slurry biome aggregation](#slurrybiomeaggregation) - - [Aggregation](#genericaggregation) - - [Biological material sample](#biologicalmaterialsample) - - [Biome aggregation sample](#biomeaggregation) - - [Bundle biome aggregation](#bundlebiomeaggregation) - - [Slurry biome aggregation](#slurrybiomeaggregation) - - [Organism part](#organismpart) - - [Organism product](#organismproduct) - - [Whole organism material sample](#wholeorganism) - - [Fluid in container](#fluidincontainer) - - [Non biologic solid object](#nonbiologicsolidobject) - - [Artifact](#artifact) - - [Fossil](#fossil) - - [Other solid object](#othersolidobject) - - [Solid material sample](#solidmaterialsample) - - [Research product](#researchproduct) - - [Analytical preparation](#analyticalpreparation) - - [Experiment product](#experimentalproduct) - -## Material sample - -[]{#materialsample} - -Concept: [`materialsample`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/materialsample) - -A material entity that represents an entity of interest in whole or in -part (http://rs.tdwg.org/dwc/terms/MaterialSample). Top concept in -material sample object type hierarchy. Represents any material sample -object. - -### Any aggregation material sample - -[]{#anyaggregation} - -Concept: [`anyaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/anyaggregation) - -Child of: - [`materialsample`](#materialsample) - -Sample consists of a bunch of material fragments, not related to the -same object (e.g. not a bunch of broken pot sherds that might be -reassembled), but taken together representative of the sampled -feature. Examples: loose soil, sediment, crushed rock, particulate, -bunches of unrelated pot sherd, human production waste, filtrates and -residues. The sample requires some kind of container to keep it -together. Cores of loosely consolidated material are considered 'Solid -material specimen' when preserved such that the internal parts have -spatial relationships (e.g. upper part, lower part, sedimentary -structures). - -#### Anthropogenic aggregation - -[]{#anthropogenicaggregation} - -Concept: [`anthropogenicaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/anthropogenicaggregation) - -Child of: - [`anyaggregation`](#anyaggregation) - -An aggregate material sample consisting of fragments of material -produced by human activity, not described individually, and generally -not all originating from the same object. Includes pottery in an -excavation unit that gets an aggregate description, production waste, -production raw-materials, or other residues (broken bits of plaster -from a destroyed wall), synthetic powders. - -#### Biome aggregation sample - -[]{#biomeaggregation} - -Concept: [`biomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/biomeaggregation) - -Child of: - [`anyaggregation`](#anyaggregation) - [`biologicalmaterialsample`](#biologicalmaterialsample) - -Material sample that is an aggregation of whole or fragmentary parts -of multiple organisms, microscopic or megascopic, representative of -some sampled feature. - -##### Bundle biome aggregation - -[]{#bundlebiomeaggregation} - -Concept: [`bundlebiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/bundlebiomeaggregation) - -Child of: - [`biomeaggregation`](#biomeaggregation) - -Material sample that is an aggregation of whole organisms -representative of some biome. - -##### Slurry biome aggregation - -[]{#slurrybiomeaggregation} - -Concept: [`slurrybiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/slurrybiomeaggregation) - -Child of: - [`biomeaggregation`](#biomeaggregation) - -Material sample that consists of mixed organic and inorganic material, -including whole organisms and organism fragments. - -#### Aggregation - -[]{#genericaggregation} - -Concept: [`genericaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/genericaggregation) - -Child of: - [`anyaggregation`](#anyaggregation) - -An aggregate material sample that is not biogenic or composed of -anthropogenic material fragments. Examples: loose soil or sediment -(e.g. in a bag), rock chips, particulate filtrate or precipitate; rock -powders. - -### Biological material sample - -[]{#biologicalmaterialsample} - -Concept: [`biologicalmaterialsample`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/biologicalmaterialsample) - -Child of: - [`materialsample`](#materialsample) - -Material sample representative of one or more living organisms from a -particular biome context, megascopic or microscopic - -#### Biome aggregation sample - -[]{#biomeaggregation} - -Concept: [`biomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/biomeaggregation) - -Child of: - [`anyaggregation`](#anyaggregation) - [`biologicalmaterialsample`](#biologicalmaterialsample) - -Material sample that is an aggregation of whole or fragmentary parts -of multiple organisms, microscopic or megascopic, representative of -some sampled feature. - -##### Bundle biome aggregation - -[]{#bundlebiomeaggregation} - -Concept: [`bundlebiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/bundlebiomeaggregation) - -Child of: - [`biomeaggregation`](#biomeaggregation) - -Material sample that is an aggregation of whole organisms -representative of some biome. - -##### Slurry biome aggregation - -[]{#slurrybiomeaggregation} - -Concept: [`slurrybiomeaggregation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/slurrybiomeaggregation) - -Child of: - [`biomeaggregation`](#biomeaggregation) - -Material sample that consists of mixed organic and inorganic material, -including whole organisms and organism fragments. - -#### Organism part - -[]{#organismpart} - -Concept: [`organismpart`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismpart) - -Child of: - [`biologicalmaterialsample`](#biologicalmaterialsample) - -Material sample that is part of an organism, e.g. a tissue sample, -plant leaf, flower, bird feather. Include internal parts not composed -of organic material (e.g. teeth, bone), and hard body parts that are -not shed (hoof, horn, tusk, claw). Hair is tricky, include here for -now. Does not necessarily imply existance of parent sample. Not -fossilized; generally includes organism parts native to deposits of -Holocene to Recent age. - -#### Organism product - -[]{#organismproduct} - -Concept: [`organismproduct`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/organismproduct) - -Child of: - [`biologicalmaterialsample`](#biologicalmaterialsample) - -Material sample is a thing produced by some organism, generally not -composed of organic material or including biological tissue, e.g. -Shell, antler, egg shell, coral skeleton (organic tissue not -included), fecal matter, cocoon, web. Consider internal parts not -composed of organic material (e.g. teeth, bone) and hard body parts -that are not shed (hoof, horn, tusk) to be organism parts. - -#### Whole organism material sample - -[]{#wholeorganism} - -Concept: [`wholeorganism`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/wholeorganism) - -Child of: - [`biologicalmaterialsample`](#biologicalmaterialsample) - -Material sample consists of the bodies of one or more entire organisms -of the same species, from any kingdom. - -### Fluid in container - -[]{#fluidincontainer} - -Concept: [`fluidincontainer`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/fluidincontainer) - -Child of: - [`materialsample`](#materialsample) - -Material sample is a liquid, gas, or mixed dominantly fluid phase -material that is necessarily inside some container. Fluids might -include minor solid particles. The container is typically human made, -but also includes natural fluid containers, e.g. a fluid inclusion in -a mineral grain. Fluids might be colloids, foams, gels, or -suspensions. The sample is the fluid substance; fluid samples -collected to analyze the contained biome should be considered 'Biome -aggregation sample' - -### Non biologic solid object - -[]{#nonbiologicsolidobject} - -Concept: [`nonbiologicsolidobject`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/nonbiologicsolidobject) - -Child of: - [`materialsample`](#materialsample) - -Individual solid object, the substance of which is not formed directly -by or part of a living organism - -#### Artifact - -[]{#artifact} - -Concept: [`artifact`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/artifact) - -Child of: - [`nonbiologicsolidobject`](#nonbiologicsolidobject) - -An object made (manufactured, shaped, modified) by a human being, or -precursor hominid. Include a set of pieces belonging originally to a -single object and treated as a single sample. - -#### Fossil - -[]{#fossil} - -Concept: [`fossil`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/fossil) - -Child of: - [`nonbiologicsolidobject`](#nonbiologicsolidobject) - -Material sample is the remains or trace of one or more organisms -preserved in rock; includes whole body, body parts (usually bone or -shell), and trace fossils. An organism or organism part becomes a -fossil when it has undergone some fossilization process that entails -physical and chemical changes akin to diagenesis in a sedimentary -rock. Includes trace fossils, which are manifestations of biologic -activity preserved in a rock body (typically sedimentary), without -included preserved body parts. - -#### Other solid object - -[]{#othersolidobject} - -Concept: [`othersolidobject`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/othersolidobject) - -Child of: - [`nonbiologicsolidobject`](#nonbiologicsolidobject) - -A non-biologic solid object that is not one of the other types. - -#### Solid material sample - -[]{#solidmaterialsample} - -Concept: [`solidmaterialsample`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/solidmaterialsample) - -Child of: - [`nonbiologicsolidobject`](#nonbiologicsolidobject) - -Individual solid object, not formed directly by or part of a living -organism, that is intended to be representative of some material. - -### Research product - -[]{#researchproduct} - -Concept: [`researchproduct`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/researchproduct) - -Child of: - [`materialsample`](#materialsample) - -Material sample is a product of some research workflow, e.g. a thin -section, an XRF pellet, a grain mount, SEM stub, synthetic rock or -mineral ... In general there should be a link to a parent material -sample from which this was derived. Might be aggregation (e.g. a -synthetic material powder) or a solid object. - -#### Analytical preparation - -[]{#analyticalpreparation} - -Concept: [`analyticalpreparation`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/analyticalpreparation) - -Child of: - [`researchproduct`](#researchproduct) - -Material sample is a product of processing required for some -observation procedure, e.g. thin section, XRF bead, SEM stub, rock -powder. If identified separately, this should have a ‘parent’ link to -the original sample - -#### Experiment product - -[]{#experimentalproduct} - -Concept: [`experimentalproduct`](https://w3id.org/isample/vocabulary/materialsampleobjecttype/experimentalproduct) - -Child of: - [`researchproduct`](#researchproduct) - -Material sample that is the product of an experimental procedure (e.g. -synthetic material) - - diff --git a/models/generated/vocabularies/material_type.qmd b/models/generated/vocabularies/material_type.qmd deleted file mode 100644 index 964fda3..0000000 --- a/models/generated/vocabularies/material_type.qmd +++ /dev/null @@ -1,377 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "iSamples Materials Vocabulary" -date: "2025-12-11T02:41:26.834919+00:00" -subtitle: | - High level vocabulary to specify the kind of material that constitutes a physical sample -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/material_type.ttl`](https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/material_type.ttl) - - -Namespace: -[`https://w3id.org/isample/vocabulary/material/materialsvocabulary`](https://w3id.org/isample/vocabulary/material/materialsvocabulary) - -**History** - -* 2022-01-05 SMR version 0.9, change base uri to https://w3id.org/isample/vocabulary/material/0.9/ for testing with ESIP COR and w3id uri resolution -* 2022-03-11 SMR change definitions from rdfs:comment to skos:definition. Minor fixes to some definitions. Add skos matches to URIs from other vocabularies; 2023-11-05 version 1.0, in preparation for release. -* 2024-08-14 SMR, various updates since 2023-12: change seeAlso to closeMatch for Rock mapping to http://resource.geosciml.org/classifier/cgi/lithology/rock; minor edits to align with manuscript about the metadata schema; update vocabularies to use 'material sample' instead of 'specimen'; update schema.org namespace to http://; add provider and codeRepository in conceptScheme metadata; minor typo fixes and definition edits. -* 2024-09-13 remove version numbers from URI - -**Concepts** - -- [Material ](#material) - - [Anthropogenic material](#anyanthropogenicmaterial) - - [Anthropogenic metal material ](#anthropogenicmetal) - - [Other anthropogenic material](#otheranthropogenicmaterial) - - [Any ice](#anyice) - - [Frozen water](#waterice) - - [Biogenic non-organic material](#biogenicnonorganicmaterial) - - [Dispersed media](#dispersedmedia) - - [Natural Solid Material](#earthmaterial) - - [Mineral ](#mineral) - - [Mixed soil sediment or rock](#mixedsoilsedimentrock) - - [Particulate](#particulate) - - [Rock or sediment](#rockorsediment) - - [Rock](#rock) - - [Sediment](#sediment) - - [Soil](#soil) - - [Fluid material](#fluid) - - [Gaseous material](#gas) - - [Liquid water](#liquidwater) - - [Non-aqueous liquid material ](#nonaqueousliquid) - - [Organic material](#organicmaterial) - -## Material - -[]{#material} - -Concept: [`material`](https://w3id.org/isample/vocabulary/material/material) - -Top Concept in iSamples Material Category scheme - -### Anthropogenic material - -[]{#anyanthropogenicmaterial} - -Concept: [`anyanthropogenicmaterial`](https://w3id.org/isample/vocabulary/material/anyanthropogenicmaterial) - -Child of: - [`material`](#material) - -Material produced by human activity. - -#### Anthropogenic metal material - -[]{#anthropogenicmetal} - -Concept: [`anthropogenicmetal`](https://w3id.org/isample/vocabulary/material/anthropogenicmetal) - -Child of: - [`anyanthropogenicmaterial`](#anyanthropogenicmaterial) - -Metal that has been produced or used by humans. Samples of naturally -occurring metallic material (e.g. native copper, gold nuggets) should -be considered mineral material. Metallic material is material that -when polished or fractured, shows a lustrous appearance, and conducts -electricity and heat relatively well. Metals are typically malleable -(they can be hammered into thin sheets) or ductile (can be drawn into -wires). The boundaries between metals, nonmetals, and metalloids -fluctuate slightly due to a lack of universally accepted definitions -of the categories involved. (https://en.wikipedia.org/wiki/Metal, c.f. -http://purl.obolibrary.org/obo/ENVO_01001069) - -#### Other anthropogenic material - -[]{#otheranthropogenicmaterial} - -Concept: [`otheranthropogenicmaterial`](https://w3id.org/isample/vocabulary/material/otheranthropogenicmaterial) - -Child of: - [`anyanthropogenicmaterial`](#anyanthropogenicmaterial) - -Non-metallic material produced by human activity. Organic products of -agricultural activity are both anthropogenic and organic. Include lab -preparations like XRF pellet and rock powders. Examples: ceramics, -concrete, slag, (anthropogenic) glass, mine tailing, plaster, waste. - -### Any ice - -[]{#anyice} - -Concept: [`anyice`](https://w3id.org/isample/vocabulary/material/anyice) - -Child of: - [`material`](#material) - -a material that is in a solid state under the temperature and pressure -conditions of the preserved sample, but is a liquid or gas at Standard -Temperature and Pressure (STP). - -#### Frozen water - -[]{#waterice} - -Concept: [`waterice`](https://w3id.org/isample/vocabulary/material/waterice) - -Child of: - [`anyice`](#anyice) - -Water that is in a solid state. - -### Biogenic non-organic material - -[]{#biogenicnonorganicmaterial} - -Concept: [`biogenicnonorganicmaterial`](https://w3id.org/isample/vocabulary/material/biogenicnonorganicmaterial) - -Child of: - [`material`](#material) - -Material produced by an organism but not composed of 'very large -molecules of biological origin.' E.g. bone, tooth, shell, coral -skeleton, - -### Dispersed media - -[]{#dispersedmedia} - -Concept: [`dispersedmedia`](https://w3id.org/isample/vocabulary/material/dispersedmedia) - -Child of: - [`material`](#material) - -Material that contains discrete elements of some material dispersed in -a continuous fluid medium. The dispersed component can be a gas, a -liquid or a solid (based on -https://en.wikipedia.org/wiki/Dispersed_media). Does not include -mixtures of granular material like soil, sediment, particulate, or -solids that would be considered rock material. - -### Natural Solid Material - -[]{#earthmaterial} - -Concept: [`earthmaterial`](https://w3id.org/isample/vocabulary/material/earthmaterial) - -Child of: - [`material`](#material) - -A naturally occurring solid material that is not anthropogenic, -biogenic, or ice. - -#### Mineral - -[]{#mineral} - -Concept: [`mineral`](https://w3id.org/isample/vocabulary/material/mineral) - -Child of: - [`earthmaterial`](#earthmaterial) - -Material consists of a single mineral or mineraloid phase. 'A mineral -is an element or chemical compound that is normally crystalline and -that has been formed as a result of geological processes.' (Nickel, -Ernest H. (1995), The definition of a mineral, The Canadian -Mineralogist. 33 (3): 689–90). Include mineraloids. ... A material -primarily composed of some substance that is naturally occurring, -solid and stable at room temperature, representable by a chemical -formula, usually abiogenic, and that has an ordered atomic structure. -(http://purl.obolibrary.org/obo/ENVO_01000256). The identity of a -mineral species is defined by a crystal structure and a chemical -composition that might include various specific elemental -substitutions in that structure. Mineraloid: A naturally occurring -mineral-like substance that does not demonstrate crystallinity. -Mineraloids possess chemical compositions that vary beyond the -generally accepted ranges for specific minerals. Examples: obsidian, -Opal. (https://en.wikipedia.org/wiki/Mineraloid) - -#### Mixed soil sediment or rock - -[]{#mixedsoilsedimentrock} - -Concept: [`mixedsoilsedimentrock`](https://w3id.org/isample/vocabulary/material/mixedsoilsedimentrock) - -Child of: - [`earthmaterial`](#earthmaterial) - -Material is mixed aggregation of fragments of undifferentiated soil, -sediment or rock origin. e.g. cuttings from some boreholes (rock -fragments and caved soil or sediment). - -#### Particulate - -[]{#particulate} - -Concept: [`particulate`](https://w3id.org/isample/vocabulary/material/particulate) - -Child of: - [`earthmaterial`](#earthmaterial) - -Material consists of microscopic particulate material derived by -precipitation, filtering, or settling from suspension in a fluid, e.g. -filtrate from water, deposition from atmosphere, astro material -particles. Might include mineral, organic, or biological material. -ENVO definition (ENVO_01000060) has "composed of microscopic portions -of solid or liquid material suspended in another environmental -material." Refine here to define as the solid particles, distinct from -a material in which they are suspended. A material that includes solid -or liquid particles suspended in another material would be a -dispersed_media in this scheme, not defined in ENVO. Human -manufactured particulates (e.g. rock powder) should be categorized as -'Anthropogenic material' as well as 'Particulate' - -#### Rock or sediment - -[]{#rockorsediment} - -Concept: [`rockorsediment`](https://w3id.org/isample/vocabulary/material/rockorsediment) - -Child of: - [`earthmaterial`](#earthmaterial) - -Material is rock or sediment. For example core from boreholes that -likely penetrate sediment near the surface and rock at greater depth, -with descriptions that do not clearly distinguish non-consolidated -sediment from rock. - -##### Rock - -[]{#rock} - -Concept: [`rock`](https://w3id.org/isample/vocabulary/material/rock) - -Child of: - [`rockorsediment`](#rockorsediment) - -Consolidated aggregate of particles (grains) of rock, mineral -(including native elements), mineraloid, or solid organic material. -Includes mineral aggregates such as granite, shale, marble; natural -glass such as obsidian; organic material formed by geologic processes -such a coal; extraterrestrial material in meteorites; and crushed -rock fragments like drill cuttings from rock. (based on -http://resource.geosciml.org/classifier/cgi/lithology/rock, same as -http://purl.obolibrary.org/obo/ENVO_00001995) - -##### Sediment - -[]{#sediment} - -Concept: [`sediment`](https://w3id.org/isample/vocabulary/material/sediment) - -Child of: - [`rockorsediment`](#rockorsediment) - -Solid granular material transported by wind, water, or gravity, not -modified by interaction with biosphere or atmosphere (to differentiate -from soil). Particles might be derived by erosion of pre-existing -rock, from shell or other body parts from organisms, precipitated -chemically in the surficial environment, or generated by explosive -volcanic activity. -(http://resource.geosciml.org/classifier/cgi/lithology/sediment). -Sediment is not consolidated, i.e. the particulate constituents do not -adhere to each other strongly enough that the aggregate can be -considered a solid material in its own right. Similar to -http://purl.obolibrary.org/obo/ENVO_00002007 - -#### Soil - -[]{#soil} - -Concept: [`soil`](https://w3id.org/isample/vocabulary/material/soil) - -Child of: - [`earthmaterial`](#earthmaterial) - -Mixed granular mineral and organic matter modified by interaction -between earth material, biosphere, and atmosphere, consisting of -varying proportions of sand, silt, and clay, organic material such as -humus, gases, liquids, and a broad range of resident micro- and -macroorganisms. (https://en.wikipedia.org/wiki/Soil) Soil consists of -horizons near the Earth's surface that, in contrast to the underlying -parent material, have been altered by the interactions of climate, -relief, and living organisms over time. (http://www.nrcs.usda.gov/wps/ -portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280) -(http://purl.obolibrary.org/obo/ENVO_00001998) - -See Also: - -* [](http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280) - -### Fluid material - -[]{#fluid} - -Concept: [`fluid`](https://w3id.org/isample/vocabulary/material/fluid) - -Child of: - [`material`](#material) - -Substance that continually deforms (flows) under an applied shear -stress, or external force. Fluids are a phase of matter and include -liquids, gases and plasmas. They are substances with zero or small -shear modulus, and flow at a perceptible rate under any shear force -applied to them. (https://en.wikipedia.org/wiki/Fluid) - -#### Gaseous material - -[]{#gas} - -Concept: [`gas`](https://w3id.org/isample/vocabulary/material/gas) - -Child of: - [`fluid`](#fluid) - -Material composed of one or more chemical entities that has neither -independent shape nor volume but tends to expand indefinitely -(http://purl.obolibrary.org/obo/ENVO_01000797). Infer that the sample -is curated in some kind of container. - -#### Liquid water - -[]{#liquidwater} - -Concept: [`liquidwater`](https://w3id.org/isample/vocabulary/material/liquidwater) - -Child of: - [`fluid`](#fluid) - -A material primarily composed of dihydrogen oxide in its liquid form; -infer that the sample is curated in some kind of container. - -#### Non-aqueous liquid material - -[]{#nonaqueousliquid} - -Concept: [`nonaqueousliquid`](https://w3id.org/isample/vocabulary/material/nonaqueousliquid) - -Child of: - [`fluid`](#fluid) - -Liquid composed dominantly of material other than water. Includes -liquids that do not fit in any other category. E.g. alcohol, -petroleum. - -### Organic material - -[]{#organicmaterial} - -Concept: [`organicmaterial`](https://w3id.org/isample/vocabulary/material/organicmaterial) - -Child of: - [`material`](#material) - -Material derived from living organisms and composed primarily of one -or more very large molecules of biological origin. Examples: body -(animal or plant), body part, fecal matter, seeds, wood, tissue, -biological fluids, biological waste, algal material, biofilm, -necromass, plankton. source: -http://purl.obolibrary.org/obo/ENVO_01000155 - - diff --git a/models/generated/vocabularies/sampled_feature_type.qmd b/models/generated/vocabularies/sampled_feature_type.qmd deleted file mode 100644 index da28979..0000000 --- a/models/generated/vocabularies/sampled_feature_type.qmd +++ /dev/null @@ -1,310 +0,0 @@ ---- -comment: | - WARNING: This file is generated. Any edits will be lost! -title: "Sampled Feature Type vocabulary" -date: "2025-12-11T02:41:27.623699+00:00" -subtitle: | - Categories to specify the broad context that a sample is intended to represent. -execute: - echo: false -categories: ["vocabulary"] ---- - -Source: -[`https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/sampled_feature_type.ttl`](https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/sampled_feature_type.ttl) - - -Namespace: -[`https://w3id.org/isample/vocabulary/sampledfeature/sampledfeaturevocabulary`](https://w3id.org/isample/vocabulary/sampledfeature/sampledfeaturevocabulary) - -**History** - -* 2021-07-09 Remove Marine biome, Subaerial terrestrial environment, Subaqueous terrestrial environment per github issue https://github.com/isamplesorg/metadata/issues/41. Make Experiment setting and Laboratory or curatorial environment subclasses of Active human occupation site. -* 2021-12-10 SMR add missing skos:inScheme statements -* 2022-01-07 SMR change to https://w3id.org/isample/ uri base, make the ConceptScheme an ontology as well. For uploading to ESIP COR and w3id resolution redirect set up. Add some mappings to other ontologies using seeAlso, closeMatch, narrowMatch. -* 2022-03-11 SMR change definitions from rdfs:comment to skos:definition. Minor fixes in definitions. Add skos matches to URIs from other vocabularies. Fix typo in glacierenvrionment URI (changed the URI to glacierenvironment) -* 2022-09-07 SMR update some of the skos mappings to other vocabularies; remove references to other vocabularies as NamedIndividual. Remove rocksample class, it was not linked in hierarchy and inconsistent with design. -* 2022-09-30 add biological entity as sampled feature, per issue https://github.com/isamplesorg/metadata/issues/107. This update was lost at some point and added back in 2022-12-09. -* 2023-11-05 SMR update version to 1.0, prep for release -* 2024-04-19 SMR update definitions to remove use of 'specimen'. Edit some definitions for better clarity -* 2024-09-13 remove version numbers from URI - -**Concepts** - -- [Any sampled feature](#anysampledfeature) - - [Anthropogenic environment](#anthropogenicenvironment) - - [Active human occupation site](#activehumanoccupationsite) - - [Experiment setting](#experimentsetting) - - [Laboratory or curatorial environment](#laboratorycuratorialenvironment) - - [Site of past human activities](#pasthumanoccupationsite) - - [Biological entity](#biologicalentity) - - [Earth environment](#earthenvironment) - - [Atmosphere](#atmosphere) - - [Earth interior](#earthinterior) - - [Earth surface](#earthsurface) - - [Lake river or stream bottom](#lakeriverstreambottom) - - [Marine water body bottom](#marinewaterbodybottom) - - [Subaerial surface environment](#subaerialsurfaceenvironment) - - [Glacier environment](#glacierenvironment) - - [Subsurface fluid reservoir](#subsurfacefluidreservoir) - - [Water body](#waterbody) - - [Marine environment](#marinewaterbody) - - [Terrestrial water body](#terrestrialwaterbody) - - [Extraterrestrial environment](#extraterrestrialenvironment) - -## Any sampled feature - -[]{#anysampledfeature} - -Concept: [`anysampledfeature`](https://w3id.org/isample/vocabulary/sampledfeature/anysampledfeature) - -Any thing that can be sampled. Top concept in sampled feature type -vocabulary. - -### Anthropogenic environment - -[]{#anthropogenicenvironment} - -Concept: [`anthropogenicenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/anthropogenicenvironment) - -Child of: - [`anysampledfeature`](#anysampledfeature) - -Sampled feature is produced by or related to human activity past or -present. - -#### Active human occupation site - -[]{#activehumanoccupationsite} - -Concept: [`activehumanoccupationsite`](https://w3id.org/isample/vocabulary/sampledfeature/activehumanoccupationsite) - -Child of: - [`anthropogenicenvironment`](#anthropogenicenvironment) - -sampled feature is a site at which there are ongoing human activities - -##### Experiment setting - -[]{#experimentsetting} - -Concept: [`experimentsetting`](https://w3id.org/isample/vocabulary/sampledfeature/experimentsetting) - -Child of: - [`activehumanoccupationsite`](#activehumanoccupationsite) - -Sampled feature is an experimental set up that produced the sample; -the sample is the product of the experiment. - -##### Laboratory or curatorial environment - -[]{#laboratorycuratorialenvironment} - -Concept: [`laboratorycuratorialenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/laboratorycuratorialenvironment) - -Child of: - [`activehumanoccupationsite`](#activehumanoccupationsite) - -Sampled feature is a laboratory or other research site, collected with -intention of characterizing the environment in which data are -collected or other research conducted, that might affect results or -safety; e.g. lab blank measurements. - -#### Site of past human activities - -[]{#pasthumanoccupationsite} - -Concept: [`pasthumanoccupationsite`](https://w3id.org/isample/vocabulary/sampledfeature/pasthumanoccupationsite) - -Child of: - [`anthropogenicenvironment`](#anthropogenicenvironment) - -sampled feature is a place where humans have been and left evidence of -their activity. Includes prehistoric and paleo hominid sites - -### Biological entity - -[]{#biologicalentity} - -Concept: [`biologicalentity`](https://w3id.org/isample/vocabulary/sampledfeature/biologicalentity) - -Child of: - [`anysampledfeature`](#anysampledfeature) - -Sampled feature is an organism. Use for samples that represent some -species of organism as the proximate sampled feature, not the -environment that the organism inhabits. - -### Earth environment - -[]{#earthenvironment} - -Concept: [`earthenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/earthenvironment) - -Child of: - [`anysampledfeature`](#anysampledfeature) - -Sampled feature is the natural Earth environment - -See Also: - -* [](http://purl.bioontology.org/ontology/MESH/D004777) -* [](http://semanticscience.org/resource/SIO_000955) - -#### Atmosphere - -[]{#atmosphere} - -Concept: [`atmosphere`](https://w3id.org/isample/vocabulary/sampledfeature/atmosphere) - -Child of: - [`earthenvironment`](#earthenvironment) - -Sampled feature is the Earth's atmosphere - -See Also: - -* [obo:ENVO_01000267](http://purl.obolibrary.org/obo/ENVO_01000267) -* [obo:RBO_00000018](http://purl.obolibrary.org/obo/RBO_00000018) - -#### Earth interior - -[]{#earthinterior} - -Concept: [`earthinterior`](https://w3id.org/isample/vocabulary/sampledfeature/earthinterior) - -Child of: - [`earthenvironment`](#earthenvironment) - -Sampled feature is solid material from within the Earth - -#### Earth surface - -[]{#earthsurface} - -Concept: [`earthsurface`](https://w3id.org/isample/vocabulary/sampledfeature/earthsurface) - -Child of: - [`earthenvironment`](#earthenvironment) - -Sampled feature is the interface between solid earth and hydrosphere -or atmosphere. Includes samples representing things collected on the -surface, in the uppermost part of the material below the surface, or -air or water directly at the contact with the Earth surface. - -##### Lake river or stream bottom - -[]{#lakeriverstreambottom} - -Concept: [`lakeriverstreambottom`](https://w3id.org/isample/vocabulary/sampledfeature/lakeriverstreambottom) - -Child of: - [`earthsurface`](#earthsurface) - -Sampled feature is the interface between the solid Earth interface and -a lake or flowing water body. - -##### Marine water body bottom - -[]{#marinewaterbodybottom} - -Concept: [`marinewaterbodybottom`](https://w3id.org/isample/vocabulary/sampledfeature/marinewaterbodybottom) - -Child of: - [`earthsurface`](#earthsurface) - -Sampled feature is the interface between the solid Earth and a marine -or brackish water body. Includes benthic boundary layer: the bottom -layer of water and the uppermost layer of sediment directly influenced -by the overlying water. - -##### Subaerial surface environment - -[]{#subaerialsurfaceenvironment} - -Concept: [`subaerialsurfaceenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/subaerialsurfaceenvironment) - -Child of: - [`earthsurface`](#earthsurface) - -sampled feature is the interface between solid Earth and atmosphere. -Sample is collected on the surface, or immediately below surface (zone -of bioturbation). Include soil and recently deposited subaerial -sediment at the surface. - -#### Glacier environment - -[]{#glacierenvironment} - -Concept: [`glacierenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/glacierenvironment) - -Child of: - [`earthenvironment`](#earthenvironment) - -Sampled feature is a glacier, ice sheet, ice shelf, iceberg, or rock -or water directly under or on top of such ice. - -#### Subsurface fluid reservoir - -[]{#subsurfacefluidreservoir} - -Concept: [`subsurfacefluidreservoir`](https://w3id.org/isample/vocabulary/sampledfeature/subsurfacefluidreservoir) - -Child of: - [`earthenvironment`](#earthenvironment) - -Sampled feature is fluid that resides in fractures, intergranular -porosity or other open space in the solid earth. - -#### Water body - -[]{#waterbody} - -Concept: [`waterbody`](https://w3id.org/isample/vocabulary/sampledfeature/waterbody) - -Child of: - [`earthenvironment`](#earthenvironment) - -Sampled feature is the Earth's hydrosphere. - -##### Marine environment - -[]{#marinewaterbody} - -Concept: [`marinewaterbody`](https://w3id.org/isample/vocabulary/sampledfeature/marinewaterbody) - -Child of: - [`waterbody`](#waterbody) - -Sampled feature is the marine hydrosphere. - -See Also: - -* [obo:ENVO_01000686](http://purl.obolibrary.org/obo/ENVO_01000686) - -##### Terrestrial water body - -[]{#terrestrialwaterbody} - -Concept: [`terrestrialwaterbody`](https://w3id.org/isample/vocabulary/sampledfeature/terrestrialwaterbody) - -Child of: - [`waterbody`](#waterbody) - -Sampled feature is terrestrial hydrosphere-- lake, other standing -water, or a flowing water body (river, stream..). Include saline water -in terrestrial evaporite environments. - -### Extraterrestrial environment - -[]{#extraterrestrialenvironment} - -Concept: [`extraterrestrialenvironment`](https://w3id.org/isample/vocabulary/sampledfeature/extraterrestrialenvironment) - -Child of: - [`anysampledfeature`](#anysampledfeature) - -Sampled feature is the environment outside of solid earth, -hydrosphere, or atmosphere. - - diff --git a/scripts/generate_vocab_docs.sh b/scripts/generate_vocab_docs.sh index b93ca72..5eff275 100755 --- a/scripts/generate_vocab_docs.sh +++ b/scripts/generate_vocab_docs.sh @@ -6,7 +6,6 @@ # get the core sample type vocabularies SCRIPT_FOLDER="$(dirname ${0})" -#SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata/develop/src/vocabularies/" SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/" @@ -17,7 +16,6 @@ for src in ${SOURCES[@]}; do fname="${src%%.*}.qmd" echo "Generating ${fname}..." python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" -# vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" done # @@ -36,7 +34,6 @@ for src in ${SOURCES[@]}; do fname="${src%%.*}.md" echo "Generating ${fname}..." python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" -# vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" done SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/" @@ -47,7 +44,6 @@ for src in ${SOURCES[@]}; do fname="${src%%.*}.md" echo "Generating ${fname}..." python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" -# vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" done SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_biology/main/vocabulary/" @@ -58,7 +54,6 @@ for src in ${SOURCES[@]}; do fname="${src%%.*}.md" echo "Generating ${fname}..." python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" -# vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}" done echo "Done."