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[ 1 ]
Manchester Centre for Integrative Systems Biology
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(May 7, 2008)
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...Events Resources Links About UsResourcesCV expand CV expand is a text mining tool for automatic expansion of controlled vocabularies as a practical alternative to tailor-made named entity recognition methods. SpecificationImplementationPublicationsPeopleContact detailsSpecification We describe a text mining (TM) method for efficient corpus-based term acquisition as a...data resources for time- and cost-effective development of a text mining tool for expansion of CVs across various domains, as a...
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Facilitating the development of controlled vocabularies for metabolomics technologies with text mining.
(Apr 29, 2008)
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining.
(Apr 29, 2008)
[ 2 ]
ontogene
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(Jun 6, 2014)
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...curation (NIH)VetSuissepast projectsRocheSASEBioBioTermEvomogAssisted curationODIN: descriptionpharmgkbCTDRegulonDBhome  Text Mining, Information Extraction,     and Assisted Curation in the biomedical domain OntoGene/BioMeXT is a research initiative which aims at pushing the boundaries of text mining for the biomedical literature. Our core...provide an independent and unbiased evaluation of text mining tools. We participated in the BioCreative challenges...
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[ 3 ]
Argo | A Web-based Text Mining Workbench
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(Mar 21, 2012)
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...charset=utf-8 Argo | A Web-based Text Mining Workbench A Web-based Text Mining WorkbenchLaunch now! Currently supported browsers: Chrome, Firefox...of components includes natural language processing and text mining analytics as well as user-interactive components...is developed by The National Centre for Text Mining (NaCTeM) at The University of Manchester. By using Argo you agree to the Terms and Conditions. Content copyright © 2012-2014, The National Centre for Text Mining, The University of Manchester This website is...
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Argo: an integrative, interactive, text mining-based workbench supporting curation.
(2012)
Argo: an integrative, interactive, text mining-based workbench supporting curation.
(2012)
[ 4 ]
Compendium of Text Mining applications for life sciences (Bio-NLP tools)
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(Oct 6, 2008)
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...text/html; charset=us-ascii Compendium of Text Mining applications for life sciences (Bio-NLP tools) Bio-NLP resources database (BioNLPdb) This page provides a compendium of Information Retrieval (IR), Information Extraction (IE), Text Mining and literature processing applications developed for providing...overview of currently existing applications in biomedical text mining: Krallinger M, Valencia A. and Hirschman L. Linking genes to literature: text mining, information extraction, and retrieval applications for biology...
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[ 5 ]
hPRINT | Human Predicted Protein Interactome » Search
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(Nov 4, 2011)
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...approaches in order to integrate various evidences (text mining, genetic relationships, evolutionary information, and domain profiles...STRING)coexpression (STRING)experimental (STRING)database (STRING)text mining (STRING)STRINGHiMapBioversetextmining cellular componenttextmining molecular functiontextmining biological...STRING)coexpression (STRING)experimental (STRING)database (STRING)text mining (STRING)STRINGHiMapBioversetextmining cellular componenttextmining molecular functiontextmining biological...STRING)coexpression (STRING)experimental (STRING)database (STRING)text mining (STRING)STRINGHiMapBioversetextmining cellular componenttextmining molecular functiontextmining biological...
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Large-scale De Novo Prediction of Physical Protein-Protein Association.
(Nov, 2011)
Large-scale De Novo Prediction of Physical Protein-Protein Association.
(Nov, 2011)
[ 6 ]
BioCreative - Track 1- Collaborative Biocurator Assistant Task (BioC)
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(Sep 3, 2016)
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...of biomedical literature, finding biological evidence through text mining techniques has been a main research topic in the bio-text mining community. However, there have been few successes for improving biocuration throughput using text mining [5].The purpose of this task is...can assist in biocuration tasks by bringing text mining tool developers and database curators together. But, no attempt has been made to integrate text mining modules developed in the formal BioCreative PPI...
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[ 7 ]
BioCreative - Track II- Workflow
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(Nov 19, 2012)
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...the issues that would be useful to text mining developers who are seeking to produce algorithms...cases? dictionary? wikipedia? other database?Use of text mining tools a. What text mining tools do you currently employ in your workflow and what problems do these algorithms solve for you? b. What problems do you have that are not currently solved, but which you think could be amenable to a text mining solution (i.e., for which steps text...
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Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.
(2012)
Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.
(2012)
[ 8 ]
PubMed-EX
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(Nov 5, 2009)
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...with additional information retrieved from IISR & IASL text-mining services. PubMed-EX’s page mark-up includes section categorization, gene/disease name, and relation. The mark-ups of PubMed-EX can help researchers quickly focus on key information in retrieved abstracts and can provide additional background information on key terms. Furthermore, our text-mining server carries out all text-mining processing...
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PubMed-EX: a web browser extension to enhance PubMed search with text mining features.
(Nov 15, 2009)
PubMed-EX: a web browser extension to enhance PubMed search with text mining features.
(Nov 15, 2009)
[ 9 ]
National Centre for Text Mining — NaCTeM — PathText2
Updated:
(Jul 1, 2013)
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...html; charset=us-ascii National Centre for Text Mining — NaCTeM — PathText2 You are in: Home | PathText2 Home Aims & Objectives NaCTeM Services Text Mining Tools Text Mining Infrastructures Resources Terms & Conditions FAQ News & Events...carried out at the National Centre for Text Mining (NaCTeM), School of Computer Science, University of...
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A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text.
(Jul 1, 2013)
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text.
(Jul 1, 2013)
[ 10 ]
National Centre for Text Mining — NaCTeM — Paragraph Vector-based Topic Detection
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(Aug 15, 2016)
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...html; charset=us-ascii National Centre for Text Mining — NaCTeM — Paragraph Vector-based Topic Detection You are in: Home | PV-based Topic DetectionHome Aims & Objectives NaCTeM Services Text Mining Tools Text Mining Infrastructures Resources Terms & Conditions FAQ News & Events...copyright © 2016, The National Centre for Text Mining — University of ManchesterSite maintained by Paul Thompson...
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[ 11 ]
National Centre for Text Mining — NaCTeM — Anatomical Entity Tagger
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(Mar 19, 2014)
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...html; charset=us-ascii National Centre for Text Mining — NaCTeM — Anatomical Entity Tagger You are in: Home | Anatomical Entity TaggerHome Aims & Objectives NaCTeM Services Text Mining Tools Text Mining Infrastructures Resources Terms & Conditions FAQ News & Events...copyright © 2016, The National Centre for Text Mining — University of ManchesterSite maintained by Paul Thompson...
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[ 12 ]
PolySearch
Updated:
(Jun 30, 2008)
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...2.0! A key challenge in biomedical text mining is to handle "comprehensive" or "associative" queries...also exploits a variety of techniques in text mining and information retrieval to identify, highlight and...S., Wishart D.S. PolySearch: a web-based text mining system for extracting relationships between human diseases...
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[ 13 ]
NutriChem 1.0 Server
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(Jan 16, 2015)
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...0 server is a database generated by text mining of 21 million MEDLINE abstracts, with information that links plant-based foods with their small molecule components and human disease phenotypes. The server contains text-mined data for 18,478 pairs of 1...Panagiotou G. and Kouskoumvekaki I. (2014) Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health...
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[ 14 ]
plan2l
Updated:
(Jun 30, 2009)
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...ascii PLAN2L : PLant ANnotation to Literature: a text mining and information extraction system for Arabidopsis thaliana PLAN2L (Plant annotation to literature) is a web tool for integrated text mining and literature-derived bio-entity relation extraction...Valencia: PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucl...
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PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.
(Jul, 2009)
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.
(Jul, 2009)
[ 15 ]
National Centre for Text Mining — NaCTeM — EventMine
Updated:
(Jun 25, 2012)
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...html; charset=us-ascii National Centre for Text Mining — NaCTeM — EventMine You are in: Home | EventMine Home Aims & Objectives NaCTeM Services Text Mining Tools Text Mining Infrastructures Resources Terms & Conditions FAQ News & Events...copyright © 2016, The National Centre for Text Mining — University of ManchesterSite maintained by Paul Thompson...
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Boosting automatic event extraction from the literature using domain adaptation and coreference resolution.
(Jul 1, 2012)
Boosting automatic event extraction from the literature using domain adaptation and coreference resolution.
(Jul 1, 2012)
[ 16 ]
Acromine dictionary
Updated:
(Apr 26, 2010)
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...an abbreviation dictionary is necessary for advanced text-mining tasks to establish associations between abbreviations and...found the service. The National Centre for Text Mining is funded by JISC. Content copyright © 2012, The National Centre for Text Mining — University of ManchesterSite maintained by Paul Thompson...
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Building a high-quality sense inventory for improved abbreviation disambiguation.
(May 1, 2010)
Building a high-quality sense inventory for improved abbreviation disambiguation.
(May 1, 2010)
[ 17 ]
PolySearch2
Updated:
(Jul 3, 2015)
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...UsWelcome to PolySearch2A critical task in biomedical text mining is to discover potential associations between various types of biomedical entities. PolySearch 2.0 (polysearch.ca) is an online text-mining system for identifying relationships between human diseases...2015) PolySearch 2.0: A significantly improved text-mining system for discovering associations between human diseases...
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[ 18 ]
gnTEAM | Text extraction, analytics, mining
Updated:
(Apr 24, 2012)
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...host-pathogen interactions; conflicting statements in scientific texts. Mining Of Scientific Methodologies From Literature Capturing best and common practice for in-silico experiments. Mining Semi-Structured Reports Data quality in question-answer reports. Who we are?We are part of the Text Mining/NLP research group within the School of...
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[ 19 ]
National Centre for Text Mining — NaCTeM — MLEE
Updated:
(Sep 10, 2012)
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...html; charset=us-ascii National Centre for Text Mining — NaCTeM — MLEE You are in: Home | MLEE Home Aims & Objectives NaCTeM Services Text Mining Tools Text Mining Infrastructures Resources Corpora ACE Meta-Knowledge Anatomy...copyright © 2016, The National Centre for Text Mining — University of ManchesterSite maintained by Paul Thompson...
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Event extraction across multiple levels of biological organization.
(Sep 15, 2012)
Event extraction across multiple levels of biological organization.
(Sep 15, 2012)
[ 20 ]
DisGeNET - a database of gene-disease associations
NEW
Updated:
(Jun 22, 2011)
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...negative associations has been removed from the text mining sources (BeFree, GAD, and LHGDN) using regular...associated to disease have been annotated using text mining. Check some examples here. More information coming...2.1). We have new data from text mining using our BeFree system . April 26-27...info and data from two new resources: Text mining (TEXTM) and Rat Genome Database (RGD). December...
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DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.
(Nov 15, 2010)
DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.
(Nov 15, 2010)
[ 21 ]
MutationFinder
Updated:
(Jan 3, 2008)
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...our lab.) Intrinsic evaluation of text mining tools may not predict performance on realistic tasks J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, and Lawrence Hunter; Pacific Symposium on Biocomputing 13:640-651(2008). PDF(A discussion on how the performance of text mining systems on gold standard data relates to...
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Rapid pattern development for concept recognition systems: application to point mutations.
(Dec, 2007)
Rapid pattern development for concept recognition systems: application to point mutations.
(Dec, 2007)
[ 22 ]
Apoptosis database
Updated:
(May 4, 2012)
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...KeyWord search using BIANA8 or using ProMiner text mining tool9.We obtain a p-Value for our predictions given by: were P is the set of proteins in teh network, C the set of candiates, V the set of proteins in teh validation set and I the set of candidate proteins validated by text mining. The chance of success p corresponds to...
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Extending signaling pathways with protein-interaction networks. Application to apoptosis.
(May, 2012)
Extending signaling pathways with protein-interaction networks. Application to apoptosis.
(May, 2012)
[ 23 ]
Manchester Centre for Integrative Systems Biology
Updated:
(May 15, 2009)
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...very partial results. We have developed a text mining approach that retrieves relevant scientific publications and annotates them with information required for the kinetic modelling of a given pathway. Results: We developed an integrative approach, combining publicly available data and software resources, for the time- and cost-effective development of text mining tools for retrieval of information relevant to...
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[ 24 ]
DIEGO Lab
Updated:
(May 8, 2015)
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...Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction...International Conference on. Vol. 2. IEEE, 2010.Text mining approaches for stock market prediction.Nikfarjam, Azadeh, Ehsan Emadzadeh, and Saravanan Muthaiyah."Text mining approaches for stock market prediction." Computer and...Bioinformatics 2008, 24(16):i126-i132.Glycoinformatics: Text Mining Lectin and Glycan Interactions in BioprocessesSamli, Kausar N., et al. "Glycoinformatics: Text Mining Lectin and Glycan Interactions in Bioprocesses." GLYCOBIOLOGY...
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[ 25 ]
U-Compare - Share and Compare with UIMA
Updated:
(May 21, 2013)
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...ComponentsContactU-Compare homepageU-Compare is an integrated text mining/natural language processing system based on the...© 2012-2017, The National Centre for Text Mining â The University of ManchesterTerms & Conditions...
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[ 26 ]
mirtex
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(Sep 26, 2015)
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...-8 Toggle navigation miRTexRESTful APIsPublicationContactmiRTex is a text-mining system that extracts miRNA-gene regulation relations...Vijay-Shanker. 2015. âmiRTex: A Text Mining System for miRNA-Gene Relation Extraction.â...
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[ 27 ]
iProLINK [PIR - Protein Information Resource]
Updated:
(Sep 11, 2015)
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...Knowledge) is a resource with access to text mining tools and annotated corpora developed in house...and phosphorylation-dependent protein-protein interactionseGIFT: a text mining tool that identifies informative terms (iTerms) and...
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[ 28 ]
NaturalLanguage/FlySlip - CL Wiki (read only)
Updated:
(Apr 28, 2008)
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...is to develop advanced technology for biomedical text mining, which can be tightly integrated into existing manual methods of literature curation with FlyBase serving as the main paradigm. We compiled new resources for development and evaluation and published the results of our research in the main text mining fora. An overview of the project is...
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[ 29 ]
ibi.imim.es
Updated:
(Oct 11, 2006)
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...pharmaceutical industry and health care by applying text mining and knowledge management, network biology and real...and machine learning, natural language processing and text mining, network and systems biology. Another important aspect...
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OSIRIS: a tool for retrieving literature about sequence variants.
(Oct 15, 2006)
OSIRIS: a tool for retrieving literature about sequence variants.
(Oct 15, 2006)
[ 30 ]
Dragon Exploratory System on Hepatitis C Virus (DESHCV)
Updated:
(May 30, 2011)
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...on Hepatitis C Virus (DESHCV), a biomedical text-mining and relationship exploring knowledgebase is the first reported comprehensive Hepatitis C Virus (HCV) customized biomedical text-mining based online web resource. Users can retrieve...
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[ 31 ]
Acromine Disambiguation
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(Apr 26, 2010)
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...found the service. The National Centre for Text Mining is funded by JISC. Content copyright © 2012, The National Centre for Text Mining — University of ManchesterSite maintained by Paul Thompson...
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Building a high-quality sense inventory for improved abbreviation disambiguation.
(May 1, 2010)
Building a high-quality sense inventory for improved abbreviation disambiguation.
(May 1, 2010)
[ 32 ]
The herb-chemical corpus
Updated:
(Sep 21, 2016)
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...large-scale way if we apply a text mining approach. Thus, we constructed a corpus for plant and chemical entities and for the relationships between them to develop and evaluate such text mining approaches. The corpus currently contains 267 plant...
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[ 33 ]
Data - DSV, Department of Computer and Systems Sciences - Stockholm University
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(Oct 13, 2011)
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...Hercules DalianisBookmark and shareTell a friendFocus areasClinical text mining Data science Mobile health Healthcare analytics Health modeling Health communitiesContactsHercules Dalianis, professorUno Fors, professor Henrik Boström, professor Read moreStories of Health InformaticsInformation sheet Download the .pdf file Health informatics (239 Kb) Health Technology Blog Clinical Text Mining GroupHEALTH BANK - Swedish Health Record Research Bank...
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[ 34 ]
PRINCIPLE: PRINCE Plugin
Updated:
(Nov 25, 2011)
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...on van Driel et al. (2006) A text-mining analysis of the human phenome. Eur J Hum Genet 14: 535-542 Phenotypic disease similarity (zipped)2011-09-1569MBPhenSim.zipDisease-disease phenotypic similarity, based on van Driel et al. (2006) A text-mining analysis of the human phenome. Eur J...
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PRINCIPLE: a tool for associating genes with diseases via network propagation.
(Dec 1, 2011)
PRINCIPLE: a tool for associating genes with diseases via network propagation.
(Dec 1, 2011)
[ 35 ]
SynLethDB
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(Jan 7, 2016)
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...assays, other related databases, computational predictions and text mining. In total, SynLethDB contains 34,089 synthetic...shRNA screenings (DECIPHER), computational predictions (DAISY) and Text Mining-based results. The pie chart on the...
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SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets.
(Jan 4, 2016)
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets.
(Jan 4, 2016)
[ 36 ]
Center for non-coding RNA in Technology and Health
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(Aug 30, 2012)
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...file containing a synonym dictionary used for text-mining miRNA co-occurrences. String_protein_dictionary.gzA tab delimited text file derived from String containing a synonym dictionary used for text-mining miRNA co-occurrences. 1 and 2 element...
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[ 37 ]
Manchester Institute of Biotechnology
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(Feb 15, 2006)
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...Supporting evidence-based public health interventions using text mining.Conformer selected top down sequencing - A novel...Supporting evidence-based public health interventions using text mining. Conformer selected top down sequencing - A novel...
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[ 38 ]
BioContext
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(Aug 8, 2012)
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...html; charset=us-ascii BioContextBioContextBioContext is a text mining system for extracting information about molecular processes...Bergman, Goran Nenadic. (2012) BioContext: an integrated text mining system for large-scale extraction and contextualisation...
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BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.
(Aug 15, 2012)
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.
(Aug 15, 2012)
[ 39 ]
iSimp: A Sentence Simplification System for Biomedical Text
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(May 22, 2014)
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...the development of natural language processing and text mining tools. For this purpose, we developed iSimp...make iSimp readily usable in NLP and text mining tools, we participate in BioCreative IV Track...
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[ 40 ]
LINNAEUS
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(Mar 11, 2010)
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...million open access full-text articles.Open text mining initiative: Initiative to bypass copyright issues when releasing full-text articles for text-mining purposes (currently not maintained). Last updated: December...
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LINNAEUS: a species name identification system for biomedical literature.
(Feb 11, 2010)
LINNAEUS: a species name identification system for biomedical literature.
(Feb 11, 2010)
[ 41 ]
Literature Based Kinase-Substrate Library at the Phosphosite Level
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(Feb 26, 2009)
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...Literature Mining This library was made by text mining abstracts from papers that describe specific phosphosites...Literature Mining This library was made by text mining abstracts from papers that describe specific phosphosites...
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[ 42 ]
myExperiment - Workflows
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(Sep 18, 2009)
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...13 entrez 13 KeggID 13 text 13 text mining 12 abstracts 11More...Filter by licence by-sa 73 by-nd 16 by 1Filter by group SabrOndexProject 32 PhD Supplementary Information 9 Text mining network 5 eLicoTutorial 3 Bonn eScience Workshop...
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[ 43 ]
T-HOD:Text-mined Hypertension, Obesity, and Diabetes candidate genes database
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(Feb 14, 2013)
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...text/html; charset=us-ascii T-HOD:Text-mined Hypertension, Obesity, and Diabetes candidate genes database...
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T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes.
(2013)
T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes.
(2013)
[ 44 ]
e-LiSe - text mining tool for Medline data - run
Updated:
(Apr 14, 2008)
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...text/html; charset=us-ascii e-LiSe - text mining tool for Medline data - runToggle navigation e...
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e-LiSe--an online tool for finding needles in the '(Medline) haystack'.
(Apr 15, 2008)
e-LiSe--an online tool for finding needles in the '(Medline) haystack'.
(Apr 15, 2008)
[ 45 ]
BIRI: BioInformatics Resources Inventory - Biomedical Informatics Group (UPM)
Updated:
(Oct 23, 2009)
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...literature and indexed using Natural Language and Text Mining techniques. The index is automatically updated by...
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[ 46 ]
drugQuest
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(Jun 14, 2016)
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...us-ascii drugQuest Home Help DrugQuest - A Text Mining Workflow for Drug Association Discovery DrugQuest accepts...
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[ 47 ]
e-MIR2: Electronic Medical Informatics Repository of Resources
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(Sep 14, 2012)
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...literature and indexed using Natural Language and Text Mining techniques. The index is automatically updated by...
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[ 48 ]
ProNormz
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(Mar 10, 2014)
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...Name © 2013 by Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore...
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[ 49 ]
Welcome to BioTextQuest
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(Nov 7, 2014)
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...to BioTextQuest Home About Help A Biomedical Text Mining Suite for Concept Discovery BioTextQuest accepts a...
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[ 50 ]
LitInspector - Literature and Pathway mining made easy!
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(Jun 30, 2009)
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...Software Suite today.LitInspector performs large scale text mining on more than 20 million PubMed entries...
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LitInspector: literature and signal transduction pathway mining in PubMed abstracts.
(Jul, 2009)
LitInspector: literature and signal transduction pathway mining in PubMed abstracts.
(Jul, 2009)
