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monarch-initiative
slimmer should return species evidence from IBA evidence
TL;DR
Expand https://api.monarchinitiative.org/api/#!/bioentityset%2Fslimmer/get_entity_set_slimmer to include taxon and taxon_label.
===
https://api.monarchinitiative.org/api/#!/bioentityset%2Fslimmer/get_entity_set_slimmer
For example for this: https://www.alliancegenome.org/gene/WB:WBGene00015203
returns IBA evidence (among others). However, the GO term: http://amigo.geneontology.org/amigo/term/GO:0010468
has a relevant species attached, which would be useful here, as well.
The biolink call is here:
https://api.monarchinitiative.org/api/bioentityset/slimmer/function?&slim=GO:0003824&slim=GO:0004872&slim=GO:0005102&slim=GO:0005215&slim=GO:0005198&slim=GO:0008092&slim=GO:0003677&slim=GO:0003723&slim=GO:0001071&slim=GO:0036094&slim=GO:0046872&slim=GO:0030246&slim=GO:0003674&slim=GO:0008283&slim=GO:0071840&slim=GO:0051179&slim=GO:0032502&slim=GO:0000003&slim=GO:0002376&slim=GO:0050877&slim=GO:0050896&slim=GO:0023052&slim=GO:0010467&slim=GO:0019538&slim=GO:0006259&slim=GO:0044281&slim=GO:0050789&slim=GO:0042592&slim=GO:0007610&slim=GO:0008150&slim=GO:0005576&slim=GO:0005737&slim=GO:0005856&slim=GO:0005739&slim=GO:0005634&slim=GO:0005694&slim=GO:0016020&slim=GO:0031982&slim=GO:0071944&slim=GO:0030054&slim=GO:0042995&slim=GO:0032991&slim=GO:0045202&slim=GO:0005575&subject=WB:WBGene00015203
The similar GO call is here:
http://golr.geneontology.org/solr/select?defType=edismax&qt=standard&indent=on&wt=json&rows=10&start=0&fl=,score&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&hl=true&hl.simple.pre=%3Cem%20class=%22hilite%22%3E&hl.snippets=1000&fq=document_category:%22annotation%22&fq=regulates_closure:%22GO:0010468%22&facet.field=aspect&facet.field=taxon_subset_closure_label&facet.field=type&facet.field=evidence_subset_closure_label&facet.field=regulates_closure_label&facet.field=annotation_class_label&facet.field=qualifier&facet.field=annotation_extension_class_closure_label&facet.field=assigned_by&facet.field=panther_family_label&q=:*&packet=1&callback_type=search&json.wrf=jQuery21400567218873571087_1527615692031&_=1527615692032
Looks like the return has taxon`` data that we could just grab directly from the closure and the taxon_label```
FYI @cmungall / @kltm From the GO meeting this morning. I think we just need to bring two additional fields through.
@deepakunni3 is this something you do when you have a moment. Important, but not urgent.
@nathandunn I don't think I follow.
The biolink API query is slimming GO terms associated to WB:WBGene00015203. Are you expecting a taxon_label and taxon_label_closure on the attached GO Terms?
The GO call highlighted above is actually a call to get just one GO term: GO:0010468. This call will return the term and its closure.
i.e. the calls are not similar.
@deepakunni3 Was just trying to find something close to see if the data was available with the realization that they are different terms.
But you are right, I'm mostly looking for the taxon and taxon_label. Closure would be fine as well, but I sense for this purpose we may not use it.
Yes, in the results for slimmer the taxon property is pinned to the gene entity, which is what you normally want. The taxon property contains id and label. The GO term itself wouldn't have the taxon since what you are getting as result is gene -> GO term association.
Unless I am misunderstanding the use-case here.
It's a misunderstanding. Yes, we do get a taxon property for the gene that has been annotated.
However, in many cases the basis for the annotation is from a second gene (what is in the GAF 'with' column) and what is returned from biolink in the "evidence__with" property. For example, the follow query: https://api.monarchinitiative.org/api/bioentityset/slimmer/function?&slim=GO:0003824&slim=GO:0004872&slim=GO:0005102&slim=GO:0005215&slim=GO:0005198&slim=GO:0008092&slim=GO:0003677&slim=GO:0003723&slim=GO:0001071&slim=GO:0036094&slim=GO:0046872&slim=GO:0030246&slim=GO:0003674&slim=GO:0008283&slim=GO:0071840&slim=GO:0051179&slim=GO:0032502&slim=GO:0000003&slim=GO:0002376&slim=GO:0050877&slim=GO:0050896&slim=GO:0023052&slim=GO:0010467&slim=GO:0019538&slim=GO:0006259&slim=GO:0044281&slim=GO:0050789&slim=GO:0042592&slim=GO:0007610&slim=GO:0008150&slim=GO:0005576&slim=GO:0005737&slim=GO:0005856&slim=GO:0005739&slim=GO:0005634&slim=GO:0005694&slim=GO:0016020&slim=GO:0031982&slim=GO:0071944&slim=GO:0030054&slim=GO:0042995&slim=GO:0032991&slim=GO:0045202&slim=GO:0005575&subject=MGI:MGI:97490
returns
- evidence_with:
[
- "MGI:MGI:1856155" ], And we have to cobble together (based on the prefix) a guess of the taxon for this gene. You'd likely have to do something similar since no one is actually providing this information. When it is a UniProt identifier it may be human, or sea anemone, or elk, or ...
Particularly for human it would be nice to get the taxon.
On Mon, Jun 4, 2018 at 1:02 PM, Deepak [email protected] wrote:
Yes, in the results for slimmer the taxon property is pinned to the gene entity, which is what you normally want. The taxon property contains id and label. The GO term itself wouldn't have the taxon since what you are getting as result is gene -> GO term association.
Unless I am misunderstanding the use-case here.
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We could do it that way, but I think that the there is a taxon for that specific evidence, as well, which is displayed on the AmiGO page I showed further down. But, maybe I misunderstood.
Nathan
On Jun 6, 2018, at 1:54 PM, Suzanna Lewis [email protected] wrote:
It's a misunderstanding. Yes, we do get a taxon property for the gene that has been annotated.
However, in many cases the basis for the annotation is from a second gene (what is in the GAF 'with' column) and what is returned from biolink in the "evidence__with" property. For example, the follow query: https://api.monarchinitiative.org/api/bioentityset/slimmer/function?&slim=GO:0003824&slim=GO:0004872&slim=GO:0005102&slim=GO:0005215&slim=GO:0005198&slim=GO:0008092&slim=GO:0003677&slim=GO:0003723&slim=GO:0001071&slim=GO:0036094&slim=GO:0046872&slim=GO:0030246&slim=GO:0003674&slim=GO:0008283&slim=GO:0071840&slim=GO:0051179&slim=GO:0032502&slim=GO:0000003&slim=GO:0002376&slim=GO:0050877&slim=GO:0050896&slim=GO:0023052&slim=GO:0010467&slim=GO:0019538&slim=GO:0006259&slim=GO:0044281&slim=GO:0050789&slim=GO:0042592&slim=GO:0007610&slim=GO:0008150&slim=GO:0005576&slim=GO:0005737&slim=GO:0005856&slim=GO:0005739&slim=GO:0005634&slim=GO:0005694&slim=GO:0016020&slim=GO:0031982&slim=GO:0071944&slim=GO:0030054&slim=GO:0042995&slim=GO:0032991&slim=GO:0045202&slim=GO:0005575&subject=MGI:MGI:97490
returns
- evidence_with: [
- "MGI:MGI:1856155" ], And we have to cobble together (based on the prefix) a guess of the taxon for this gene. You'd likely have to do something similar since no one is actually providing this information. When it is a UniProt identifier it may be human, or sea anemone, or elk, or ...
Particularly for human it would be nice to get the taxon.
On Mon, Jun 4, 2018 at 1:02 PM, Deepak [email protected] wrote:
Yes, in the results for slimmer the taxon property is pinned to the gene entity, which is what you normally want. The taxon property contains id and label. The GO term itself wouldn't have the taxon since what you are getting as result is gene -> GO term association.
Unless I am misunderstanding the use-case here.
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