-
Notifications
You must be signed in to change notification settings - Fork 11
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
Handling letter-case in IDs in a consistent, easy-to-maintain way #735
Comments
The first step is figuring out the identifier-case formats for each of the namespaces we use. I'm likely the lead on this. It'll take a bit of time, but not be too difficult, to review the namespaces we use and find those with lower-case letters in their IDs (aka the exceptions). (It's unnecessary to make a list of all namespaces we use, which ones of those have IDs w/ letters, which ones of those have all-caps...) But there's an issue that I think needs untangling: I'm not clear on Translator's standards for identifier-case format. It's not clear from a quick look at the biolink-model repo...
|
FWIW, NodeNorm doesn't expect identifiers to be purely numerical. Here is the current distribution of CURIE prefixes with non-numerical identifiers in NodeNorm:
If the list of all those identifiers will be useful to you (it's 2.9G compressed), please let me know and I can send it over! |
This table of namespaces + example IDs is great. We don't need a list of all IDs for a namespace; the examples here are fine. |
Note to self: there are examples where there's a mix of lettercase in the ID itself - FB (flybase) and WormBase. See Gaurav's list above. |
I had a discussion with Sierra Moxon (Translator data-modeling team), on my concerns with Translator standards:
However, it's unclear how to resolve the issues/discrepancies (Translator-wide)
|
Background
During the JQ work, we encountered an issue with an external API (CTD) and the letter-case of the bioentity IDs in its responses (ref: Jackson's comment and my reply):
KEGG.PATHWAY
IDs should have lower-case letters (ex:hsa05323
) but our api-response-transform module code was transforming the response's ID strings to all-caps.Issue
We realized that this was a larger issue (ref: my braindump here, a "current situation" post here):
The text was updated successfully, but these errors were encountered: