19th International CODATA Conference
Category: Interoperability

Some Applications of Ontologies in Biodiversity Informatics

Wolfgang Lipp (w.lipp@bgbm.org)
BGBM Berlin, Germany

An import goal in present-day biodiversity informatics is the opening of many millions of data items for research. The domain of semantics is seemingly only now coming into the reach of technology. I would like to define 'ontology' as a 'semantic topology', namely, a mostly graph-like space of terms between which links may exist. The result is a structured vocabulary, of which ABCD and Darwin Core are examples. Applications of ontologies include, but are not limited to, the following:

**Describe Objects And Object Data**
    1)  **Declare Data Source Mappings** -- terms of ontologies like ABCD are used to provide labels for attributes of databases.
    2)  **Provide The Names** -- terms of ontologies like ABCD are used to provide names for pieces of data exchanged during a request/response communication.
    3)  **Provide The Values** -- terms of ontologies may be used to provide the values of pieces of data exchanged during a request/response communication.

**Describe Data Sources and Data Sinks**
    1)  **Give A Description Of Data Sources** -- ontologies are used to describe a database e.g. in terms of scientific fields covered, in order to ease performing point 1.1, above, and to inform the network infrastructure as well as data end users ('I provide pictures of algae').
    2)  **Give A Description Of Data Clients** -- ontologies are used to describe a request ('I need observations of algae'), so results may be filtered and sorted.

**Describe Descriptions**
    1)  **Declare Ontologies**
    2)  **Describe Ontologies In Terms Of Each Other** -- basically, mappings on ontology like Darwin Core to terms of another one, e.g. ABCD.
    3)  **Bind External Data To Terms Of Ontologies** -- extend and annotate ontologies.

Reviewing points 1.2 and 1.3, we can see that a semantic annotation of data may be performed *both* on the naming side (frame) as well as on the value side (filling) of a name/value pair. This opens a wide space of opportunities for data exchange, as it makes it possible to balance burdens between authors of ontologies.

It further seems possible to put together 2.1, 3.1, and 3.3 -- to describe data sources in terms of a special purpose ontology that is linked through a number of assessments by way of data binding to a data schema like ABCD -- to give users a map and a compass for ABCD. The ontology designed for the purpose, called :bion: for Biology Information Ontology, is small but growing; we try to make do with an approach that only includes the relationships parent / child, logical implication, and equivalence between terms.