Reorganise the hierarchy under fluorescent protein tag#10
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Add classes to group the fluorescent protein tag terms according to the colour of the protein tag (`green fluorescent protein tag`, `yellow fluorescent protein tag`, etc.). Re-classify all existing fluorescent protein tag terms under the grouping terms that are appropriate for them. For example, `EGFP` is classify as both: - `green fluorescent protein tag` - `fluorescent protein derived from Aequorea` We then redefine `Green fluorescent protein from Aequorea` to be equivalent to `green fluorescent tag AND fluorescent protein derived from Aequorea`, so that EGFP gets automatically classified accordingly. Likewise for all other similar terms.
PA-GFP is a photoactivatable variant of EGFP, so it can be explicitly classified as a subclass of EGFP. Likewise for a few other photoactivatable or photoswitchable tags.
Labels should not start with an uppercase letter, unless the label refers to a proper noun.
lubianat
approved these changes
Jan 30, 2026
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I did not check in Protégé, but it seems correct as far as I can tell. At least the terms look better sorted now. |
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This PR implements the reorganisation proposed in #8.
That is, it add classes to group the fluorescent protein tag terms according to the colour of the tag (
green fluorescent protein tag,yellow fluorescent protein tag, etc.).Then, all existing terms for fluorescent protein tags are re-classified under the appropriate grouping terms. For example,
EGFPis reclassified as, simultaneously:green fluorescent protein tag, andfluorescent protein derived from Aequorea.Lastly, the existing terms that group the tags according to both their colour and their organism of origin are redefined using a logical definition. For example,
Green fluorescent protein from Aequoreais redefined to be equivalent'green fluorescent tag' and 'fluorescent protein derived from Aequorea'.(Ideally, I’d like to axiomatise the statements about the organisms of origin, but this is tricky as the terms here really represent visualisation methods, not the actual protein tags. So we can’t really say, for example, that
EGFPderives fromAequorea victoria– regardless of which relation we use for that – because it would be wrong to say that a visualisation method derives from an organism…)