The Ontology for open Digital Specimens (ODS) situates open Digital Specimens in the relevant OBO Foundry ontologies and extends from those roots to define the new concepts needed to support mass digitization and Digital Specimens on the Internet.
The relevant OBO Foundry Ontologies are the following:
- Ontology for Biomedical Investigations (OBI): OBI is an ontology for the description of life-science and clinical investigations;
- Biological Collections Ontology (BCO): BCO is an ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys; and,
- Information Artifact Ontology (IAO): IAO is an ontology of information entities.
For an explanation of how the BCO is related to the OBI and IAO ontologies, this recent (2018) book chapter on "Integrating and Managing Biodiversity Data with the Biocollections Ontology" by Ramona Walls et al. is helpful.
With reference to the following figure,
In the OBI there is the concept of a ‘planned_process’ (OBI_0000011) that captures the idea of performing some kind of process that has previously been planned. Present examples (subclasses) include: carrying out investigations, assays, creating datasets, developing software and (of immediate relevance) collecting specimens ('specimen_collection_process',OBI_000659).
The result of a specimen_collection_process is a specimen (OBI_0100051), which can be further elaborated as a PreservedSpecimen or a LivingSpecimen. And here we arrive at the conjunction between the ontologies of the OBO Foundry and the terms vocabularies/schema of TDWG Darwin Core (DwC) and Access to Biological Collections Data (ABCD) and its Extension for Geosciences (EFG).
The concepts 'specimen_collection_process' and 'specimen' are replicated forward into the BCO as BCO:OBI_0000659 and BCO:OBI_0100051 respectively.
ODS situates the act of planned digitization activities as a new kind of OBI:planned_process that we name as 'digitization_event' or 'digitization_process' (ODS_00000nn). This sits alongside the familiar notion of collecting specimens as another major activity performed by institutions holding natural science collections.
The output of a digitization_process is a new class ‘digital specimen’ (ODS_00000nn). This must be considered as a new subclass of ‘information_content_entity’ (IAO:0000030) in the IAO), being ‘a result of a digitisation event or process’. We consdier a new subclass because the existing subclasses don't seem appropriate. Subclass 'data_item' (IAO:0000027) seems rather too general.
To do: digitization_event or digitization_process? Go back to earlier notes and have a look at why is event rather than process.
To do: assign numbers/IRI to the new concepts in ODS - two above.
END.