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Update editor guidelines re: standardising database_cross_reference and contributor annotations #2058

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21 changes: 20 additions & 1 deletion docs/editing_guidelines.md
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Expand Up @@ -78,7 +78,7 @@ The following considerations apply both to all human-readable fields (names, tex


## Cross-references to the literature
Assertions in textual definitions, evidence provided in comments, and synonyms should be as much as possible backed up by citing the appropriate literature.
Assertions in textual definitions, evidence provided in comments, and synonyms should be backed up by citing the appropriate literature.

Citations are made by cross-references, that is by adding `http://www.geneontology.org/formats/oboInOwl#hasDbXref` annotations to the definition, comment, and synonym annotations. Add one such annotation per reference, using the CURIE syntax with well-known prefixes:

Expand All @@ -90,6 +90,25 @@ If the main source for an assertion is a term in another ontology, the short ide

ORCID identifiers may also be used when the only available source for an assertion is an individual researcher. This should be done sparingly.

**Technical details of adding a cross-reference using Protégé**:

For all: In the "Create Annotation" window, select the annotation property **database_cross_reference**.

If the cross-reference can be represented as a CURIE and is not an ORCID: Enter the CURIE, using the bioregistry standard prefix, as a Value on the "Literal" tab. Leave Datatype empty.
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Non-CURIE values (e.g., URLs) are discouraged, but when used are also entered the same way, i.e., as a literal string with no Datatype selected.
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In cases where more than one CURIE is available for a resource, e.g., both a PMID and a doi are available, there is no preference for one over the other.
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If the cross-reference is an ORCID, enter the ORCID as an IRI in the IRI field on the “IRI Editor” tab.
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To restate, in all cases except ORCIDs, the CURIE is preferred and entered as a literal string. For ORCIDs, the IRI is preferred and is entered as an IRI.
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The above instructions apply whether the cross-reference is added to another annotation (e.g., annotating a text defintion or comment) or adding to the overall class (i.e., not an annotation of another annotation).

## Term contributors

When adding an ORCID to identify a term contributor, in the "Create Annotation" window, select the annotation property **dcterms:contributor**. The ORCID is still entered as an IRI on the “IRI Editor” tab.
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## Formal definitions
The formal definition of a class is made up of all the logical axioms about the class (as opposed to the annotation assertion axioms). This includes classification assertions, relationship assertions, equivalence assertions, and disjointness assertions.
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