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A Semantic Web for bioinformatics: goals, tools, systems, applications
2008
BMC Bioinformatics
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A Semantic Web for bioinformatics The session on Semantic Web tools and applications is represented in this Supplement by five contributions. ...
medium and long term perspectives in applying Semantic Web technologies to bioinformatics. ...
Publish with Bio Med Central and every scientist can read your work free of charge http://www.biomedcentral.com/1471-2105/9/S4/S1 ...
doi:10.1186/1471-2105-9-s4-s1
pmid:18460170
pmcid:PMC2367628
fatcat:axiel3c56vgo5ajdw4uv6riz6q
Efficient functional bioinformatics tools: towards understanding biological processes
2010
EMBnet journal
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In this contribution we review different methodologies and applications for functional bioinformatics in the context of automated data and text analysis in biology. ...
Experimental high-throughput techniques in biology are generating large amounts of data related to genes and proteins at different levels. ...
Tools and methodologies able to efficiently process the huge amounts of data that are generated in this field are still demanded by the molecular biology community. ...
doi:10.14806/ej.16.1.184
fatcat:ohe3oznt3zd2rnxj4udoqr6to4
Mining Semantic Descriptions of Bioinformatics Web Resources from the Literature
[chapter]
2009
Lecture Notes in Computer Science
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A number of projects (myGrid, BioMOBY, etc.) have recently been initiated in order to organise emerging bioinformatics Web Services and provide their semantic descriptions. ...
The method combines terminological processing and dependency parsing of journal articles, and applies information extraction techniques to profile Web services using informative textual passages, related ...
This work was partially supported by the UK Biotechnology and Biological Science Research Council (BBSRC) via the projects "Mining Term Associations from Literature to Support Knowledge Discovery in Biology ...
doi:10.1007/978-3-642-02121-3_40
fatcat:dtpm6iflsrcgbdn74lt2rnu6py
NETTAB 2013: Semantic, social, and mobile applications for bioinformatics and biomedical laboratories
2014
BMC Bioinformatics
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Topics included issues, methods, algorithms, and technologies for the design and development of tools and platforms able to provide semantic, social, and mobile applications supporting bioinformatics and ...
The thirteenth NETTAB workshop, NETTAB 2013, was devoted to semantic, social, and mobile applications for bioinformatics and biomedical laboratories. ...
This article has been published as part of BMC Bioinformatics Volume 15 Supplement 14, 2014: Semantic, social, mobile applications for bioinformatics and biomedical laboratories: selected works from the ...
doi:10.1186/1471-2105-15-s14-s1
pmid:25471662
pmcid:PMC4255736
fatcat:t65i3f6azze6plr54d5dv7hufy
The role of parallelism, web services and ontologies in bioinformatics and omics data management and analysis
2013
EMBnet journal
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The increasing availability of omics data poses new challenges to bioinformatics applications regarding the efficient storage and integration of experimental data, their efficient and high-throughput preprocessing ...
This paper presents an overview of how parallelism, service orientation, and knowledge management techniques can be used to face those challenges presenting some recent bioinformatics tools and projects ...
By modeling the application domain of a bioinformatics application and the analysis techniques used to analyse data, ontologies may be used to guide the development of bioinformatics workflows, suggesting ...
doi:10.14806/ej.19.b.731
fatcat:i3tffcagufhd5ijk5cq5enzwxe
Accelerating Knowledge Discovery through Community Data Sharing and Integration
2009
IMIA Yearbook of Medical Informatics
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Objectives To summarize current excellent research in the field of bioinformatics. Method Synopsis of the articles selected for the IMIA Yearbook 2009. ...
Advances in systems biology, bio-ontologies and text-ming can also be noted. ...
Acknowledgement I would like to acknowledge the support of Martina Hutter and the reviewers in the selection process of the IMIA Yearbook. ...
doi:10.1055/s-0038-1638650
fatcat:dmird6o2g5buldu7pnhbfirvoi
Guest Editorial: Special Section on Grid, Web Services, Software Agents, and Ontology Applications for Life Sciences
2007
IEEE Transactions on Nanobioscience
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Others are concerned with advanced techniques and methodologies, like Web services and agent-based systems. ...
R ECENT progress in the application of bioinformatics, computational biology, and systems biology to biomedicine has made it essential to devise technological platforms able to ensure appropriate support ...
doi:10.1109/tnb.2007.897434
fatcat:kihmne4uazcivazs5vgh36c6py
The Eighth Annual Bio-Ontologies Meeting
2005
PLoS Computational Biology
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Bio-ontologies offer a variety of large, rapidly changing examples of ontologies with which knowledge representation techniques, methodologies, and tools can be developed and tested. ...
The Semantic Web vision now being actively promoted as the ''next generation'' Web-which aims to make the Web open to automatic computational use-makes heavy use of ontological technology (http://www.w3 ...
doi:10.1371/journal.pcbi.0010077
pmid:16758004
pmcid:PMC1323465
fatcat:5aipqp5ajbduxbyq6t74sjavna
Guided Composition of Tasks with Logical Information Systems - Application to Data Analysis Workflows in Bioinformatics
[chapter]
2013
Lecture Notes in Computer Science
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The objective is to use semantics to describe bioinformatic tasks and to adapt the guided approach of Sewelis, a LIS semantic web tool, to the composition of tasks. ...
The composition of tasks is however difficult due to the distributed and heterogeneous resources of bioinformatics. ...
Evaluation methodology GenOuest 4 is a bioinformatic platform that provides a large collection of tools and services for data analysis. ...
doi:10.1007/978-3-642-38288-8_47
fatcat:qvzfu62ytnbfdfdkehyqfr4n7y
Data Integration in Bioinformatics: Current Efforts and Challenges
[chapter]
2011
Bioinformatics - Trends and Methodologies
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Application of the Semantic Web technologies to biological data integration is a significant advancement for bioinformatics, enabling automated data processing and reasoning. ...
However, the Semantic Web continues to evolve and its application in biological data integration has several limitations. ...
Because of the rapid development of new technologies in molecular biology, new bioinformatic techniques emerge accordingly to keep the pace of in silico development of life science. ...
doi:10.5772/21654
fatcat:zaiy3lxhgrdwhgqdqnjrqg3gbm
Query Answering Using Ontologies in Agent-based Resource Sharing Environment for Biological Web Information Integrating
2003
International Joint Conference on Artificial Intelligence
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How to rapidly capture, utilize and integrate hundreds of biological databases on the Web is one of the most critical issues in bioinformatics. ...
This approach makes the details of querying Web resources transparent to the biologists and allows them to query biological resources on the Web in the terms of their domain knowledge. ...
Acknowledgments We wish to thank Rita Huang and bi omedical scientists at the Institute of Biomedical Science, Academia Sinica for their helpful comments on this work. ...
dblp:conf/ijcai/LuH03
fatcat:jpekbid44fgopdd2o5e3d27cg4
Ontology Engineering Techniques for Biological Data
2014
Journal of Computers
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Our goal is to provide new technique for gene-ontology to increase the efficiency, completeness and correctness of ontology engineering technique as compared to the previous ontologies developed by different ...
Data integration is being provided through a series of tools and techniques but lack of reliable terminologies and concepts cause hurdles. ...
To overcome this problem semantic web has been introduced that is the extension of the current web [7] . ...
doi:10.4304/jcp.9.9.2151-2158
fatcat:dckwvugrhnguxdgoqnohbbukqe
Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance
2013
Wiley Interdisciplinary Reviews. Computational Molecular Science
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The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous ...
and properly curated metadata; and an understanding of the contribution that the Semantic Web can make at all stages of the research lifecycle. ...
and Repositories Programmes, and HEFCE/UMF). ...
doi:10.1002/wcms.1127
pmid:24432050
pmcid:PMC3884755
fatcat:vpqawnligbbyrgjepzznugq3vi
Knowledge Representation and Management
2010
IMIA Yearbook of Medical Informatics
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- ing sharing and reusability across applications, domains, and institutions thus contributing to building capacities worldwide. ...
Combining the newest techniques in computational linguistics and natural language processing with the latest methods in statistical data analysis, machine learning and text mining has proved to be efficient ...
Acknowledgement I greatly acknowledge the support of Martina Hutter and of the reviewers in the selection process of the IMIA Yearbook. ...
doi:10.1055/s-0038-1638691
fatcat:eiq4m2tu4fhvvekby6aayhrfsi
Cancer bioinformatics: A new approach to systems clinical medicine
2012
BMC Bioinformatics
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For example, the Semantic Web technology was used to understand high throughput clinical data and develop quantitative semantic models retrieved from Corvus, a data warehouse which provides a uniform interface ...
There is a need to develop cancer bioinformatics-specific methodologies or introduce new and advanced bioinformatics tools to answer the specific question of cancer. ...
Submit your next manuscript to BioMed Central and take full advantage of: ...
doi:10.1186/1471-2105-13-71
pmid:22549015
pmcid:PMC3424139
fatcat:zgqcyimh35ezloeg2ky5fkmpn4
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