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monarch-initiative / monarch-legacy

Monarch web application and API
BSD 3-Clause "New" or "Revised" License
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Add links to bio-lark pheno-discuss #648

Open mellybelly opened 9 years ago

mellybelly commented 9 years ago

In Monarch app, we need some mechanism for users to comment on any given disease or phenotype ontology definition. At first this would just be for HPO and diseases. Perhaps add a button or link that says "edit this concept" on those pages, with links to HPO-Bio-lark phenodiscuss: For example, see: http://hpo.bio-lark.org/#/phenotypes/324

see https://github.com/Bio-LarK/hpo @tudorgroza can assist.

mellybelly commented 9 years ago

assigning back to @tudorgroza for recent ideas on how to integrate in short term. @nlwashington @kshefchek can answer questions.

tudorgroza commented 9 years ago

The color palette of the HPO editor is now closer to the Monarch skin and we have included links on each term to the Monarch page. Next step: re-design the back-end and feed it data directly from SciGraph.

nlwashington commented 9 years ago

how would you like us to link to bio-lark? should there be a button on a given phenotype page? does bio-lark only serve HP?

tudorgroza commented 9 years ago

Good questions :) ... Well ... it does have OMIM disorders as well, but they do not have a proper identification system for them - or for HPO terms as a matter of fact. Honestly, not sure if at this point it makes sense to add links back. Let us replace the backend and implement the proper URI scheme before. What do you say?

cmungall commented 9 years ago

@tudorgroza when you say feed data directly from SciGraph, which parts do you mean? So far we haven't been using SG as any kind of permanent store.

My ideal architecture would be to use the github APIs and use github as a backend for anything involving modifications, proposed changes or comments. Power users could do things via GH (e.g. fork the ontology, use the tracker directly), domain experts would have a nice biolark view. Of course we're not even using gh for hpo yet so this may be some way off, and there are fundamental issues with maintaining a large owl ontology in git but we should be thinking towards the future.

jmcmurry commented 9 years ago

This has multiple sub-tasks short and long term, but lets a) outline them and b) make make at least some progress by thanksgiving release.

jmcmurry commented 8 years ago

@cmungall would INCA speak to any components of this? If so what exactly?