diff --git a/docker/run-local.sh b/docker/run-local.sh
index e5dc61d..2b7869b 100755
--- a/docker/run-local.sh
+++ b/docker/run-local.sh
@@ -27,4 +27,4 @@ if [ ! -d "$S_DOC_DIR/docs" ]
echo "docs directory expected, but not found at $S_DOC_DIR/docs"; exit 1;
fi
-docker run -it -p4000:4000 -v $S_DOC_DIR:/software-docs github-pages-server_local:latest
+docker run -it -p4000:4000 -v $S_DOC_DIR:/software-docs hubmap/github-pages-server
\ No newline at end of file
diff --git a/docs/avr/example-avrs-v2.tsv b/docs/avr/example-avrs-v2.tsv
index ee34b43..2b3242b 100644
--- a/docs/avr/example-avrs-v2.tsv
+++ b/docs/avr/example-avrs-v2.tsv
@@ -1,2 +1,2 @@
-uniprot_accession_number hgnc_id target_symbol host isotype clonality clone_id vendor catalog_number lot_number recombinant concentration_value dilution_factor conjugate rrid method tissue_preservation cycle_number fluorescent_reporter protocol_doi manuscript_doi author_orcids vendor_affiliation organ organ_uberon_id antigen_retrieval omap_id avr_pdf_filename previous_version_id metadata_schema_id
-P04637 HGNC:11998 PDCD1 Mouse IgG2b monoclonal DO-7 Dako M7001 20082640 No 2.5 Cy5 AB_2206626 Cell DIVE FFPE 10 https://dx.doi.org/10.17504/protocols.io.bqjimuke https://doi.org/10.1101/2022.03.30.486438 0000-0001-7524-8260 Dako skin UBERON:0002097 6 p53_AVR.pdf 677908ff-24b6-4585-a324-c1d71284b5d0
+uniprot_accession_number hgnc_id target_symbol host isotype clonality clone_id vendor catalog_number lot_number recombinant concentration_value dilution_factor conjugate rrid method tissue_preservation cycle_number fluorescent_reporter protocol_doi manuscript_doi author_orcids vendor_affiliation organ organ_uberon_id antigen_retrieval omap_id avr_pdf_filename previous_version_id metadata_schema_id constorium
+P04637 HGNC:11998 PDCD1 Mouse IgG2b monoclonal DO-7 Dako M7001 20082640 No 2.5 Cy5 AB_2206626 Cell DIVE FFPE 10 https://dx.doi.org/10.17504/protocols.io.bqjimuke https://doi.org/10.1101/2022.03.30.486438 0000-0001-7524-8260 Dako skin UBERON:0002097 6 p53_AVR.pdf 677908ff-24b6-4585-a324-c1d71284b5d0 HuBMAP
\ No newline at end of file
diff --git a/docs/avr/tsv-format-v2.md b/docs/avr/tsv-format-v2.md
index 46858d3..b73117b 100644
--- a/docs/avr/tsv-format-v2.md
+++ b/docs/avr/tsv-format-v2.md
@@ -1,39 +1,45 @@
---
layout: page
---
+
# HuBMAP Antibody Validation Report Structure
-With each submission of AVR documents associated header/metadata information must be include for each AVR document. This information is provided as a .tsv file. It is recommended to start with the blank (header only) [template tsv file](/avr/avr-template-v2.tsv), use Excel or other spreadsheet to enter the data, then export as a comma separated value (tsv) file. An example [example AVR tsv file](/avr/example-avrs-v2.tsv) is also available. All columns in the tsv file are required, with the definitions of the columns here:
+With each submission of AVR documents associated header/metadata information must be include for each AVR document. This
+information is provided as a .tsv file. It is recommended to start with the blank (header
+only) [template tsv file](/avr/avr-template-v2.tsv), use Excel or other spreadsheet to enter the data, then export as a
+comma separated value (tsv) file. An example [example AVR tsv file](/avr/example-avrs-v2.tsv) is also available. All
+columns in the tsv file are required, with the definitions of the columns here:
-| attribute (tsv column) | description |
-|--------------------------|--------------------------------------------------------------------------------|
-| uniprot_accession_number | This can typically be found on the vendor’s website, but can also be found by searching UniProt.org directly. Please note that different species have different UniProt accession numbers for the same protein. If your data was acquired using human tissue, be sure you are choosing the UniProt accession for the human protein. |
-|hgnc_id | Gene identification number from Human Gene Ontology Nomenclature Committee (HGNC) https://www.genenames.org/ encoding the target protein. HGNC:####|
-|target_symbol | This is the symbol of the protein that the antibody is targeting. Please list the UniProt protein name. This may be different from the common name for the protein. |
-|isotype | Describes the antibody isotype. Please write out any symbols. (e.g. IgG, IgG1, IgG1 kappa)|
-| host | This is the species that was used to generate the antibody (e.g. mouse, rabbit, etc). |
-|clonality| This will be either Monoclonal or Polyclonal.|
-|clone_id | A unique identifier for a laboratory-generated antibody produced either by hybridoma cells or through recombinant DNA technology.|
-|vendor | This is the company that sells the antibody. |
-|catalog_number | Provides catalog number from vendor for the source of the antibody.|
-|lot_number | This is the lot number for the antibody that was validated. |
-|recombinant | Simple Yes or No if the antibody was recombinant. Recombinant antibodies (rAbs) are monoclonal antibodies which are generated in vitro using synthetic genes.|
-|concentration_value | Provides a recommended usage in standardized units (μg/mL). Numeric only (units standardized) If providing dilution instead, leave this field blank. Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP). |
-|dilution_factor | Provides a recommended dilution factor. If providing a concentration instead, leave this field blank. (e.g. for 1:100 dilution put "100" for the dilution factor): Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP).|
-|conjugate | Specifies addition to the antibody (e.g., fluorophore, heavy metal, oligonucleotide) enabling detection, if applicable. If no conjugate, leave blank.|
-|rrid | This can usually be found on the vendor’s website, but can also be found by searching at https://scicrunch.org/resources/Antibodies/search or htps://antibodyregistry.org. If there is no RRID, you can create one here: https://scicrunch.org/resources/about/resource. |
-|method | This is the downstream assay that was used (e.g. CODEX, MIBI, etc). |
-|tissue_preservation | Preservation technique used. If fixative other than formalin, indicate the percentage of fixative indicated (e.g., 1% or 4%). Use a common abbreviation format (e.g., FFPE for formalin fixed paraffin embedded).|
-|protocol_doi | All validation pipelines need an accompanying protocol on protocols.io. or another open protocol repository. Details the protocol used to validate the antibody, including positive and negative controls and example images. If the validation procedure is the same for all antibodies your which lab tests, then a single protocol can be used. If validation procedures differ, then different methods will need different validation protocols. |
-|manuscript_doi | DOI for the published manuscript that details the use of the antibody and the associated OMAP.|
-| author_orcids | This is needed for whomever is submitting the validation data. This will be used to differentiate the same antibodies being tested across different groups. Identifies the individuals who validated the antibody used in the assay; Format ####-####-####-#### (the last digit may be X) See https://info.orcid.org/researchers/ |
-| vendor_affiliation | Identities whether the antibody validation was done by commercial entity (antibody vendor or multiplexed technology provider). Vendor name. If not applicable, please leave this field blank. (e.g. Cell Signaling Technology, Bio-Techne, Abcam, Biolegend, Akoya Biosciences, Leica Microsystems)|
-| organ | This is the tissue that was used to acquire the validation data. This should be the same tissue that was used in the downstream assay. |
-|organ_uberon_id | Uberon multi-species anatomy ontology ID for organ (e.g. for kidney UBERON:0002113). Accessible via the Ontology look-up service (OLS): https://www.ebi.ac.uk/ols/search?ontology=uberon |
-| antigen_retrieval | If applicable, indicate general conditions under which antigen retrieval was performed. Additional details should be available in the referenced protocol (see protocol_doi field).Required format: pH values; if multiple, separate by commas. |
-| avr_pdf_filename | The name of the corresponding AVR document in PDF format that this row of metadata is associated with. This name must match the file uploaded in the Antibody PDF section of the AVR upload screen during submission. An example AVR document can be found here.|
-| omap_id | Unique identifier assigned to Organ Mapping Antibody Panel (OMAP) at time of publication. OMAP with number based on date created (e.g. OMAP-1, OMAP-2) (optional field)|
-| cycle_number | Identifies the cycle number in which an antibody was either applied to the tissue or, in the case of CODEX,visualized with a fluorescent reporter. For non-cyclic methods use 1 for all cycles. Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP).|
-|fluorescent_reporter | For indirect visualization (e.g., oligo-conjugated antibodies), define the fluorescent reporter utilized in the corresponding cycle. For metal or fluorophore-conjugated antibodies, please leave blank. Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP).|
-| previous_version_id | The HuBMAP ID for the Antibody Validation Report that this upload is a revision of if applicable.|
-| metadata_schema_id | The schema ID for the Cedar template used to validate the fields in the TSV. The ID must be used for every row. For the AVR, the ID is 677908ff-24b6-4585-a324-c1d71284b5d0. This template may be viewed [here](https://cedar.metadatacenter.org/templates/edit/https://repo.metadatacenter.org/templates/677908ff-24b6-4585-a324-c1d71284b5d0?folderId=https:%2F%2Frepo.metadatacenter.org%2Ffolders%2F98c178d0-562e-4b04-b2b5-6e65ee6f9f58). A Cedar account is required to view the template.
\ No newline at end of file
+| attribute (tsv column) | description |
+|--------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| uniprot_accession_number | This can typically be found on the vendor’s website, but can also be found by searching UniProt.org directly. Please note that different species have different UniProt accession numbers for the same protein. If your data was acquired using human tissue, be sure you are choosing the UniProt accession for the human protein. |
+| hgnc_id | Gene identification number from Human Gene Ontology Nomenclature Committee (HGNC) https://www.genenames.org/ encoding the target protein. HGNC:#### |
+| target_symbol | This is the symbol of the protein that the antibody is targeting. Please list the UniProt protein name. This may be different from the common name for the protein. |
+| isotype | Describes the antibody isotype. Please write out any symbols. (e.g. IgG, IgG1, IgG1 kappa) |
+| host | This is the species that was used to generate the antibody (e.g. mouse, rabbit, etc). |
+| clonality | This will be either Monoclonal or Polyclonal. |
+| clone_id | A unique identifier for a laboratory-generated antibody produced either by hybridoma cells or through recombinant DNA technology. |
+| vendor | This is the company that sells the antibody. |
+| catalog_number | Provides catalog number from vendor for the source of the antibody. |
+| lot_number | This is the lot number for the antibody that was validated. |
+| recombinant | Simple Yes or No if the antibody was recombinant. Recombinant antibodies (rAbs) are monoclonal antibodies which are generated in vitro using synthetic genes. |
+| concentration_value | Provides a recommended usage in standardized units (μg/mL). Numeric only (units standardized) If providing dilution instead, leave this field blank. Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP). |
+| dilution_factor | Provides a recommended dilution factor. If providing a concentration instead, leave this field blank. (e.g. for 1:100 dilution put "100" for the dilution factor): Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP). |
+| conjugate | Specifies addition to the antibody (e.g., fluorophore, heavy metal, oligonucleotide) enabling detection, if applicable. If no conjugate, leave blank. |
+| rrid | This can usually be found on the vendor’s website, but can also be found by searching at https://scicrunch.org/resources/Antibodies/search or htps://antibodyregistry.org. If there is no RRID, you can create one here: https://scicrunch.org/resources/about/resource. |
+| method | This is the downstream assay that was used (e.g. CODEX, MIBI, etc). |
+| tissue_preservation | Preservation technique used. If fixative other than formalin, indicate the percentage of fixative indicated (e.g., 1% or 4%). Use a common abbreviation format (e.g., FFPE for formalin fixed paraffin embedded). |
+| protocol_doi | All validation pipelines need an accompanying protocol on protocols.io. or another open protocol repository. Details the protocol used to validate the antibody, including positive and negative controls and example images. If the validation procedure is the same for all antibodies your which lab tests, then a single protocol can be used. If validation procedures differ, then different methods will need different validation protocols. |
+| manuscript_doi | DOI for the published manuscript that details the use of the antibody and the associated OMAP. |
+| author_orcids | This is needed for whomever is submitting the validation data. This will be used to differentiate the same antibodies being tested across different groups. Identifies the individuals who validated the antibody used in the assay; Format ####-####-####-#### (the last digit may be X) See https://info.orcid.org/researchers/ |
+| vendor_affiliation | Identities whether the antibody validation was done by commercial entity (antibody vendor or multiplexed technology provider). Vendor name. If not applicable, please leave this field blank. (e.g. Cell Signaling Technology, Bio-Techne, Abcam, Biolegend, Akoya Biosciences, Leica Microsystems) |
+| organ | This is the tissue that was used to acquire the validation data. This should be the same tissue that was used in the downstream assay. |
+| organ_uberon_id | Uberon multi-species anatomy ontology ID for organ (e.g. for kidney UBERON:0002113). Accessible via the Ontology look-up service (OLS): https://www.ebi.ac.uk/ols/search?ontology=uberon |
+| antigen_retrieval | If applicable, indicate general conditions under which antigen retrieval was performed. Additional details should be available in the referenced protocol (see protocol_doi field).Required format: pH values; if multiple, separate by commas. |
+| avr_pdf_filename | The name of the corresponding AVR document in PDF format that this row of metadata is associated with. This name must match the file uploaded in the Antibody PDF section of the AVR upload screen during submission. An example AVR document can be found here. |
+| omap_id | Unique identifier assigned to Organ Mapping Antibody Panel (OMAP) at time of publication. OMAP with number based on date created (e.g. OMAP-1, OMAP-2) (optional field) |
+| cycle_number | Identifies the cycle number in which an antibody was either applied to the tissue or, in the case of CODEX,visualized with a fluorescent reporter. For non-cyclic methods use 1 for all cycles. Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP). |
+| fluorescent_reporter | For indirect visualization (e.g., oligo-conjugated antibodies), define the fluorescent reporter utilized in the corresponding cycle. For metal or fluorophore-conjugated antibodies, please leave blank. Required field if AVR is part of an Organ Mapping Antibody Panel (OMAP). |
+| previous_version_id | The HuBMAP ID for the Antibody Validation Report that this upload is a revision of if applicable. |
+| metadata_schema_id | The schema ID for the Cedar template used to validate the fields in the TSV. The ID must be used for every row. For the AVR, the ID is 677908ff-24b6-4585-a324-c1d71284b5d0. This template may be viewed [here](https://cedar.metadatacenter.org/templates/edit/https://repo.metadatacenter.org/templates/677908ff-24b6-4585-a324-c1d71284b5d0?folderId=https:%2F%2Frepo.metadatacenter.org%2Ffolders%2F98c178d0-562e-4b04-b2b5-6e65ee6f9f58). A Cedar account is required to view the template. |
+| consortium | The consortium or project this report is associated with (e.g. HuBMAP, SenNet, KPMP). |
\ No newline at end of file