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Chado schema is well spread and manages ontologies using the CV module. In this module, the cvterm table as constraint that basically says: "a given term name can only appear once in a same controlled vocabulary".
This means, for instance, we can not load more than one "green" (shared by colour charts A and B) or "other" (shared by many traits) terms in the Banana_ontology controlled vocabulary. It will also be an issue when we are dealing with a 1996 and a 2016 scale. A workarround is to create a different namespace for each scale. The Chado ontology (obo) loader will load terms in separate controlled vocuabularies.
Doing so, for instance for "rachis appearance scale (1 to 5)" and "bunch shape scale (1 to 5)" (and others), we would have 2 different namespaces, both having a dedicated "other" term. Likewise, we would have a BananaScaleColourChartA and a BananaScaleColourChartB namespaces wich will both have a "green" term without issue. However, those 2 namespaces will be shared accross traits using thoses scales.
But there is still an issue with this solution for colour scales: how to say that, for a given trait, only a subset of colours in a chart can be used? And also, to what colour corresponds a given numeric code for a given trait; for instance "6.3.6 Petiole margin colour" color 1 is "Cream" and "6.3.22 Pigmentation of outer surface of cigar leaf" color 1 is "Green" while both uses the colour chart A.
The text was updated successfully, but these errors were encountered:
Chado schema is well spread and manages ontologies using the CV module. In this module, the cvterm table as constraint that basically says: "a given term name can only appear once in a same controlled vocabulary".
This means, for instance, we can not load more than one "green" (shared by colour charts A and B) or "other" (shared by many traits) terms in the Banana_ontology controlled vocabulary. It will also be an issue when we are dealing with a 1996 and a 2016 scale. A workarround is to create a different namespace for each scale. The Chado ontology (obo) loader will load terms in separate controlled vocuabularies.
Doing so, for instance for "rachis appearance scale (1 to 5)" and "bunch shape scale (1 to 5)" (and others), we would have 2 different namespaces, both having a dedicated "other" term. Likewise, we would have a BananaScaleColourChartA and a BananaScaleColourChartB namespaces wich will both have a "green" term without issue. However, those 2 namespaces will be shared accross traits using thoses scales.
But there is still an issue with this solution for colour scales: how to say that, for a given trait, only a subset of colours in a chart can be used? And also, to what colour corresponds a given numeric code for a given trait; for instance "6.3.6 Petiole margin colour" color 1 is "Cream" and "6.3.22 Pigmentation of outer surface of cigar leaf" color 1 is "Green" while both uses the colour chart A.
The text was updated successfully, but these errors were encountered: