elixir-europe / biohackathon-projects-2019 Goto Github PK

• BridgeDb
• Validator
• queryExpander
• IdentitifierMappingService

Maybe with HDT files?

• BridgeDb
• Validator
• queryExpander
• IdentityMappingService

I got complaints that, particularly, Team Green is not FAIR. For example, we don't have identifiers for players (ORCID has been suggested) and we don't have ontologies to describe our skills. I mean, seriously, I cannot find anything on BioPortal for "I would kill for the nomination"! :(

Making them more findable, accesible, interoperable, and reusable.

See discussion on Gitter.

Folder structure with just numbers is very hard to navigate if you don't know the number ...
https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects

The text in this project does not appear to line up with the title:

• Development of a Pulsar toolkit

The text for the Pulsar project appears to be in this project:

• Updating the Galaksio workflow management interface for Galaxy and migrating it to Vue.js

And others are swapped as well.

For now, we have local mapping files for genes+protein IDs, metabolites and interactions.
I believe there are quite some projects here also working on (rare) diseases.
So I've started to create the code to create these mappings, based on Wikidata. Tests in Jenkins are green now, so time to extend the approach. The code now works for:

• Wikidata ID
• OMIM ID
• Disease Ontology ID

I would like to add the following (but need to make some changes to main BridgeDb code to accommodate for new databases which were previously not supported/available):

• Disease Ontology ID
• UMLS CUI
• OrphaNet ID (at least on of the projects here is working with that database)
• MeSH descriptor ID

These databases will be added separately (combining -CM and regular form):

• ICD 9
• ICD 10
• ICD 11

After these are available in BridgeDb, I will write the remaining code to add the databases mentioned above.

If there is anyone who has a database with disease IDs (and willing to share these CC0), or is missing some database which is part of Wikidata already, please let me know so I can add that as well!

Over last year @egonw and me added quite some more (metabolite) mappings to the WikiPathways RDF, originating from BridgeDb; we should add some more example queries so it's easier for people to use those mappings in the RDF.

See also:

• Support for Compact Identifiers in the library API bridgedb/BridgeDb#134
• Support for Compact Identifiers bridgedb/BridgeDb#133
• support Compact Identifiers as webservice output bridgedb/BridgeDb#83