BlueBrain/nexus-schemas

genric

@genric

but unless they are published there is no way to try them :) workbench tests are good but I think they don't cover all possibilities

Oliver Schmid

@olinux

This would also mean that we would wipe and re-instantiate the integration environment on a regular base.

genric

@genric

this sound great, it will minimize the version bumping

nevertheless we need to discuss versioning strategies

Oliver Schmid

@olinux

@MFSY what do you think about having some staging in INCF? I think it's crucial because we have to be sure that a schema in master is final.

@genric - I agree - this is a complex topic and it would be good to have a common understanding

Mohameth François SY

@MFSY

Let have a meeting and discuss all of this. I set up one.

Oliver Schmid

@olinux

:thumbsup: thanks!

Andrew Davison

@apdavison

I'm unclear how things work with the various OntologyTermShapes. For example, with the SexOntologyTermShape, I guess somewhere there should be something that specifies the possible values for validation, e.g. "male", "female", but I don't see where that is.

Mohameth François SY

@MFSY

Hi @apdavison ,

I’ve opened while ago an issue on INCF/neuroshapes describing (proposing actually) a way to handle ontologies

INCF/neuroshapes#53

The idea is as follows:

we should provide relevant defaults for people to use. I think of ontology terms from NIFSTD (We can add relevant ontologies that HBP and BBP are using)
we should allow users to use their own ontology term

we should allow users that don’t have ontology terms ot still be able to use the schemas

We should avoid global constraint on the schemas at INCF/neuroshapes and enable each data integration/curation team platform enforce the ontologies they want.

Mohameth François SY

@MFSY

I think the strategy is quite generic (unless objections). I would suggest we identify relevant defaults that both HBP and BBP use in term of brain regions, brain parcels, species, strains, cell types ….. and add those in the ontology term shapes

Mohameth François SY

@MFSY

For the sex ontology terms we can start by this:

{
      "@id": “this:SexShape",
      "@type": "sh:NodeShape",
      "or": [
        {
          "label": "The expected sex value is an ontology/vocabulary term: identified by an IRI.",
          "node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.0/shapes/LabeledOntologyEntityShape"
        },{
          "label": "The expected sex value is from a specific sex term from an ontology: identified by an IRI.",
          "node": "{{base}}/schemas/neurosciencegraph/commons/typedlabeledontologyterm/v0.1.0/shapes/SexOntologyTermShape"
        },{
         "label": "The expected sex value is a free plain text taken from a controlled list of values.",
          "datatype": "xsd:string”,
“in”:[“male”,”female”]
        }
      ]
    }

Tell me if this works for you

Andrew Davison

@apdavison

Thanks, I had seen that issue, but forgotten about it.
For context, I'm thinking about automatically populating a drop-down list in a GUI.

I was thinking that the IRI of the ontology could be specified as part of the constraint, and then the GUI could go fetch the list of valid ontology terms.

Mohameth François SY

@MFSY

Populating a drop down list from a root ontology term referenced in a schema is definitely a main (and nice) use case for this.

The question is which IRI to use for sex for example. The challenge is to find defaults IRIs that are commonly accepted in the community (From NIFSTD). I’m open to suggestion.

If you have IRIs for the sex ontology terms we can add them

even though putting male and female under nsg namespace will not hurt and is perfectly feasible

thoughts ?

Mohameth François SY

@MFSY

Will the following work ?:

{
      "@id": “this:SexShape",
      "@type": "sh:NodeShape",
      "or": [
        {
          "label": "The expected sex value is an ontology/vocabulary term: identified by an IRI.",
          "node": "{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.0/shapes/LabeledOntologyEntityShape"
        },{
          "label": "The expected sex value is from a specific sex term from an ontology: identified by an IRI.",
          "node": "{{base}}/schemas/neurosciencegraph/commons/typedlabeledontologyterm/v0.1.0/shapes/SexOntologyTermShape"
        },{
         "label": "The expected sex value is  taken from a controlled list of values.",
          “nodeKind": “sh:IRI”,
“in”:[“nsg:Male”,”nsg:Female”]
        }
      ]
    }

Now I’m aware that sex taxonomy is made of more terms (https://bioportal.bioontology.org/ontologies/NIFDYS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000047)

Andrew Davison

@apdavison

I'm having problems with the ProtocolShape defined here (the old "No data was selected for validation" error): https://github.com/INCF/neuroshapes/tree/master/modules/core/src/main/resources/schemas/neurosciencegraph/core/protocol
and I note that there are no test data for this schema. Would it be possible to add some tests for this? I can then probably figure out where I'm going wrong.
Also to note there is a typo in the HadProtocolValueShape: "sh:PropetyShape"

Mohameth François SY

@MFSY

Hi Andrew

I’ll add the test

What version of neurosciencegraph/core/protocol are you using ?

But a "No data was selected for validation” issue is usually caused by a type difference between the submitted instance ( the protocol in your case) and the targetedClass in the schema.

Mohameth François SY

@MFSY

Also to note there is a typo in the HadProtocolValueShape: "sh:PropetyShape”

indeed

Mohameth François SY

@MFSY

HadProtocolValueShape is fixed:

INCF/neuroshapes#85

Andrew Davison

@apdavison

@MFSY I still can't get Protocol (or the new ExperimentalProtocol) working. When you have time, it would be really helpful to see a test for these shapes.

Mohameth François SY

@MFSY

Thank you for reporting this

I’ll have a look today and generate some tests for those

It would help a lot to see the type of errors you get

Mohameth François SY

@MFSY

There is a new version of the protocols shapes in review INCF/neuroshapes#172. We’ll add the tests there.

Mohameth François SY

@MFSY

The PR is now merged.

Where communities thrive

People

Repo info

Activity