DISEASES: Text mining and data integration of disease–gene associations

[1]  Christian Stolte,et al.  COMPARTMENTS: unification and visualization of protein subcellular localization evidence , 2014, Database J. Biol. Databases Curation.

[2]  Damian Szklarczyk,et al.  STITCH 4: integration of protein–chemical interactions with user data , 2013, Nucleic Acids Res..

[3]  Jan Gorodkin,et al.  Protein-driven inference of miRNA–disease associations , 2013, Bioinform..

[4]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[5]  Barry Smith,et al.  The environment ontology: contextualising biological and biomedical entities , 2013, Journal of Biomedical Semantics.

[6]  Thomas C. Wiegers,et al.  A CTD–Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug–disease and drug–phenotype interactions , 2013, Database J. Biol. Databases Curation.

[7]  S. Gammie,et al.  Development of a versatile enrichment analysis tool reveals associations between the maternal brain and mental health disorders, including autism , 2013, BMC Neuroscience.

[8]  P. Stenson,et al.  The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine , 2013, Human Genetics.

[9]  L. Jensen,et al.  The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text , 2013, PloS one.

[10]  Robert Eriksson,et al.  Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text , 2013, J. Am. Medical Informatics Assoc..

[11]  Damian Szklarczyk,et al.  STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..

[12]  Elspeth A. Bruford,et al.  Genenames.org: the HGNC resources in 2013 , 2012, Nucleic Acids Res..

[13]  Thomas C. Wiegers,et al.  The Comparative Toxicogenomics Database: update 2013 , 2012, Nucleic Acids Res..

[14]  S. Brunak,et al.  Mining electronic health records: towards better research applications and clinical care , 2012, Nature Reviews Genetics.

[15]  Pak Chung Sham,et al.  GWASdb: a database for human genetic variants identified by genome-wide association studies , 2011, Nucleic Acids Res..

[16]  Gang Feng,et al.  Disease Ontology: a backbone for disease semantic integration , 2011, Nucleic Acids Res..

[17]  Lars Juhl Jensen,et al.  DistiLD Database: diseases and traits in linkage disequilibrium blocks , 2011, Nucleic Acids Res..

[18]  Halil Kilicoglu,et al.  Constructing a semantic predication gold standard from the biomedical literature , 2011, BMC Bioinformatics.

[19]  Søren Brunak,et al.  Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts , 2011, PLoS Comput. Biol..

[20]  Sophia Ananiadou,et al.  Discovering and visualizing indirect associations between biomedical concepts , 2011, Bioinform..

[21]  Jacob de Vlieg,et al.  CoPub update: CoPub 5.0 a text mining system to answer biological questions , 2011, Nucleic Acids Res..

[22]  Sunghwan Sohn,et al.  Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications , 2010, J. Am. Medical Informatics Assoc..

[23]  Tsviya Olender,et al.  GeneCards Version 3: the human gene integrator , 2010, Database J. Biol. Databases Curation.

[24]  Alan R. Aronson,et al.  An overview of MetaMap: historical perspective and recent advances , 2010, J. Am. Medical Informatics Assoc..

[25]  W. Kibbe,et al.  Annotating the human genome with Disease Ontology , 2009, BMC Genomics.

[26]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[27]  Debasis Dash,et al.  HGVbaseG2P: a central genetic association database , 2008, Nucleic Acids Res..

[28]  M. Daly,et al.  Genetic Mapping in Human Disease , 2008, Science.

[29]  Sophia Ananiadou,et al.  FACTA: a text search engine for finding associated biomedical concepts , 2008, Bioinform..

[30]  Montgomery Slatkin,et al.  Linkage disequilibrium — understanding the evolutionary past and mapping the medical future , 2008, Nature Reviews Genetics.

[31]  M. McCarthy,et al.  Genome-wide association studies for complex traits: consensus, uncertainty and challenges , 2008, Nature Reviews Genetics.

[32]  S A Forbes,et al.  The Catalogue of Somatic Mutations in Cancer (COSMIC) , 2008, Current protocols in human genetics.

[33]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[34]  Joyce A. Mitchell,et al.  Challenges and strategies of the Genetics Home Reference. , 2006, Journal of the Medical Library Association : JMLA.

[35]  P. Bork,et al.  Literature mining for the biologist: from information retrieval to biological discovery , 2006, Nature Reviews Genetics.

[36]  Dietrich Rebholz-Schuhmann,et al.  BIOINFORMATICS ORIGINAL PAPER Data and text mining Resolving abbreviations to their senses in Medline , 2005 .

[37]  Burr Settles,et al.  ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text , 2005 .

[38]  Daniel Hanisch,et al.  ProMiner: rule-based protein and gene entity recognition , 2005, BMC Bioinformatics.

[39]  Jian Su,et al.  Recognition of protein/gene names from text using an ensemble of classifiers , 2005, BMC Bioinformatics.

[40]  Hongfang Liu,et al.  Gene name ambiguity of eukaryotic nomenclatures , 2005, Bioinform..

[41]  M. Olivier A haplotype map of the human genome. , 2003, Nature.

[42]  M. Olivier A haplotype map of the human genome , 2003, Nature.

[43]  Rob Jelier,et al.  CoPub Mapper: mining MEDLINE based on search term co-publication , 2005, BMC Bioinformatics.

[44]  Jonathan D. Wren,et al.  Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network , 2004, Bioinform..

[45]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[46]  E. Wilson The encyclopedia of life , 2003 .

[47]  Daniel Berleant,et al.  Mining MEDLINE: Abstracts, Sentences, or Phrases? , 2001, Pacific Symposium on Biocomputing.

[48]  T. Jenssen,et al.  A literature network of human genes for high-throughput analysis of gene expression , 2001, Nature Genetics.

[49]  Hongfang Liu,et al.  Evaluating the UMLS as a source of lexical knowledge for medical language processing , 2001, AMIA.

[50]  T. Takagi,et al.  Toward information extraction: identifying protein names from biological papers. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.