ArticleJournal of biomedical semantics2014
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.
Article in Journal of biomedical semantics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.Metabolomics : Official journal of the Metabolomic Society · 2023Pooled it
- BioAgents: Bridging the gap in bioinformatics analysis with multi-agent systems.Scientific reports · 2025Article
- Improving data sharing and knowledge transfer via the Neuroelectrophysiology Analysis Ontology (NEAO).Scientific data · 2025Article
- ENCORE: a practical implementation to improve reproducibility and transparency of computational research.Nature communications · 2024Article
- Dermoscopy Differential Diagnosis Explorer (D3X) Ontology to Aggregate and Link Dermoscopic Patterns to Differential Diagnoses: Development and Usability Study.JMIR medical informatics · 2024Article
- Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research.Proceedings of the ... International World-Wide Web Conference. International WWW Conference · 2023Article
- An ontology-driven framework for knowledge representation of digital extortion attacks.Computers in human behavior · 2023Article
- A Linked Open Data-Based Terminology to Describe Libre/Free and Open-source Software: Incremental Development Study.JMIR medical informatics · 2023Article
- Ontologies for increasing the FAIRness of plant research data.Frontiers in plant science · 2023Review
- Toward a standard formal semantic representation of the model card report.BMC bioinformatics · 2022Article
- A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research.Metabolites · 2022Review
- The role of software in science: a knowledge graph-based analysis of software mentions in PubMed Central.PeerJ. Computer science · 2022Article
- The role of metadata in reproducible computational research.Patterns (New York, N.Y.) · 2021Review
- Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.Briefings in bioinformatics · 2021Article
- Article
- Dataset of ontology competency questions to SPARQL-OWL queries translations.Data in brief · 2020Article
- The Knowledge Object Reference Ontology (KORO): A formalism to support management and sharing of computable biomedical knowledge for learning health systems.Learning health systems · 2018Article
- Bio-TDS: bioscience query tool discovery system.Nucleic acids research · 2017Article
- The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.Journal of biomedical semantics · 2016Article
- Where next for the reproducibility agenda in computational biology?BMC systems biology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationBiomedical 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.
resultsThe 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.
conclusionThe 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. AVAILABILITY: 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.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.