GO Timeline

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

• Cull %.ontology files. Announced on GO friends; done August 2009

Forthcoming changes

June-July 2009

• Incorporate internal cross-products (using intersection_of tags)

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)