Difference between revisions of "2017 Berkeley GO Editors Workshop II"

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= Party! (or at least dinner together) =
 
*Where: [https://goo.gl/maps/UsbWRZLMFMy 2 Biehs Court, Oakland, CA 94618]
 
*When: Wednesday, August 16 (whenever the meeting closes down and you get over there)
 
*Ideas for what you'd like to eat? And drink?
 
  
 
= Agenda (Draft) =
 
= Agenda (Draft) =
Line 8: Line 4:
 
== Tuesday 15th ==
 
== Tuesday 15th ==
  
=== Tue Morning ===
+
Note: Jim may have a hard time calling in on wed afternoon, tue better, so we may rearrange to accomodate
 +
 
 +
=== Tue Morning 9am-12pm ===
  
 
* Intro, goals (Chris)
 
* Intro, goals (Chris)
 
* Advanced OWL Tutorial (Chris, DOS)
 
* Advanced OWL Tutorial (Chris, DOS)
 
** Work through exercises: https://github.com/geneontology/protege-tutorial
 
** Work through exercises: https://github.com/geneontology/protege-tutorial
 +
*** Disjoint classes
 +
*** Imports
 
** Improving the tutorial for others
 
** Improving the tutorial for others
 
* Advanced concepts
 
* Advanced concepts
** GCIs
+
** GCIs (General Class Inclusion)
 
** Hidden GCIs
 
** Hidden GCIs
 
** How to write good logical definitions
 
** How to write good logical definitions
  
=== Tue Afternoon ===
+
=== Tue Afternoon 1pm-5pm ===
 +
 
 +
sparkly swirly things
 +
 
 +
* SPARQL (Eric, Chris)
 +
* SWRL (DavidOS)
  
 
How to do cool stuff on the command line
 
How to do cool stuff on the command line
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* [https://github.com/ontodev/robot ROBOT] tutorial
 
* [https://github.com/ontodev/robot ROBOT] tutorial
 
** Setup (Eric)
 
** Setup (Eric)
 +
** Owltools https://github.com/owlcollab/owltools/
 
** Commands (Chris)
 
** Commands (Chris)
 
* You'll love Makefiles. No, really you will
 
* You'll love Makefiles. No, really you will
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== Wednesday 16th ==
 
== Wednesday 16th ==
  
=== Wed Morning ===
+
=== Wed Morning 9am-12pm ===
  
 
DOSDPs, yaml, INCA is the new TermGenie
 
DOSDPs, yaml, INCA is the new TermGenie
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* Discussion: What would an ideal ontology development environment be like?
 
* Discussion: What would an ideal ontology development environment be like?
  
=== Wed Afternoon ===
+
=== Wed Afternoon 1pm-5pm ===
  
 
* RO
 
* RO
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** Debugging using the explanation panel
 
** Debugging using the explanation panel
 
** Table Mode demo (Dan) 4pm
 
** Table Mode demo (Dan) 4pm
 +
 +
=== Wed Evening: Party! (or at least dinner together) ===
 +
 +
*Where: [https://goo.gl/maps/UsbWRZLMFMy 2 Biehs Court, Oakland, CA 94618]
 +
*When: Wednesday, August 16 (whenever the meeting closes down and you get over there)
 +
*Ideas for what you'd like to eat? And drink?
  
 
== Thursday 17th ==
 
== Thursday 17th ==
  
=== Morning ===
+
=== Morning 9am-12pm ===
  
 
Ontology Content
 
Ontology Content
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**Kimberly [https://github.com/geneontology/go-ontology/issues/13944 #13944 protein quality control]
 
**Kimberly [https://github.com/geneontology/go-ontology/issues/13944 #13944 protein quality control]
 
**Kimberly [https://github.com/geneontology/go-ontology/issues/12272 #12272 receptor agonist activity]
 
**Kimberly [https://github.com/geneontology/go-ontology/issues/12272 #12272 receptor agonist activity]
 +
***Receptor agonist activity is being classified as a 'signal transducer activity' but the annotation documentation says that ligands cannot be annotated to 'signal transducer activity'
 
* Update on status of Molecular Function re-factor
 
* Update on status of Molecular Function re-factor
 
* Review the accumulated use cases for GO from ontology ticket #13606. Discuss how we can continue to best meet the needs of our various communities.
 
* Review the accumulated use cases for GO from ontology ticket #13606. Discuss how we can continue to best meet the needs of our various communities.
 
* Review all documentation of SOPs for ontology editors.
 
* Review all documentation of SOPs for ontology editors.
  
 
+
=== Afternoon 1pm-5pm ===
=== Afternoon ===
 
  
 
* Improving editors documentation
 
* Improving editors documentation
 
* Goals for signaling workshop
 
* Goals for signaling workshop
 +
**Design templates for MFs for signaling pathway components
 +
***Ligands, e.g. Wnt, EGFs, Delta/Serrate
 +
***Receptors
 +
***Downstream cascade components, e.g. protein kinases, scaffolds
 +
***Transcription factors
  
 
== Topics ==
 
== Topics ==
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== Parking ==
 
== Parking ==
  
Visitor parking is available, see:
+
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:
  
 
* http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/
 
* http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/
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Aim to be at the lab for 9am
 
Aim to be at the lab for 9am
 +
 +
  
 
== Participants ==
 
== Participants ==
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| Matt Horridge  
 
| Matt Horridge  
 
| Stanford
 
| Stanford
| possible
+
|
 +
|-
 +
| Donghui Li
 +
| CZI
 +
| wed only?
 
|-
 
|-
 
|}
 
|}
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* Suzi Lewis
 
* Suzi Lewis
  
 
+
[[Category:Workshops]]
[[Category:Meetings]]
 
 
[[Category:Protege]]
 
[[Category:Protege]]

Latest revision as of 07:09, 15 April 2019

Agenda (Draft)

Tuesday 15th

Note: Jim may have a hard time calling in on wed afternoon, tue better, so we may rearrange to accomodate

Tue Morning 9am-12pm

  • Intro, goals (Chris)
  • Advanced OWL Tutorial (Chris, DOS)
  • Advanced concepts
    • GCIs (General Class Inclusion)
    • Hidden GCIs
    • How to write good logical definitions

Tue Afternoon 1pm-5pm

sparkly swirly things

  • SPARQL (Eric, Chris)
  • SWRL (DavidOS)

How to do cool stuff on the command line

Pipes and stuff

  • Pipelines and Continuous Integration (Chris, Seth, Eric)
    • Travis deep dive
    • How to figure out WTF went wrong with your pull request
    • Jenkins Release pipeline (Seth)

Wednesday 16th

Wed Morning 9am-12pm

DOSDPs, yaml, INCA is the new TermGenie

  • TermGenie Replacement
    • Plan Overview (Chris)
    • yaml design pattern overview (Nicole V, David OS)
    • INCAForm demo (Nicole V)
  • Exercises
    • Add a new term in INCAForm
    • Make a new design pattern
  • Discussion
    • Reusing templates in Noctua
    • Getting stricter about accepting compositional terms

Planning for the future

  • Protege and WebProtege (Tentative) (Matt H)
  • Discussion: What would an ideal ontology development environment be like?

Wed Afternoon 1pm-5pm

  • RO
    • Overview (DavidOS, Chris)
      • Gene product to class relations (KVA)
    • Exercise: making an RO pull request
    • GORel (for extensions) (DavidOS)
    • Discussion
      • retiring GORel
    • Documentathon: documenting RO for curators
    • ABox Ontologies (DavidOS)
  • Noctua
    • Ontology-based QC of Noctua (Chris)
    • The Arachne reasoner (Chris, or Jim if he can call in)
    • Debugging using the explanation panel
    • Table Mode demo (Dan) 4pm

Wed Evening: Party! (or at least dinner together)

  • Where: 2 Biehs Court, Oakland, CA 94618
  • When: Wednesday, August 16 (whenever the meeting closes down and you get over there)
  • Ideas for what you'd like to eat? And drink?

Thursday 17th

Morning 9am-12pm

Ontology Content

  • Problematic GitHub tickets/mini Projects, backlog
  • Update on status of Molecular Function re-factor
  • Review the accumulated use cases for GO from ontology ticket #13606. Discuss how we can continue to best meet the needs of our various communities.
  • Review all documentation of SOPs for ontology editors.

Afternoon 1pm-5pm

  • Improving editors documentation
  • Goals for signaling workshop
    • Design templates for MFs for signaling pathway components
      • Ligands, e.g. Wnt, EGFs, Delta/Serrate
      • Receptors
      • Downstream cascade components, e.g. protein kinases, scaffolds
      • Transcription factors

Topics

Fundamentals

  • Understanding OWL reasoning. A practical sessions with problem solving exercises, covering:
    • Equivalent Class, SubClass; Relations: Characteristics, disjoints, hierarchy, chains, domain and range; GCIs; advanced querying; explanations.
  • Understanding the current GO relation set. (A practical session with problem solving exercises + aim to develop better doc)
  • The art of designing robust equivalence axioms & design patterns ( editors would like more guidelines on how to construct these.)

Infrastructure

  • Design pattern infrastructure
  • Pipelines and how they run, both imports and file output. Starting jobs with ROBOT.
  • Build failures
    • Document the various fail messages and how to correct the issues.
  • Ontology work for GO-CAM
    • QC-checking property chains and relations that will be used for GPAD generation
    • Removing the part_of o regulates chains--- Do we want to instantiate all of the current inferences before removal?
    • How will design patterns be implemented in Noctua?
      • What design patterns should have priority for Noctua?

Logistics

Accommodations

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
Harold Drabkin Jackson Laboratory
Kimberly Van Auken Caltech Arriving SFO Monday, 8/14, 5:03PM
Pascale Gaudet SIB Swiss Institute of Bioinformatics
David Osumi-Sutherland EBI
Karen Christie Jackson Laboratory
Tanya Berardini TAIR/Phoenix
Huaiyu Mi USC
Nicole Vasilevsky OHSU
Matt Horridge Stanford
Donghui Li CZI wed only?

LBL:

  • Chris Mungall
  • Eric Douglass
  • Monica Munoz-Torres
  • Seth Carbon
  • Suzi Lewis