ArticleJournal of cheminformatics2019
Interoperable chemical structure search service.
Article in Journal of cheminformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 10 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
10 citing papers in PubMed.
- The IDSM mass spectrometry extension: searching mass spectra using SPARQL.Bioinformatics (Oxford, England) · 2024Article
- The SIB Swiss Institute of Bioinformatics Semantic Web of data.Nucleic acids research · 2024Article
- Annotation of biologically relevant ligands in UniProtKB using ChEBI.Bioinformatics (Oxford, England) · 2023Article
- Article
- Representation of molecules for drug response prediction.Briefings in bioinformatics · 2022Review
- Rhea, the reaction knowledgebase in 2022.Nucleic acids research · 2022Article
- IDSM ChemWebRDF: SPARQLing small-molecule datasets.Journal of cheminformatics · 2021Article
- Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB.Metabolites · 2021Article
- Enzyme annotation in UniProtKB using Rhea.Bioinformatics (Oxford, England) · 2020Article
- Correction to: Interoperable chemical structure search service.Journal of cheminformatics · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
motivationThe existing connections between large databases of chemicals, proteins, metabolites and assays offer valuable resources for research in fields ranging from drug design to metabolomics. Transparent search across multiple databases provides a way to efficiently utilize these resources. To simplify such searches, many databases have adopted semantic technologies that allow interoperable querying of the datasets using SPARQL query language. However, the interoperable interfaces of the chemical databases still lack the functionality of structure-driven chemical search, which is a fundamental method of data discovery in the chemical search space.
resultsWe present a SPARQL service that augments existing semantic services by making interoperable substructure and similarity searches in small-molecule databases possible. The service thus offers new possibilities for querying interoperable databases, and simplifies writing of heterogeneous queries that include chemical-structure search terms. AVAILABILITY: The service is freely available and accessible using a standard SPARQL endpoint interface. The service documentation and user-oriented demonstration interfaces that allow quick explorative querying of datasets are available at https://idsm.elixir-czech.cz .
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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.