+ Multi-organism GO annotation David Osumi-Sutherland Gene Ontology.

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Presentation transcript:

+ Multi-organism GO annotation David Osumi-Sutherland Gene Ontology

+

+ “rif... [is] expressed on the infected red [blood] cell surface.” Plasmodium falciparum GP of one organism in CC of another

+ Plasmodium falciparum | Homo sapiens The species in the interaction are recorded... by entering two taxon IDs in the Taxon column: First taxon ID: species encoding the gene product First taxon ID: other species in the interaction. GP of one organism in CC of another

+ Plasmodium falciparum | Homo sapiens The species in the interaction are recorded... by entering two taxon IDs in the Taxon column: First taxon ID: species encoding the gene product First taxon ID: other species in the interaction. Why not just plasma membrane? GP of one organism in CC of another

+ A duplicate cell component branch is growing under host-cell Why? Keeps annotations of gene products located in CCs of host organism separate from regular GO CC annotations.

+ A duplicate cell component branch is growing under host-cell Many terms duplicate the regular cell component hierarchy. THIS IS NOT SUSTAINABLE Some terms refer to components that are formed from the interaction of 2 organisms. Add new parent class for these: multi-organism cell component

+ Proposed solution Plasmodium falciparum parasite_of Homo sapiens located_in GO: plasma membrane + annotation extension: part_of Homo sapiens

+ Proposed solution Plasmodium falciparum parasite_of Homo sapiens located_in GO: plasma membrane When used, replaces part_of as default GP to CC relation in GPAD Tools used for grouping annotations need to group these annotations separately. Precedent: NOT New qualifier / GP to CC relation: located_in + annotation extension: part_of Homo sapiens

+ Proposed solution Plasmodium falciparum parasite_of Homo sapiens located_in GO: plasma membrane New qualifier / GP to CC relation: located_in + annotation extension: part_of Homo sapiens Replace host CC term with regular one, recording the taxon of the organism it is part of in the annotation extension.

+ Proposed solution Plasmodium falciparum parasite_of Homo sapiens located_in GO: plasma membrane Taxon extension – using standard relations between organisms : host_of, symbiont_of, parasite_of vector_for… Relations defined with population and community ontology (PCO) + annotation extension: part_of Homo sapiens

+ Proposed solution – retrofit when host not recorded Plasmodium falciparum symbiont_of host organism * located_in GO: plasma membrane + annotation extension: part_of host organism * * Generic host organism class from PCO

+ Homo sapiens | Human rhinovirus 3 Multi-organism process annotation

+ Homo sapiens host_of Human rhinovirus 3 Proposed solution + annotation extension: occurs_in Homo sapiens Optionally record where the process takes place

+ mate_of host_of, parasite_of, vector_for host_of/parasite_of bitten_by ? pregnant_mother_of ? / fetus_of ?

+ Acknowledgments Jane Lomax Rebecca Foulger Chris Mungall Ramona Walls (PCO – relation defs) Jie Zheng (PCO – relation defs)