A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1–20)

Abstract

This paper describes a new ontology of human developmental anatomy covering the first 49 days [Carnegie stages (CS)1-20], primarily structured around the parts of organ systems and their development. The ontology includes more than 2000 anatomical entities (AEs) that range from the whole embryo, through organ systems and organ parts down to simple or leaf tissues (groups of cells with the same morphological phenotype), as well as features such as cavities. Each AE has assigned to it a set of facts of the form <AE><relationship><parent>, with the relationships including starts_at and ends_at (CSs), part_of (there can be several parents) and is_a (this gives the type of tissue, from an organ system down to one of~80 simple tissues predominantly composed of a single cell kind, which is also specified). Leaf tissues also have a develops_from link to its parent tissue. The ontology includes~14 000 such facts, which are mainly from the literature and an earlier ontology of human developmental anatomy (EHDAA, now withdrawn). The relationships enable these facts to be integrated into a single, complex hierarchy (or mathematical graph) that was made and can be viewed in the OBO-Edit browser (oboedit.org). Each AE has an EHDAA2 ID that may be useful in an informatics context, while the ontology as a whole can be used for organizing databases of human development. It is also a knowledge resource: a user can trace the lineage of any tissue back to the egg, study the changes in cell phenotype that occur as a tissue develops, and use the structure to add further (e.g. molecular) information. The ontology may be downloaded from www.obofoundry.org. Queries and corrections should be sent to j.bard@ed.ac.uk. Key words: anatomical classification; bioinformatics; Carnegie staging; human development; ontology. IntroductionBioinformatics needs formal anatomies (anatomy ontologies) primarily to structure databases that handle tissueassociated data (Burger et al. 2008). Such formalisms not only provide numerical identifiers (IDs) that can be used for searching and for providing normal data for mutant material, but can also make available to the user information that goes well beyond what might be found in anatomy textbooks (e.g. a hierarchy of all the tissues present at a given stage of development). There is now a wide range of such ontologies for adult and developing model organisms, and they are available at www.obofoundry.org (the location for all ontologies mentioned in this paper, other than the FMA). Standard ontology editors such as OBO-Edit (oboedit.org/) integrate and display the ontology as a parts or classification hierarchy.A very detailed ontology of adult human anatomy, the FMA 1 (Rosse & Mejino, 2008) is now available. The current ontology for human developmental anatomy (ID: EHDA; Hunter et al. 2003) is less complete: it comprises a set of ontologies, one for each Carnegie stage (CS) (1-20) that only includes basic part_of data. Its structure was derived from the original ontology of mouse developmental anatomy...

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