Term Definitions and References
This page describes the conventions used for constructing textual and logical definitions, and ways to cite references for ontology term components (definitions, synonyms, etc.).
Textual term definitions facilitate the consistent use of a term in annotation of different data types by curators. We follow the convention that each term should have a textual definition of the genus-differentia form (i.e., a subclass structure of A is an A that has properties X and Y that distinguish it from the other subclass structures of A (Smith et al. 2007). Distinguishing characteristics typically include structural criteria, location, shape, development and/or a list of the parts of the entity.
The following are examples of genus-differentia definitions in the TAO. Note that the definition begins with the name of the parent term ("dermal bone") followed by the characteristics that differentiate the defined term from all other dermal bones:
Antorbital: Dermal bone that is located on the anterior margin of the infraorbital series, dorsal to the first infraorbital and lateral to the nasal
Dentary: Dermal bone that forms the anterolateral part of the lower jaw.
Definitions are written so that they apply universally to the taxon under consideration. However, some taxonomic information, such as the presence of the structure or its variation in some quality across taxa, can be helpful to the user for general understanding and identification of the structure. Such taxonomic statements are recorded in the "Comment" field for the term. For example, 'Weberian apparatus' (TAO: 0001188) has the following definition: “Anatomical cluster that consists of the modified anteriormost vertebrae and associated structures that connect the swim bladder to the inner ear” and the following is recorded in the comment field: “Vertebra 1-4, and sometimes vertebra 5 in some catfishes, are part of the Weberian apparatus. Weberian apparatus is present in Otophysi.”
Logical definitions, or cross-products, are computable forms of textual definitions, and also take the form of genus-differentia definitions. They are created by combining ontology terms with a relation, enabling reasoners to perform automated tasks such as inferring is_a relationships among terms.
- Creating cross-products in Obo-Edit
Documenting term references
There are several ways to record references for the origin of definitions or synonyms. These include DOIs or Pubmed IDs to reference a publication. Older publications typically lack these identifiers, and in these cases, a PSPUB identifier (see below) can created for the reference. URLs can also be used to reference a term tracker item or website. Finally, a curator's initials is used in cases where the curator created a basic definition without the use of external references.
Phenoscape Publication Identifiers (PSPUB)
PSPUB identifiers are identifiers created to store references to journal articles which lack DOI or Pubmed identifiers. They are also used to reference meetings or workshops during which ontology design decisions were made. Examples of how these are used given below.
- Reference for the origin of a definition:
id: VAO:0000000 name: cartilaginous element def: "Skeletal element that is composed of cartilage tissue and may be permanent or transient." [PSPUB:0000170]
- PSPUB:0000170: Phenoscape Skeletal Anatomy Jamboree (2010). Brian K. Hall (Dalhousie University), Matthew Vickaryous (Ontario Veterinary College, University of Guelph), David Blackburn, University of Kansas; Wasila Dahdul, University of South Dakota and NESCent; Alexander Diehl, Mouse Genome Informatics (MGI); Melissa Haendel, Oregon Health Sciences University; John G. Lundberg, Department of Ichthyology, Academy of Natural Sciences, Philadelphia; Paula Mabee, Department of Biology, University of South Dakota; Martin Ringwald, Mouse Genome Informatics (MGI); Erik Segerdell, Oregon Health Sciences University; Ceri Van Slyke, Zebrafish Information Network (ZFIN); Monte Westerfield, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon. 2010. Skeletal terms and relationships were created and revised at the Skeletal Anatomy Jamboree held by Phenoscape (NSF grant BDI-0641025) and hosted by the National Evolutionary Synthesis Center (NESCent), April 9-10, 2010.
- Reference for a synonym
id: TAO:0000169 name: basisphenoid def: "An endochondral bone that is located ventral to the pterosphenoid and dorsal to the parasphenoid. Basisphenoid is a median bone that is usually Y-shaped." [TAO:wd] synonym: "basisphénoïde (French)" EXACT [PSPUB:0000164]
- PSPUB:0000164: Chanet, B. and Desoutter-Meniger (2008). "French-English glossary of terms found in Chabanaud’s published works on Pleuronectiformes." Cybium E1: 1-23.