SWUG:Meeting 2007 09 19

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Meeting notes

Present: Chris, Suzi, Mary, Seth, Ben

Review of previous action items

  • ID Tracking : Chris, Mary to send RQs to Stan


  • Create mapping files (Dan)


  • Ben to add tests for graph loading issues


  • Loading orthology into main database

Mary has tried local DB, had problems. Added 2 tables, for targets and orthology

TODO: Schema review at princeton

Mary will also come across to Berkeley. Will discuss dates next week.

  • Inter-ontology intra-GO ontology linkages. Document this (Chris)
 Discussed implications for database loading in particular graph_path filling. Plan: Use the OBO-Edit code for building path table in future.


Meeting prep


  1. Is everyone going to the mtg next week?
  2. Who is staying for refgenomes?
  3. Any agenda items to add?

Ben coming for advisors

  • Berkeley + Mary to meet on saturday night. Send numbers

Of relevance to SWUG:

Sunday Morning:

  • Aim1, ontology development. ontology structure: Chris
  • Aim2, refGenomes. Mention web presence here?
  • Aim3, annotation. Obo-Edit(???) John reporting
  • Aim4, Providing annotations and tools to Users. Production: Ben. AmiGO: Chris and Amelia

- Chris will report on database in AmiGO section

Monday afternoon

  • Cross-products
  • GO - taxon links

- John will report on ORB/term requests


  • refG tools (Chris, with help fromm Mary and Seth)

Action items from last GOC meeting

We will go through action items of relevance to the SWUG to help speed things up at the GOC meeting

Taken from: http://gocwiki.geneontology.org/index.php/Action_Items

  • 2. Action Item (Hub): Make proposals for various displays of reference genome data
  • 10. Action Item for John: Add a term creation date to the .obo file.
  • 22. Action Item for John: Link OBO-Edit docs to geneontology.org from oboedit.org.
  • 32. Action Item (AWG): Explore whether this [Mary's graphs] would be a useful addition to AmiGO 2.0.
  • 33. Action Item (AWG): There should be more tracking of what users are doing in the next AmiGO; explore the options.
  • 34. Action Item (Seth & AWG): Discussed that these changes should be reflected in AmiGO.
  • 38. Action Item (AmiGO Working Group): Change AmiGO to hide (by default) structured comments of certain types. Obsolete comments will not be shown. Structured comments that don’t belong will not be shown. Have option to hide comments.

We think this is a bad action item

ACTION: fix gene_ontology_edit.obo

  • 50. Action Item (MGI, SGD): Change all pipes to commas.
  • 51. Action Item (Chris, Ben): Work through any database implications.


  • 74. Action Item (Chris, Jane, Harold): Create concrete proposal for linking between all GO ontologies, get relationship ontology up to speed, do pilot project in metabolism.
  • 75. Action Item (Amelia): Talk to Stanford about monthly archive release notes.


Progress report for NIH

  • Suzi will send today

Reports and Discussion


  • Reasoner speedups x10
  • office hours are v useful
  • XP editor


  • Architecture refactoring
  • Biaxial
  • map2slim and termfinder chained together

Reference Genomes

  • RoR curation interface status - still to look up
  • Mary will send schema details to list

Documentation & Outreach

Software Architecture, Schema and Modeling

  • go-perl release on CPAN
  • DBStag release on CPAN
  • latest schema changes
  • consider/replaced_by
  • synonymtypedefs
  • by-species gene product counts
  • taxon


  • gp2protein reports
  • integrating latest changes into production
  • sequence loading speedups
  • NCBI sequence taxonomy updated

Presentations and papers

  • amigo paper


Review of Action Items