20th GO Consortium Meeting: Difference between revisions
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* PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members. Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutions. Also will touch on alternate taxon id resources that we might want to incoroporate. (Candace and Michelle) | * PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members. Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutions. Also will touch on alternate taxon id resources that we might want to incoroporate. (Candace and Michelle) | ||
* Update on loading dual taxon into database/AmiGO. Also will touch on alternate taxon id resources that we might want to incoroporate. (Michelle and Chris) | * Update on loading dual taxon into database/AmiGO. Also will touch on alternate taxon id resources that we might want to incoroporate. (Michelle and Chris?) | ||
==22 OCT AM: Reference Genome 1/2 day== | ==22 OCT AM: Reference Genome 1/2 day== |
Revision as of 10:05, 19 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)
- Michelle will be ECO editor
- HTP evidence code? (Eurie)
- Electronically curated flag in GAF proposal
- New subcodes of IGC will be going into ECO: inferred from system reconstruction (ISR) and inferred from genome cluster (ICL). Currently IGC encompasses more than one type of evidence - it includes both pathway reconstruction/protein complex reconstruction and also operon structure/synteny. In order to be able to more precisely describe which was used we want to have the two new codes. These are currently being used by the Bioinformatics Resource Centers (BRCs). This was discussed on the evidence code mail list and there was no objection. (Michelle)
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
PAMGO report on successes and some problem annotations from consortium members
- PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members. Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutions. Also will touch on alternate taxon id resources that we might want to incoroporate. (Candace and Michelle)
- Update on loading dual taxon into database/AmiGO. Also will touch on alternate taxon id resources that we might want to incoroporate. (Michelle and Chris?)
22 OCT AM: Reference Genome 1/2 day
8:30 Progress Report
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?)
8:45 progress on homology sets and homology inference
Paul and Kara
- generating homology sets, including protein set generation
- new paradigm for making homology inferences
- process and implementation for homology set selection, and homology inferences
Discussion about protein set generation
Paul
- Issues:
- incompleteness
- splice forms vs canonical protein
- complete proteome; partial gene predictions
- possible solution: try to work with Swiss Prot?
- Paul will present problems identified so far
- We will add documentation as to how to generate files and protein sequences
- 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??
10:45 Annotation Consistency and Quality Issues
Pascale
- How to improve documentation
- How to address the QC issue
- Make working groups for recurrent problems:
- binding
- regulation
- most evidence codes
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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