ArticleBriefings in bioinformatics2012
Mining the pharmacogenomics literature--a survey of the state of the art.
Article in Briefings in bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed.
- Extracting knowledge networks from plant scientific literature: potato tuber flesh color as an exemplary trait.BMC plant biology · 2021Article
- PGxCorpus, a manually annotated corpus for pharmacogenomics.Scientific data · 2020Article
- Computational drug repositioning using meta-path-based semantic network analysis.BMC systems biology · 2018Article
- Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.Briefings in bioinformatics · 2018Article
- Use of ontology structure and Bayesian models to aid the crowdsourcing of ICD-11 sanctioning rules.Journal of biomedical informatics · 2017Article
- Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery.Briefings in bioinformatics · 2016Review
- Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health.Advances in experimental medicine and biology · 2016Review
- Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research.BMC bioinformatics · 2015Article
- An Overview of Biomolecular Event Extraction from Scientific Documents.Computational and mathematical methods in medicine · 2015Review
- Mining adverse drug reactions from online healthcare forums using hidden Markov model.BMC medical informatics and decision making · 2014Article
- Big data in medicine is driving big changes.Yearbook of medical informatics · 2014Review
- A knowledge-driven approach to extract disease-related biomarkers from the literature.BioMed research international · 2014Review
- Literature mining of genetic variants for curation: quantifying the importance of supplementary material.Database : the journal of biological databases and curation · 2014Article
- A machine learning approach to identify clinical trials involving nanodrugs and nanodevices from ClinicalTrials.gov.PloS one · 2014Article
- Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.Journal of biomedical semantics · 2013Article
- Discovery of novel biomarkers and phenotypes by semantic technologies.BMC bioinformatics · 2013Article
- Automated Metabolic Phenotyping of Cytochrome Polymorphisms Using PubMed Abstract Mining.AMIA ... Annual Symposium proceedings. AMIA SymposiumArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011. Pharmacogenomics (or pharmacogenetics) is the field that studies how human genetic variation impacts drug response. Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years. This survey covers efforts dealing with the automatic recognition of relevant named entities (e.g. genes, gene variants and proteins, diseases and other pathological phenomena, drugs and other chemicals relevant for medical treatment), as well as various forms of relations between them. A wide range of text genres is considered, such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives. We also discuss infrastructure and resources needed for advanced text analytics, e.g. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensive ways to disseminate and interact with the typically huge amounts of semiformal knowledge structures extracted by text mining tools. Finally, we consider some of the novel applications that have already been developed in the field of pharmacogenomic text mining and point out perspectives for future research.
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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.