Submitter: Trish Whetzel
Affiliation: University of Pennsylvania
1413 Blockley Hall
423 Gaurdian Drive
Philadelphia, PA 19104

Title: Status of the Functional Genomics Investigation Ontology (FuGO)

Patricia L. Whetzel presenting on behalf of the FuGO Working Group

Email address:

FuGO Working Group:


The application of high-throughput functional genomics technologies such as microarrays and mass spectrometry to a wide variety of biological conditions has facilitated the investigation of new kinds of biological questions and has also resulted in the generation of massive amounts of data and metadata. The Functional Genomics Investigation Ontology (FuGO) is being developed as a collaborative, international effort to build an ontology that will provide a common resource of terms to annotate functional genomics investigations as well as assays that generate large amounts of data and metadata (Whetzel et al., The Development of FuGO - An Ontology for Functional Genomics Investigations, OMICS (in press)). Those involved in the FuGO project represent biological and technological domains and currently include representatives from the following communities: Metabolomics, Proteomics, Transcriptomics, Crop Sciences, Environmental Genomics, Flow Cytometry, Genome Sequence, Immunogenomics, Nutrigenomics, Polymorphism, Toxicogenomics. Although these are diverse communities, there is a shared need for terms to describe universal features of investigations such as the design, protocols, assays, material, and units of measurement. The scope of FuGO will cover both terms that are universal to all functional genomics investigations and those that are domain specific. In addition, FuGO will reference out to existing mature ontologies for additional domain content, e.g. Foundational Model of Anatomy, to avoid the need to duplicate these resources, and will do so in such a way as to foster their ease of use in annotation.

The initial ontology building process includes the collection of use cases from communities, the identification of terms of interest for annotation. From these use cases, and the binning of terms into top-level containers such as Object and Process. In the process of building FuGO, a style guide is being developed to provide recommendations for naming conventions for terms, formats for definitions and policies for the development of the ontology such as those for the addition of synonyms and numeric identifiers for terms. In addition to these style recommendations, FuGO is being developed as an OBO Foundry Application ontology and will meet OBO requirements (

During our first FuGO workshop in February, a draft version of FuGO was developed using Protégé/OWL. This initial version of the ontology focuses on the need for universal terms from the involved communities and includes an extension for technology specific terms for the Proteomics community. Thus far, the ontology building process has focused on the development of is_a relations, while noting where other relations, such as part_of, are needed. Future development of FuGO will proceed as an iterative process in which a section of the ontology will be reviewed by all interested communities allowing terms, both universal and community specific, to be added to the ontology. In addition, non-is_a relations will also be added to join the branches of the ontology. In conclusion, FuGO is being developed to provide a common resource for annotation of functional genomics investigations and in this way, the ontology will serve as the "semantic glue" to provide a common understanding of the annotated data from across disparate data sources.