Gene Wiki Project

Gregory Stupp, Andra Waagmeester

Andrew Su Lab

The Scripps Research Institute

San Diego, CA, USA

wikicite

What drugs interact with proteins whose genes are associated with prostate cancer?

Physically interacts with

Encoded by

Genetic association

Metformin

Solute carrier family 22 member 3

SLC22A3

Prostate Cancer

https://doi.org/10.1136/amiajnl-2014-002649

Actively being studied!

http://tinyurl.com/m74tnxq

Curated Knowledge

Crowd-sourced Knowledge

Wikidata Crowdsourcing Model for Enhancing DO Curation

Add xref: DOID:0060177 -> MESH:C535328

curation

Gene Wiki Future (Use Cases)

• Wikibase for non-CC0 data
• Wikibase for research data
• Non-Clinical data, experimental data, text-mined data
• Data (that is not "knowledge") that is not appropriate for wikidata
• Wikibase for staging, development, testing (shex) bots
• WDQS with less restrictions on
• Federated queries
• Time outs

Implementation (problems and opportunities)

• Wikibase configuration customization
• How do i change URIs, ports, etc.
• Wikidata Integrator support
• Syncing local properties with properties from another Wikibase
• Some sort of query interface wrapper/helper that can simplify the property -> skos:exactMatch lookups across wikibases to facilitate writing more legible federated queries
• Going from wikidata to external wikibases
• Scalability:
• Can it handle a billion edges?
• Multiple synchronous queries?
• User/data authentication (private data)
• ...

Lightning Talk: WDI

• Fixing WDI to work correctly with Wikibase
• Changing expected URIs
• Fix fast run mode
• Fix sparql queries
• https://github.com/SuLab/WikidataIntegrator

Lightning Talk: Syncing local properties with properties from another Wikibase

How do we link PIDs and QIDs that are the same between Wikidata and local wikibase?

One solution:

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Test Implementation: SemmedDB

Text-mined biomedical edges from all of Pubmed Abstracts

• Scaled down (normalized, grouped version):
• 200k nodes
• 10 million edges