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[ 1 ] BioCreative - Track II- Workflow  
Updated: (Nov 19, 2012)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
23160416 Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II. Manual curation of data from the biomedical literature is a rate-limiting factor for many expert curated databases. Despite the continuing advances in biomedical text mining and the pressing needs of biocurators for better tools, few existing text-mining tools have been successfully integrated into production literature curation systems such...
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[ 2 ] Manchester Centre for Integrative Systems Biology  
Updated: (May 7, 2008)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
18460187 Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and...source of technology-specific terms as opposed to paper abstracts. We suggest a text mining method for efficient corpus-based term acquisition as a way of rapidly expanding...
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[ 3 ] Compendium of Text Mining applications for life sciences (Bio-NLP tools)  
Updated: (Oct 6, 2008)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
18834499 Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Efficient access...of web-based applications for analyzing biological data, new text-mining and information extraction strategies are being implemented. These systems...to the main characteristics and applications of currently available text-mining systems for life sciences in terms of the following: the type of biological information demands being addressed; the level of information granularity of both user queries and results; and the features and methods commonly exploited by these applications. The current trend in biomedical text mining points toward an increasing diversification in terms of...
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[ 4 ] Brain Regions Co-occurrences  
Updated: (Jun 15, 2015)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...approaches would be useful. We propose to use text-mining models to automatically suggest potential targets from the neuroscientific literature, full-text articles and abstracts, so that they can be used for anatomical connection studies and more specifically for tractography. We applied text-mining models to three structures: two well-studied structures...
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[ 5 ] Linguamatics  
Updated: (Jul 14, 2009)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...or "upregulation". The I2E system uses a flexible text-mining approach, supporting both of these strategies, as well...usLife SciencesHealthcareProducts & ServicesNews & BlogEventsSupportResourcesContact us The world's leading text mining platformLinguamatics I2E makes sense of a world increasingly filled with big data and unstructured text. Using advanced Natural Language Processing, it reads and understands that data, helping you find insights, discoveries and connections that would otherwise remain hidden. What is text mining?The I2E platformWho uses I2E?Life sciencesHealthcareLinguamatics Text...
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[ 6 ] Argo | A Web-based Text Mining Workbench  
Updated: (Mar 21, 2012)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
22434844 Argo: an integrative, interactive, text mining-based workbench supporting curation. Curation of biomedical literature is often supported by the automatic analysis of textual content that generally involves a sequence of individual processing components. Text mining (TM) has been used to enhance the...charset=utf-8 Argo | A Web-based Text Mining Workbench   A Web-based Text Mining WorkbenchLaunch now! Currently supported browsers: Chrome, Firefox...
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[ 7 ] miRSel: tab Search  
Updated: (Mar 26, 2010)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...not very reliable. We propose to use text mining of publication abstracts for extracting microRNA-gene associations including microRNA-target relations to complement current repositories. The microRNA-gene association database miRSel combines text-mining results with existing databases and computational predictions. Text mining enables the reliable extraction of microRNA, gene...
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[ 8 ] miRCancer - microRNA Cancer Association Database  
Updated: (Feb 27, 2013)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...a microRNA-cancer association database constructed by text mining on literature. Research interests in microRNAs have...propose to extract microRNA-cancer associations by text mining and store them in a database called miRCancer. The text mining is based on 75 rules we have constructed, which represent the common sentence structures typically used to state microRNA expressions in cancers. The microRNA-cancer association database, miRCancer, is updated regularly by running the text mining algorithm against PubMed. All miRNA-cancer...
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[ 9 ] PubMed-EX  
Updated: (Nov 5, 2009)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...browser extension to enhance PubMed search with text mining features. PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which...with additional information retrieved from IISR & IASL text-mining services. PubMed-EX’s page mark-up...background information on key terms. Furthermore, our text-mining server carries out all text-mining processing, freeing up users’ resources. More screen...
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[ 10 ] mirtex  
Updated: (Sep 26, 2015)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
26407127 miRTex: A Text Mining System for miRNA-Gene Relation Extraction. MicroRNAs (miRNAs) regulate a wide range of cellular and developmental processes through gene expression suppression or mRNA degradation. Experimentally validated miRNA gene targets are often reported in the literature. In this paper, we describe miRTex, a text mining system that extracts miRNA-target relations, as...
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[ 11 ] U-Compare - Share and Compare with UIMA  
Updated: (May 21, 2013)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...as web services. U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. Users can rapidly develop biomedical text mining workflows by mixing and matching U-Compare's...
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Deploying and sharing U-Compare workflows as web services.   Paper Page   (Feb 18, 2013)  
[ 12 ] PolySearch  
Updated: (Jun 30, 2008)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
18487273 PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. A particular challenge in biomedical text mining is to find ways of handling 'comprehensive'...also exploits a variety of techniques in text mining and information retrieval to identify, highlight and...2.0! A key challenge in biomedical text mining is to handle "comprehensive" or "associative" queries...
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[ 13 ] gnTEAM | Text extraction, analytics, mining  
Updated: (Apr 24, 2012)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
22529179 21388573 Towards semi-automated curation: using text mining to recreate the HIV-1, human protein...mentions in 3090 articles. The advancement of text-mining (TM) techniques has offered a possibility to...http://gnode1.mib.man.ac.uk/HIV1-text-mining. MeSH:Data Mining / methods * MeSH:Databases, Protein...by the bioinformatics community. We present a text mining approach that utilises the literature to automatically...
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[ 14 ] ontogene  
Updated: (Jun 6, 2014)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...conditions in this corpus. Using the OntoGene text-mining system (http://www.ontogene.org), we extracted...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...
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[ 15 ] PubstractHelper  
Updated: (Dec 16, 2014)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
25512689 PubstractHelper: A Web-based Text-Mining Tool for Marking Sentences in Abstracts from PubMed Using Multiple User-Defined Keywords. While a huge amount of information about biological literature can be obtained by searching the PubMed database, reading through all the titles and abstracts resulting from such a search for useful information is inefficient. Text mining makes it possible to increase this...
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[ 16 ] DISEASES - Search  
Updated: (Feb 23, 2015)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
25484339 DISEASES: text mining and data integration of disease-gene associations. Text mining is a flexible technology that can be...positive rate of only 0.16%. Nonetheless, text mining should not stand alone, but be combined with other types of evidence. For this reason, we have developed the DISEASES resource, which integrates the results from text mining with manually curated disease-gene associations, cancer...
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[ 17 ] BioCreative - Track 1- Collaborative Biocurator Assistant Task (BioC)  
Updated: (Sep 3, 2016)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...the convenient gene/protein curation tool based on text mining.Database URL: http://www.biocreative.org/tasks/biocreative...increase 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 to...
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[ 18 ] drugQuest  
Updated: (Jun 14, 2016)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
27295093 DrugQuest - a text mining workflow for drug association discovery. Text mining and data integration methods are gaining ground...as chemical databases. Herein, we apply a text mining approach on the DrugBank database in order...user-friendly web interface. DrugQuest is a text mining tool for knowledge discovery: it is designed...
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[ 19 ] National Centre for Text Mining — NaCTeM — PathText2  
Updated: (Jul 1, 2013)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...then turns them into queries for three text mining-based MEDLINE literature search systems. These queries...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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[ 20 ] NutriChem 1.0 Server  
Updated: (Jan 16, 2015)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...services/NutriChem-1.0, a database generated by text mining of 21 million MEDLINE abstracts for information that links plant-based foods with their small molecule components and human disease phenotypes. NutriChem contains text-mined data for 18478 pairs of 1772 plant...0 server is a database generated by text mining of 21 million MEDLINE abstracts, with information...
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[ 21 ] Serine Protease Mutation Database  
Updated: (Feb 19, 2008)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...K-dependent coagulation serine proteases using a text-mining tool. Central repositories of mutations that combine...development of new database management tools. A text mining tool automatically scans full-length references to identify and extract mutations. High recall rates between 96 and 99% and precision rates of 87 to 93% were achieved. Text mining significantly reduces the time and expertise required...
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[ 22 ] Dragon Exploratory System on Hepatitis C Virus (DESHCV)    
Updated: (May 30, 2011)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...cycle and functions of its proteins. Biomedical text-mining is a useful approach for analyzing the increasing corpus of published scientific literature on HCV. We report here the first comprehensive HCV customized biomedical text-mining based online web resource, dragon exploratory system on hepatitis C virus (DESHCV), a biomedical text-mining and relationship exploring knowledge base was developed...
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Dragon exploratory system on Hepatitis C Virus (DESHCV).   Paper Page   (Jun, 2011)  
[ 23 ] plan2l  
Updated: (Jun 30, 2009)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
19520768 PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. There is an increasing interest in using literature mining techniques to complement information extracted from annotation databases or generated by bioinformatics applications. Here we present PLAN2L, a web-based online search system that integrates text mining and information extraction techniques to access systematically...
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[ 24 ] Form1  
Updated: (May 6, 2016)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...Building a glaucoma interaction network using a text mining approach. The volume of biomedical literature and...study reports on the results of a text mining approach to extract gene interactions from the data warehouse of published experimental results which are then used to benchmark an interaction network associated with glaucoma. To the best of our knowledge, there is, as yet, no glaucoma interaction network derived solely from text mining approaches. The presence of such a network...
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[ 25 ] hPRINT | Human Predicted Protein Interactome » Search  
Updated: (Nov 4, 2011)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...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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[ 26 ] PolySearch2  
Updated: (Jul 3, 2015)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
25925572 PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. PolySearch2 (http://polysearch.ca) is an online text-mining system for identifying relationships between biomedical entities...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...
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[ 27 ] NCBI Text Mining Tools  
Updated: (Jun 16, 2016)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...26187250 Beyond accuracy: creating interoperable and scalable text-mining web services. The biomedical literature is a knowledge-rich resource and an important foundation for future research. With over 24 million articles in PubMed and an increasing growth rate, research in automated text processing is becoming increasingly important. We report here our recently developed web-based text mining services for biomedical concept recognition and normalization...
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[ 28 ] Center for non-coding RNA in Technology and Health  
Updated: (Aug 30, 2012)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...to other genes and each other using text mining, TF promoter binding site and 6 different miRNA binding site prediction methods. In the first approach text mining of PubMed abstracts reveal statistically significant associations...targets to any degree. Our manually validated text-mining results also suggests that miRNAs may be...
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[ 29 ] LiverCancerMarkerRIF Home Page  
Updated: (Aug 29, 2014)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...liver cancer biomarker interactive curation system combining text mining and expert annotations. Biomarkers are biomolecules in...cancer as the target and developed a text-mining-based curation system named LiverCancerMarkerRIF, which allows...provides a user-friendly method for accessing text-mining-aided information and a concise interface to assist curators while they remain at the PubMed Web site. Biomedical text-mining techniques are applied to automatically recognize biomedical...
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[ 30 ] T-HOD:Text-mined Hypertension, Obesity, and Diabetes candidate genes database  
Updated: (Feb 14, 2013)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...exponential increase in gene mapping studies. The Text-mined Hypertension, Obesity and Diabetes candidate gene database...T-HOD employed the state-of-art text-mining technologies, including a gene/disease identification system...T-HOD is regularly updated by our text-mining system and verified by domain experts. The...text/html; charset=us-ascii T-HOD:Text-mined Hypertension, Obesity, and Diabetes candidate genes database...
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[ 31 ] Index of /download/  
Updated: (Apr 24, 2013)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...from literature with multi-level gene normalization. Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles...
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[ 32 ] Chilibot: finding gene and protein relationships from MEDLINE - a text mining approach  
Updated: (Nov 16, 2004)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...the scientific community. Despite the existence of text-mining methods that identify biological relationships based on...the public. We present a NLP-based text-mining approach, Chilibot, which constructs content-rich relationship...gene and protein relationships from MEDLINE - a text mining approach You need frame support to view this page. Chilibot is a web-based text mining application that extracts gene protein and drug...
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[ 33 ] DiMeX homepage  
Updated: (Apr 14, 2016)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
27073839 DiMeX: A Text Mining System for Mutation-Disease Association Extraction. The...have addressed this problem by developing a text-mining system (DiMeX) to extract mutation to disease...dimex/. We conclude that this high-throughput text-mining approach has the potential to significantly assist...of Mutation association to DiseasesDiMeX is a text mining system that extracts mutation to disease associations...
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[ 34 ] BioNLP'09 Shared Task on Event Extraction - Home  
Updated: (Sep 8, 2010)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
20823321 Discriminative and informative features for biomolecular text mining with ensemble feature selection. In the field of biomolecular text mining, black box behavior of machine learning systems...classification performance of state-of-the-art text mining algorithms. Furthermore, we illustrate how FS can...the opportunity to considerably improve upon current text mining tools. The FS algorithms and classifiers are...
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[ 35 ] 1471-2105-10-177-S2  
Updated: (Jul 1, 2009)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
19515247 Text-mining of PubMed abstracts by natural language processing...constitute the core of our recently deployed text mining application. Our Text Mining application is available online on the ERIC...annotations and adding value to both the text-mining and annotations systems. MeSH:Abstracting and Indexing...
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[ 36 ] Angiogenesis Events Extraction  
Updated: (Sep 28, 2011)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...research novelties are: a) customise deep semantic text mining techniques to extract protein-bioprocess associations automatically; b) to extract biological events pertaining to protein-disease associations automatically from the literature; c) to support the semi-automatic production of annotated texts pertaining to biological information for text mining applications; d) to identify automatically bioprocesses linked...
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Automatic extraction of angiogenesis bioprocess from text.   Paper Page   (Oct 1, 2011)  
[ 37 ] OpenNICTA | Variome  
Updated: (Apr 15, 2013)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...important new resource for the development of text mining solutions that address relationships among patient cohorts, disease and genetic variation, and therefore, we also discuss the role text mining might play in the curation of information...textual data for training and evaluation of text mining systems.Here, we introduce the Variome Annotation...
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[ 38 ] 1471-2105-10-177-S1  
Updated: (Jul 1, 2009)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
19515247 Text-mining of PubMed abstracts by natural language processing...constitute the core of our recently deployed text mining application. Our Text Mining application is available online on the ERIC...annotations and adding value to both the text-mining and annotations systems. MeSH:Abstracting and Indexing...
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[ 39 ] iProLINK [PIR - Protein Information Resource]  
Updated: (Sep 11, 2015)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...biological databases. Motivated by the promise of text mining methodologies, but at the same time, the...data sources that can be utilized for text mining research in the areas of bibliography mapping...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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[ 40 ] National Centre for Text Mining — NaCTeM — Paragraph Vector-based Topic Detection  
Updated: (Aug 15, 2016)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...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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[ 41 ] egas  
Updated: (Jun 9, 2016)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...Egas is a web-based platform for text-mining assisted literature curation that focuses on usability...Users can inspect, correct or remove automatic text-mining results, manually add new annotations, and export...Egas, a web-based platform for biomedical text mining and assisted curation with highly usable interfaces...is a web-based platform for biomedical text mining and collaborative curation, supporting manual and automatic...
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[ 42 ] Java Machine Learning Library (Java-ML)  
Updated: (Sep 8, 2010)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
20823321 Discriminative and informative features for biomolecular text mining with ensemble feature selection. In the field of biomolecular text mining, black box behavior of machine learning systems...classification performance of state-of-the-art text mining algorithms. Furthermore, we illustrate how FS can...the opportunity to considerably improve upon current text mining tools. The FS algorithms and classifiers are...
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[ 43 ] BioContext  
Updated: (Aug 8, 2012)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
22711795 BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. Although the amount of data in biology is rapidly increasing, critical information for understanding biological events like phosphorylation or gene expression remains locked in the biomedical literature. Most current text mining (TM) approaches to extract information about biological...
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[ 44 ] National Centre for Text Mining — NaCTeM — Anatomical Entity Tagger  
Updated: (Mar 19, 2014)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...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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[ 45 ] tmVar  
Updated: (May 23, 2013)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
23564842 tmVar: a text mining approach for extracting sequence variants in biomedical literature. Text-mining mutation information from the literature becomes a...high accuracy. Here, we report tmVar, a text-mining approach based on conditional random field (CRF...
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[ 46 ] Proceedings | BioLINK Special Interest Group  
Updated: (Jan 10, 2015)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...theme of the workshop was 'Roles for text mining in biomedical knowledge discovery and translational medicine'. This summary reviews the outcomes of the workshop. Meeting themes included concept annotation methods and applications, extraction of biological relationships and the use of text-mined data for biological data analysis. All articles...the {BioLINK SIG} 2013: {R}oles for text mining in biomedical knowledge discovery and translational medicine...
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[ 47 ] Moara project  
Updated: (Apr 9, 2010)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...are important preliminary steps for many biological text mining tasks, such as information retrieval, protein-protein...in the workflow of a more general text mining system. MeSH:Data Mining / methods * MeSH:Databases...Biotecnologia (CNB) for the development of biological text mining tools. It consists of a Java library...
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[ 48 ] gimli  
Updated: (Nov 15, 2013)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...usability still hinder their wider application outside text mining research. We present Gimli, an open-source...Advanced users can integrate Gimli in their text mining workflows through the provided library, and extend...with Neji?With Neji you can build text mining processing pipelines for:Rapidly create REST services and interactive web pages for text mining tasksConcept recognition:Dictionary-based, Machine learning-based...
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[ 49 ] 1471-2105-11-135-S1  
Updated: (Mar 26, 2010)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...not very reliable. We propose to use text mining of publication abstracts for extracting microRNA-gene associations including microRNA-target relations to complement current repositories. The microRNA-gene association database miRSel combines text-mining results with existing databases and computational predictions. Text mining enables the reliable extraction of microRNA, gene...
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[ 50 ] Ondex - data integration and biological network analysis  
Updated: (Apr 8, 2010)   Rate Avg: ☆☆☆☆☆ ( no ratings )  
...the Ondex data integration framework that uses text mining techniques over Medline abstracts as a method...In conclusion, we show that the additional text mining features are able to highlight proteins using the scientific literature that would not have been seen using data integration alone. Ondex is an open-source software project and can be downloaded, together with the text mining features described here, from www.ondex.org...
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