20th GO Consortium Meeting: Difference between revisions
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* Issues: | * Issues: | ||
** augumentation: try to work with Swiss Prot? | ** augumentation: try to work with Swiss Prot? | ||
** isoforms vs canonical protein | ** isoforms vs canonical protein : try to work with Swiss Prot? | ||
** complete proteome; partial gene predictions | ** complete proteome; partial gene predictions | ||
Revision as of 10:58, 18 October 2008
Logistics
Agenda
ALERT: GO Top needs to sign off on agenda prior to these meetings. If there is no action item, or discussion point proposed in advance, the meeting is not the forum for first initiating a discussion.
Action Items
http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting_Minutes_April_2008#ACTION_ITEMS
Ontology Content Development
Work in progress
- MF-BP links : Function-Process_Links
- (Note from the managers' meeting: Chris has been updating the wiki pages; we should probably organize that by 'types' of links to be adding; this also involves the new relations to be added)
- Outline of scope of project, progress report (Chris, ~25 slides)
- relations to be used - part_of, has_part and regulates
- Implementation plan
- Automatically extracting links from pathway databases
- Manually curated links - pilot projects (Jennifer, Harold)
- The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 Slides)
- Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered
- Ontology content QC
- Ongoing regulation-term QC (David, Tanya, Chris) - think this is covered?
- Category:Cross Products - use of XP defs and logical reasoning to do QC. See XP:Progress 2008. (~5 slides, Chris)
- "Trigger" files for annotation QC - first set based on taxon correlation (Jennifer, Chris)(Jennifer presenting 11 Slides)
- Signal transduction - New high level term proposal (Jennifer, David)
- Jennifer and David have been working on a proposal for a new set of high level signaling terms. The new terms are ready to go live and we present them for comment. (~5 min talk) Slides
- Processes affecting cellular components, e.g. CC organization and biogenesis (Midori, Jane, David?)
- PAMGO collaboration - brief report on new term additions and QC (Jane)
- Collaboration with IMG to map to IMG terms to GO terms (Jane)
- Peptidase activity terms - reorganization completed
Ontology development discussion topics
- Setting priorities across different types of content development task
- How to allocate effort among (a) overall logical enhancements (e.g. improving genus-differentia aspects of definitions or adding new relationship types); (b) keeping up with SF submissions; (c) content meeting changes; anything else
- More generally, what's the right balance between retrofitting the existing ontology (definition style, relationship types just two examples) versus new additions?
OBO-Edit
- Update on latest version (Amina)
- Using Reasoner and Cross-product definitions for Ontology QC and automated ontology management (Amina and Chris)
- OBO-Edit progress statistics
- Michael Schroeder et al. plug-in
- Sourceforge Bug Tracker
- Sourceforge Feature Requests
- Download the latest OBO-Edit2 beta
Organization/Management
- SourceForge clearout done
- Possible forthcoming changes to day-to-day editing practices (David, Midori, Chris?)
- Creating and using cross-products
- Using new relationship types
- Integrating QC into editing pipeline
General Annotation
Evidence Codes
- Using the ECO as the primary source (and definition) for evidence codes. The documentation should reflect (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.
Plan to get some people together to work on it for 2-3 days and fix it (somewhat)
- Electronically curated flag in GAF proposal
Annotation and ontologies
- A (re-)introduction to the new column 16, Annotation_Cross_Products
- Ontological relationships between gene products and functions, processes and components
GO Database
- APIs
- GHOUL GO Hibernate Object Utility Layer. An API to the GO database for Java programmers
- Lucene indexing
- Regular reporting of statistics, sanity checks, and such on the GO database.
- New way of calculating the Transitive_closure
Taxa
- How to address the problem that comes up in trying to do dual taxon annotations when one of the partners has no taxon ID number at NCBI [e.g. when a microbe is interacting with a plant which has no taxon ID number (and this also is a problem because different cultivars of a plant also do not have different ID numbers)]. Can we discuss how to handle the requirement for a taxon ID (especially the second one in the Dual Taxon situation) when one has not yet been assigned by NCBI? -Candace Collmer
- Update on loading dual taxon into database/AmiGO
22 OCT AM: Reference Genome 1/2 day
8:30 PANTHER update
Paul and Kara
- generating homology sets, including protein set generation
- process for making ISS inferences
Discussion about protein set generation
Paul (add documentation)
- Regarding gp2protein files: The original aim was to support BLAST server.
- Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??
- Issues:
- augumentation: try to work with Swiss Prot?
- isoforms vs canonical protein : try to work with Swiss Prot?
- complete proteome; partial gene predictions
Progress on tracking/curation tool (TCT)
- Chris will be presenting the tracking tool
- Suzi : Curation tool
Improvements in annotation depth and breadth
(Chris and Mike's data)
Improvement in ontology structure
- Examples of ontology changes stemming from Reference Genome annotation (David?)
Annotation Consistency and Quality Issues
Pascale
- HTP evidence code?
- Discuss use of binding/regulation terms (GOC meeting)
- Establish guidelines for annotation to a process versus regulation of that process
- Process IC or IDA? (from Jamboree 18 July 2008-minutes; example : GCH1)
- There will likely be several other topics to discuss from the two electronic jamborees; so far: Reference_Genome_Annotation_Project#Annotation_Consistency_Issues
Web presence, Outreach and User Advocacy
Outreach
- Short update on Outreach going on throughout the Consortium. Highlights presented by Tanya Berardini (Author submission of annotations - 3 Slides) and Michelle Gwinn-Giglio (PAMGO outreach and University of Maryland Annotation courses - 6 Slides).
- Swiss-Prot to do GO annotations (Michael)
AmiGO 1.6 for Reference Genome (Seth & Amelia)
- Present progress on AmiGO graphical views
Resource Usage statistics (Mike)
User Support
- Evaluation of helpdesk performance
GO Papers, Publications and Presentations
- Ref Genome paper status report
- AmiGO app. note
- News letter impact
Other items
Consortium meetings
- Next GOC meeting : Coordinate with Third International Biocurator Meeting, Berlin, April 16-19, 2009?
Breakout sessions to fit in somehow
- Final preparations for SAB meeting
- Amina, Chris and OBO-Edit users (including cross-products)
- Pascale, Suzi and reference genome curators
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