2018 Berkeley GO Docathon: Difference between revisions
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*[https://docs.google.com/document/d/18ihslb7prB6CWtu2yjF-pMHZBTY1-AdXJAu-ZyuyXS4/edit# GO-CAM Guidelines (this is the old Google doc)] | *[https://docs.google.com/document/d/18ihslb7prB6CWtu2yjF-pMHZBTY1-AdXJAu-ZyuyXS4/edit# GO-CAM Guidelines (this is the old Google doc)] | ||
**[https://github.com/oborel/obo-relations Relations - definitions, examples] | **[https://github.com/oborel/obo-relations Relations - definitions, examples] | ||
*[https://docs.google.com/spreadsheets/d/1ZESgrKU0c8vI6mBFtwPA1g-rtl-4AVzCjUQmnBdo-zI/edit#gid=916411263 Spreadsheet with testing scenarios] | |||
== Tuesday, January 23rd == | == Tuesday, January 23rd == |
Revision as of 16:27, 19 January 2018
Logistics
Rooms
- 153 has been reserved on Tuesday, January 23rd. 248 is reserved for the other 4 days.
Agenda (Draft)
Monday, January 22nd
Which Noctua/GO-CAM documentation to keep and where?
- Noctua landing page - click on About link at upper right
- Noctua Quick Start Guide
- Paul's Noctua Guide on the wiki
- GO-CAM Guidelines (this is the old Google doc)
- Spreadsheet with testing scenarios
Tuesday, January 23rd
- GO-CAM Guidelines
- Relations - definitions, examples
- This is applicable not only to GO-CAM but to conventional annotation as well
- New CC relations proposal
- Reasoning, inferred annotations
- Use of evidence
- Relations - definitions, examples
- 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
- Review landing page on Annotation for correct information (e.g. what do we mean by 'GO Consortium')
- 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
- Request from Pascale:
Documentation on design patterns:
- How to test that an equivalence axiom is necessary and sufficient
- Contents of the design pattern file: tsv + yaml files
- Naming conventions for design patterns
- IDs for design patterns
- Procedure for updates and obsoletion
- Existing documentation (that I could find):
- https://github.com/dosumis/dead_simple_owl_design_patterns/blob/master/spec/dosdp_tsv_schema.md
- https://github.com/dosumis/dead_simple_owl_design_patterns/tree/master/spec
- https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/README.md
- https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/templates/generic_go_pattern_outline.yaml
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: edit the geneontology.org site directly
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 top of the page "Reviewed on YYYY-MM-DD"
For geneontology.org pages
(Needs to be decided - ideally we would work directly from the geneontology.org Drupal)
- List of all pages and their review status: https://docs.google.com/spreadsheets/d/1uIf64upvTolKVM6_6smZNFocvhATleMUPHawsoe_oco/edit?usp=sharing
- For each page, copy content to wiki
- review content:
- make sure it's up to date
- edit to remove content too detailed for external users
- The content intended for users get moved back to the web site, with a link to the wiki as appropriate
- Detailed content appropriate for curators/project members goes to the wiki
- For 'Current' pages that have been reviewed, and for which content is up to date, add at the top of the page "Reviewed on YYYY-MM-DD"
Google docs
GO Google docs are considered 'sandbox items' - they are drafts, etc and we don't aim to maintain them up to date or have any indication of their status.
- Exceptions*:
- Consortium meeting minutes
- Progress reports
- Annotation Review Requests
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
- Walk, 1.3 miles
- Free Hollis Shuttle
- Taxi/Lyft/Uber
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 | Available until ~1pm PST |
Huaiyu Mi | USC |
LBL:
- Chris Mungall
- Eric Douglass
- Seth Carbon
- Suzi Lewis