lpalbou
lpalbou
I was doing some comparisons between jupyter and r notebooks while accessing S3 and found out paws currently has issues listing files: With prefix "A/B", I get 0 R files...
https://nbviewer.jupyter.org/github/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb and binder: https://hub.gke.mybinder.org/user/biolink-ontobio-actww75g/notebooks/notebooks/Phenotype_Enrichment.ipynb The notebook creates but step 7 doesn't create an enrichment list:  I have tried locally and it's the...
We got a message this morning on the alliance helpdesk that the ribbon wasn't working for a new HGNC id: https://agr-jira.atlassian.net/browse/AGRHELP-74 (may require jira account to access) I checked the...
Sending this query: curl 'http://api.geneontology.org/api/ontology/ribbon/?subset=goslim_agr&subject=ZFIN:ZDB-GENE-980526-166&subject=HGNC:10848&subject=MGI:98297&subject=RGD:3673&subject=FB:FBgn0004644&subject=WB:WBGene00001700&subject=WB:WBGene00001691&subject=WB:WBGene00004264&subject=WB:WBGene00006952&exclude_PB=true&exclude_IBA=true' -H 'Content-Type: application/json' -I Will return a 400 due to the content-type
**Proposal**: add a new parameter exclude_slim to the bioentityset/slimmer/function route to exclude in the result set all annotations that are mapped to any slim of exclude_slim **Why**: creating the "other"...
There are some divergences between the GO & Monarch API. Some can be resolved (e.g. adding parameters to the slimmer route), but some will need more discussions (e.g. implementation specific...
The current API implementation is returning a list of all ids but not a set. As a consequence, there are duplicated pmids: https://api.monarchinitiative.org/api/bioentity/function/GO%3A0044598/publications?start=0&rows=100
It's great to now have the aspect field for each object of the association. I think however it would make more sense if instead of showing the label of the...
Test query: https://api.monarchinitiative.org/api/bioentityset/slimmer/function?slim=GO:0016043&subject=MGI:88276&rows=-1 Look for "regulation of histone demethylase activity (H3-K4 specific)". There are two associations for that GO term but except for the association id, those are duplicate. Looking...
When executing a [slimmer / function query](https://api.monarchinitiative.org/api/bioentityset/slimmer/function?&slim=GO:0016491&slim=GO:0016787&slim=GO:0016740&slim=GO:0016874&slim=GO:0030234&slim=GO:0038023&slim=GO:0005102&slim=GO:0005215&slim=GO:0005198&slim=GO:0008092&slim=GO:0003677&slim=GO:0003723&slim=GO:0003700&slim=GO:0008134&slim=GO:0036094&slim=GO:0046872&slim=GO:0030246&slim=GO:0097367&slim=GO:0008289&slim=GO:0003674&slim=GO:0007049&slim=GO:0016043&slim=GO:0051234&slim=GO:0008283&slim=GO:0030154&slim=GO:0008219&slim=GO:0032502&slim=GO:0000003&slim=GO:0002376&slim=GO:0050877&slim=GO:0050896&slim=GO:0023052&slim=GO:0006259&slim=GO:0016070&slim=GO:0019538&slim=GO:0005975&slim=GO:1901135&slim=GO:0006629&slim=GO:0042592&slim=GO:0009056&slim=GO:0065009&slim=GO:0050789&slim=GO:0007610&slim=GO:0008150&slim=GO:0005576&slim=GO:0005886&slim=GO:0045202&slim=GO:0030054&slim=GO:0042995&slim=GO:0031410&slim=GO:0005768&slim=GO:0005773&slim=GO:0005794&slim=GO:0005783&slim=GO:0005829&slim=GO:0005739&slim=GO:0005634&slim=GO:0005694&slim=GO:0005856&slim=GO:0032991&slim=GO:0005575&subject=MGI:88276&rows=-1): @cmungall @deepakunni3 is it ok to change the response to add a field "aspect" in assocs/object ? Current response: ``` [ { "subject":...