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

Blaise T F Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman, Guido Jenster
2005 BMC Bioinformatics  
In addition, all genes versus keywords were hierarchical clustered to reveal a complete grouping of published genes based on co-occurrence.  ...  MEDLINE search strings for 15,621 known genes and 3,731 keywords were generated and validated.  ...  Acknowledgements We thank Edwin van den Heuvel, Victor de Jager, Rene van Schaik, Jacob de Vlieg, and BioASP for their support, NLM (National Library of Medicine) for licensing of MEDLINE and Jan Kors  ... 
doi:10.1186/1471-2105-6-51 pmid:15760478 pmcid:PMC1274248 fatcat:qbmbo6du2nantcskwg376wmq44

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Martin Krallinger, Alfonso Valencia, Lynette Hirschman
2008 Genome Biology  
Following the increasing popularity of web-based applications for analyzing biological data, new text-mining and information extraction strategies are being implemented.  ...  The current trend in biomedical text mining points toward an increasing diversification in terms of application types and techniques, together with integration of domain-specific resources such as ontologies  ...  Systems such as the CoPub Mapper [65] provide online access to ranked co-occurrence associations extracted from PubMed between genes and biological terms (for instance, from GO or disease names) and  ... 
doi:10.1186/gb-2008-9-s2-s8 pmid:18834499 pmcid:PMC2559992 fatcat:oeqr7ctzgjeo5nnw53fimelwxa

Recent progress in automatically extracting information from the pharmacogenomic literature

Yael Garten, Adrien Coulet, Russ B Altman
2010 Pharmacogenomics (London)  
Acknowledgements The authors would like to thank Connie M Oshiro for comments on the manuscript and Nicholas P Tatonetti for useful discussions and assistance creating the figures.  ...  Chang et al., XPlorMed, FACTA and CoPub Mapper used abstract level co-occurrence, while methods such as AliBaba, EBIMed, iHOP, and Pharmspresso identify co-occurrence of drugs, genes and diseases at the  ...  When searching the scientific literature, documents are journal publications and typically PubMed is the interface used to search the MEDLINE repository of over 19,000,000 publications.  ... 
doi:10.2217/pgs.10.136 pmid:21047206 pmcid:PMC3035632 fatcat:7g3jwc4hjfetbb5phmzstzhjeu

Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)

Elina Tjioe, Michael W Berry, Ramin Homayouni
2010 BMC Bioinformatics  
Searching the enormous amount of information available in biomedical literature to extract novel functional relationships among genes remains a challenge in the field of bioinformatics.  ...  FAUN is tested on three manually constructed gene document collections. Its utility and performance as a knowledge discovery tool is demonstrated using a set of genes associated with Autism.  ...  [20] have developed CoPub Mapper which identifies shared terms that co-occurred with gene names in MEDLINE abstracts.  ... 
doi:10.1186/1471-2105-11-s6-s14 pmid:20946597 pmcid:PMC3026361 fatcat:bfkhgpyt2bdkzac6mccrmxcke4

Navigating the Functional Landscape of Transcription Factors via Non-Negative Tensor Factorization Analysis of MEDLINE Abstracts

Sujoy Roy, Daqing Yun, Behrouz Madahian, Michael W. Berry, Lih-Yuan Deng, Daniel Goldowitz, Ramin Homayouni
2017 Frontiers in Bioengineering and Biotechnology  
of sets of genes, transcription factors (TFs), and terms from MEDLINE abstracts.  ...  One advantage of this method is that it can discover potentially new gene-TF associations from the literature.  ...  Several co-occurrence based-LBD approaches, such as CoPub Mapper (Alako et al., 2005) , PubGene (Jenssen et al., 2001) , Chilibot (Chen and Sharp, 2004) , and GeneWays (Rzhetsky et al., 2004) , have  ... 
doi:10.3389/fbioe.2017.00048 pmid:28894735 fatcat:td3fnjulevctfbrtorugiwv4zq

DEVELOPMENT OF A HEPATITIS C VIRUS KNOWLEDGEBASE WITH COMPUTATIONAL PREDICTION OF FUNCTIONAL HYPOTHESIS OF THERAPEUTIC RELEVANCE KOJO KWOFIE SAMUEL

Vladimir Bajic, Alan Christoffels
2011 unpublished
This research thesis report the development of two freely available HCV-specific web-based resources: (i) Dragon Exploratory System on Hepatitis C Virus (DESHCV) accessible via DESHCV is a text mining  ...  system implemented using named concept recognition and co-occurrence based approaches to computationally analyze about 32, 000 HCV related abstracts obtained from PubMed.  ...  CoPub Mapper: mining MEDLINE based on search term co-publication.BMC Bioinformatics, 6, 51. Aphinyanaphongs, Y., & Aliferis, C. F. (2003).  ... 
fatcat:khbuvbkjujbk3dvhoinrnwxqq4

DEVELOPMENT OF A HEPATITIS C VIRUS KNOWLEDGEBASE WITH COMPUTATIONAL PREDICTION OF FUNCTIONAL HYPOTHESIS OF THERAPEUTIC RELEVANCE KOJO KWOFIE SAMUEL

Vladimir Bajic, Alan Christoffels
2011 unpublished
This research thesis report the development of two freely available HCV-specific web-based resources: (i) Dragon Exploratory System on Hepatitis C Virus (DESHCV) accessible via DESHCV is a text mining  ...  system implemented using named concept recognition and co-occurrence based approaches to computationally analyze about 32, 000 HCV related abstracts obtained from PubMed.  ...  CoPub Mapper: mining MEDLINE based on search term co-publication.BMC Bioinformatics, 6, 51. Aphinyanaphongs, Y., & Aliferis, C. F. (2003).  ... 
fatcat:dxh5kptlxfdojbqc7dngtunu4a