title: The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.
abstract: BACKGROUND
  Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility.
  
  
  RESULTS
  The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications.
  
  
  CONCLUSIONS
  The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user's needs.
  
  
  BACKGROUND
  The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com.
authors: EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK.
authors: James
authors: J
authors: Malone
authors: School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
authors: Andy
authors: A
authors: Brown
authors: School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
authors: Allyson L
authors: AL
authors: Lister
authors: EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK.
authors: Jon
authors: J
authors: Ison
authors: School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
authors: Duncan
authors: D
authors: Hull
authors: EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK.
authors: Helen
authors: H
authors: Parkinson
authors: School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
authors: Robert
authors: R
authors: Stevens