Correct root node for study_type ontology

[bcorrie]

Mostly for @bussec to review...

The current root node for the study_type ontology is:

                ontology:
                    draft: true
                    name: NCIT
                    url: https://ncit.nci.nih.gov/ncitbrowser/
                    top_node:
                        id: C15320
                        value: Study Design

The example in the spec is

            example:
                id: C15197
                value: Case-Control Study

This "Case-Control Study" node is not a child of the "Study Design" root node. There is a root node called "Study" under which this lies. "Study" and "Study Design" are siblings in the tree...

I think we might want "Study" to be the root node???

                ontology:
                    draft: true
                    name: NCIT
                    url: https://ncit.nci.nih.gov/ncitbrowser/
                    top_node:
                        id: C63536
                        value: Study

[bcorrie]

FYI here are the children nodes of "Study":

     Animal Study
     Case Series
     Case Study
     Case-Control Study
     Clinical Study
     Controlled Study
     DICOM Study
     Genetic Study
     Laboratory Study
     Liver Study
     Nonclinical Study
     Nutritional Study
     Panel Study
     Pharmacological Study
     Pilot Study
     Population Based Study
     Preclinical Study
     Study Branch
     Study of Disease Management
     Study of Disease Mechanisms
     Study Type
     Supportive Care Study
     Trial Blinding Schema

[bcorrie]

@bussec any comments on this... We are about to go through and change the repertoire metadata on all of our studies, and I don't want to go down the incorrect path... Emily had a look at this and seems to agree that the "Study" node seems to make more sense as the root node.

[bussec]

@bcorrie, I agree that "Study" (C63536) is the node that we would like to use, I assume this was a mistake during the initial annotation. Therefore please change the Schema accordingly. One more thing: I just realized that the URL does not point to obolibrary. Is the url field in the object primarily for human entertainment or is this something that we expect a repository to access/parse?

[bcorrie]

@bcorrie, I agree that "Study" (C63536) is the node that we would like to use, I assume this was a mistake during the initial annotation. Therefore please change the Schema accordingly.

@bussec will do...

One more thing: I just realized that the URL does not point to obolibrary. Is the url field in the object primarily for human entertainment or is this something that we expect a repository to access/parse?

I believe the URL is something that we want to be usable by application programs for sure, but we haven't really defined how to do that. By that I mean there isn't a definition anywhere that says you should be able to perform function X with the URL to get information about a specific ontology term or ID. I am not sure how practical that is, given the breadth of the ontologies that we might end up referencing, but I would hope that would be a goal... 8-) So for now, a human needs to look at the URL and try to find out how to look up an ontology term and information about it using that URL...

[bcorrie]

I have updated the root node in the spec. Currently the OBO site seems to be down so I can't confirm what the correct URL is so that will have to wait...

Branch https://github.com/airr-community/airr-standards/tree/ontology-patch-1

[bcorrie]

Changed the URL for the ontology to use the ontobee one to be consistent with others. Is this what we want?

https://github.com/airr-community/airr-standards/commit/5e3877f820903296c397347cc9c0bb3e69658dd4

[bcorrie]

If so, should we use this for NCBI Taxonomy: http://www.ontobee.org/ontology/ncbitaxon and this for Cell Ontology: http://www.ontobee.org/ontology/cl

If so, should we document this as a recommendation at the Ontology node in the schema as per:

                url:
                    type: string
                    description: Ontology URL

could become:

                url:
                    type: string
                    description: Ontology URL. If the Ontology is included in the Open Biological and Biomedical Ontology (OBO) Foundry set of ontologies, the OBO URL link should be used.

[bussec]

@bcorrie +1 for using one default provider for ontologies. I'm ok with using ontobee.org for now, but if we are thinking about programmatic access I would like to pitch in EBI's Ontology Lookup Service, as they are providing an ontology crossreference service (called OxO), which I assume will become necessary at some point.

Maybe that's a job for the OntoVoc Team ;-)

[bcorrie]

@bcorrie +1 for using one default provider for ontologies. I'm ok with using ontobee.org for now, but if we are thinking about programmatic access I would like to pitch in EBI's Ontology Lookup Service, as they are providing an ontology crossreference service (called OxO), which I assume will become necessary at some point.

Yes, I was looking at that service, as I think one of the Ontologies was pointing at that originally... I have to admit that I have found ontobee to be a bit unresponsive the last couple of days while I was doing the harmonization... Web pages for ontologies hanging for a significant amount of time... So maybe we should switch over to EBI, as I think as a supported service that might be more robust - not that I have a lot of experience one way or the other...

[bussec]

I have found ontobee to be a bit unresponsive the last couple of days while I was doing the harmonization

I made the same observation, just wasn't sure whether this was due to being on the other side of the pond. Commit 4d3c45c now uses OLS (and resolves a sync problem with the schema copies).