Add link-outs on our end - Main ticket

[lwinfree]

Summary: Most of these sources now have links TO Monarch, but many do not have hyperlinks FROM Monarch yet. Most are listed on Monarch pages, but are not hyperlinked (See https://github.com/monarch-initiative/monarch-app/issues/1517).

Source	DONE our side	DONE their side	Contacted?	Heard back?	Need to email	Where	Links on our end?	Github issue
VarSome	Y	Y	Y	Y	N	We are on their gene pages	Y	https://github.com/monarch-initiative/monarch-app/issues/1526
NCBI	Y	Y	Y	Y	N	have added links to 85 genes!	Y	https://github.com/monarch-initiative/monarch-app/issues/1450
HGNC	Y	Y	Y	Y	N	They will add links to their beta site	Y
MODs: MGI, ZFIN, Xenbase	N	N			??	AGR??
UCSC Genome browser	N	N	N, need to set up a track hub: https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html; Melissa has a contact		??	I don't see a place for us to be linked
STRING (Melissa contact)	N	N	revisit this later		Y	I don't see a good place for us to be linked
Reactome	N	N	Y	Y	N	external database
GeneWeaver	N	N			Y	Ask if we can be added to their LinkOuts for specific genes; they have multiple species - is there 1 we could start with?		https://github.com/monarch-initiative/monarch-app/issues/1422
OMIM	N	Y	Y	Y	N		Have IDs but not hyperlinked
GeneCards	N	Y	Y	Y	N	have approved links	N
ENSEMBL	N	Y	Y	Y	N	Linked in June release	Have IDs but not hyperlinked
GARD	N	Y	N		N	our links are on here already	N
NORD	N	Y	Y	Y	N	Resources or References section?	N
Biogps with andrew’s group.	N	Y	Y	Y	N	http://biogps.org/plugin/1154/monarch-gene/	N	https://github.com/monarch-initiative/monarch-app/issues/1477
DDI resources	N	Y	N/A		N	we are on their site under "collaborators"	N
IMPC	N	Y	N/A		N	we are listed on their site under “tools”	need to confirm: Have IDs but not hyperlinked
MMRRC (melissa contact Kent Lloyd)	N	Y	N/A		N	we are on their site under "Other Resources"	need to add hyperlinks - under source column

NEXT STEPS:

• adding hyperlinks to external IDs
• Track hub for UCSC genome browser
• meeting with Reactome Apr 2nd

[lwinfree]

cc @jmcmurry. Here is the table above as a spreadsheet.

[jmcmurry]

This is dependent on a game plan wrt linkouts more broadly. Probably depends on something backend to be more sensible. cc: @TomConlin . Ultimately this will be reflected in the new release.