gorule-0000013.md

layout	id	title	type	fail_mode	status	contact	implementations
rule	GORULE:0000013	Taxon-appropriate annotation check	report	soft	approved	go-quality@lists.stanford.edu	language source python https://github.com/biolink/ontobio/blob/master/ontobio/io/qc.py

• GO taxon constraints ensure that annotations are not made to inappropriate species or sets of species. This information is obtained from the only_in_taxon and never_in_taxon tags in the ontology (maintained in go-ontology/tree/master/src/taxon_constraints).
• Experimental annotations (1) failing the taxon constraints are reported in the error reports but unchanged; non-experimental annotations (2) are filtered out of the pipeline products. (1) EXP evidence codes: EXP, IDA, IEP, IGC, IGI, IMP, IPI, HDA, HEP, HGI, HMP, HTP. (2) non EXP annotations: IBA, IKR, IRD, IC, ISA, ISM, ISO, ISS, NAS, RCA, TAS, IEA.
• Taxon constraints DO NOT apply to negated (NOT qualifier in GPAD/GAF) annotations.

Implementation Notes

The current implementation of this in GO makes use of the Elk reasoner, wrapped by the gaferencer tool. This tool produces a gaferences.json file (see this example file), which includes all OWL inferences over the GAF. A subset of these are taxon violations.

An example:

{
    "annotation":{
        "annotation":{
            "relation":"http://purl.obolibrary.org/obo/RO_0002331",
            "term":"http://purl.obolibrary.org/obo/GO_0098706"
        },
        "taxon":"http://purl.obolibrary.org/obo/NCBITaxon_10090",
        "extension":[
            
        ]
    },
    "inferences":[
        
    ],
    "satisfiable":false,
    "taxonProblem":true
}

This particular class is not valid for Mouse (NCBITaxon:10090)

The gaferences files is processed in the pipeline via ontobio and includes alongside other GO rules reports.

Publications

See http://www.biomedcentral.com/1471-2105/11/530 for more details.