Protein Ontology: a controlled structured network of protein entities.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to UniProtKB in that PRO's organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO's representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments.

A Metrics Ontology. An intellectual infrastructure for defining, managing, and applying metrics.

This paper presents the beginnings of a comprehensive ontology for organizing information about metrics and its potential application to defining and managing metrics in the CTSA (Clinical and Translational Science Award) project. The aim is to support an integrated database of all metrics used by CTSA components. The ontology is given as an entity-relationship conceptual data schema. Its completion should draw on metrics definition templates that can be found in many places.