The Gene Wiki project: Looking to the future v.2017

The Gene Wiki project has been generously funded by the National Institutes for General Medical Sciences (NIGMS) since 2009. As the second funding period is wrapping up early next year, it was time to once again look forward and think about our vision for the next 4-5 years. Posted below is what we came up with, submitted earlier this week to the NIH as a competing renewal proposal with Lynn Schriml and Kristian Andersen as co-Investigators. Fingers crossed!

Also a fine time to recognize that this proposal resulted from the direct and indirect contributions of so many people — postdocs, grad students, staff, past and current collaborators, Wikidata and Wikipedia communities, etc etc — far too many to name individually here. For a mostly comprehensive list, please see our grant-related publications.


3 Comments

  1. Sam Smith

    I would applaud your activities to integrate to the degree possible your work with the Wikidata movement. To me, GeneWiki, GO and related projects have achieved a degree of ontological rigor that is missing in Wikidata, so you have something to contribute, as well as something to gain.

  2. Federico Leva

    Data integration is great. Do you plan some federated Wikibase, or a staging Wikibase server like the EAGLE wiki did, or something else? I didn’t understand the “database connector” part of the proposal.

    • Andrew Su

      Hi Federico, we plan on using Wikidata directly rather than creating another instance of the Wikibase software. Of course, the Wikidata SPARQL query server does allow some reasonably complex federated queries, as outlined at https://www.wikidata.org/wiki/User:ProteinBoxBot/SPARQL_Examples#Federated_Queries .

      The “database connector” was in reference to our “Wikidata Integrator” python library (https://github.com/SuLab/wikidataintegrator). While it’s a very functional bot-building library now, we plan to extend it to perform more write-time data validation checks. In a relational database, you would be prevented from adding a record that didn’t match the table schema — we want to do a similar thing based on the ShEx models described in Aim 1B.

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