Literature mining for the biologist: from information retrieval to biological discovery (Q30002370)

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.

Europe PubMed Central

title

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

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main subject

information retrieval

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1

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Peer Bork

series ordinal

3

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Jasmin Saric

series ordinal

2

object named as

Jasmin Saric

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publication date

February 2006

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published in

Nature Reviews Genetics

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volume

7

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page(s)

119-129

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issue

2

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cites work

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Somatomedin C and arginine: implicit connections between mutually isolated literatures

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Linking estrogen to Alzheimer's disease: An informatics approach

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Of truth and pathways: chasing bits of information through myriads of articles.

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Facts from text--is text mining ready to deliver?

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Automated extraction of information in molecular biology

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Accomplishments and challenges in literature data mining for biology

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Genomics and natural language processing

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Concerted mechanism of Swe1/Wee1 regulation by multiple kinases in budding yeast.

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An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts

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Mining literature for protein-protein interactions.

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PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine

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Extraction of transcript diversity from scientific literature

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Ranking the whole MEDLINE database according to a large training set using text indexing

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MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling

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A gene network for navigating the literature

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Tagging gene and protein names in biomedical text

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GAPSCORE: finding gene and protein names one word at a time.

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Identifying gene and protein mentions in text using conditional random fields

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ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text

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Recognition of protein/gene names from text using an ensemble of classifiers

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Using BLAST for identifying gene and protein names in journal articles.

31 March 2020

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Finding relevant references to genes and proteins in Medline using a Bayesian approach

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Protein names precisely peeled off free text.

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Exploring the boundaries: gene and protein identification in biomedical text

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Automatically annotating documents with normalized gene lists

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A simple approach for protein name identification: prospects and limits

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ProMiner: rule-based protein and gene entity recognition

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Gene name ambiguity of eukaryotic nomenclatures

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Resolving abbreviations to their senses in Medline.

31 March 2020

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Thesaurus-based disambiguation of gene symbols

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Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information

31 March 2020

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Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

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STRING: known and predicted protein-protein associations, integrated and transferred across organisms

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From gene networks to gene function

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Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network

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

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Integration of text- and data-mining using ontologies successfully selects disease gene candidates

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Learning statistical models for annotating proteins with function information using biomedical text

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Beyond the clause: extraction of phosphorylation information from medline abstracts

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Extraction of regulatory gene/protein networks from Medline

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Extracting human protein interactions from MEDLINE using a full-sentence parser

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Extraction of protein interaction information from unstructured text using a context-free grammar

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Mining MEDLINE for implicit links between dietary substances and diseases

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Extending the mutual information measure to rank inferred literature relationships

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Using literature-based discovery to identify disease candidate genes.

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HSF and Msn2/4p can exclusively or cooperatively activate the yeast HSP104 gene

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Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase

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Genetic factors that regulate the attenuation of the general stress response of yeast

31 March 2020

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The Ccr4-Not complex independently controls both Msn2-dependent transcriptional activation--via a newly identified Glc7/Bud14 type I protein phosphatase module--and TFIID promoter distribution.

31 March 2020

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Shared roles of yeast glycogen synthase kinase 3 family members in nitrogen-responsive phosphorylation of meiotic regulator Ume6p

31 March 2020

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Expression of the INO2 regulatory gene of Saccharomyces cerevisiae is controlled by positive and negative promoter elements and an upstream open reading frame

31 March 2020

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Transcriptional regulation of the squalene synthase gene (ERG9) in the yeast Saccharomyces cerevisiae

31 March 2020

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Life cycles of successful genes

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Dynamic Complex Formation During the Yeast Cell Cycle

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Differential activities of murine single minded 1 (SIM1) and SIM2 on a hypoxic response element. Cross-talk between basic helix-loop-helix/per-Arnt-Sim homology transcription factors

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Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families

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Mining functional information associated with expression arrays

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Use of keyword hierarchies to interpret gene expression patterns.

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Mining microarray expression data by literature profiling

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Using text analysis to identify functionally coherent gene groups

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The computational analysis of scientific literature to define and recognize gene expression clusters

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TXTGate: profiling gene groups with text-based information

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Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease.

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Systematic association of genes to phenotypes by genome and literature mining

31 March 2020

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Information extraction from full text scientific articles: where are the keywords?

31 March 2020

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Distribution of information in biomedical abstracts and full-text publications.

31 March 2020

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Assessing the accuracy of prediction algorithms for classification: an overview

31 March 2020

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Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup.

31 March 2020

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Overview of BioCreAtIvE: critical assessment of information extraction for biology

31 March 2020

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Worldwide scientific publishing activity

31 March 2020

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31 March 2020

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Coauthorship networks and patterns of scientific collaboration

31 March 2020

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31 March 2020

Identifiers

DOI

10.1038/NRG1768

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Consolidated OpenCitations Corpus – April 2017

Dimensions Publication ID

2095216

1011616497

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2095216

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Consolidated OpenCitations Corpus – April 2017

Consolidated OpenCitations Corpus – April 2017

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