Difference between revisions of "2018 Berkeley GO Docathon"

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= Logistics =
 +
 +
== Rooms ==
 +
*153 has been reserved on Tuesday, January 23rd.  248 is reserved for the other 4 days.
 +
  
 
= Agenda (Draft) =
 
= Agenda (Draft) =
  
== Rooms: ==
+
== Meeting MInutes ==
*153 has been reserved on Tuesday, January 23rd. 248 is reserved for the other 4 days.
+
*[https://docs.google.com/document/d/1d5f_uGNhE4BJpUbMFsKvaHkgmxq4tMWec0EyYmt7Gsc/edit# Minutes on Google Drive]
 +
 
 +
== User Stories/Use Cases ==
 +
*[https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit# Draft of user stories on Google drive]
  
 
== Monday, January 22nd ==
 
== Monday, January 22nd ==
*Noctua landing page
+
=== Which Noctua/GO-CAM documentation to keep and where? ===
*Noctua Quick Start
+
*[http://noctua.geneontology.org/ Noctua landing page - click on About link at upper right]
*GO-CAM Guidelines (more detailed, on wiki or readthedocs?)
+
*[http://noctua.geneontology.org/doc/quick-start-guide Noctua Quick Start Guide]
**Relations - definitions, examples
+
*[http://wiki.geneontology.org/index.php/Noctua Paul's Noctua Guide on the wiki]
 +
*[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://docs.google.com/spreadsheets/d/1ZESgrKU0c8vI6mBFtwPA1g-rtl-4AVzCjUQmnBdo-zI/edit#gid=916411263 Spreadsheet with testing scenarios]
  
 
== Tuesday, January 23rd ==
 
== Tuesday, January 23rd ==
 
*GO-CAM Guidelines
 
*GO-CAM Guidelines
 
**Relations - definitions, examples
 
**Relations - definitions, examples
 +
***This is applicable not only to GO-CAM but to conventional annotation as well
 +
***New CC relations proposal
 +
****https://github.com/geneontology/go-annotation/issues/1639
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****gene products as complex members
 +
****gene products active in a given CC
 +
*****[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002432 is active in (RO:0002432)]
 +
****gene products localized to a given CC but not necessarily active
 +
**Reasoning, inferred annotations
 +
**Use of evidence
 +
*GO-CAM Paper
 
*Annotation File Pipelines
 
*Annotation File Pipelines
 
**File submissions
 
**File submissions
 
**Jenkins jobs and reports
 
**Jenkins jobs and reports
 +
**GO rules
  
 
== Wednesday, January 24th ==
 
== Wednesday, January 24th ==
 
*GOC website - move more detailed documentation off of the website, but provide links to internal (i.e. wiki or readthedocs) pages
 
*GOC website - move more detailed documentation off of the website, but provide links to internal (i.e. wiki or readthedocs) pages
 +
*[https://docs.google.com/spreadsheets/d/1uIf64upvTolKVM6_6smZNFocvhATleMUPHawsoe_oco/edit#gid=0 List of all published on geneontology.org Drupal as of 2018-01-17]
 +
*We'll start by reviewing and focusing on the page marked very high and high priority
 +
**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
 
**Annotation Guidelines - use GO handbook chapters wherever possible
 
***Overall GO philosophy
 
***Overall GO philosophy
Line 27: Line 52:
 
***Types of gene products, e.g. transmembrane proteins
 
***Types of gene products, e.g. transmembrane proteins
 
***Evidence Codes
 
***Evidence Codes
 +
***Annotation Extension
 +
***File Format Guide
  
 
== Thursday, January 25th ==
 
== Thursday, January 25th ==
 +
*9am PST - Jim joining; look at evidence, how relations are chaining, annotation extensions
 
*GOC website - move more detailed documentation off of the website, but provide links to internal (i.e. wiki or readthedocs) pages
 
*GOC website - move more detailed documentation off of the website, but provide links to internal (i.e. wiki or readthedocs) pages
 
**FAQs
 
**FAQs
 
**Ontology Documentation
 
**Ontology Documentation
 +
**GO Database
  
 
== Friday, January 26th ==
 
== 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"
 +
* For pages that we want to remove, use the 'Unpublish' option, don't DELETE
 +
 +
===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 =
 
= Logistics =
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| Pascale Gaudet
 
| Pascale Gaudet
 
| SIB Swiss Institute of Bioinformatics
 
| SIB Swiss Institute of Bioinformatics
 +
| Available until ~1pm PST
 +
|-
 +
| Huaiyu Mi
 +
| USC
 
|  
 
|  
 
|-
 
|-

Latest revision as of 11:17, 28 March 2019

Logistics

Rooms

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


Agenda (Draft)

Meeting MInutes

User Stories/Use Cases

Monday, January 22nd

Which Noctua/GO-CAM documentation to keep and where?

Tuesday, January 23rd

  • GO-CAM Guidelines
  • 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
  • List of all published on geneontology.org Drupal as of 2018-01-17
  • We'll start by reviewing and focusing on the page marked very high and high priority
    • 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

  • 9am PST - Jim joining; look at evidence, how relations are chaining, annotation extensions
  • 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:


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"
  • For pages that we want to remove, use the 'Unpublish' option, don't DELETE

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

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