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Classification of information fusion methods in systems biology

Jane Synnergren, Björn Olsson, Jonas Gamalielsson
2009 In Silico Biology  
In addition, there is also an increasing need for integrative analysis, where knowledge about the biological system is derived by data fusion, using heterogeneous data sets as input.  ...  Due to these high-throughput technologies, the study of biological systems has evolved from focusing on single components (e.g. genes) to encompassing large sets of components (e.g. all genes in an entire  ...  The information retrieval module can retrieve up to 20 different types of data for each gene in a gene set, including Gene Ontology (GO) annotations [15] , tissue expression patterns, chromosomal distributions  ... 
pmid:19795566 fatcat:fnri743i7nfwhg6ch327ewevmq

Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology [chapter]

Christian Blaschke, Lynette Hirschman, Hagit Shatkay, Alfonso Valencia
2010 Lecture Notes in Computer Science  
In the biomedical domain, research has focused on several complex text-based applications, including the identification of relevant literature (information retrieval) for specific information needs, the  ...  The broad area of biomedical text mining is concerned with using methods from natural language processing, information extraction, information retrieval and summarization to automate knowledge discovery  ...  In the biomedical domain, research has focused on several complex text-based applications, including the identification of relevant literature (information retrieval) for specific information needs, the  ... 
doi:10.1007/978-3-642-13131-8_1 fatcat:42nm5vxcdnafjkogcz4wcoasoa

Thinking PubMed: an Innovative System for Mental Health Domain

Maja Hadzic, Russel D'Souza, Fedja Hadzic, Tharam Dillon
2008 2008 21st IEEE International Symposium on Computer-Based Medical Systems  
when needed.  ...  Furthermore, the Thinking PubMed analyzes and links the retrieved information, and extracts hidden patterns and knowledge using data mining algorithms.  ...  BioIE [8] is an extraction system of the information covering biological interactions. It annotates the results using the terms of Gene Ontology.  ... 
doi:10.1109/cbms.2008.20 dblp:conf/cbms/HadzicDHD08 fatcat:aanc6fx3ebaa3k42ras7nb4cee

PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning

James M. Melott, John N. Weinstein, Bradley M. Broom
2015 Bioinformatics  
PathwaysWeb is a resource-based, well-documented web system that provides publicly available information on genes, biological pathways, Gene Ontology (GO) terms, gene-gene interaction networks (importantly  ...  The PathwaysWeb API simplifies the construction of applications that need to retrieve and interrelate information across multiple, pathway-related data types from a variety of original data sources.  ...  Although many databases and application programming interfaces (APIs) exist for retrieving pathway-related data for use in biological research, they provide data that are incomplete, use different data  ... 
doi:10.1093/bioinformatics/btv554 pmid:26400039 pmcid:PMC4907393 fatcat:av5xjxs4zvg5fn7jethvj6wsou

Text-mining and information-retrieval services for molecular biology

Martin Krallinger, Alfonso Valencia
2005 Genome Biology  
Text-mining in molecular biology -- defined as the automatic extraction of information about genes, proteins and their functional relationships from text documents -- has emerged as a hybrid discipline  ...  A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators.  ...  We thank Robert Hoffmann for providing Figure 2 and Christian Blaschke, as well as all the members of the group, for interesting discussions.  ... 
doi:10.1186/gb-2005-6-7-224 pmid:15998455 pmcid:PMC1175978 fatcat:7r2q7lkyybdpxj6j2zsvnwyftm

Evaluating gene/protein name tagging and mapping for article retrieval

Chong Min Lee, Manabu Torii, Zhang-Zhi Hu, Yi-Ting Tsai, Jinesh Shah, Hongfang Liu
2010 International Symposium for Semantic Mining in Biomedicine  
Approaches and data resources for gene/protein tagging and mapping need to be selected appropriately for individual practical tasks.  ...  system trained on the BioCreAtIvE II gene mention corpus.  ...  For example, Textpresso (Muller, Kenny et al. 2004 ) is an information retrieval system that can retrieve sentences from fulllength articles.  ... 
dblp:conf/smbm/LeeTHTSL10 fatcat:gkxaplqv7fexvctlx7uyomumcy

ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database

A. Kossenkov, F. J. Manion, E. Korotkov, T. D. Moloshok, M. F. Ochs
2003 Bioinformatics  
The system allows easy use of the output from one search as the input for a new search, as well as the filtering of results.  ...  The database is used to store formats and parameters and information for parsing data from web sites.  ...  ACKNOWLEDGEMENTS We would like to thank Dr Kenneth Zaret for providing the initial impetus for this project. We thank the National Institutes of Health, National Cancer Institute  ... 
doi:10.1093/bioinformatics/btg056 pmid:12651736 fatcat:fcyhmlq73ra75agvc2qljhefwm

Hairpins in bookstacks: Information retrieval from biomedical text

H. Shatkay
2005 Briefings in Bioinformatics  
She is an active member of the biomedical text-mining community, and one of the first researchers in the area of text mining and information retrieval for bioinformatics.  ...  For these, the related genes identified by the system typically shared the same biological function, and on average, three or four of the top five terms assigned by the system to each gene correctly indicated  ...  This focused set of documents can also provide the relevant literature needed for analysing and explaining experimental results (on which other automated mining systems may operate).  ... 
doi:10.1093/bib/6.3.222 pmid:16212771 fatcat:2liwpccfq5dhza5mmdw66q7m2m

PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature

G. R. Grimes, T. Q. Wen, M. Mewissen, R. M. Baxter, S. Moodie, J. S. Beattie, P. Ghazal
2006 Bioinformatics  
ACKNOWLEDGEMENTS The authors thank their colleagues at the GTI and collaborators Alan Pemberton, Varrie Oglivie, Elaine Marshall, Mathieu Blanc and Mick Rae for contributing to this resource.  ...  INTRODUCTION High-throughput technologies are now widely used for the global and parallel measurement of gene and protein activity within biological systems.  ...  A major challenge for biologists, therefore, is to rapidly derive comprehensive information about the biological processes for each of the specific genes or proteins in the list and to identify where domain-specific  ... 
doi:10.1093/bioinformatics/btl342 pmid:16809392 fatcat:sbeu2pe2xbcaxjlzzplza3bfuu

Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager

A. R. Shah, M. Singhal, K. R. Klicker, E. G. Stephan, H. S. Wiley, K. M. Waters
2007 Bioinformatics  
The Bioinformatics Resource Manager (BRM) is a software environment that provides the user with data management, retrieval and integration capabilities.  ...  BRM is developed using Java TM and other open-source technologies for free distribution.  ...  ACKNOWLEDGEMENTS The research described in this article was conducted under the LDRD Program at the Pacific Northwest National Laboratory, a multiprogram national laboratory operated by Battelle for the  ... 
doi:10.1093/bioinformatics/btm031 pmid:17324940 fatcat:6zcslqw2avgy3ag26dnqus7gji

Text mining in life sciences [chapter]

J. Fluck, H. Deneke, C. Gieger
2005 Text Mining and its Applications to Intelligence, CRM and Knowledge Management  
Now the immense volume of literature makes it almost impossible for biologists and clinical researchers to retrieve all relevant information on a specific topic and to keep up with current research.  ...  Text mining provides the methods to automatically retrieve and extract information contained in free text.  ...  Usage of ontologies to define the fields in databases allows for highly accurate information retrieval and easy combination of information from different databases due to the underlying structure.  ... 
doi:10.2495/978-1-85312-995-7/17 fatcat:l55iiv3op5hqhpsd5nfz4yxc7y


2006 Biocomputing 2007  
Scientists working on genomics projects are often faced with the difficult task of sifting through large amounts of biological information dispersed across various online data sources that are relevant  ...  Many groups have attempted to address the annotation backlog through automated annotation systems that are geared toward specific organisms, and which may thus not possess the necessary flexibility and  ...  for their technical assistance.  ... 
doi:10.1142/9789812772435_0033 fatcat:wdtebs732zhpdpjd37tz27ijvy

A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries

Kalpana Raja, Matthew Patrick, Yilin Gao, Desmond Madu, Yuyang Yang, Lam C. Tsoi
2017 International Journal of Genomics  
Text mining (also known as literature mining) is one of the commonly used approaches for automated generation of biological knowledge from the huge number of published articles.  ...  Different bioinformatics approaches have been developed to streamline the downstream analyzes by providing independent information to interpret and provide biological inference.  ...  For example, automated high-throughput clinical applications can be developed to support clinicians' information needs [68] .  ... 
doi:10.1155/2017/6213474 pmid:28331849 pmcid:PMC5346376 fatcat:7yhwtsgyqndabcrhpx7uxsx7da

Reconstructing transcriptional Regulatory Networks using data integration and Text Mining

Rafael T. Pereira, Hugo Costa, Sonia Carneiro, Miguel Rocha, Rui Mendes
2015 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
In this work, we developed an integrated approach for the reconstruction of TRNs that retrieve the relevant information from important biological databases and insert it into a unique repository, named  ...  extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors).  ...  This entails that there is an increasing amount of biological information that can be retrieved from these databases.  ... 
doi:10.1109/bibm.2015.7359907 dblp:conf/bibm/PereiraCCRM15 fatcat:ywerjm5k2rhwtjcxovbpnoav4q

A text-mining perspective on the requirements for electronically annotated abstracts

Florian Leitner, Alfonso Valencia
2008 FEBS Letters  
A second generation of systems could then attempt to address the problems of annotating protein interactions and protein/gene functions, a more difficult task for text-mining systems.  ...  The recent introduction of the first meta-server for the annotation of biological text, with the possibility of collecting annotations from available text-mining systems, adds credibility to the technical  ...  Acknowledgements: The authors would like to thank Martin Krallinger for insightful discussions.  ... 
doi:10.1016/j.febslet.2008.02.072 pmid:18328824 fatcat:umlsoplbdrds5ope6fzexaxmv4
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