ArticlePacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2014
Towards pathway curation through literature mining--a case study using PharmGKB.
Article in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Use of Network Pharmacology and Experiment Validation to Uncover the Mechanism of Jianshen Lishui Prescription in the Treatment of Intracerebral Hemorrhage.Combinatorial chemistry & high throughput screening · 2025Article
- PharmGKB, an Integrated Resource of Pharmacogenomic Knowledge.Current protocols · 2021Article
- BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences.Database : the journal of biological databases and curation · 2017Article
- Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2016Article
- Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.BMC bioinformatics · 2015Article
- Extracting Concepts for Precision Oncology from the Biomedical Literature.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational ScienceArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The creation of biological pathway knowledge bases is largely driven by manual effort to curate based on evidences from the scientific literature. It is highly challenging for the curators to keep up with the literature. Text mining applications have been developed in the last decade to assist human curators to speed up the curation pace where majority of them aim to identify the most relevant papers for curation with little attempt to directly extract the pathway information from text. In this paper, we describe a rule-based literature mining system to extract pathway information from text. We evaluated the system using curated pharmacokinetic (PK) and pharmacodynamic (PD) pathways in PharmGKB. The system achieved an F-measure of 63.11% and 34.99% for entity extraction and event extraction respectively against all PubMed abstracts cited in PharmGKB. It may be possible to improve the system performance by incorporating using statistical machine learning approaches. This study also helped us gain insights into the barriers towards automated event extraction from text for pathway curation.
Indexed as
Identifiers
24297561PMC3902837What OpenQuestion holds
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.