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What is what

What is an Ontology ?#

Ontologies formally represent knowledge about a certain domain and store it in a structured and machine readable way. Fraunhofer SCAI restricts its interest to Ontologies in Life Sciences. Ontologies are widely used in Life Sciences and there exists an Ontology for almost every major topic in Biology and Life Sciences.

What is .owl ?#

The majority of biomedical ontologies are formalized using the Web Ontology Language (OWL) , a language based on Description Logic (a decidable fragment of first order predicate logic). [https://en.wikipedia.org/wiki/First-order_logic]. Technically .owl files are written using the RDF syntax.

What is Protege ?#

Protege is a free software published by the Stanford University and is one of the most important tools when it comes to create and modify Ontologies. It can be downloaded here: [https://protege.stanford.edu/] and there is a very good tutorial here : [https://protegewiki.stanford.edu/wiki/Protege4Pizzas10Minutes]. Protege can be used to view, delete and add things to the Ontology.

What is the Obo Foundry and Obo Principles?#

The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles.

  • P1) Open - The ontology MUST be openly available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed in altered form under the original name or with the same identifiers.
  • P2) Common Format - The ontology is made available in a common formal language in an accepted concrete syntax.
  • P3) URI/Identifier Space - Each ontology MUST have a unique IRI in the form of an OBO Foundry permanent URL (PURL).
  • P4) Versioning - The ontology provider has documented procedures for versioning the ontology, and different versions of ontology are marked, stored, and officially released.
  • P5) Scope - The scope of an ontology is the extent of the domain or subject matter it intends to cover. The ontology must have a clearly specified scope and content that adheres to that scope.
  • P6) Textual Definitions - The ontology has textual definitions for the majority of its classes and for top level terms in particular.
  • P7) Relations - Relations should be reused from the Relations Ontology (RO).
  • P8) Documentation - The owners of the ontology should strive to provide as much documentation as possible.
  • P9) Documented Plurality of Users - The ontology developers should document that the ontology is used by multiple independent people or organizations.
  • P10) Commitment To Collaboration - OBO Foundry ontology development, in common with many other standards-oriented scientific activities, should be carried out in a collaborative fashion.
  • P11) Locus of Authority - There should be a person who is responsible for communications between the community and the ontology developers, for communicating with the Foundry on all Foundry-related matters, for mediating discussions involving maintenance in the light of scientific advance, and for ensuring that all user feedback is addressed.
  • P12) Naming Conventions - The names (primary labels) for elements (classes, properties, etc.) in an ontology must be intelligible to scientists and amenable to natural language processing. Primary labels should be unique among OBO Library ontologies.
  • P16) Maintenance - The ontology needs to reflect changes in scientific consensus to remain accurate over time.
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