missing homologs

[mellybelly]

on this page:
https://monarchinitiative.org/gene/NCBIGene%3A494115
autocomplete shows additional species RBMXL1 but these are not on the homolog tab
@TomConlin @kshefchek @cmungall

same on beta.

[cmungall]

Tom, do you know how to go about debugging this?

First look at panther.ttl, we expect to find the HGNC ID in there. If
it's not, further investigate and report upstream to panther

On 20 Apr 2016, at 6:13, Melissa Haendel wrote:

on this page:
https://monarchinitiative.org/gene/NCBIGene%3A494115
autocomplete shows additional species RBMXL1 but these are not on the
homolog tab
@TomConlin @kshefchek @cmungall

same on beta.

---

You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub:
https://github.com/monarch-initiative/monarch-app/issues/1237

[TomConlin]

panther dipper is producing HGNC identifiers in its output
but HGNC:25073 was not produced in the run I have on hand from ~6 weeks ago.
the identifier does not exist in either of the raw input files we have

grep HGNC:25073 RefGenomeOrthologs
grep HGNC:25073 Orthologs_HCOP

will be in meetings for the next while

[TomConlin]

On the panther website the HGNC identifier for RBMXL1 does exists now.
http://www.pantherdb.org/genes/gene.do?acc=HUMAN|HGNC=25073|UniProtKB=Q96E39
as a sparse looking record. Nothing on the page indicates when it was added.

Will try building a current set of panther triples.

[jmcmurry]

This thread reminded me to document the inherent complexity in HGNC identifiers. Just want to make sure we are aware of it prefixcommons/operations#19

1. ambiguity about what identifier is
2. multiple entity types
3. multiple identifier types
4. Type-specific URL patterns combined with lack of deterministic typing in local ID

[TomConlin]

Will note that after a failed search with an ideal identifier it is routine to repeat with degenerate identifiers in an ad hoc fashion.

[TomConlin]

rerunning with currently available data does not change anything w.r.t HGNC:25073

[kshefchek]

This data is not in panther, so not a bug on our side.