2018 Berkeley GO Docathon

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Revision as of 13:26, 12 January 2018 by Pascale (talk | contribs)
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Logistics

Rooms

  • 153 has been reserved on Tuesday, January 23rd. 248 is reserved for the other 4 days.


Agenda (Draft)

Monday, January 22nd

Tuesday, January 23rd

  • GO-CAM Guidelines
    • Relations - definitions, examples
    • Reasoning, inferred annotations
    • Use of evidence
  • GO-CAM Paper
  • Annotation File Pipelines
    • File submissions
    • Jenkins jobs and reports
    • GO rules

Wednesday, January 24th

  • GOC website - move more detailed documentation off of the website, but provide links to internal (i.e. wiki or readthedocs) pages
    • Annotation Guidelines - use GO handbook chapters wherever possible
      • Overall GO philosophy
      • Annotation of specific areas of biology, e.g. apoptosis, signaling, transcription
        • Give GO-CAM examples wherever possible
      • Annotation of specific types of experiments, e.g. ChIP
      • Types of gene products, e.g. transmembrane proteins
      • Evidence Codes
      • Annotation Extension
      • File Format Guide

Thursday, January 25th

  • GOC website - move more detailed documentation off of the website, but provide links to internal (i.e. wiki or readthedocs) pages
    • FAQs
    • Ontology Documentation
    • GO Database

Friday, January 26th

  • GOC website - move more detailed documentation off of the website, but provide links to internal (i.e. wiki or readthedocs) pages
    • Annotation Tools, Downloads, and Beyond
    • Contributing to GO
    • Submitting GO Annotations
    • Other Useful Links

Procedure

  • All documentation will be reviewed based on the priority listed in the agenda (all is the objective)
  • Documentation may be located in the wiki, google docs, geneontology.org, GitHub and ReadTheDocs. The goal of the Docathon is to consolidate.
    • Curators: first on the wiki, and later we will decide if this is the final location.
    • Ontology documentation: first: clean up the wiki, and see what needs to be moved (either on readthedocs or on the wiki- to be decided)
    • Software developer documentation: GitHub
    • User documentation: first on the wiki, later on the geneontology.org

wiki pages

  • we will use the categories Archived and Retired
    • Archived‏‎: For reports and other documents we want to save (old but still relevant)
    • Retired: old and irrelevant (content out-of date).
      • Add to the page the category
      • Move the page to PageName (Archived) or PageName (Retired) as appropriate.
    • For 'Current' pages that have been reviewed, and for which content is up to date, add at the bottom "Reviewed on YYYY-MM-DD"

For geneontology.org pages

Logistics

Accommodations

There are two ways travelers can secure their reservation:

1. By Phone- 1-800-325-3535 and mention "Gene Ontology" 2. Via the Web- https://www.starwoodmeeting.com/Book/GeneOntology


Getting there:

Taxis also available from either MacArthur or Ashby

Parking

We will try to reserve as many spots outside the front entrance as we can. Look for spots that say "GO meeting". if you see one, take it.

If there is none available, don't worry. Park temporarily and grab a parking pass from the person at the gate, you can then park in the garage:

Meeting Location

Berkeley Lab, Aquatic Park Offices

Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley Physical address: 717 Potter Street, Berkeley, CA 94710

Meeting room: room 181

Travel between hotel and meeting

Aim to be at the lab for 9am


Participants

Name Organization Comments
David Hill Jackson Laboratory
Kimberly Van Auken Caltech
Pascale Gaudet SIB Swiss Institute of Bioinformatics
Huaiyu Mi USC

LBL:

  • Chris Mungall
  • Eric Douglass
  • Seth Carbon
  • Suzi Lewis