---
layout: rule
id: GORULE:0000013
title: "Taxon-appropriate annotation check"
type: report
fail_mode: soft
status: approved
contact: "go-quality@lists.stanford.edu"
implementations:
  - language: python
    source: 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](https://github.com/geneontology/gaferencer) tool. This tool produces a gaferences.json file (see [this example file](http://release.geneontology.org/2021-02-01/reports/mgi.gaferences.json)), which includes all OWL inferences over the GAF. A subset of these are taxon violations. 

An example:

```json
{
    "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](http://www.biomedcentral.com/1471-2105/11/530)
for more details.