Semiotes: a semantics for sharing.

Area of Science:

• Bioinformatics
• Computational Biology
• Semantic Web Technologies

Background:

• Automated biological information exchange necessitates semantic declaration.
• Existing methods lack interoperability due to diverse data models and schemas.
• Independent databases and algorithms require a common semantic framework.

Purpose of the Study:

• To present an approach for semantic declaration enabling independent systems to communicate.
• To introduce Glossa, a formal language for defining biological semantics.
• To facilitate the exchange of information and computations between distributed biological databases and algorithms.

Main Methods:

• Utilizing Glossa, a formal language, to executably define semantics via semiotes.
• Employing semiotes as axiomatic definitions for simple notions.
• Implementing mappings between local notions and semiotes for data translation.
• Developing parsers for translating between indigenous ideas and semiotic messages.

Main Results:

• Glossa enables the definition of complex ideas and computations through semiotes.
• Semiotes act as a shared, abstract layer for semantic definitions.
• Systems can locally interpret and process semiotic messages.
• Independent computational entities can lightly federate capabilities using Glossa.

Conclusions:

• Glossa and semiotes provide a computable framework for semantic interoperability in biology.
• This approach allows independent systems to exchange information and computations without rigid coordination.
• It supports the federation of capabilities while preserving unique perspectives on scientific and technical questions.