ArticleBMC systems biology2013
PathNER: a tool for systematic identification of biological pathway mentions in the literature.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Large language models and their applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- ASpedia-R: a package to retrieve junction-incorporating features and knowledge-based functions of human alternative splicing events.Bioinformatics advances · 2024Article
- Splicing signature database development to delineate cancer pathways using literature mining and transcriptome machine learning.Computational and structural biotechnology journal · 2023Article
- New reasons for biologists to write with a formal language.Database : the journal of biological databases and curation · 2022Article
- Bio-TDS: bioscience query tool discovery system.Nucleic acids research · 2017Article
- Network Analysis of a Comprehensive Knowledge Repository Reveals a Dual Role for Ceramide in Alzheimer's Disease.PloS one · 2016Article
- Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events.BMC systems biology · 2015Article
- Systematic analysis of the associations between adverse drug reactions and pathways.BioMed research international · 2015Review
- KneeTex: an ontology-driven system for information extraction from MRI reports.Journal of biomedical semantics · 2015Article
- Molecular profiling of thyroid cancer subtypes using large-scale text mining.BMC medical genomics · 2014Article
- InCoB2013 introduces Systems Biology as a major conference theme.BMC systems biology · 2013Article
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3 authors.
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Abstract
backgroundBiological pathways are central to many biomedical studies and are frequently discussed in the literature. Several curated databases have been established to collate the knowledge of molecular processes constituting pathways. Yet, there has been little focus on enabling systematic detection of pathway mentions in the literature.
resultsWe developed a tool, named PathNER (Pathway Named Entity Recognition), for the systematic identification of pathway mentions in the literature. PathNER is based on soft dictionary matching and rules, with the dictionary generated from public pathway databases. The rules utilise general pathway-specific keywords, syntactic information and gene/protein mentions. Detection results from both components are merged. On a gold-standard corpus, PathNER achieved an F1-score of 84%. To illustrate its potential, we applied PathNER on a collection of articles related to Alzheimer's disease to identify associated pathways, highlighting cases that can complement an existing manually curated knowledgebase.
conclusionsIn contrast to existing text-mining efforts that target the automatic reconstruction of pathway details from molecular interactions mentioned in the literature, PathNER focuses on identifying specific named pathway mentions. These mentions can be used to support large-scale curation and pathway-related systems biology applications, as demonstrated in the example of Alzheimer's disease. PathNER is implemented in Java and made freely available online at http://sourceforge.net/projects/pathner/.
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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.