GO Timeline

From GO Wiki
Jump to navigation Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

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)