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...t assumption behind what has been said so far is that the theories or specifications all live within the one and the same formalism. However, viewpoint specifications [3] and heterogeneous ontologies =-=[18]-=-, which both have received attention recently, involve different specification formalisms. In such heterogeneous settings (typically based on a graph of logics), colimits and amalgamation can be obtai...

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...t formalisms, like description logics, first-order logic, and modal (first-order) logics, combinations of ontologies need to be constructed across different institutions, as is argued convincingly in =-=[32]-=-. To obtain heterogeneous logical theories, one first needs to fix some graph of logics and logic translations, usually formalised as institutions and so-called institution comorphisms, mapping signat...

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...ption logic such as OWL 2.0 is being used in their development. However, the use of a logical representation language alone is clearly not enough to ensure the high quality of an information resource =-=[3]-=-, and even ontologies employing the same formal language are often not combinable into a single resource because of incompatibilities between the ways this language is used by different groups. [4] Th...

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...integration of two ontologies (O1 and O2) into a third ontology O is any operation by which O1, O2 are ‘re-interpreted’ from the (global) point of view of O. This has been utilized in the approach of =-=[31]-=- (called semantic integration), which integrates two ontologies by mapping (or translating) them into a common reference ontology. The main feature here is that semantic consequence is preserved upwar...

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...ossakowski et al. 2006). Moreover, the appendix contains additional details about the syntax of Casl (and HetCasl introduced below) as well as example specifications. 2.2 Heterogeneous Ontologies As (=-=Schorlemmer & Kalfoglou 2008-=-) argue convincingly, since ontologies are being written in many different formalisms, like relation schemata, description logics, first-order logic, and modal (first-order) logics, alignments of onto...

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...rminologies and ontologies used in EHRs. Achieving this was the second objective of our endeavor. 2.3 Ensure compatibility with the OBO Foundry framework Many of the ontologies being employed in specific life science disciplines and in associated clinical specialisms are still built by groups working independently or with no resort to common ontological standards. Increasingly, one or other version of description logic such as OWL DL is being used in their development. However, the use of a logical representation language is clearly not enough to ensure high quality of an information resource [6], and even ontologies employing the same formal language are often not combinable into a single resource because of multiple incompatibilities between the ways this language is used by different groups to express biological or clinical information. [7] The goal of the OBO (Open Biomedical Ontologies) Foundry is to counter such tendencies by promoting the creation of a single, expanding family of ontologies designed to be interoperable and logically well-formed and to incorporate accurate representations of biological reality by adhering to a set of common principles [8], of which the most impo...