Loading into Protege

[janelomax]

Hi - what's the best way to load all the biopharma ontologies into Protege please? I've tried loading using https://github.com/iofoundry/ontology/blob/biopharma-dev/biopharma/AboutBiopharmaceuticalManufacturingDev.rdf but it looks like it isn't pulling in all the imports.

[ElisaKendall]

@janelomax - I'll take a look at that Jane, but it's likely that you are correct. I'm not sure what was done to move from NIIMBL to the IOF GitHub repo and structure, but will see if I can assist, or reach out to the right folks to have them revise the about file accordingly.

[ElisaKendall]

@janelomax After a bit more investigation, aside from the QUDT errors, which happen when you use QUDT (i.e., they are issues that we are ignoring for the purposes of IOF for now), it appears to have loaded the bio-pharma ontologies. I spot-checked classes for several of bio-pharma ontologies using Protege's search capability and found them, including all of the metadata, etc. There are some odd things happening, for example, view by label doesn't appear to work properly so I'm seeing them with their camel case class names (the ones from IOF - the BFO classes work as anticipated), which might have to do with something happening with the IOF namespaces, but otherwise the content appears to have loaded correctly.

Can you identify anything specific that you think is missing?

[steveraysteveray]

I couldn't help notice the mention of QUDT. I see you are importing http://qudt.org/2.1/schema/qudt/. If you import http://qudt.org/3.1.2/schema/qudt/ or just the latest (no version in the URI), http://qudt.org/schema/qudt/ it should load QUDT without error. I just tested this with Protege 5.6.4.

Of course, if you want the actual units, etc. you should just import http://qudt.org/vocab/unit/ instead, which will bring in all the rest.

[ElisaKendall]

@steveraysteveray Thanks, Steve, I hadn't paid attention to that, but recognized the issues from other project. I knew from some discussion with other IOF team members that some things had been addressed. @MilosDrobnjakovic would you please fix the BopPharma load files when you have a moment?

[MilosDrobnjakovic]

Hi @ElisaKendall thank you so much for looking into this issue!
I have just double checked from my end and the qudt present on this branch in the cached folder renders without any errors in protege and it doesnt have any hermit issues. Our policy is to use cached ontologies from external resources. If you load the cached version what specific error do you have?
Thank you steve for also contributing to this thread. I will check in the following days the changes introduced by qudt schema v3 and if needed update the cache to it.
As for the label rendering it might be due to protege settings: all labels should render properly if you have the en-us, en, en-US in your render view.
@janelomax, https://github.com/iofoundry/ontology/blob/biopharma-dev/biopharma/AboutBiopharmaceuticalManufacturingDev.rdf is the way to load all of them. Please make sure you are doing local imports and not pulling it from the web.
If issues persist, I am also available for a call to go over any protege loading/rendering issues with you.

[ElisaKendall]

@MilosDrobnjakovic The issue is with the about file and possibly internal to the bio-pharma ontologies, which explicitly reference the older version of QUDT. SO even if you have to right version cached, the bio-pharma ontologies don't point to that version.

And thanks for the rendering hint - I thought I had that set properly, but with a number of reboots lately due to microsoft updates, it might have reverted to default.

[janelomax]

Ah, so those import URIs don't resolve? We wanted to add this to a pipeline so creating local imports isn't ideal. Do you have plans to create purls for those files at all?

[wsobel]

I think we can create resolvable IRI using the spec.instustrialontologies.org. It will not be exactly as the final IRI since it will resolve to a branch. It will look something like the following: https://spec.industrialontologies.org/ontology/biopharma-dev/latest/biopharma/Agent.rdf (for example). This resolves, but is not too pretty.

I think if we add a metadata file to the directory and the top level to make the machinery work. I can take a crack at it and see if I can get some of the content to resolve a bit better from the spec... IRI.

Would this be somethng that would make things easier to use? It won't be very pretty, but should be a lot better.

[wsobel]

I have created a branch biopharma-metadata off of biopharma-dev that contains the metadata necessary to get the machinery to hopefully provide IRIs we can resolve. I will be seeing what is required to get protege to resolve the IRIs and make it aware.

I will need feedback from you if this is acceptable. I moved all you ontologies into the biopharma domain, for example:

   https://spec.industrialontologies.org/ontology/agent/

becomes

   https://spec.industrialontologies.org/ontology/biopharma/Agent/

[wsobel]

To load the entire ontology, use the following IRI in Protege (File -> Open From Url...):

https://spec.industrialontologies.org/ontology/biopharma-metadata/latest/biopharma/AboutBiopharmaceuticalManufacturingDev/

Any individual ontologies can be loaded as follows:

https://spec.industrialontologies.org/ontology/biopharma-metadata/latest/biopharma/Agent/
https://spec.industrialontologies.org/ontology/biopharma-metadata/latest/biopharma/ManufacturingExecution/
https://spec.industrialontologies.org/ontology/biopharma-metadata/latest/biopharma/Material/
etc...

If we merge into biopharma-dev, the IRI will change to the following for Agent (for example):

https://spec.industrialontologies.org/ontology/biopharma-dev/latest/biopharma/Agent/

[wsobel]

Does this solve the problem?

btw: There is still an issue with MaterialProcurementAndStorage not being recognized as provisonal, even though there is a maturity:

		<iof-av:maturity rdf:resource="&iof-av;Provisional"/>

I'm not sure how to fix it. It is just something that does not show up correctly in the viewer. Otherwise no other issues.

@ElisaKendall , can someone from EDM Council take a look?

[mereolog]

Does this solve the problem?

btw: There is still an issue with MaterialProcurementAndStorage not being recognized as provisonal, even though there is a maturity:

  <iof-av:maturity rdf:resource="&iof-av;Provisional"/>

I'm not sure how to fix it. It is just something that does not show up correctly in the viewer. Otherwise no other issues.

@ElisaKendall , can someone from EDM Council take a look?

@wsobel you need to "register" all new ontologies in https://github.com/iofoundry/ontology/blob/biopharma-metadata/catalog-v001.xml.

Currently, the publishing process creates theses errors:

[34mMerging all dev ontologies into one RDF file�[0m
	ERROR(<https://spec.industrialontologies.org/ontology/biopharma/MonitoringAndControl/>): collect_ontologies: "HTTP Error 404: Not Found"
	ERROR(<https://spec.industrialontologies.org/ontology/biopharma/Equipment/>): collect_ontologies: "HTTP Error 404: Not Found"
	ERROR(<https://spec.industrialontologies.org/ontology/biopharma/Material/>): collect_ontologies: "HTTP Error 404: Not Found"
	ERROR(<https://spec.industrialontologies.org/ontology/biopharma/Physical/>): collect_ontologies: "HTTP Error 404: Not Found"
	ERROR(<https://spec.industrialontologies.org/ontology/biopharma/Agent/>): collect_ontologies: "HTTP Error 404: Not Found"
	ERROR(<https://spec.industrialontologies.org/ontology/biopharma/Recipe/>): collect_ontologies: "HTTP Error 404: Not Found"
	ERROR(<https://spec.industrialontologies.org/ontology/biopharma/ManufacturingExecution/>): collect_ontologies: "HTTP Error 404: Not Found"
	ERROR(<https://spec.industrialontologies.org/ontology/biopharma/Parameter/>): collect_ontologies: "HTTP Error 404: Not Found"
	ERROR(<https://spec.industrialontologies.org/ontology/biopharma/MaterialProcurementAndStorage/>): collect_ontologies: "HTTP Error 404: Not Found"
�[34mMerging dev ontologies encountered problem(s), so hygiene test results may be incomplete.�[0m

[wsobel]

The IRIs will not resolve since it is not merged to master. It only resides in the branch so the version IRIs resolve after processing. The catalog works fine with protege locally, that has not been an issue. I updated all the IRIs to match the ontologies.

That is another issue since this cannot work given that the IRIs will only resolve locally.

The specific issue is regarding the ontoviewer not recognizing that MaterialProcurementAndStorage is not provisional. It is marked as such in the ontology.