GO Timeline

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Changes made to date

  • start publishing go_ext (contains the MF-MF intraontology links and the BP-MF interontology links)
  • put in place process for conversion of files

old pipeline:

go_write --cp--> obof1.2 --> obo2obo --> obof1.0

new pipeline:

go_write --cp--> go_ext  --filter links and tags --> obof1.2 --> obo2obo --> obof1.0
Filter step removes bleeding-edge links and tags
  • MF-MF regulates links (March 2009)
  • MF-BP links
    • regulates (March 2009)
    • part_of (May 2009)
  • has_part links (coming June-July2009)
  • intersection_of tags (coming June-July 2009)
  • created_by and creation_date metadata tags
  • release of Inter-Ontology 'regulates' links
  • OE2 live: will include created_by and creation_date tags (this info will get filtered out as well for now)
  • Test incorporation of has_part links; release into go_write and go_ext

Forthcoming changes

June-July 2009

  1. Regulation (see XP:biological_process_xp_regulation, XP:molecular_function_xp_regulators, and Regulation_cross-products
  2. Subset of XP:biological_process_xp_self that use has_part differentiae
  3. Subset of XP:cellular_component_xp_self that use has_part differentiae
  4. XP:cellular_component_xp_go
  • Q: how to present the intersection_of tags in AmiGO, make them human readable


3rd quarter 2009

  • switch to using the go-db-reasoner.pl (new way of filling in the graph path table, takes into account the relations -- see Transitive_closure)
  • Relation filter in Amigo (uses go-db-reasoner.pl)
  • Population of godb from go_all (ignore intersection_of tags when loading into db)

Anytime, not dependent on any of the other changes above

  • Release of gene_association file, col16 (annotation cross-products) - March 2009
Test cases
MGI: cross products to cell ontology (relations: located_in, occurs_in)
TAIR: cross products to plant ontology (check relations used in conjunction with PO terms)
population in db (April 2009)
AmiGO (Dec. 2009)
  • Release of gene_association file, col17 (gene product) - March 2009
Test cases
Wormbase, MGI, TAIR
population in db (April 2009)
AmiGO (Dec. 2009)


Further on

Transition to XML for gene_association files, instead of tab-delimited (still provide the 'flattened' files for consumer)