New namespace request: DWCOBO

[Ramona Walls]

I am requesting a new OBO Foundry namespace for an OWL interpretation of Darwin Core (DwC) as RDF. Please see full details at https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1390 and https://github.com/BiodiversityOntologies/dwcobo.

I have created these ontologies for use within the BCO, but I expect that other ontologies will want to import DwC properties. These ontologies will provide a ready-made and standard way for anyone to reuse DwC within OBO ontologies. They also allow BCO to be more modular.

Ramona

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Ramona L. Walls, Ph.D.
Assistant Research Professor, Bio5 Institute, University of Arizona

Part-time artist (https://www.instagram.com/omnivoresgratitutude/)

[Hilmar Lapp]

Hi Ramona,

You’re probably familiar with DarwinCore-SW, which has been published a few year ago:

http://www.semantic-web-journal.net/content/darwin-sw-darwin-core-based-terms-expressing-biodiversity-data-rdf-1

Can you say how this effort would relate to or build on that?

  -hilmar

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Hilmar Lapp -:- lappland.io

[Ramona Walls]

Good question, Hilmar. DarwinCore-SW is more comparable to BCO, in that it models the relationships among the Darwin Core classes. A key difference  between dwc-sw and bco is that bco fits within the OBO Foundry framework and is rooted in BFO. Because BCO follows OBO Foundry best and common practices, it is easily integrated with other OBO Foundry ontologies.

The new ontologies I am proposing are semantically light, and just provide an OWL representation of the DwC as RDF. They are slightly more semantically rich than dwc as rdf, because I have chosen to transform the DwC grouping classes into actual domains for the dwc properties. I'm happy to hear feedback about this idea.

Ramona

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Ramona L. Walls, Ph.D.
Assistant Research Professor, Bio5 Institute, University of Arizona

Part-time artist (https://www.instagram.com/omnivoresgratitutude/)

[Chris Mungall]

It feels a bit outside the scope of OBO. But I like your idea of making BCO the OBO-ified artefact, and have mappings to DWC (as well as MIxS, NEON, IGSN/Sesar/etc?).

I think your richer version of DWC is useful, but it still feels outside the scope of OBO:

 - I don't think the IRIs are correctly formed, is your intent to reuse DWC ones, or to make a new namespace in OBO

 - A lot of the terms already appear in existing OBO ontologies: dwc:behavior, dwc:country, dwc:habitat, dwc:lifeStage, dwc:Dataset

 - A lot of terms appear to conflict, but represent different concepts than how they are currently used by members of the OBO community; e.g. dwc:pathway, dwc:class

 - The modeling seems in conflict with OBO modeling - e.g. dataset is represented as an individual, not a class; there are duplicate IRIs for all concepts, with datatype and object property versions

I fully support the goals of making a semantically richer DWC data dictionary (we both want to do a similar thing for MIxS, along with others like Jie Zheng). But I'm not sure what is gained by registering this product with OBO and making parallel OBO PURLs? Ideally your richer representation could be folded back into the main DWC, but absent that do you lose anything by registering on say w3id.org and submitting to bioportal? Also is there not a danger in now having *four* URIs for each DWC property ({obo,dwc} x {OP,DP})?

I don't mean to shut this down, I think there is a clear need for OBO-adjacent efforts such as providing semantically enhanced data dictionaries, and OBO provides a lot of the useful technology for doing this, there is a legitimate discussion about extending OBO vs creating a parallel infrastructure (an analogous situation exists for conversions of databases into "ontologies" and knowledge graphs).

I think it would be useful to 'clone' OBO for a broader registry of 'semantic artefacts' that are OBO-adjacent. This would include schemas and data dictionaries in the environmental/diversity sciences (MIxS, NEON, IGSN/Sesar, DWC). A lot of the same technology could be leveraged (e.g. cloned OLS/BioPortal/OntoBee instances - or even overloading the existing ones).

To view this discussion on the web visit https://groups.google.com/d/msgid/obo-discuss/CAJYF1k5zRr_2PjFvMgW2yDOZSG1Qqg8LOdJ2e_kdk6q8kMEVeg%40mail.gmail.com.

[Ramona Walls]

Chris, 

The intention is reuse the dwc IDs for each term, not create new ones. I was only looking for an OBO Foundry IRI for the ontology artefacts. Yes, w3c would work, and perhaps that is a better idea! I guess I just thought first of what I am most familiar with. In fact, my hope of being able to use OBO tooling with these ontologies wouldn't be so simple anyway, given that the term IRIs would not be obo-formatted PURLs. Also, the conflicts with OBO modeling that you point out (and others that you did not point out), make it far from simple to just plug in DwC to the suite of OBO ontologies. I like your idea of nurturing obo-adjacent artefacts.

I am not sure about the prospects of this OWL representation being folded back into TDWG. Even if it does come to pass, it will likely take years, and we need to have it functional for our BCO-based projects in the short term. I have filed an issue on the DwC RDF tracker (https://github.com/tdwg/rs.tdwg.org/issues/67) and hope to have some discussion there.

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Assistant Research Professor, Bio5 Institute, University of Arizona

Part-time artist (https://www.instagram.com/omnivoresgratitutude/)