ArticleJournal of biomedical semantics2011
Linking the Resource Description Framework to cheminformatics and proteochemometrics.
Article in Journal of biomedical semantics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Chemical reaction network knowledge graphs: the OntoRXN ontology.Journal of cheminformatics · 2022Article
- Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence.Annual review of biomedical data science · 2020Article
- NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease.Journal of biomedical semantics · 2016Article
- Many InChIs and quite some feat.Journal of computer-aided molecular design · 2015Article
- Semantic enrichment of longitudinal clinical study data using the CDISC standards and the semantic statistics vocabularies.Journal of biomedical semantics · 2015Article
- Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance.Wiley interdisciplinary reviews. Computational molecular science · 2013Article
- The ChEMBL database as linked open data.Journal of cheminformatics · 2013Article
- Applications of the InChI in cheminformatics with the CDK and Bioclipse.Journal of cheminformatics · 2013Article
- Bioclipse-R: integrating management and visualization of life science data with statistical analysis.Bioinformatics (Oxford, England) · 2013Article
- Redefining Cheminformatics with Intuitive Collaborative Mobile Apps.Molecular informatics · 2012Article
- Computational toxicology using the OpenTox application programming interface and Bioclipse.BMC research notes · 2011Article
- Brunn: an open source laboratory information system for microplates with a graphical plate layout design process.BMC bioinformatics · 2011Article
- Biomedical semantics in the Semantic Web.Journal of biomedical semantics · 2011Article
- The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.PloS one · 2011Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSemantic web technologies are finding their way into the life sciences. Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet. The semantic web technology Resource Description Framework (RDF) and related methods show to be sufficiently versatile to change that situation.
resultsThe work presented here focuses on linking RDF approaches to existing molecular chemometrics fields, including cheminformatics, QSAR modeling and proteochemometrics. Applications are presented that link RDF technologies to methods from statistics and cheminformatics, including data aggregation, visualization, chemical identification, and property prediction. They demonstrate how this can be done using various existing RDF standards and cheminformatics libraries. For example, we show how IC50 and Ki values are modeled for a number of biological targets using data from the ChEMBL database.
conclusionsWe have shown that existing RDF standards can suitably be integrated into existing molecular chemometrics methods. Platforms that unite these technologies, like Bioclipse, makes this even simpler and more transparent. Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility. The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows.
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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.