ArticleBMC bioinformatics2008
Mapping proteins to disease terminologies: from UniProt to MeSH.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- FuDiCo: Gene Fusion-Initiated Path Propagation for Disease Comorbidity Prediction.Current issues in molecular biology · 2026Article
- Drug repurposing for Parkinson's disease by biological pathway based edge-weighted network proximity analysis.Scientific reports · 2024Article
- Disease gene prioritization with quantum walks.Bioinformatics (Oxford, England) · 2024Article
- An experimentally validated approach to automated biological evidence generation in drug discovery using knowledge graphs.Nature communications · 2024Article
- MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering.Bioinformatics (Oxford, England) · 2023Article
- Exploring Drug Treatment Patterns Based on the Action of Drug and Multilayer Network Model.International journal of molecular sciences · 2020Article
- Network-based characterization of disease-disease relationships in terms of drugs and therapeutic targets.Bioinformatics (Oxford, England) · 2020Article
- Network-principled deep generative models for designing drug combinations as graph sets.Bioinformatics (Oxford, England) · 2020Article
- Computational Methods for Identifying Similar Diseases.Molecular therapy. Nucleic acids · 2019Review
- Self-Weighted Multi-Kernel Multi-Label Learning for Potential miRNA-Disease Association Prediction.Molecular therapy. Nucleic acids · 2019Article
- Automatic extraction of protein-protein interactions using grammatical relationship graph.BMC medical informatics and decision making · 2018Article
- Conserved Disease Modules Extracted From Multilayer Heterogeneous Disease and Gene Networks for Understanding Disease Mechanisms and Predicting Disease Treatments.Frontiers in genetics · 2018Article
- MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank.Journal of biomedical semantics · 2017Article
- Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations.Bioinformatics and biology insights · 2017Article
- Tissue Specificity of Human Disease Module.Scientific reports · 2016Article
- A knowledge-based approach for predicting gene-disease associations.Bioinformatics (Oxford, England) · 2016Article
- Network-based in silico drug efficacy screening.Nature communications · 2016Article
- A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome.PLoS computational biology · 2015Article
- Disease networks. Uncovering disease-disease relationships through the incomplete interactome.Science (New York, N.Y.) · 2015Article
- Development and tuning of an original search engine for patent libraries in medicinal chemistry.BMC bioinformatics · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlthough the UniProt KnowledgeBase is not a medical-oriented database, it contains information on more than 2,000 human proteins involved in pathologies. However, these annotations are not standardized, which impairs the interoperability between biological and clinical resources. In order to make these data easily accessible to clinical researchers, we have developed a procedure to link diseases described in the UniProtKB/Swiss-Prot entries to the MeSH disease terminology.
resultsWe mapped disease names extracted either from the UniProtKB/Swiss-Prot entry comment lines or from the corresponding OMIM entry to the MeSH. Different methods were assessed on a benchmark set of 200 disease names manually mapped to MeSH terms. The performance of the retained procedure in term of precision and recall was 86% and 64% respectively. Using the same procedure, more than 3,000 disease names in Swiss-Prot were mapped to MeSH with comparable efficiency.
conclusionsThis study is a first attempt to link proteins in UniProtKB to the medical resources. The indexing we provided will help clinicians and researchers navigate from diseases to genes and from genes to diseases in an efficient way. The mapping is available at: http://research.isb-sib.ch/unimed.
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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.