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Cited by 11Biomedical Text Mining and OntologiesComputational Drug Discovery MethodsSemantic Web and Ontologies

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

The functional therapeutic chemical classification system

Open access
Croset, Samuel, Overington, John P., Rebholz-Schuhmann, Dietrich·2014·Bioinformatics
DOI 10.1093/bioinformatics/btt628PMC PMC3957075
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Abstract

Motivation: Drug repositioning is the discovery of new indications for compounds that have already been approved and used in a clinical setting. Recently, some computational approaches have been suggested to unveil new opportunities in a systematic fashion, by taking into consideration gene expression signatures or chemical features for instance. We present here a novel method based on knowledge integration using semantic technologies, to capture the functional role of approved chemical compounds. Results: In order to computationally generate repositioning hypotheses, we used the Web Ontology Language to formally define the semantics of over 20 000 terms with axioms to correctly denote various modes of action (MoA). Based on an integration of public data, we have automatically assigned over a thousand of approved drugs into these MoA categories. The resulting new resource is called the Functional Therapeutic Chemical Classification System and was further evaluated against the content of the traditional Anatomical Therapeutic Chemical Classification System. We illustrate how the new classification can be used to generate drug repurposing hypotheses, using Alzheimers disease as a use-case. Availability: https://www.ebi.ac.uk/chembl/ftc; https://github.com/loopasam/ftc. Contact: croset@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

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  • Statins (atorvastatin, simvastatin, rosuvastatin, fluvastatin) and ezetimibe were suggested as viable AD repurposing candidates by other studies.

    “Still, statins (atorvastatin, simvastatin, rosuvastatin, fluvastatin) and ezetimibe were suggested as viable AD repurposing candidates by other studies”

    From Drug repurposing for Alzheimer’s disease from 2012–2022—a 10-year literature review (2023) · cites this paper as Croset et al., 2014

    Section 2.3 identifies ezetimibe as a potential Alzheimer’s disease repurposing candidate and discusses statins as a possible approach. It does not name atorvastatin, simvastatin, rosuvastatin, or fluvastatin, and says early studies had not clearly shown a benefit, so it does not establish the listed drugs as viable candidates suggested by other studies. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Reported negative outcomes may not entirely discredit the candidacy of certain drugs.

    “suggesting that reported negative outcomes may not entirely discredit the candidacy of certain drugs (Cheung et al., 2014;Croset et al., 2014;Kondo et al., 2017;Bauzon et al., 2020;Wu et al., 2021).”

    From Drug repurposing for Alzheimer’s disease from 2012–2022—a 10-year literature review (2023) · cites this paper as Croset et al., 2014

  • Demecarium was first suggested as an AD repurposing candidate in 2014, with subsequent support in two studies; after 2016, the drug was not mentioned again.

    “demecarium was first suggested as an AD repurposing candidate in 2014 (Croset et al., 2014), with subsequent support in two studies (Jamal et al., 2015;Zhang et al., 2016); however, after 2016, the drug was not mentioned again.”

    From Drug repurposing for Alzheimer’s disease from 2012–2022—a 10-year literature review (2023) · cites this paper as Croset et al., 2014

    Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.

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Research works printed but not linked: 29

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Metadata

Authors
Croset, S., Overington, J. P., & Rebholz-Schuhmann, D.
Affiliations
  • European Bioinformatics Institute (GB)
  • European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
Corresponding author
Croset, Samuel
ORCID
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2013-10-30
Volume
30
Issue
6
Pages
876-883
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/btt628
PMC
PMC3957075
OpenAlex
W2127050796
Cited by
11
References
1
Citations by year
2026: 1 · 2024: 1 · 2023: 1 · 2021: 1 · 2019: 1 · 2017: 1 · 2016: 2 · 2015: 1 · 2014: 1 · 2013: 1
FWCI
0.75
Type
journal article
Language
en
Open access
Licence
Locations
  • Bioinformatics (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • ICBO
Funders
European Molecular Biology Laboratory
Topics
  • Health Sciences › Medicine › Health Informatics › Biomedical Text Mining and Ontologies
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
  • Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
Keywords
drug repurposing, mechanism of action, semantic technologies, Web Ontology Language, knowledge integration, approved drugs, Alzheimer's disease, ATC classification
MeSH terms
Alzheimer Disease, Pharmaceutical Preparations, Humans, Internet, Drug Repositioning, Polypharmacology

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