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sys-bio / libOmexMeta

libOmexMeta is a library aimed at providing developer-level support for reading, writing, editing and managing semantic annotations for biosimulation models.
https://sys-bio.github.io/libOmexMeta/
Apache License 2.0
8 stars 6 forks source link

Create OMEX files from Biomodels rdf files and check them #42

Open hsauro opened 3 years ago

hsauro commented 3 years ago

All models from biomodels had their annotations extracted and put into rdf files. Create the equivalent omex files that combine the rdf file and associated model. Send biomodels a link to the list of omex files.

nickerso commented 3 years ago

also need to check if the inferred semantic annotations in libOmexMeta match those generated when doing this in SemGen.

CiaranWelsh commented 3 years ago

Releant to the first step in this issue: What is the best way to download the curated section of biomodels is these days? I used to use BioServices.BioModels() in Python, but it now appears broken. I also once wrote a simple web scraper using Python requests module, but that's a bit of a pain. What is the official way to do this?

CiaranWelsh commented 3 years ago

https://sys-bio.github.io/libOmexMeta/docs-build/download_biomodels/download_biomodels.html

jonrkarr commented 3 years ago

@CiaranWelsh BioModels provides a REST API: https://www.ebi.ac.uk/biomodels/docs/

Lucian and I have also been working on cleaning up BioModels. This is in a Git repo: https://github.com/sys-bio/temp-biomodels. If you just need temporary access, you can simply clone the repo to get all of the SBML files.

jonrkarr commented 3 years ago

@hsauro where are these RDF files? They're not on the BioModels website or available from the REST API?

If we can see this, we try to make BioSimulations as consistent with this as possible.