This is such a wide-reaching statement that few curators would want to make.
This rule only applies to GO:0005515; children of this term can be qualified with not, as further information on the type of binding is then supplied in the GO term; e.g. not + NFAT4 protein binding ; GO:0051529 would be fine, as the negative binding statement only applies to the NFAT4 protein.
For more information, see the binding guidelines on the GO wiki.
]]>For more information, see the binding guidelines on the GO wiki.
]]>This will be a soft QC; a script will make these inferences and it is up to each MOD to evaluate and include the inferences in their GAF/DB.
For more information, see the binding guidelines on the GO wiki.
]]>
gene product: protein A
GO term: protein binding ; GO:0005515
evidence: IPI
reference: PMID:123456
with/from: with protein A
this annotation line can be interpreted as: protein A was found to carry out the 'protein binding' activity in PMID:12345, and that this function was Inferred from the results of a Physicial Interaction (IPI) assay, which involved protein X
However if we would like to transfer this annotation to protein A's ortholog 'protein B', the ISS annotation that would be created would be:
gene product: protein B
GO term: protein binding ; GO:0005515
evidence: ISS
reference: GO_REF:curator_judgement
with/from: with protein A
This is interpreted as 'it is inferred that protein B carries out protein binding activity due to its sequence similarity (curator determined) with protein A, which was experimentally shown to carry out 'protein binding'.
Therefore the ISS annotation will not display the the interacting protein X accession. Such an annotation display can be confusing, as the value in the 'with' column just provides further information on why the ISS/IPI or IGI annotation was created. This means that an ISS projection from protein binding is not particularly useful as you are only really telling the user that you think an homologous protein binds a protein, based on overall sequence similarity.
This rule only applies to GO:0005515, as descendant terms such as mitogen-activated protein kinase p38 binding ; GO:0048273 used as ISS annotations are informative as the GO term name contains far more specific information as to the identity of the interactor.
For more information, see the binding guidelines on the GO wiki.
]]>For more information, see the binding guidelines on the GO wiki.
]]>For more information, see the catalytic activity annotation guide on the GO wiki.
]]>We provide and maintain the list of too high-level terms as two subsets in the ontology:
Both subsets denote high level terms, not to be used for any manual annotation.
For inferred electronic annotations (IEAs), we allow the use of terms from the gocheck_do_not_manually_annotate subset. These terms may still offer some general information, but a human curator should always be able to find a more specific annotation.
]]>This is proposed as a HARD QC check: incorrectly formatted references will be removed.
]]>The SQL code identifies all ND annotations that do not use GO_REF:0000015 or one of the alternative internal references listed for it in the GO references file.
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