Nathan Dunn

autocomplete returns a funny GO idea

1

http://api.geneontology.org/api/search/entity/autocomplete/GO:0070996?rows=20&prefix=GO  ``` {"docs": [{"id": "GO:0070996", "label": ["type 1 melanocortin receptor binding"], "match": "GO:0070996", "category": ["molecular function"], "taxon": "", "taxon_label": "", "highlight": "GO:0070996", "has_highlight": true}, {"id": "GO:0070966", "label": ["nuclear-transcribed mRNA...

ribbon / slimmer function: "evidence_with" should include - label, id, and taxon - for each entry

4

not sure how doable this is within biolink: https://github.com/geneontology/ribbon/issues/50

support "expression" category for slimmer function

5

Currently we support `function` and `phenotype`. We should do the same to support an `expression` category. FYI @cmungall / @selewis

slimmer should return species evidence from IBA evidence

7

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,...

create route for Genome Features / Variants that aligns with current Apollo track / variant services

6

- align gene, etc. https://github.com/biolink/biolink-api/blob/master/biolink/datamodel/serializers.py#L177-L224 . to correspond to Apollo web-services output (which should correspond to JBrowse, as well) - add corresponding biolink api routes. - /biotentity/gene/{id}/features - /biotentity/gene/{location}/features (location...

add ribbon to monarch

7

There was some discussion about doing this. Not sure when it happens, but wanted a placeholder for it. https://github.com/geneontology/ribbon

grails3-neo4j-hibernate example transaction fails on grails 4

1

Not sure if we should just use gorm-micronaut bindings everywhere instead for grails 4, but I wanted to provide these fixes either way. - you can't run these embedded unless...

Added support for RS256

3

I tried to change the get algorithm to RS256 to match the client. ``` plugin: springsecurity: rest: token: generation: jwt: algorithm: "RS256" ``` However, it JwtService only seems to return...

fix zfin links to no longer use ZFIN_jump

2

https://agr-jira.atlassian.net/browse/AGR-1350 http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-020724-1 should use: http://identifiers.org:ZFIN:ZDB-PUB-020724-1 if the organization is known (for the ZFIN curie prefix) or http://zfin.org/ZDB-PUB-020724-1 if not (but I think we always know): should handle all other cases,...