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A prototype system for retrieval of gene functional information

Lillian C Folk, Timothy B Patrick, Joyce S Pattison, Russell D Wolfinger, Joyce A Mitchell
2003 AMIA Annual Symposium Proceedings  
For experiments generating thousands of genes of interest, retrieval of functional information can become a significant bottleneck.  ...  To address this issue, we are currently developing a prototype system to automate the process of retrieval of functional information from multiple on-line sources.  ...  Gary Allen, University of Missouri-Columbia, for their support of this project.  ... 
pmid:14728346 pmcid:PMC1480332 fatcat:q66stidtuncvhjwpl4ugtsmra4

BIOBIBLIOMETRICS: INFORMATION RETRIEVAL AND VISUALIZATION FROM CO-OCCURRENCES OF GENE NAMES IN MEDLINE ABSTRACTS

B. J. STAPLEY, G. BENOIT
1999 Biocomputing 2000  
Walmsley for Saccharomyces cerevisiae expertise. BJS is the recipient of a Postdoctoral Scholarship from the Center for Computational Science, University of Kentucky.  ...  for the prototype system.  ...  System and Methods We have constructed a prototype system for biomedical information retrieval and visualization using the Saccharomyces cerevisiae genome (SGD) b 18 and a set of Medline documents published  ... 
doi:10.1142/9789814447331_0050 fatcat:qg6atpeb5ndfvpt5r7zfz63mmq

A system for knowledge management in bioinformatics

Sudeshna Adak, Vishal S. Batra, Deo N. Bhardwaj, P. V. Kamesam, Pankaj Kankar, Manish P. Kurhekar, Biplav Srivastava
2002 Proceedings of the eleventh international conference on Information and knowledge management - CIKM '02  
We address this problem in a comprehensive system for knowledge management in bioinformatics called e2e.  ...  We have implemented an e2e prototype that enables a biologist to analyze her gene expression data in GEML or from a public site like Stanford, and discover knowledge through operations like querying on  ...  The underlying infrastructure for e2e is a view integration middleware (called Enterprise Information System to emphasize the fact that it should be able to handle large data sizes) which can retrieve  ... 
doi:10.1145/584792.584905 dblp:conf/cikm/AdakBBKKKS02 fatcat:ueh36lhoeng6zpsvzqbayn56sq

Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics

Michael Gruenberger, Rudi Alberts, Damian Smedley, Morris Swertz, Paul Schofield, Casimir Consortium, Klaus Schughart
2010 BMC Research Notes  
The application for the phenotype-centric use-case, "MUSIG-Phen", is based on a similar concept and starting from phenotype descriptions retrieves information for associated genes.  ...  The application for the gene-centric use-case, "MUSIG-Gen" starts from a list of gene names and collects a wide range of data types from several distributed databases in a "shopping cart"-like manner.  ...  Acknowledgements We thank George Gkoutos for helpful discussions on the technical developments of the use cases and all the members of the international advisory board of the CASIMIR consortium http://  ... 
doi:10.1186/1756-0500-3-16 pmid:20205870 pmcid:PMC2826352 fatcat:mkuczyzcnfdbdh3ydnhayc7mlq

Bi2SoN

Benjamin Köhncke, Sascha Tönnies, Wolf-Tilo Balke
2012 Proceedings of the 12th ACM/IEEE-CS joint conference on Digital Libraries - JCDL '12  
The presented system focuses on all aspects needed for suitable data integration and retrieval for domain experts from the field of biology.  ...  The resulting prototype was presented to a group of domain experts who confirmed that the system delivers suitable results supporting the scientists by their literature search.  ...  We have shown in a first prototype that the integration of different sources for synonym enrichment already leads to pleasant retrieval results.  ... 
doi:10.1145/2232817.2232888 dblp:conf/jcdl/KohnckeTB12 fatcat:tz6g4cmutbcybafysawrlsbs5y

Gene indexing: characterization and analysis of NLM's GeneRIFs

Joyce A Mitchell, Alan R Aronson, James G Mork, Lillian C Folk, Susanne M Humphrey, Janice M Ward
2003 AMIA Annual Symposium Proceedings  
We developed a prototype functional alerting system for researchers based on the GeneRIFs, and a strategy to find all of the literature related to genes.  ...  The result is an entry called a Gene Reference Into Function (GeneRIF) within the LocusLink database.  ...  We have created a prototype but functional GeneRIF Automated Alerting System (GRAAS) to illustrate this point.  ... 
pmid:14728215 pmcid:PMC1480312 fatcat:qlgzmsxwv5brngbnsu6r5q2r4q

Clinical decision support for whole genome sequence information leveraging a service-oriented architecture: a prototype

Brandon M Welch, Salvador Rodriguez-Loya, Karen Eilbeck, Kensaku Kawamoto
2014 AMIA Annual Symposium Proceedings  
To demonstrate the functionality of this prototype, we implemented a clinical scenario of a hypothetical patient at high risk for Lynch Syndrome based on his genomic information.  ...  In this manuscript, we describe the development of a prototype CDS system that is capable of providing genome-guided CDS at the point of care and within the clinical workflow.  ...  This manuscript describes our effort to build a functional prototype of the previously proposed CDS architecture for WGS information 12 .  ... 
pmid:25954430 pmcid:PMC4419907 fatcat:6wdko7la7nhevaj7cyi4uljnhm

IMGT/LIGM-DB: a systematized approach for ImMunoGeneTics database coherence and data distribution improvement

V Giudicelli, D Chaume, M P Lefranc
1998 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
We developed a systematized approach and defined LIGM-DB systems which manage and realize the major tasks for the database survey.  ...  LIGM-DB accurate immunogenetics data is based on the standardization of biological knowledge related to keywords, annotation labels and gene identification.  ...  Acknowledgments We thank Chantal Busin (LIGM) for the IMGT WWW interface design, ValŽrie BarbiŽ (EUROGENTEC) for the development of IMGT/PRIMER-DB, GŽraldine Folch, Nathalie Pallar•s, Manuel Ruiz and Dominique  ... 
pmid:9783210 fatcat:2wchtsf2wndqto63trn26hwltq

A Method for Querying Complete Genomes by Viewing Them as Structured Documents

Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto
1998 Genome Informatics Series  
Acknowledgements This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas, `Genome Science', from the Ministry of Education, Science, Sports and Culture of Japan.  ...  Experimental Results Based on our query language, we have implemented a prototype system for querying complete genomes, using the Perl language.  ...  Our system was thus able to obtain a result that accurately suggests a functional relationship between gene pairs.  ... 
doi:10.11234/gi1990.9.314 fatcat:hyp5zdmznzcz5lxxzz6siawygu

iNGS: a prototype tool for genome interpretation and annotation

Ismael Navas-Delgado, Maria Jesús García Godoy, Fátima Arjona-Pulido, Trinidad Castillo-Castillo, Ana Isabel Ramos-Ostio, José F. Aldana-Montes
2013 EMBnet journal  
In this work, we have started designing a platform for integrating, in a first step, existing analysis tools and adding annotations from public databases to the findings of these tools.  ...  This platform can be used to produce tools for different kind of users.  ...  Acknowledgements The Project Grant [TIN2011-25840) (Spanish Ministry of Education and Science) and P11-TIC-7529 (Innovation, Science and Enterprise Ministry of the regional government of the Junta de Andalucía  ... 
doi:10.14806/ej.19.b.723 fatcat:fcqorqt765badl7os5pcz7bsmi

MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanks

M. Masseroli, A. Stella, N. Meani, M. Alcalay, F. Pinciroli
2004 Bioinformatics  
Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTML format.  ...  Although some databanks provide batch retrieval of data via FTP, this requires expertise and resources for locally reimplementing the databank.  ...  ACKNOWLEDGEMENTS We thank Heiko Muller for suggesting the initial idea from which we started the development of MyWEST and the method it implements illustrated here.  ... 
doi:10.1093/bioinformatics/bth392 pmid:15247102 fatcat:6knhsawx35er3ol5nzgdgfn5xm

EpoDB: a database of genes expressed during vertebrate erythropoiesis

F Salas
1998 Nucleic Acids Research  
EpoDB is a database designed for the study of gene regulation during differentiation and development of vertebrate red blood cells.  ...  The database is organized around biological features, e.g., genes, rather than sequences, which are supported by a controlled and consistent vocabulary for gene names and gene family names.  ...  ACKNOWLEDGEMENTS This work was supported by a grant number R01-RR04026-07A2 from the National Center for Research Resources, NIH.  ... 
doi:10.1093/nar/26.1.288 pmid:9399855 pmcid:PMC147174 fatcat:hchb26sr6nfmfek7z76fxj3qna

Container Stacking And Retrieval Prototype Using Genetic Algorithms

Azizi Ab. Aziz, Azizi Zakaria
2003 Jurnal Teknologi  
This prototype was developed at Artificial Intelligence System Development Laboratory (AISDEL), Sirim Berhad.  ...  As a result it will increase the operational costs. This paper proposed a genetic algorithms technique to solve container-stacking problem, where a prototype has been developed.  ...  ACKNOWLEDGEMENT The authors wish to express their sincere thanks to researchers at Artificial Intelligence System Development Laboratory (AISDEL) SIRIM Berhad for their help and fruitful discussion throughout  ... 
doi:10.11113/jt.v38.483 fatcat:o3zpx3irjjfqpj473fu52ylxo4

Web mining: a survey in the fuzzy framework

Dragos Arotaritei, Sushmita Mitra
2004 Fuzzy sets and systems (Print)  
A hybridization of fuzzy sets with genetic algorithms (another soft computing tool) is described for information retrieval. An extensive bibliography is also included.  ...  This article provides a survey of the available literature on fuzzy Web mining.  ...  Fuzzy genes are used as intelligent agents for information retrieval from the Web [22] .  ... 
doi:10.1016/j.fss.2004.03.003 fatcat:xtnbbibicjh73g7av34nm2acoy

EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis

C. J. Stoeckert, F. Salas, B. Brunk, G. C. Overton
1999 Nucleic Acids Research  
EpoDB is a database of genes expressed in vertebrate red blood cells. It is also a prototype for the creation of cell and tissue-specific databases from multiple external sources.  ...  We have also enhanced the queries for retrieving sequence from specified genes by the addition of MEME, a motif discovery tool, to the integrated analysis tools which include CLUSTALW and TESS.  ...  ACKNOWLEDGEMENTS We wish to thank Dr Jian Wang for her help with the recent update and Arthur Lin and Zhaoliang Lu for their help on the EpoDB web site.  ... 
doi:10.1093/nar/27.1.200 pmid:9847180 pmcid:PMC148135 fatcat:zwbd24nqejhxvitufevsrv252m
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