2017 Berkeley GO Editors Workshop II: Difference between revisions
(Created page with "= Agenda = == Topics == * Equivalence axioms - editors would like more guidelines on how to construct these. * OWL GCIs- Where do they live and how do they work? * Advan...") |
mNo edit summary |
||
(60 intermediate revisions by 10 users not shown) | |||
Line 1: | Line 1: | ||
= Agenda = | |||
= 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) | |||
** Work through exercises: https://github.com/geneontology/protege-tutorial | |||
*** Disjoint classes | |||
*** Imports | |||
** Improving the tutorial for others | |||
* 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 | |||
* [https://github.com/ontodev/robot ROBOT] tutorial | |||
** Setup (Eric) | |||
** Owltools https://github.com/owlcollab/owltools/ | |||
** Commands (Chris) | |||
* You'll love Makefiles. No, really you will | |||
** Makefile concepts | |||
** Overview of the GO makefile | |||
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 | |||
* [https://github.com/geneontology/go-ontology/issues/13692 TermGenie Replacement] | |||
** [https://docs.google.com/presentation/d/17hXXSWBiqP4mg0c3MX_vIO5OgwVvfa2b8i-sqoUMY9c/edit?usp=sharing 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: [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 == | |||
=== Morning 9am-12pm === | |||
Ontology Content | |||
* Problematic GitHub tickets/mini Projects, backlog | |||
** Pascale: https://github.com/geneontology/go-ontology/issues/13731 | |||
**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] | |||
***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 | |||
* 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 == | == 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 = | = Logistics = | ||
Line 23: | Line 145: | ||
Taxis also available from either MacArthur or Ashby | 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: | |||
* http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/ | |||
== Meeting Location == | == Meeting Location == | ||
Line 30: | Line 160: | ||
Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley | Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley | ||
Physical address: 717 Potter Street, Berkeley, CA 94710 | Physical address: 717 Potter Street, Berkeley, CA 94710 | ||
Meeting room: room 181 | |||
=== Travel between hotel and meeting === | === Travel between hotel and meeting === | ||
Line 38: | Line 170: | ||
Aim to be at the lab for 9am | Aim to be at the lab for 9am | ||
== Participants == | == Participants == | ||
Line 50: | Line 184: | ||
| Jackson Laboratory | | Jackson Laboratory | ||
| | | | ||
| | |||
|- | |||
|Harold Drabkin | |||
| Jackson Laboratory | |||
| | | | ||
|- | |- | ||
| Kimberly Van Auken | | Kimberly Van Auken | ||
| Caltech | | Caltech | ||
| | | Arriving SFO Monday, 8/14, 5:03PM | ||
|- | |- | ||
| Pascale Gaudet | | Pascale Gaudet | ||
Line 62: | Line 200: | ||
| David Osumi-Sutherland | | David Osumi-Sutherland | ||
| EBI | | EBI | ||
| | |||
|- | |||
| Karen Christie | |||
| Jackson Laboratory | |||
| | |||
|- | |||
| Tanya Berardini | |||
| TAIR/Phoenix | |||
| | |||
|- | |||
| Huaiyu Mi | |||
| USC | |||
| | | | ||
|- | |||
| Nicole Vasilevsky | |||
| OHSU | |||
| | |||
|- | |||
| Matt Horridge | |||
| Stanford | |||
| | |||
|- | |||
| Donghui Li | |||
| CZI | |||
| wed only? | |||
|- | |- | ||
|} | |} | ||
[[Category: | LBL: | ||
* Chris Mungall | |||
* Eric Douglass | |||
* Monica Munoz-Torres | |||
* Seth Carbon | |||
* Suzi Lewis | |||
[[Category:Workshops]] | |||
[[Category:Protege]] | [[Category:Protege]] |
Latest revision as of 10:09, 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)
- Work through exercises: https://github.com/geneontology/protege-tutorial
- Disjoint classes
- Imports
- Improving the tutorial for others
- Work through exercises: https://github.com/geneontology/protege-tutorial
- 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
- ROBOT tutorial
- Setup (Eric)
- Owltools https://github.com/owlcollab/owltools/
- Commands (Chris)
- You'll love Makefiles. No, really you will
- Makefile concepts
- Overview of the GO makefile
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)
- Overview (DavidOS, Chris)
- 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
- Pascale: https://github.com/geneontology/go-ontology/issues/13731
- Kimberly #13944 protein quality control
- Kimberly #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
- 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
- Design templates for MFs for signaling pathway components
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
- 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 | ||
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