hattrill
commented
5 months ago Noctua is done. P2GO needs more information:
Hi Helen,
Regarding loading FlyBase anatomy into Protein2GO, this is the information we have from WormBase.
We’d need to know which branch of Fly anatomy we should load, and if it has a GO equivalence.
Also, we need to know for each of the extension relations, which top Fly anatomy term is allowed.
Can you provide this information ? Let me know if it’s not clear.
Thanks, Pascale
Here what the GOA database has to enable annotation extensions as an examples from WB.
From GO-UPPER.OBO you can see
[Term] id: WBbt:0004017 is_a: GO:0005623 ! cell
result in the GOA database in following entity->parent relation
WBbt:0004017 GO:0005623
following data from go-upper.obo also extracted
WBbt:0005766 UBERON:0001062 WBls:0000002 WBls:0000075 WBls:0000075 nematoda life stage UBERON:0000105 WBls:0000091 WBls:0000075 WBls:0000101 WBls:0000075
From GOREL.OBO in "property_value: local_range":
[Typedef] id: has_end_location name: has end location def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: AE_cell_or_anatomical subset: AE_cellular_component subset: display_for_curators subset: ro-eco subset: valid_for_annotation_extension xref: RO:0002232 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string property_value: local_domain BFO:0000015 xsd:string property_value: local_range "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1" xsd:string property_value: usage "Use this relation to relate a biological process to the location (cell component, cell type, anatomical location) in which the process ends. Examples include recording the cell-type or cellular compartment in which a cell-cell signalling process ends. To record a location in which the entire process occurs, please use 'occurs in'." xsd:string domain: BFO:0000015 range: BFO:0000004 is_a: go_annotation_extension_relation ! go annotation extension relation is_a: has_part_that_occurs_in ! has part that occurs in
results in the GOA DB as following
has_end_location WBbt:0004017 has_end_location WBbt:0005766
and for other relations data extracted as bellow. Something similar needs to be added for FlyBase.
Thanks,
Alex
acts_on_population_of WBbt:0004017 results_in_determination_of WBbt:0004017 results_in_commitment_to WBbt:0004017 results_in_acquisition_of_features_of WBbt:0004017 regulates_o_results_in_specification_of WBbt:0004017 regulates_o_results_in_movement_of WBbt:0004017 has_start_location WBbt:0004017 results_in_movement_of WBbt:0004017 occurs_in WBbt:0004017 results_in_morphogenesis_of WBbt:0004017 part_of WBbt:0004017 results_in_maturation_of WBbt:0004017 results_in_division_of WBbt:0004017 regulates_o_occurs_in WBbt:0004017 results_in_formation_of WBbt:0004017 regulates_o_results_in_acquisition_of_features_of WBbt:0004017 results_in_specification_of WBbt:0004017 regulates_o_results_in_development_of WBbt:0004017 results_in_development_of WBbt:0004017
results_in_development_of WBbt:0005766 regulates_o_results_in_development_of WBbt:0005766 regulates_o_occurs_in WBbt:0005766 part_of WBbt:0005766 occurs_in WBbt:0005766 has_start_location WBbt:0005766 regulates_o_results_in_acquisition_of_features_of WBbt:0005766 results_in_morphogenesis_of WBbt:0005766 results_in_maturation_of WBbt:0005766 results_in_formation_of WBbt:0005766
existence_overlaps WBls:0000075 exists_during WBls:0000075 existence_starts_and_ends_during WBls:0000075 happens_during WBls:0000075 part_of WBls:0000075
Talk to GOC and P2GO about adding FBdv and FBbt to annotation tools.