Wikipedia:WikiProject Molecular Biology/Computational Biology/EBI hackathon on September 4, 2015

About

This page serves the organization of a hackathon at the European Bioinformatics Institute in Hinxton on September 4, 2015, as a satellite event to the Wikipedia Science Conference held on September 2-3 at the Welcome Trust and the accompanying hackathon on September 5 (both in London).

Potential Topics

We find the following topics interesting to discuss but if you have any other topics in your mind please add them below.

• How OA figures could be shared between Europe PMC and Wikipedia
• How we might co-develop annotation systems
• Citation counts of Europe PMC in Wikipedia.
• How to share the outputs of scientific text mining with Wikipedia space e.g. accession number
• Conversely - how Wikipedia content could be used in scientific resources?
• Facilitate the addition of bibliographic metadata to Wikidata
  • most of the fields in queries to Citoid, CrossRef and elsewhere can readily be mapped to existing Wikidata properties included in the draft data model for bibliographic metadata for scholarly articles in Wikidata, which would allow to add the information to the respective Wikidata items (or to create those items if need be), e.g. by way of a gadget or through tools like QuickStatements
    • prototype tool now exists
• looking up species with Wikidata API [PMR et al.]

Useful links

• Wikipedia:Database download
• MetaMine (ContentMine) demo
• AutoList tool to get Wikidata item lists based on Queries
  • Example: Birds with NCBI ID
• Wikidata Query command description
• BioJS
• main species extracted from IJSEM by ContentMine and list of all un/resolved in [1]
• ORCID & Wikipedia cites of Europe PMC articles
• Web annotation tool and Web annodation data model
• DOIs added and removed to Wikipedia - live!
• Wikidata API docs to get information about a specific item
  • Example for Douglas Adams
• Wikibase
• mw:Manual:Pywikibot
• Searching Wikidata for multiple items:
  • http://wdq.wmflabs.org/api?q=string[225:%22Mus%20musculus%22,225:%22Homo%20sapiens%22]&props=225
• Wikidata for authority control

Interested participants

Please note that if you are from outside the Wellcome Trust Genome Campus, you need to e-mail Senay Kafkas (kafkas@ebi.ac.uk) and let us know more formally that you are coming, so we can notify the campus security to actually let you in.

• -- Daniel Mietchen (talk) 16:51, 8 June 2015 (UTC)
• -- Senay Kafkas (EMBL-EBI)
• -- Jo McEntyre (EMBL-EBI)
• -- Peter Murray-Rust (Cambridge and EBI) Petermr (talk) 11:33, 9 June 2015 (UTC)
• -- Dan Bolser (talk) 12:15, 9 June 2015 (UTC)
• -- Jenny Molloy (ContentMine and University of Cambridge)
• -- Alexbateman (talk) 10:39, 15 June 2015 (UTC) (EMBL-EBI)
• -- Audrey Hamelers (talk) (EMBL-EBI)
• -- Martin Fenner (PLOS)
• -- Magnus Manske (talk) (WTSI)
• -- Jee-Hyub Kim (EMBL-EBI)
• -- Thomas Arrow

Venue & Logistics

• The Hackathon will take place in the Ickleton room, the EMBL-EBI South Building.
• How to get to the Wellcome Trust Genome Campus, EMBL-EBI, accommodation etc: http://www.ebi.ac.uk/about/travel
• When you arrive to the campus, please go to the Security building, which is on your left just before the booths. You will be issued a badge.
• We will start at 9am and finish at 5pm
• We have space for up to 20 people.
• We will provide lunch for the visitors.