10 November 2020 PAINT Conference Call

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Discussion Topics

Default qualifiers

See https://github.com/pantherdb/fullgo_paint_update/issues/45


   BP -> involved_in
   MF -> enables
   CC -> is_active_in
   CC -> children of protein-containing complexes -> part_of


-> OK, Dustin has coded this already.

Following up on previous items

Contradictory NOT annotations

see PTHR47279 - bad example because I removed the primary annotations - but iso-2 was annotated to

  • NOT GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific

and

  • NOT GO:0006357 regulation of transcription by RNA polymerase II

(maybe this is still there - depending on the release cycles of the respective resources)

-> Anushya and Huaiyu say this is already implemented, the node is pink, Anushya will send an example => Example: PTHR23103 ACTION ITEM: Pascale to add to documentation

Mismatches Reference proteomes and MOD taxon IDs

Paul generated a spreadsheet with species with > 100 EXP annotations https://docs.google.com/spreadsheets/d/1jN2hrTkGIRNqOb1hSCX4MGSuzzXydS7C-YhUzXb01X4/edit#gid=0

I’ve highlighted in red the ones where the taxon IDs do not match between PANTHER/UniProt and GO (four total), and in yellow the ones where there is a distinct gene/protein ID space used in the GAF that we might want to double check to make sure it’s in the UniProt mapping file so we can ensure that we can match those up. I assume the standard MOD IDs will be in the mapping files, so I didn’t highlight those. I’ve also noted several other cases, where there are additional experimental GO annotations but to a distinct taxon ID. Not sure how we want to handle this.


Known issues:

  • For pombe, UniProt Reference Proteomes uses taxon:284812, while pombase uses taxon:4896 (see email exchange 'pombe taxon').
  • For Aspergillus fumigatus, the GAF is submitted by AspGD using taxID 746128, and UniProt has mapped those annotations to sequences with taxID 330879 (which NCBI shows as a child strain of 746128), so this one is similar to the S. pombe case in that UniProt uses the strain level rather than the species.
  • For Leishmania major, the GAF is submitted by GeneDB using taxID 347515, and UniProt has mapped those annotations to sequences with taxID 5664 (which NCBI shows as a parent species to strain 347515), so this one is opposite to the S. pombe case in that UniProt uses the species level rather than strain.
  • Maria Martin also write about S. cerevisiae: This is also true for S.cerevisiae where UniProt uses the reference strain S288c (taxon:559292), and there even less of the annotations are actually coming from experiments in that particular strain, yet UniProt (and SGD) annotate everything in GO to that taxon.
  • WRT species, this is what UniProt/GOA does (from Alex):

Hi Huaiyu, We are using mapping provided by aspergillusgenome.org here http://www.aspergillusgenome.org/download/External_id_mappings/ If it has mapping to UniProt accessions, which belong to strain taxID, that what is used. We don't do mappings ourself we relaying on the DB authority to assign mapping to UniProt. I guess they are doing their best to do so. In the QuickGO fro example we include descendants by default if you filter by taxID. https://www.ebi.ac.uk/QuickGO/annotations?taxonId=746128&taxonUsage=descendants I'm not sure, but perhaps similar strategy can be applied to PAINT annotations. Best regards, Alex

ACTION ITEM: Marc to check with Sandrine Pilbout at Swiss-Prot to see if taxon can be harmonized

Update on Taxon constraints

  • Dustin prepares a table at every release
  • ACTION: Dustin to check with Jim on where are the 'full' taxon constraints are, so that we use the same.

ACTION ITEM: Follow up again

New discussion points

common_name in go-reference-species.yaml is not unique

https://github.com/geneontology/go-site/issues/1564 -> We could probably just use the genus, instead of 'bacteria' => ACTION ITEM: Dustin to see if we can use 'names' from this table: http://pantherdb.org/panther/summaryStats.jsp

Review tree

PTHR42918 Lys tRNA synthetase & inflammation - see https://github.com/geneontology/go-annotation/issues/3224 How much evidence is enough ? ACTION ITEM: Assign to whoever curated the tree for review

Adding a limit for the with/from field output in the IBA GAFs ?

For example GO term GO:0007275 has a ton of descendant terms and this gene is in a large family (PTHR24416[1] - 1747 genes) so more genes to source exp annotations from.

 for example: 
  UniProtKB	P54764	EPHA4		GO:0007275	PMID:21873635	IBA	PANTHER:PTN001230349|FB:FBgn0025936|MGI:MGI:98277|ZFIN:ZDB-GENE-980526-307|MGI:MGI:95522|FB:FBgn0040505|UniProtKB:P21802|RGD:2561|RGD:2425|RGD:2621|ZFIN:ZDB-GENE-020503-1|UniProtKB:Q02763|WB:WBGene00004740|UniProtKB:Q16288|RGD:2869|ZFIN:ZDB-GENE-980526-255|WB:WBGene00006897|MGI:MGI:95294|UniProtKB:Q91987|MGI:MGI:97902|UniProtKB:P11362|UniProtKB:P30530|WB:WBGene00003007|FB:FBgn0033791|MGI:MGI:1345277|WB:WBGene00017381|ZFIN:ZDB-GENE-980526-326|WB:WBGene00000289|ZFIN:ZDB-GENE-050407-1|WB:WBGene00001184|RGD:3285|RGD:620144|MGI:MGI:95558|MGI:MGI:104294|ZFIN:ZDB-GENE-041001-112|FB:FBgn0283499|MGI:MGI:96969|UniProtKB:P04629|MGI:MGI:96433|MGI:MGI:97383|UniProtKB:P54760|MGI:MGI:99216|UniProtKB:P10721|WB:WBGene00002299|MGI:MGI:95411|MGI:MGI:104770|RGD:620486|UniProtKB:P36888|UniProtKB:P28693|ZFIN:ZDB-GENE-041014-1|RGD:628622|RGD:1305275|UniProtKB:P29317|RGD:620028|UniProtKB:P35968|UniProtKB:P07333|MGI:MGI:1096337|MGI:MGI:1347520|MGI:MGI:99611|ZFIN:ZDB-GENE-031118-121|ZFIN:ZDB-GENE-030323-1|RGD:2965|MGI:MGI:109378|ZFIN:ZDB-GENE-010126-3|RGD:61308|FB:FBgn0024245|ZFIN:ZDB-GENE-020503-2|FB:FBgn0015380|RGD:620713|MGI:MGI:98664|WB:WBGene00006896|RGD:621642|MGI:MGI:97531|ZFIN:ZDB-GENE-030918-1|UniProtKB:P54756|MGI:MGI:103305|RGD:620831|ZFIN:ZDB-GENE-030131-6458|ZFIN:ZDB-GENE-990415-65|ZFIN:ZDB-GENE-001205-1|MGI:MGI:95524|UniProtKB:P54762|WB:WBGene00006894|ZFIN:ZDB-GENE-050916-2|WB:WBGene00000898|ZFIN:ZDB-GENE-010724-10|MGI:MGI:1346037|WB:WBGene00020504|MGI:MGI:1347521|RGD:620980|MGI:MGI:97384|MGI:MGI:95559|ZFIN:ZDB-GENE-050107-1|UniProtKB:Q9PUF6|ZFIN:ZDB-GENE-060427-5|UniProtKB:F1NHC7|ZFIN:ZDB-GENE-030826-6|MGI:MGI:95278|FB:FBgn0010407|FB:FBgn0032006|UniProtKB:Q15303|ZFIN:ZDB-GENE-990415-62|RGD:3214|UniProtKB:A0A2R8QHE8|MGI:MGI:96575|FB:FBgn0285896|RGD:2611|MGI:MGI:1339758|RGD:3211|FB:FBgn0003731|ZFIN:ZDB-GENE-020503-4|MGI:MGI:97530|RGD:3213|UniProtKB:P35916|RGD:620568|MGI:MGI:95276|RGD:3556|FB:FBgn0020391|MGI:MGI:104771|RGD:1560587|FB:FBgn0003733|MGI:MGI:99906|FB:FBgn0010389|UniProtKB:P08581|MGI:MGI:95410|MGI:MGI:95561|RGD:69323|RGD:1559469|ZFIN:ZDB-GENE-070713-2|MGI:MGI:104757|MGI:MGI:95523|ZFIN:ZDB-GENE-010126-2|MGI:MGI:96965|RGD:2252|RGD:2543|WB:WBGene00016104|MGI:MGI:1347244|MGI:MGI:96677|MGI:MGI:99612|MGI:MGI:99654|WB:WBGene00003863|RGD:2556|ZFIN:ZDB-GENE-001207-7|MGI:MGI:97385|RGD:2917|WB:WBGene00006868|ZFIN:ZDB-GENE-000705-1|ZFIN:ZDB-GENE-990415-208|RGD:3082|MGI:MGI:101766|ZFIN:ZDB-GENE-071218-3|ZFIN:ZDB-GENE-050114-4|RGD:3284|FB:FBgn0003366|ZFIN:ZDB-GENE-070209-277|UniProtKB:P06213|MGI:MGI:95525|ZFIN:ZDB-GENE-990415-56|MGI:MGI:96683|ZFIN:ZDB-GENE-030918-4|FB:FBgn0011829|ZFIN:ZDB-GENE-990415-55|ZFIN:ZDB-GENE-020503-3	P	Ephrin type-A receptor 4	UniProtKB:P54764|PTN002521356	protein	taxon:9606	20201025	GO_Central	

Not sure if this is the problem annotation, but this breaks the QuickGO/GOA parser (expects fewer characters) ACTION ITEM: Pascale tell Alex that this is the data - we dont plan to change it, we export all evidence