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- Title
The IDSM mass spectrometry extension: searching mass spectra using SPARQL.
- Authors
Galgonek, Jakub; Vondrášek, Jiří
- Abstract
Summary The Integrated Database of Small Molecules (IDSM) integrates data from small-molecule datasets, making them accessible through the SPARQL query language. Its unique feature is the ability to search for compounds through SPARQL based on their molecular structure. We extended IDSM to enable mass spectra databases to be integrated and searched for based on mass spectrum similarity. As sources of mass spectra, we employed the MassBank of North America database and the In Silico Spectral Database of natural products. Availability and implementation The extension is an integral part of IDSM, which is available at https://idsm.elixir-czech.cz. The manual and usage examples are available at https://idsm.elixir-czech.cz/docs/ms. The source codes of all IDSM parts are available under open-source licences at https://github.com/idsm-src.
- Subjects
NORTH America; MASS spectrometry; SPARQL (Computer program language); MOLECULAR structure; DATABASES; CROWDSOURCING; MASS spectrometers
- Publication
Bioinformatics, 2024, Vol 40, Issue 4, p1
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btae174