Frequently Asked Questions

In this setting, an ontology is a controlled vocabulary with structure. The actual meanings of the terms in the ontology are given in the definitions provided with each term. Terms in the ontology are said to have parent-child relationships. A parent term, representing a broader concept, may have one or several more specific child terms, representing parts of the parent concept or instances of it.

The structure of the FAO is a directed acyclic graph (DAG). This is similar to a hierarchy, except that in a hierarchy, a term may have only one parent, while in a DAG, a term may have more than one parent. This is to ensure that a concept is represented in all relevant biological contexts. For more details on the structure of ontologies and a graphical representation of a DAG, see the SGD GO Help page.

The flat file version of the FAO and its definitions can be viewed here. The top of the file shows the last revision date. Each term is represented on a line, with its ID number and synonym(s). Term names are preceded by the symbol '%' if the term is an instance of its parent term (e.g., a 'lichen thallus' is an instance of a 'composite structure'), or by the symbol '<' if the term is part of its parent term (e.g., a 'stipe' is part of a 'basidiocarp'). Parent-child relationships are represented by indentation: child terms are represented below the parent term, and indented relative to it. If a term has multiple parents, then it will be shown below each parent term in the flat file.

Every term is unique and has a unique identifier, the FAO_id, with the syntax 'FAO:nnnnnnn', where nnnnnnn is a zero-padded integer of seven digits. If users and developers agree that a term is defunct, then it is removed from its place in the ontology and made a child of the meta term "obsolete;" its definition is preserved. When two terms are merged, e.g., term A and term B are merged as term A, then the FAO_id of term B is made a secondary FAO_id. Secondary FAO_id's are presented as a comma-separated list, e.g.:

term A ; FAO:id term A, FAO:id term B, FAO:id term C, ...

A freely available Java application, DAG-Edit, has been developed to facilitate viewing and editing ontologies. The FAO ontology and definitions files may be downloaded from the Open Biological Ontology CVS site for viewing using DAG-Edit. This program displays the ontology graphically, making it easier to visualize the relationships between terms, and displays the definition for a selected term.

The FAO can be used to describe the structural localization of gene products (which may be proteins or RNAs), or may be used in conjunction with orthogonal ontologies, such as phenotype ontologies or GO Process, Function, and Cellular Component ontologies, to provide detailed annotations for a gene product.

Recent sequencing efforts by individual communities and the Fungal Genome Initiative at MIT have led to an explosion of sequence information from diverse fungi. The use of a common vocabulary by separate databases or scientific projects to describe the entities they work with will enable direct comparisons between species or projects. Thus, implementation of FAO and other ontologies, such as GO, to functionally annotate gene products will help the greater fungal community share information.

The FAO is freely available for public use. The ontology and definitions files (fungal_anatomy.ontology and fungal_anatomy.definitions) may be downloaded from the Open Biological Ontology site. However, we ask that users do not change the FAO independently. If additions or corrections need to be made, please contact developers (via the fungal-ontology e-mail list) to make the changes.

To see how ontologies have been used to annotate gene products in fungi, check out the locus pages at the Saccharomyces Genome Database (for an example, see the SWE1 locus page.). SGD currently annotates gene products to Biological Process, Molecular Function, and Cellular Component ontologies developed by the GO Consortium. Schizosaccharomyces pombe GeneDB also annotates gene products using the Gene Ontology.