Application of text mining in the biomedical domain (Q38340254)

2 September 2017

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title

Application of text mining in the biomedical domain (English)

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2 September 2017

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Wynand Alkema

2

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author name string

Wilco W M Fleuren

series ordinal

1

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2 September 2017

30 January 2015

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2 September 2017

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2 September 2017

74

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2 September 2017

97-106

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On-line biomedical databases-the best source for quick search of the scientific information in the biomedicine.

2 September 2017

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Literature mining for the biologist: from information retrieval to biological discovery

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

GoGene: gene annotation in the fast lane

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Urine proteomics for profiling of human disease using high accuracy mass spectrometry

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Protein markers of ischemic insult in brain endothelial cells identified using 2D gel electrophoresis and ICAT-based quantitative proteomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

CoPub update: CoPub 5.0 a text mining system to answer biological questions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

TMT-HCC: a tool for text mining the biomedical literature for hepatocellular carcinoma (HCC) biomarkers identification

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Categorization of services for seeking information in biomedical literature: a typology for improvement of practice

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Frontiers of biomedical text mining: current progress

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Text-mining and information-retrieval services for molecular biology

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Mining the biomedical literature in the genomic era: an overview

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Text mining and its potential applications in systems biology

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Text mining for the biocuration workflow

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

askMEDLINE: a free-text, natural language query tool for MEDLINE/PubMed

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

XplorMed: a tool for exploring MEDLINE abstracts

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

MedlineRanker: flexible ranking of biomedical literature

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

MiSearch adaptive pubMed search tool

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

PICO element detection in medical text without metadata: are first sentences enough?

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

PubCrawler: keeping up comfortably with PubMed and GenBank

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

PubMatrix: a tool for multiplex literature mining

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

PubNet: a flexible system for visualizing literature derived networks

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Gene List significance at-a-glance with GeneValorization

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Disease and phenotype gene set analysis of disease-based gene expression in mouse and human.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Content-rich biological network constructed by mining PubMed abstracts

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Authorship trends in the surgical literature

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

AN ACTIVE VISUAL SEARCH INTERFACE FOR MEDLINE

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Discovering and visualizing indirect associations between biomedical concepts.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

PPInterFinder--a mining tool for extracting causal relations on human proteins from literature

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Reflect: augmented browsing for the life scientist

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Text processing through Web services: calling Whatizit

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

AliBaba: PubMed as a graph

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Martini: using literature keywords to compare gene sets

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

World databases of summaries of articles in the biomedical fields

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Literature-based compound profiling: application to toxicogenomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Overview of BioCreative II gene normalization

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Mining biomarker information in biomedical literature

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Improving image retrieval effectiveness via query expansion using MeSH hierarchical structure

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

NCBO Technology: Powering semantically aware applications

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Enhancing HMM-based biomedical named entity recognition by studying special phenomena

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Identification of related gene/protein names based on an HMM of name variations

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Cascaded classifiers for confidence-based chemical named entity recognition

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Automatic recognition of disorders, findings, pharmaceuticals and body structures from clinical text: an annotation and machine learning study

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Two-phase biomedical named entity recognition using CRFs.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

A kernel-based approach for biomedical named entity recognition.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Scalable biomedical Named Entity Recognition: investigation of a database-supported SVM approach

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Chemical named entities recognition: a review on approaches and applications

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Getting started in text mining

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Decreased clearance of serum retinol-binding protein and elevated levels of transthyretin in insulin-resistant ob/ob mice

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Retinol-binding protein 4 and its relation to insulin resistance in obese children before and after weight loss

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

CoPub Mapper: mining MEDLINE based on search term co-publication

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Fish oil, Raynaud's syndrome, and undiscovered public knowledge

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Migraine and magnesium: eleven neglected connections

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Somatomedin C and arginine: implicit connections between mutually isolated literatures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Literature mining for the discovery of hidden connections between drugs, genes and diseases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Mining connections between chemicals, proteins, and diseases extracted from Medline annotations

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Literature-based concept profiles for gene annotation: the issue of weighting

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Anni 2.0: a multipurpose text-mining tool for the life sciences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Prednisolone-induced changes in gene-expression profiles in healthy volunteers

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Prednisolone induces the Wnt signalling pathway in 3T3-L1 adipocytes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Towards virtual knowledge broker services for semantic integration of life science literature and data sources

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Open PHACTS: semantic interoperability for drug discovery

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Biomedical discovery acceleration, with applications to craniofacial development

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Interorgan coordination of the murine adaptive response to fasting

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Drug target identification using side-effect similarity

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Using literature-based discovery to identify disease candidate genes.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Discovery of novel biomarkers and phenotypes by semantic technologies

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Role of the angiogenic components, VEGFA, FGF2, OPN and RHOC, in urothelial cell carcinoma of the urinary bladder

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Drug repositioning: identifying and developing new uses for existing drugs

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Drug repositioning summit: finding new routes to success.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Systematic evaluation of drug-disease relationships to identify leads for novel drug uses

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Discovering breast cancer drug candidates from biomedical literature

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Identification of small molecules enhancing autophagic function from drug network analysis

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Human disease-drug network based on genomic expression profiles

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Computational approaches for drug repositioning and combination therapy design.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Drug repositioning through incomplete bi-cliques in an integrated drug-target-disease network

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

GoPubMed: exploring PubMed with the Gene Ontology

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Literature mining, ontologies and information visualization for drug repurposing

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Mining the pharmacogenomics literature--a survey of the state of the art

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Adverse drug events: database construction and in silico prediction.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Automatic detection of adverse events to predict drug label changes using text and data mining techniques

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Extraction of potential adverse drug events from medical case reports

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Benefits and drawbacks of electronic health record systems

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Mining electronic health records: towards better research applications and clinical care

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

A Large Kindred With 17q-Linked Breast and Ovarian Cancer: Genetic, Phenotypic, and Genealogical Analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

The complete BRCA2 gene and mutations in chromosome 13q-linked kindreds

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Effects of BRCA1 and BRCA2 mutations on female fertility

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Identifying phenotypic signatures of neuropsychiatric disorders from electronic medical records

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Longitudinal analysis of pain in patients with metastatic prostate cancer using natural language processing of medical record text

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

MeInfoText: associated gene methylation and cancer information from text mining

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Text-mining applied to autoimmune disease research: the Sjögren's syndrome knowledge base

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

G2Cdb: the Genes to Cognition database.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

BioCaster: detecting public health rumors with a Web-based text mining system

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

OLSVis: an animated, interactive visual browser for bio-ontologies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

BioPortal: ontologies and integrated data resources at the click of a mouse

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

Elsevier opens its papers to text-mining

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2015.01.015

10.1016/J.YMETH.2015.01.015

7 January 2021

Identifiers

DOI

1 reference

2 September 2017

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PubMed ID

25641519