Manager 20Aug2014: Difference between revisions
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[[Category: | [[Category:GO Managers Meetings]] | ||
=On call= | =On call= | ||
Judy, Suzi, Chris, Rama, Pascale, Kimberly, David, Paul T. | |||
= | =Minutes= | ||
==Trello board== | ==Trello board== | ||
https://trello.com/b/IdtTLGEt/go-priorities | https://trello.com/b/IdtTLGEt/go-priorities | ||
Line 11: | Line 11: | ||
==GOC meeting Barcelona== | ==GOC meeting Barcelona== | ||
http://wiki.geneontology.org/index.php/2014_Barcelona_GOC_Meeting_Agenda | http://wiki.geneontology.org/index.php/2014_Barcelona_GOC_Meeting_Agenda | ||
*People should add items to the wiki | |||
==Conf. Call with Phil Bourne (NIH)== | ==Conf. Call with Phil Bourne (NIH)== | ||
Line 22: | Line 24: | ||
*Resolved a number of outstanding SourceForge tickets - Paola is compiling the numbers | *Resolved a number of outstanding SourceForge tickets - Paola is compiling the numbers | ||
*By end of week, hopefully all of Val's outstanding tickets will also be resolved | *By end of week, hopefully all of Val's outstanding tickets will also be resolved | ||
==Overhaul of Molecular Function== | |||
*Ontology editors looked at the proposal and liked much of the proposed changes | *Ontology editors looked at the proposal and liked much of the proposed changes | ||
*Where would the MF overhaul fit in with ontology development priorities? | *Where would the MF overhaul fit in with ontology development priorities? | ||
*Would be good to have more people trained in ontology development | *Would be good to have more people trained in ontology development | ||
* | *Also testing out web Protege - a more long term goal | ||
==Other Areas of Ontology Development== | |||
*Working on Uberon developmental process, perhaps a bigger scope | |||
*Cell cycle - Jane continues to work on this | |||
*New terms - TermGenie | |||
*New terms - SourceForge | |||
*For SourceForge, may be necessary to move on from items if submitter doesn't respond to follow-up questions | |||
*Areas where there is poor representation in the ontology, or ontology is confusing - these can be more major projects | |||
*'''ACTION ITEM''' - need to start triaging items, but still need to discuss adding more resources to ontology development | |||
*Major items could get their own Trello cards (with sub-items, if needed) | |||
*As an example, the ubiquitination project has now become much larger, now encompasses other small protein transferases (e.g., SUMOylation, NEDDylation) - now a Trello card for this | |||
*Bring in more experts to help? | |||
==Noctua= | ==Noctua== | ||
*Chris - new release of Noctua | *Chris - new release of Noctua | ||
*Most visible change is user login | *Most visible change is user login | ||
Line 35: | Line 50: | ||
*Chris will contact | *Chris will contact | ||
=Text Mining== | ==Text Mining== | ||
*Yuling is training an enzymatic activity document classifier (SVM) | *Yuling is training an enzymatic activity document classifier (SVM) | ||
*Will investigate feasibility of SVM on PMC corpus for prioritizing papers based on data type | *Will investigate feasibility of SVM on PMC corpus for prioritizing papers based on data type | ||
==Annotation Advocacy== | |||
*Moving to Jenkins - progressing | |||
*Moni is working with Rachael and Rama on documentation for submitting annotations | |||
*Annotation extensions - ongoing education; every annotation call things come up, are discussed, and documentation is revised as needed | |||
*Annotation metrics - any work done on auto-generating reports? | |||
*Numbers are available on website; but should we also be measuring and reporting information content? | |||
*Can we tap into software support from other members to help with this? | |||
*Include GAF errors | |||
==Phylogenetic-based Annotation== | |||
*Had in-person component of the tree annotation jamboree | |||
*Went well, got lots of trees annotated, talked about metrics | |||
*Still need to have annotations committed, though | |||
*'''ACTION ITEM''' - Need to initiate the Monday Google hangout | |||
*'''ACTION ITEM''' - Remove large-scale experiments from display in PAINT, add to next PAINT call agenda | |||
==Outreach and Usability== | |||
*NAR paper in the works | |||
*Documentation updating | |||
==Software== | |||
*Still working on RDF representation of GO | |||
*TermGenie paper is out |
Latest revision as of 09:50, 15 April 2019
On call
Judy, Suzi, Chris, Rama, Pascale, Kimberly, David, Paul T.
Minutes
Trello board
https://trello.com/b/IdtTLGEt/go-priorities
GOC meeting Barcelona
http://wiki.geneontology.org/index.php/2014_Barcelona_GOC_Meeting_Agenda
- People should add items to the wiki
Conf. Call with Phil Bourne (NIH)
NAR Paper
- Judy reminder about upcoming database issue
- Moni and Harold are working on a draft
- Aiming for September 15th deadline, but will likely need a little more time
- Paper focuses on updates and enhancements to the project, also provides overall summary with key info (e.g., contact)
SourceForge Clearance Jamboree
- Resolved a number of outstanding SourceForge tickets - Paola is compiling the numbers
- By end of week, hopefully all of Val's outstanding tickets will also be resolved
Overhaul of Molecular Function
- Ontology editors looked at the proposal and liked much of the proposed changes
- Where would the MF overhaul fit in with ontology development priorities?
- Would be good to have more people trained in ontology development
- Also testing out web Protege - a more long term goal
Other Areas of Ontology Development
- Working on Uberon developmental process, perhaps a bigger scope
- Cell cycle - Jane continues to work on this
- New terms - TermGenie
- New terms - SourceForge
- For SourceForge, may be necessary to move on from items if submitter doesn't respond to follow-up questions
- Areas where there is poor representation in the ontology, or ontology is confusing - these can be more major projects
- ACTION ITEM - need to start triaging items, but still need to discuss adding more resources to ontology development
- Major items could get their own Trello cards (with sub-items, if needed)
- As an example, the ubiquitination project has now become much larger, now encompasses other small protein transferases (e.g., SUMOylation, NEDDylation) - now a Trello card for this
- Bring in more experts to help?
Noctua
- Chris - new release of Noctua
- Most visible change is user login
- Also Noctua annotations are loading into the dev version of AmiGO (will give demo at Barcelona)
- This is very useful as we get more models; curators can search for annotations in dev version of AmiGO
- Chris will contact
Text Mining
- Yuling is training an enzymatic activity document classifier (SVM)
- Will investigate feasibility of SVM on PMC corpus for prioritizing papers based on data type
Annotation Advocacy
- Moving to Jenkins - progressing
- Moni is working with Rachael and Rama on documentation for submitting annotations
- Annotation extensions - ongoing education; every annotation call things come up, are discussed, and documentation is revised as needed
- Annotation metrics - any work done on auto-generating reports?
- Numbers are available on website; but should we also be measuring and reporting information content?
- Can we tap into software support from other members to help with this?
- Include GAF errors
Phylogenetic-based Annotation
- Had in-person component of the tree annotation jamboree
- Went well, got lots of trees annotated, talked about metrics
- Still need to have annotations committed, though
- ACTION ITEM - Need to initiate the Monday Google hangout
- ACTION ITEM - Remove large-scale experiments from display in PAINT, add to next PAINT call agenda
Outreach and Usability
- NAR paper in the works
- Documentation updating
Software
- Still working on RDF representation of GO
- TermGenie paper is out