OntoSPM is distributed according to a Creative Common CC-BY-4.0 Licence

OntoSPM is a result produced by the OntoSPM Collaborative Action. It is a modular ontology, implemented in OWL 2, and composed of a main module (OntoSPM.owl) and of several modules extracted from existing ontologies.

The entities (Classes, Object properties, Data properties, Annotations) were selected from existing ontologies as much as possible. The criteria for selecting terms from existing ontologies were primarily based on relevance to the domain of Surgery and Surgical Data Science.

The main modules are listed below, together with a reference to their original license and a motivation statement and a term list guiding the extraction.

• Basic Formal Ontology (BFO 2)
  • License: CC-BY
  • Reference: https://github.com/bfo-ontology/BFO/wiki
  • Motivation: need for a foundational ontology providing a common and consistent integration framework
  • Subset: the entire file is imported

• Information Artefacts Ontology (IAO)
  • License: CC-BY
  • Reference: https://github.com/information-artifact-ontology/IAO/
  • Motivation: need for a basic entities for information content entities and measurement values
  • Subset: the list of extracted terms is available at: iao.txt

• Mouse pathology (MPATH)
  • License: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported
  • Reference: http://www.pathbase.net/
  • Motivation: need for a set of terms covering pathological anatomical structures relevant to the domain of surgery (it is quite exhaustive)
  • Subset: the list of extracted terms is available at: mpath.txt

• Phenotypic quality (PATO)
  • License: BSD 3-clause
  • Reference: https://github.com/pato-ontology/pato/
  • Motivation: need for a set of terms covering phenotypic qualities needed for representing basic qualities of organisms and measurements
  • Subset: the list of extracted terms is available at: pato.txt

• Units of measurement (UO)
  • License: CC-BY
  • Reference: https://github.com/bio-ontology-research-group/unit-ontology
  • Motivation: need for a set of terms covering phenotypic qualities needed for representing measurements
  • Subset: the list of extracted terms is available at: uo.txt

• Foundational Model of Anatomy (FMA)
  • License: Creative Commons Attribution 3.0 Unported
  • Reference: http://si.washington.edu/projects/fma
  • Motivation: need for a set of terms covering normal human anatomy (currently limited to main organs and main organ parts)
  • Subset: the list of extracted terms is available at: fma.txt