Open pgaudet opened 5 years ago
This was the previous ticket: https://github.com/geneontology/amigo/issues/532#issuecomment-430349876
Note that this seems to exist in the arbre set in the release. sjcarbon@moiraine:/tmp/foo$:( grep -i -r "T1ESS4" * PTHR12623/PTHR12623.arbre:AN94:HELRO|EnsemblGenome=HelroG162517|UniProtKB=T1ESS4;
arbre line structure appears okay, no found issues in the log with collisions. As above, most of rest of family seems to load fine. However, there seem to be a couple others missing in this family.
AN84:CAEEL|WormBase=WBGene00003107|UniProtKB=Q22002;
AN90:DROME|FlyBase=FBgn0259986|UniProtKB=Q59E55;
AN94:HELRO|EnsemblGenome=HelroG162517|UniProtKB=T1ESS4;
Now, the first two appear to be missing from the AmiGO load, possibly not in the upstream file, so it's not an issue that they do not appear (naturally). The last one, what started us, appears with partial information.
bbop@wok:/home/skyhook/release/annotations$ zgrep -i "[[:space:]]T1ESS4[[:space:]]" *.gaf.gz
goa_uniprot_all.gaf.gz:UniProtKB T1ESS4 20199624 GO:0005634 GO_REF:0000002 IEA InterPro:IPR006988|InterPro:IPR006989|InterPro:IPR039040 C Uncharacterized protein 20199624|HELRODRAFT_162517 protein taxon:6412 20181103 InterPro
goa_uniprot_all.gaf.gz:UniProtKB T1ESS4 20199624 GO:0006355 GO_REF:0000002 IEA InterPro:IPR006988|InterPro:IPR039040 P Uncharacterized protein 20199624|HELRODRAFT_162517 protein taxon:6412 20181103 InterPro
goa_uniprot_all.gaf.gz:UniProtKB T1ESS4 20199624 GO:0045892 GO_REF:0000002 IEA InterPro:IPR006989 P Uncharacterized protein 20199624|HELRODRAFT_162517 protein taxon:6412 20181103 InterPro
Okay, that's all our inputs. Note that none of these are what appears in AmiGO, which is disturbing.
bbop@wok:/home/skyhook/release/products/annotations$ zgrep -i "[[:space:]]T1ESS4[[:space:]]" paint_*.gaf.gz
paint_other.gaf.gz:UniProtKB T1ESS4 HELRODRAFT_162517 GO:0006355 PMID:21873635 IBA MGI:MGI:107563|MGI:MGI:107564|PANTHER:PTN000290064 P Uncharacterized protein UniProtKB:T1ESS4|PTN002651296 protein taxon:6412 20170228 GO_Central
paint_other.gaf.gz:UniProtKB T1ESS4 HELRODRAFT_162517 GO:0005634 PMID:21873635 IBA MGI:MGI:107563|PANTHER:PTN000290064 C Uncharacterized protein UniProtKB:T1ESS4|PTN002651296 protein taxon:6412 20170228 GO_Central
paint_other_noiea.gaf.gz:UniProtKB T1ESS4 HELRODRAFT_162517 GO:0006355 PMID:21873635 IBA PANTHER:PTN000290064|MGI:MGI:107564|MGI:MGI:107563 P Uncharacterized protein UniProtKB:T1ESS4|PTN002651296 protein taxon:6412 20170228 GO_Central
paint_other_noiea.gaf.gz:UniProtKB T1ESS4 HELRODRAFT_162517 GO:0005634 PMID:21873635 IBA PANTHER:PTN000290064|MGI:MGI:107563 CUncharacterized protein UniProtKB:T1ESS4|PTN002651296 protein taxon:6412 20170228 GO_Central
paint_other-src.gaf.gz:UniProtKB T1ESS4 HELRODRAFT_162517 GO:0006355 PMID:21873635 IBA PANTHER:PTN000290064|MGI:MGI:107564|MGI:MGI:107563 P Uncharacterized protein UniProtKB:T1ESS4|PTN002651296 protein taxon:6412 20170228 GO_Central
paint_other-src.gaf.gz:UniProtKB T1ESS4 HELRODRAFT_162517 GO:0005634 PMID:21873635 IBA PANTHER:PTN000290064|MGI:MGI:107563 CUncharacterized protein UniProtKB:T1ESS4|PTN002651296 protein taxon:6412 20170228 GO_Central
Note, the ones we want are the first two--they are not in the main products due to coming in from paint_other.
I think I have it--traced through with a modified owltools. The error seems to be an off-by-one in PANTHERTree.java in readyAnnotationDataCache.
Now picked-up on snapshot
http://amigo-exp.geneontology.io/amigo/gene_product/UniProtKB:T1ESS4
Should clear on next release.
This looks done ?
I just found another gene with the PTHR missing, CG4678 Drosophila:
Can we have a query that checks that all annotations with IBA evidence also have a PTHR family?
Thanks, Pascale
@pgaudet We currently have no query framework for items in the Solr load. That would be a separate feature request.
From the current release:
bbop@wok:/tmp/foo$ grep -r "FBgn0030778" *
PTHR11532/PTHR11532.arbre:AN457:DROME|FlyBase=FBgn0030778|UniProtKB=B7Z0Z5;
@dustine32 This is interesting. In the tree files, the gene identifiers appear to be out of sync with what the GO generally uses--there appears to be a conflation with the label for the contributor (e.g. "FlyBase") and the CURIE namespace (e.g. "FB"). For the algorithm to work as it currently does, the following replacements should be made:
FlyBase
-> FB
WormBase
-> WB
The currently used CURIE namespaces for GO are:
bbop@wok:/home/skyhook/release/annotations$ zgrep --no-filename -v "^!" *.gaf.gz | cut -f 1 | sort | uniq -c | sort -n
15 PAMGO_VMD
110 NCBI_GP
183 NCBI_NP
304 ASAP
1349 SGN
1498 ComplexPortal
3639 PseudoCAP
5119 EcoGene
26627 NCBI
31587 GeneDB
47260 GR_protein
52074 JCVI_CMR
54523 PomBase
74669 dictyBase
92619 TIGR_CMR
112832 FB
118016 WB
127308 SGD
217989 ZFIN
230582 TAIR
292089 CGD
405751 MGI
436843 RGD
634197 AspGD
13534661 RNAcentral
586123510 UniProtKB
The non-CURIE gene identifiers, as they currently appear in the tree files, are:
bbop@wok:/tmp/foo$ grep "^AN" /tmp/an.txt | tr '|' '\n' | grep -v "^AN" | tr -d ';' | cut -d '=' -f 1 | sort | uniq -c | sort -n
4 Araport
45 Gene_Name
245 GeneID
592 CGD
3237 EcoGene
3820 Gene_OrderedLocusName
4314 PomBase
4581 SGD
8227 dictyBase
10324 FlyBase
10952 Gene_ORFName
12213 Xenbase
13803 WormBase
18816 RGD
19358 HGNC
20127 TAIR
20365 ZFIN
21039 MGI
175481 Gene
278029 Ensembl
472806 EnsemblGenome
1098378 UniProtKB
These should be aligned with preference to the proper CURIE namespace.
Probably mentioned above but the amigo pipeline is pulling these mismatching identifiers from here: http://data.pantherdb.org/current/globals/tree_files.tar.gz
And this is a resource I added specifically for the amigo load. So I'm thinking we can simply transform the identifier namespaces in these files to the GO-friendly CURIE's. This would mirror the same namespace transformation logic performed by the IBA GAF generation script createGAF.pl.
@kltm Is it possible to try a test run once I generate the new tarball? Let's say I'll plan on putting it here: http://data.pantherdb.org/current_test/globals/tree_files.tar.gz
@dustine32 If you can wait until next week, after our release, you could also put them in the regular location and we can see what happens in the dailies.
@kltm Sure thing, thanks!
Hello,
Looks like this one is not yet resolved but I cannot find any open ticket. See for example: http://amigo.geneontology.org/amigo/gene_product/UniProtKB:T1ESS4
This gene has IBA annotations, technically it should belong to a family.
@kltm Can you please have a look?
Thanks, Pascale