GSOC Gene wiki Bot

[Chinmay Naik]

Hi,

I am extremely delighted to have had the opportunity to be contributing to Crowdsourcing Biology through GSOC-2013. I sincerely thank all the mentors for their invaluable guidance.
I have been in touch with the recent developments and new features rolled out by the wikidata team.
Specifically, properties can now be used by label and by their id as well.
One additional feature we can add is Template:constraint:Item  (Items should have these properties) http://www.wikidata.org/wiki/Template:Constraint:Item
I believe we can use this to specify the following
1) every gene wikidata item should have a following set of identifiers.
2) For Homologous relationships.
Kindly let me know your thoughts on this.

I had some queries regarding the project. The properties proposed to capture gene info have not yet been created. I took a look at property proposal procedure (http://www.wikidata.org/wiki/Wikidata:Property_proposal)
I am not much familiar with it but do we need upvotes from wikidata members to speed up the process of property creation?? Should i reach out to wikidata community in this regard??

I have specified the tentative timeline in my proposal and i hope to stick to it more or less.Kindly suggest whether it is on the right track.

Thanks,

Chinmay

[Salvatore Loguercio]

Hi Chinmay,

Congrats for your admission to GSoC'13!

I am not 100% sure about including Template:Constraint right now - it can be certainly useful, but remember that gene annotation can be messy and incomplete - think about identifiers in one database that are not represented in another resource. Same issue with homology. Probably easier to get started without it - we can always use it later, when we have some more defined use case for it.

As for properties, I found these related to gene info:

http://www.wikidata.org/wiki/Wikidata:Property_proposal/all#Biochemistry_and_molecular_biology_.2F_Biochemie_und_Molekularbiologie_.2F_Biochimie_et_biologie_mol.C3.A9culaire  

• 7.16.1 Mouse Genome Informatics ID
• 7.16.2 EC Number
• 7.16.3 ChEMBL
• 7.16.4 IUPHAR ID
• 7.16.5 Homologene ID
• 7.16.6 Ensembl ID

We are still missing a few of them (like Ensembl ID), but these should be enough to get started.. Meanwhile we can propose more IDs - yes, it's a vote-based process and may take a while, but I don't see reasons for not including some more popular gene identifiers.

Best,

Sal

[Chinmay Naik]

Thanks Sal for the welcome. I have started with the available properties. I have created a user sub-page to work on the template structure and a rough pywikipedia bot to fill gene items with available properties.
I will be having final examinations from tomorrow till mid of next week. As such, I will continue working on the project after my finals.

Thanks,

Chinmay

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