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
- Filter step removes bleeding-edge links and 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)
- Regulation (see XP:biological_process_xp_regulation, XP:molecular_function_xp_regulators, and Regulation_cross-products
- Subset of XP:biological_process_xp_self that use has_part differentiae
- Subset of XP:cellular_component_xp_self that use has_part differentiae
- 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)