The definition of these biomedical ontologies has evolved both in its ontological foundations, with the commitment to common upper ontologies such as the Basic Formal Ontology (BFO) [ 25], and in its representation, which has become increasingly logic based, via the adoption of ontology definition languages such as the Web Ontology Language (OWL) [ 26 29].
The proposed framework benefits from information about ontologies, such as terminology and ontology structure, to calculate a compatibility metric of ontology suitability for reuse and hence integration.
Fuzzy ontology membership values can be learned from documents or users, based around existing ontologies such as the Unified Medical Language System UMLSS).
As seen from this summary, relevant ontologies such as neuron projection regeneration, neuron projection morphogenesis, actin cytoskeleton, and microtubule cytoskeleton were altered, in line with the IPA results.
High-quality and standardized clinical data are critical for patient registries which requires the systematic use of ontologies such as the HPO (see above).
A number of upper ontologies such as Basic Formal Ontology (BFO) [25] are developed to support domain ontology building as well.
The new triple dataset uses standard ontologies including the Bibliography Ontology [13] and the Citation Typing Ontology (CiTO) [14] for literature references and citations, and domain ontologies such as the Protein Ontology[15] and the Chemical Information Ontology [16].
The biosciences have several approaches for creating ontologies, such as the Gene Ontology (GO)[26].
As for the first point, currently there are a few authoritative ontologies, such as SUMO4 (Suggested Upper Merged Ontology), standardized at IEEE, but these ontologies are not enough to address the interoperability problem.
At present, most of the ontology-driven mining in the biomedical domain uses the UMLS [57] or GO [58] ontology, but now several chemical information ontologies such as ChEBI [59] and CHEMINF [60] are available too.
