Category:Virtual biology ontologies

Ontologies are hierarchically structured vocabularies of terms and relationships that are clearly defined and designed to represent and communicate information about a particular scientific domain.

Virtual biology uses several biomedical ontologies for unambiguous, systematic descriptions of physiological, biological, chemical and physics-based entities and processes as well as their interrelations [1].

Key elements in annotating models with ontology terms include [1, 2]:

• associating codewords in the model with appropriate unambiguous ontology identifiers;
• specifying components and subcomponents in the model utilizing the hierarchical structure within an ontology;
• linking the model and its components and subcomponents to supporting measured experimental data.

The use of multiple ontologies for defining components and subcomponents of models could allow them to be compared and integrated to form composite models in an automated manner [2].

Standardizing biological information with organized vocabularies and ontologies already has proven to be valuable in formally defining components of models and representations of complex systems[1, 2]. For example, describing multiscale processes in mouse development mathematical models using a combination of GO and Cell Type Ontology terms has been shown to be effective to provide clear definitions of function and to allow comparison of function under different conditions [3].

The table below contains brief description of these ontologies.

Gene Ontology (GO) describes gene function through properties of proteins and includes hierarchical information in the three domains of cellular location, molecular functions, and biological processes.1,19

FMA http://sig.biostr.washington.edu/projects/fm/ OPB http://sbp.bhi.washington.edu/projects/the-ontology-of-physics-for-biology-opb

References

1. Error fetching PMID 22027554: [Courtot2011]
2. Error fetching PMID 22805979: [Beard2013]
3. Error fetching PMID 17566825: [Bard2007]