ArticlePLoS computational biology2016
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed.
- MolMeDB RDF: transforming a relational database about biological membranes to the RDF format to increase interoperability.Journal of cheminformatics · 2026Article
- The FAIR AOP roadmap for 2025: Advancing findability, accessibility, interoperability, and re-usability of adverse outcome pathways.Computational toxicology (Amsterdam, Netherlands) · 2025Article
- NNI Nanoinformatics Conference 2023: Movement Toward a Common Infrastructure for Federal nanoEHS Data Computational Toxicology: Short Communication.Computational toxicology (Amsterdam, Netherlands) · 2024Article
- Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations.Orphanet journal of rare diseases · 2023Article
- Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content.Applied in vitro toxicology · 2022Article
- Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions.PloS one · 2022Article
- RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data.BMC microbiology · 2021Article
- Ten simple rules for creating reusable pathway models for computational analysis and visualization.PLoS computational biology · 2021Article
- Publishing reproducible dynamic kinetic models.Briefings in bioinformatics · 2021Article
- A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses.BMC biology · 2021Article
- An empirical meta-analysis of the life sciences linked open data on the web.Scientific data · 2021Article
- WikiPathways: connecting communities.Nucleic acids research · 2021Article
- Search, access, and explore life science nanopublications on the Web.PeerJ. Computer science · 2021Article
- Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome.Frontiers in genetics · 2019Article
- Enabling Web-scale data integration in biomedicine through Linked Open Data.NPJ digital medicine · 2019Review
- WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.Nucleic acids research · 2018Article
- AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2018Article
- Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform.F1000Research · 2018Article
- Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials.Frontiers in genetics · 2018Article
- Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.
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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.