search

draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
MIT License
23 stars 7 forks source link

Update MIRIAM Registry to support new collections #80

Closed mephenor closed 4 years ago

mephenor commented 4 years ago

Current identifiers.org registry file is outdated (version from 22 Jun 2018) and should be updated.

draeger commented 4 years ago

There should be a mechanism that updates this automatically upon building the project.

matthiaskoenig commented 4 years ago

Just some information, because I have been there with another project: The old XML registry file is still working but will likely be deprecated in the near future (at least is the feedback I got when asking for changes in the dateformat). The latest registry content is now available via the api https://docs.identifiers.org/articles/api.html via the getResolverDataset

Resolver dataset

Endpoint: https://registry.api.identifiers.org/resolutionApi/getResolverDataset
Method: GET
Description: Returns a copy of the whole registry.
Example: https://registry.api.identifiers.org/resolutionApi/getResolverDataset

Not sure if you use the libmiriam/libregistry, but probably must be rewritten with the new JSON format.

Best M

mephenor commented 4 years ago

Custom parser for registry is implemented in refactoring branch now and should interact with all places in the code where annotations are handled correctly. Still need to add tests before merging into master

Edit: Current registry is pulled from identifiers.org when building ModelPolisher

Schmoho commented 2 years ago

This appears to work fine. As the issue has been closed, I am moving it to finished.