Problem with MSIO import

[teisnotte]

Hello there,

I'm new to ontology and I'm running a startup script for an ontology that I'm creating. sh seed-via-docker.sh -c -C XXX.yaml However, it seems I cannot find the MSIO file based on my configuration file. How can I solve this?

First 5 violations:
WARN	missing_definition	root node	IAO:0000115
WARN	missing_definition	description	IAO:0000115
WARN	missing_definition	license	IAO:0000115
WARN	missing_definition	title	IAO:0000115
INFO	missing_superclass	root node	rdfs:subClassOf
curl -L http://purl.obolibrary.org/obo/msio.owl --create-dirs -o tmp/msio-download.owl --retry 4 --max-time 200 && \
robot --catalog catalog-v001.xml convert -i tmp/msio-download.owl -o tmp/mirror-msio.owl
INVALID ONTOLOGY FILE ERROR Could not load a valid ontology from file: msio-download.owl
For details see: http://robot.obolibrary.org/errors#invalid-ontology-file-error
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.

This is the ontology: https://www.ebi.ac.uk/ols4/ontologies/msio

[jamesaoverton]

Sorry, MSIO has never been registered with the OBO Foundry, so it is not eligible to use the OBO PURL system.

• no match for "msio" on the OBO Foundry home page: https://obofoundry.org/
• no match for "msio" searching the OBO registry on GitHub: https://github.com/search?q=repo%3AOBOFoundry%2FOBOFoundry.github.io%20msio&type=code
• no match for "msio" in the OBO PURL repository (except for this issue Problem with MSIO import #1036): https://github.com/search?q=repo%3AOBOFoundry%2Fpurl.obolibrary.org%20msio&type=code

When I look at MSIO on OLS4 https://www.ebi.ac.uk/ols4/ontologies/msio it does say that the "Ontology IRI: http://purl.obolibrary.org/obo/msio.owl", and I see term IRIs such as http://purl.obolibrary.org/obo/MSIO_0000001. But since MSIO is not registered with OBO we (OBO) were not aware of this usage, don't support it, and can't really do anything about it except ask them to either (1) go through the OBO registration process, or (2) stop using OBO PURLs.

[teisnotte]

Thank you James! I've contacted @proccaserra to see if we can resolve this issue.

[teisnotte]

@shawntanzk Could you take a look? Thank you!

[shawntanzk]

Hey hey,

Would agree with @jamesaoverton here - given the purls dont resolve, not sure I would recommend actually using it now.

I did take a look at @proccaserra repo, and if you REALLY want to import the v1.0 in using ODK, you can configure accordingly (assuming you are using base file merging)

import_group:
  use_base_merging: TRUE
  products:
    - id: msio
      mirror_from: https://raw.githubusercontent.com/ISA-tools/MSIO/refs/heads/master/releases/1.0/MSIO-merged-reasoned.owl
      make_base: TRUE
      base_iris:
        - http://purl.obolibrary.org/obo/MSIO_

But again, the purls dont resolve and I would follow @jamesaoverton advice here - for MSIO to either get registered with OBO or change their purls so they resolve elsewhere (you can change the base_iris field if MSIO decide to resolve to a new URL)

Hope that helps

PS sorry for the ODK dark arts hack :p

[teisnotte]

Thank you Shawn, this is really helpful. Another question is if I use the temporary fix, will I be able to easily update when MSIO fix the PURLs?

[proccaserra]

@teisnotte @shawntanzk @jamesaoverton
If time is of the essence, it might be quicker to go for option-2, which could be done by minting MSIO identifier with w3id as submitting to the obofoundry might take time.

Another issue which makes MSIO release complicated relates to nmrCV, the release of which is also broken as this is non-maintained. So I rely on a local copy, to clear error and ensure proper import.

If @teisnotte @shawntanzk are able to help upgrade to using the ODK, I would not mind the assistance. much appreciated.

Status:

• replaced base iri from http://purl.obolibrary.org/obo/MSIO_ to http://w3id.org/msio/MSIO_
• correction to nmrCV.owl to clear error caused by xml:lang="de" & IRI
• preparing a new MSIO release for loading in EBI OLS4 to enable synching with w3id PR

[shawntanzk]

Hey @proccaserra

Happy to try to help convert to ODK, but I am not sure if I have the bandwidth in the short run to do this.
If the IDs are submitted to w3id, I think the immediate issue is solved, we can leave the conversion to ODK for later :)
let me know your thoughts.

Another issue which makes MSIO release complicated relates to nmrCV, the release of which is also broken as this is non-maintained. So I rely on a local copy, to clear error and ensure proper import.

Similarly happy to look into this later on, but if you have a full release product for now, then it is still useable.

Hope that helps, if not please ping me again :)

Thanks

[shawntanzk]

see ISA-tools/MSIO#15