wiki:annotationSanityChecks

Version 7 (modified by val_wood, 9 years ago) (diff)

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GO already implements some sanity checks: http://geneontology.org/GO.annotation_qc.shtml

Additional GO checks

Take care using "NOT" qualifier with GO MF annotations supported by IMP

Care if knocked out a gene and found expected process was not affected (negative result), need further experiments to deduce whether gene is responsible but role is masked by another gene product

Pombase rules based on biology:

Start to list here, group by type

Extensions scope, not encoded in obo file

tRNA as substrate is only possible with RNA pol III promoter

Matrix related

Examples

Transmembrane transport has no overlaps with DNA metabolism Transmembrane transport has no overlaps with translation

I sent a test list to Amlelia but I don't think any progress was made, I will dig out and add rules here

  • If A is true B is always true All transmembrane transporters should have integral to membrane EXCEPT (list complexes) Use for /if this then this F/P C/P is rules cannot be wired into ontology
  • Reciprocal annotations which are always true

reciprocal annotation GO/FYPO binding target of/ is substrate reciprocal annotation that can be inferred from extension i.e process dependent on localisation to -> component required_by process etc

Regulation

Matrix related