Schemas and Ontologies

TaxPub

TaxPub is an extension to the U.S. National Library of Medicine/National Center for Biotechnology Information Journal Article XML Document Type Definition (DTD) providing domain-specific markup for taxonomic information in articles published in the area of biological systematics. TaxPub is described in detall in the article TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions (See also TaxPub Documentation).

Currently, the following journals use TaxPub:

TaxonX

Taxonx is a XML schema for encoding taxonomic literature in order to

  • Create open, stable, persistent, full-text digital surrogates of taxonomic treatments
  • Identify taxonomic treatments and their major structural components to enable networked reference and citation
  • Identify lower level textual data such as scientific names, localities, morphological characters, and bibliographic citations to facilitate their extraction by and integration with external applications and resources
  • Study and describe the structure of systematics publications by creating few typical corpora of literature, such as entire journal (eg AMNH Novitates), across taxa (e.g all ant systematics papers post 1995), or faunistic (e.g. all ant systematics paper covering Madagascar ranging from 1758 to 2006)

TaxonX is a lightweight and flexible schema which can be quickly learned and applied to a wide variety of formatting present in legacy document as well as in new publications. It permits, and sometimes relies on (see use of MODS for file-level bibliographical metadata) external schemata. It has loose content requirements that allow for instances to be encoded over time and at many levels of granularity while maintaining validity through iterations. Additionally, TaxonX contains mechanisms for semantic normalization of the data contained in treatments.

Treatment Ontology

The Github repo for the ontologies used in representing data from taxonomic treatments in RDF.