Attribution for pathways

[ValWood]

We can display attribution for pathways because authors are captured in Noctua . I plan to ask the community to review the pathways as we create them. It would be nice if we could store a "reviewed-by" somewhere ....

[kimrutherford]

We can display attribution for pathways because authors are captured in Noctua .

Can you show me an example?

It would be nice if we could store a "reviewed-by" somewhere

Is "reviewed-by" something that can be stored in Noctua?

[ValWood]

Well I assumed (most likely incorrectly) that they would be exported. They are shown associated with the models on the landing page as "contributors"

http://noctua.geneontology.org/workbench/noctua-landing-page/

[ValWood]

Is "reviewed-by" something that's can be stored in Noctua?

I can ask about this. I guess it would involved the reviewers obtaining a git ID and a Noctua log in though. And I guess they would need to then distinguish between editors and reviewers. I was hoping it could be simpler because we already store the people's detail in Canto locally so we wouldn't run into GDPR issues. We could (presumably) just confirm that they are willing to review and be attributed and then store their name in a config associated with the model ID?

[kimrutherford]

Well I assumed (most likely incorrectly) that they would be exported.

I had a look. The contributors are available via RDF, at least:

<http://purl.org/dc/elements/1.1/contributor> "https://orcid.org/0000-0001-6330-7526"^^xsd:string ,
                                              "https://orcid.org/0009-0003-9059-1333"^^xsd:string ;

http://noctua.geneontology.org/download/gomodel:66187e4700001573/owl

[kimrutherford]

I can ask about this. I guess it would involved the reviewers obtaining a git ID and a Noctua log in though. And I guess they would need to then distinguish between editors and reviewers.

That seems like a good feature for Noctua.

I was hoping it could be simpler because we already store the people's detail in Canto locally so we wouldn't run into GDPR issues. We could (presumably) just confirm that they are willing to review and be attributed and then store their name in a config associated with the model ID?

Let's have a chat about that. I think if they have to log into Noctua to review, that's the point where they should confirm that they're happy about GDPR issues.

[ValWood]

I opened a ticket about this, but I should have said I'm not expecting them to log in to Noctua. They are reviewing the post-production pathways once they are on dev (I think this is easier)

[kimrutherford]

I had a look. The contributors are available via RDF, at least:

<http://purl.org/dc/elements/1.1/contributor> "https://orcid.org/0000-0001-6330-7526"^^xsd:string ,
                                             "https://orcid.org/0009-0003-9059-1333"^^xsd:string ;

I've just spent some time reading up on RDF, OWL and Turtle which I had never done before. For dealing with the GO-CAM data I don't think I can avoid it any more. OBO and GAF files aren't enough. :-)

So I think I now know why that snippet above has such odd syntax and how to parse it correctly.

I think I might need to learn a bit about SPARQL next so we can query for PomBase models.

[kimrutherford]

sounds fun ;)

It's a bit painful. The documentation for all these things is very jargony.

For example, the RDF docs mention "blank nodes" and they occur in OWL files. This is how they are described - clear as mud!:

---

The blank nodes in an RDF graph are drawn from an infinite set. This set of blank nodes, the set of all RDF URI references and the set of all literals are pairwise disjoint.

Otherwise, this set of blank nodes is arbitrary.

RDF makes no reference to any internal structure of blank nodes. Given two blank nodes, it is possible to determine whether or not they are the same.

[ValWood]

Oh my gosh.
I have no idea what that is about!
Is it worth asking on the slack channels for a useful primer?

[kimrutherford]

It's a bit painful. The documentation for all these things is very jargony.

Turns out the RDF querying of GO and pathways is going the way of the dodo, so no problem.

[kimrutherford]

Turns out the RDF querying of GO and pathways is going the way of the dodo, so no problem.

I've had a look the GO-CAM data returned by the GO API and the contributor is included. There's not an obvious place to store the contributor in Chado so I'll need to think about that.

Storing the model titles in Chado is already quite a big hack so it might make sense to store the model title and the contributors (and any other model metadata) in a JSON file in SVN rather than Chado.

[kimrutherford]

Storing the model titles in Chado is already quite a big hack

I've had a think about this and we can probably use the feature table in Chado to store the pathways. That's not really what it's for (it's meant for chromosome features) but it will make things easier. If each pathway is a feature then the title can just be the feature name and details like the contributors are easy to store in the featureprop table.

[kimrutherford]

It might help with Chado to have a PB ref for GO-CAMs. Does that make sense?

[ValWood]

Yes I think so. Draft:

GO CAMs (Causal Activity Models) are pathway models curated manually by combining standard GO annotations.
GO-CAM models can connect different pieces of information about the function of a gene product (joining together different annotations for the same gene product), and/or connect different gene products together by specifying how the activity of one gene product can affect the activity of another gene product. All connections in a GO-CAM model are made using clearly defined semantic relations from the Relations Ontology.
For more details about GO-CAM see PMID: 31548717

[kimrutherford]

Great, thanks. Can you suggest a title? Is "Causal Activity Model curation" enough?

[ValWood]

"GO-CAM Causal Activity Model curation"

[kimrutherford]

We could (presumably) just confirm that they are willing to review and be attributed and then store their name in a config associated with the model ID?

That's probably the simplest plan, have an SVN file like supporting_files/go-cam-reviewers.tsv with the GO-CAM ID, ORCID and reviewer name as the columns.

I've just added a file of PomBase ORCIDs and names which might be useful later:
pombe-embl/supporting_files/pombase_orcid_mapping.tsv

The contributors are available via RDF, at least:

Also available in the new JSON files (see #1248)

    {
      "key": "contributor",
      "value": "https://orcid.org/0000-0001-6330-7526"
    },
    {
      "key": "contributor",
      "value": "https://orcid.org/0009-0003-9059-1333"
    },

I've had a think about this and we can probably use the feature table in Chado to store the pathways.

I'm working on that now so we can store the GO-CAM contributors (and later the reviewers) in Chado.

[kimrutherford]

As a first step, I've updated the script that parses the GO-CAM model JSON files to write a single JSON file containing all the model data needed for loading into Chado:

pombe-embl/supporting_files/pombase_gocam_data_for_chado.json

[kimrutherford]

I've now re-worked how GO-CAMs are stored in Chado to be more flexible. So the contributors and date(*) from the models are now in Chado and can now be displayed on the website or used anywhere else we need them.

• (*) I need to ask what this date is. In the GO-CAM JSON files it's just called "date". It seems to be the date the model last changed but I'm not sure.

We can display attribution for pathways because authors are captured in Noctua . I plan to ask the community to review the pathways as we create them.

We need to decide where/when to display the authors/contributors.

Should we show the date?

It would be nice if we could store a "reviewed-by" somewhere ....

We now have a way to store reviewers in Chado and to pass that through to the website.

I broke last night's load with some of the changes I made yesterday so there was no update. I'll check things working on Saturday morning.

[kimrutherford]

We need to decide where/when to display the authors/contributors.

And we should chat about reviewers. Is this plan OK?:

have an SVN file like supporting_files/go-cam-reviewers.tsv with the GO-CAM ID, ORCID and reviewer name as the columns.

We could do that very quickly.

We'd need to also decide where to display the reviewer name.

(And do we have to worry about the GDPR? What a drag)

[ValWood]

This sounds like a reasonable solution.
I don't think we need to worry about GDPR because we will only add people as reviewers if they agree.

[kimrutherford]

Should we put the attribution and reviewer name only on the full page GO-CAM pages?:
https://www.pombase.org/gocam/docs/67086be200000251

[ValWood]

I think so

[kimrutherford]

Something like this?:

https://desktop.kmr.nz/gocam/docs/66187e4700001781

[kimrutherford]

I've implemented that for the morning. Let me know if I should change "Curation by:"

[ValWood]

Maybe "Curated by"?

[kimrutherford]

Maybe "Curated by"?

That makes sense. It will match "Reviewed by" when we add that.

I'll change it.