Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Same term names belonging to several scales bring issue for Chado schema #17

Open
guignonv opened this issue Jan 10, 2018 · 0 comments
Open

Comments

@guignonv
Copy link

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant