GO slim?

[grace-ac]

I am hoping to get GO slims to categorize into higher level groups

The link to one that I have from a long long time ago no longer exists http://owl.fish.washington.edu/halfshell/bu-alanine-wd/17-07-20/GO-GOslim.sorted

[grace-ac]

I see there's a bunch of options on this website: https://geneontology.org/docs/go-subset-guide/

[sr320]

Did you check handbook?

…

On Mon, Nov 3, 2025 at 6:02 PM Grace Crandall ***@***.***> wrote: *grace-ac* left a comment (RobertsLab/resources#2369) <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2369*issuecomment-3483395269__;Iw!!K-Hz7m0Vt54!hpRnd5PCQut25aUL87MQdCi60ENijzAlF3z0xOxSLl-AwtvdcT00WXoCv6HhhIRgG4twFV8a5Oh4S0-OPEVJ0rc$> I see there's a bunch of options on this website: https://geneontology.org/docs/go-subset-guide/ <https://urldefense.com/v3/__https://geneontology.org/docs/go-subset-guide/__;!!K-Hz7m0Vt54!hpRnd5PCQut25aUL87MQdCi60ENijzAlF3z0xOxSLl-AwtvdcT00WXoCv6HhhIRgG4twFV8a5Oh4S0-OAlj6V4A$> — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2369*issuecomment-3483395269__;Iw!!K-Hz7m0Vt54!hpRnd5PCQut25aUL87MQdCi60ENijzAlF3z0xOxSLl-AwtvdcT00WXoCv6HhhIRgG4twFV8a5Oh4S0-OPEVJ0rc$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABB4PN6E53L7GBPC376NVDT3273LXAVCNFSM6AAAAACLBQJHSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTIOBTGM4TKMRWHE__;!!K-Hz7m0Vt54!hpRnd5PCQut25aUL87MQdCi60ENijzAlF3z0xOxSLl-AwtvdcT00WXoCv6HhhIRgG4twFV8a5Oh4S0-O8Q8EHfY$> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[grace-ac]

i did not...

just did!
found it in the handbook!

http://current.geneontology.org/ontology/subsets/goslim_generic.obo

[grace-ac]

following the guide in the handbook

Code: (start at 275): 33-annot-DEGlists.Rmd

Issue with code chunk at line 342

[kubu4]

Check line 309 (and 310). You're assigning paths to the variables, not the column names (which is what you want, I believe).

[grace-ac]

oooh good catch!! I fixed it, but still got the same error

[kubu4]

Need to see what that data fram looks like. Run head() and/or str() command on the data frame and post here.

[grace-ac]

'data.frame':	30969 obs. of  56 variables:
 $ transcript_id                     : chr  "g19583.t1" "g12808.t1" "g5589.t1" "g12024.t1" ...
 $ PSC.423                           : int  166 440 172 34 0 0 11012 205 0 0 ...
 $ PSC.426                           : int  78 638 0 15 0 0 7564 106 0 0 ...
 $ PSC.429                           : int  99 882 0 38 9 0 11153 172 0 0 ...
 $ PSC.432                           : int  110 788 0 3 16 0 10104 158 0 0 ...
 $ PSC.435                           : int  109 1090 38 34 32 0 8493 92 0 0 ...
 $ PSC.438                           : int  127 666 290 0 55 0 9920 160 0 0 ...
 $ PSC.441                           : int  125 494 114 8 18 0 10497 175 0 0 ...
 $ PSC.444                           : int  65 658 170 0 0 0 8941 201 0 0 ...
 $ PSC.453                           : int  165 702 1283 50 242 0 5443 280 0 0 ...
 $ PSC.456                           : int  65 834 57 20 35 0 8554 278 0 0 ...
 $ PSC.465                           : int  92 1058 14 0 8 0 10118 139 0 0 ...
 $ PSC.468                           : int  164 663 16 0 4 0 7373 160 0 0 ...
 $ PSC.519                           : int  191 818 56 117 13 0 11788 108 0 0 ...
 $ PSC.522                           : int  62 732 219 13 46 0 10008 240 0 0 ...
 $ PSC.525                           : int  292 1051 247 46 16 0 12181 468 0 0 ...
 $ PSC.528                           : int  62 701 1843 26 458 0 4815 381 0 0 ...
 $ PSC.531                           : int  208 1957 0 20 0 0 13609 47 0 0 ...
 $ PSC.534                           : int  124 1004 1241 62 518 0 6212 506 0 0 ...
 $ PSC.537                           : int  170 1376 45 17 13 0 11634 53 0 0 ...
 $ PSC.540                           : int  146 616 0 13 8 0 11590 151 0 0 ...
 $ PSC.549                           : int  219 1193 0 0 0 0 9150 115 0 0 ...
 $ PSC.552                           : int  98 373 0 15 0 0 9515 125 0 0 ...
 $ PSC.561                           : int  349 755 0 0 0 0 13106 67 0 0 ...
 $ PSC.564                           : int  138 407 94 28 45 0 5866 255 0 0 ...
 $ baseMean                          : num  140.9 NA NA NA 49.7 ...
 $ log2FoldChange                    : num  0.759 NA NA NA -3.055 ...
 $ lfcSE                             : num  0.241 NA NA NA 1.052 ...
 $ stat                              : num  3.15 NA NA NA -2.91 ...
 $ pvalue                            : num  0.00162 NA NA NA 0.00367 ...
 $ padj                              : num  0.0232 NA NA NA 0.039 ...
 $ V2                                : chr  "sp" NA "sp" "sp" ...
 $ Entry                             : chr  "P59644" NA "P80146" "Q09143" ...
 $ gene_name                         : chr  "PI5PA_MOUSE" NA "SEPR_THESR" "CTR1_MOUSE" ...
 $ V5                                : num  37.9 NA 38.5 27 NA ...
 $ V6                                : int  467 NA 314 385 NA NA 413 226 NA NA ...
 $ V7                                : int  232 NA 161 249 NA NA 272 95 NA NA ...
 $ V8                                : int  8 NA 7 8 NA NA 7 1 NA NA ...
 $ V9                                : int  4 NA 81 23 NA NA 10 1 NA NA ...
 $ V10                               : int  462 NA 377 381 NA NA 420 223 NA NA ...
 $ V11                               : int  420 NA 109 80 NA NA 4 100 NA NA ...
 $ V12                               : int  836 NA 407 458 NA NA 402 325 NA NA ...
 $ V13                               : num  8.30e-95 NA 7.71e-56 2.48e-32 NA ...
 $ V14                               : num  311 NA 191 132 NA NA 194 271 NA NA ...
 $ From                              : chr  "P59644" NA "P80146" "Q09143" ...
 $ Reviewed                          : chr  "reviewed" NA "reviewed" "reviewed" ...
 $ Entry.Name                        : chr  "PI5PA_MOUSE" NA "SEPR_THESR" "CTR1_MOUSE" ...
 $ Protein.names                     : chr  "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (EC 3.1.3.36) (Inositol polyphosphate 5-phosphatase J) (P"| __truncated__ NA "Extracellular serine proteinase (EC 3.4.21.-)" "High affinity cationic amino acid transporter 1 (CAT-1) (CAT1) (Ecotropic retroviral leukemia receptor) (Ecotro"| __truncated__ ...
 $ Gene.Names                        : chr  "Inpp5j Pib5pa" NA "" "Slc7a1 Atrc1 Rec-1" ...
 $ Organism                          : chr  "Mus musculus (Mouse)" NA "Thermus sp. (strain Rt41A)" "Mus musculus (Mouse)" ...
 $ Length                            : int  1003 NA 410 622 NA NA 522 327 NA NA ...
 $ Gene.Ontology..biological.process.: chr  "negative regulation of neuron projection development [GO:0010977]; phosphatidylinositol dephosphorylation [GO:0046856]" NA "proteolysis [GO:0006508]" "L-arginine transmembrane transport [GO:1903826]; L-histidine import across plasma membrane [GO:1903810]; L-orni"| __truncated__ ...
 $ Gene.Ontology..cellular.component.: chr  "cytoplasm [GO:0005737]; dendritic shaft [GO:0043198]; growth cone [GO:0030426]; plasma membrane [GO:0005886]; r"| __truncated__ NA "extracellular space [GO:0005615]" "apical plasma membrane [GO:0016324]; basolateral plasma membrane [GO:0016323]; membrane [GO:0016020]; protein-c"| __truncated__ ...
 $ Gene.Ontology..GO.                : chr  "cytoplasm [GO:0005737]; dendritic shaft [GO:0043198]; growth cone [GO:0030426]; plasma membrane [GO:0005886]; r"| __truncated__ NA "extracellular space [GO:0005615]; serine-type endopeptidase activity [GO:0004252]; proteolysis [GO:0006508]" "apical plasma membrane [GO:0016324]; basolateral plasma membrane [GO:0016323]; membrane [GO:0016020]; protein-c"| __truncated__ ...
 $ Gene.Ontology..molecular.function.: chr  "inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity [GO:0052659]; inositol-1,4,5-trisphosphate 5-phosphat"| __truncated__ NA "serine-type endopeptidase activity [GO:0004252]" "L-arginine transmembrane transporter activity [GO:0061459]; L-histidine transmembrane transporter activity [GO:"| __truncated__ ...
 $ Gene.Ontology.IDs                 : chr  "GO:0001726; GO:0004439; GO:0004445; GO:0005737; GO:0005886; GO:0010977; GO:0017124; GO:0030426; GO:0032587; GO:"| __truncated__ NA "GO:0004252; GO:0005615; GO:0006508" "GO:0000064; GO:0001618; GO:0005290; GO:0015189; GO:0015819; GO:0016020; GO:0016323; GO:0016324; GO:0032991; GO:"| __truncated__ ...

[kubu4]

Also, is that the appropriate way to read in a column of data? Do you have to read in the entire file as a CSV first and then you can reference the column in subsequent calls?

[sr320]

I would recommend using https://github.com/sr320/workflow-annotation

[grace-ac]

I would recommend using https://github.com/sr320/workflow-annotation

this would have me re-run blast, though, right? i already ran blast and just want to annotate to GO slim

[sr320]

correct.. but in fact this might be faster. got a url to a gene fasta you can drop here?

…

On Tue, Nov 4, 2025 at 11:31 AM Grace Crandall ***@***.***> wrote: *grace-ac* left a comment (RobertsLab/resources#2369) <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2369*issuecomment-3487709552__;Iw!!K-Hz7m0Vt54!nHwMjYQBLKNMPch48aoqAZN8ZCmv7BbWj9PzszDFMbM78KpdaZ-I3TsnXiaOxpUbKkQhzw_KJZhYvNA3jT1-y64$> I would recommend using https://github.com/sr320/workflow-annotation <https://urldefense.com/v3/__https://github.com/sr320/workflow-annotation__;!!K-Hz7m0Vt54!nHwMjYQBLKNMPch48aoqAZN8ZCmv7BbWj9PzszDFMbM78KpdaZ-I3TsnXiaOxpUbKkQhzw_KJZhYvNA3g0FniOU$> this would have me re-run blast, though, right? i already ran blast and just want to annotate to GO slim — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2369*issuecomment-3487709552__;Iw!!K-Hz7m0Vt54!nHwMjYQBLKNMPch48aoqAZN8ZCmv7BbWj9PzszDFMbM78KpdaZ-I3TsnXiaOxpUbKkQhzw_KJZhYvNA3jT1-y64$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABB4PN72ULUT6Y5ZD6RHHFL33D5JBAVCNFSM6AAAAACLBQJHSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTIOBXG4YDSNJVGI__;!!K-Hz7m0Vt54!nHwMjYQBLKNMPch48aoqAZN8ZCmv7BbWj9PzszDFMbM78KpdaZ-I3TsnXiaOxpUbKkQhzw_KJZhYvNA3GNONeRg$> . You are receiving this because you commented.Message ID: ***@***.***>

[grace-ac]

https://gannet.fish.washington.edu/seashell/bu-github/paper-pycno-sswd-2021-2022/data/augustus.hints.codingseq