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A Semantic Web for bioinformatics: goals, tools, systems, applications

Nicola Cannata, Michael Schröder, Roberto Marangoni, Paolo Romano
2008 BMC Bioinformatics  
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

Alberto Pascual-Montano, Jose M Carazo
2010 EMBnet journal  
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]

Hammad Afzal, Robert Stevens, Goran Nenadic
2009 Lecture Notes in Computer Science  
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

Paolo Romano, Nicola Cannata
2014 BMC Bioinformatics  
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

Mario Cannataro, Pietro Hiram Guzzi
2013 EMBnet journal  
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

Y.L. Yip
2009 IMIA Yearbook of Medical Informatics  
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

Luciano Milanesi, Giuliano Armano, Vincent Breton, Paolo Romano
2007 IEEE Transactions on Nanobioscience  
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

Phillip Lord, Robert Stevens, James A. Butler, Robin McEntire
2005 PLoS Computational Biology  
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]

Mouhamadou Ba
2013 Lecture Notes in Computer Science  
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]

Zhang Zhang, Vladimir B., Jun Yu, Kei-Hoi Cheung, Jeffrey P.
2011 Bioinformatics - Trends and Methodologies  
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

Jiann-Jyh Lu, Chun-Nan Hsu
2003 International Joint Conference on Artificial Intelligence  
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

Asma Fardoos, Jamshaid Iqbal Janjua, Amjad Farooq
2014 Journal of Computers  
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

Jeremy G. Frey, Colin L. Bird
2013 Wiley Interdisciplinary Reviews. Computational Molecular Science  
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

A.-M. Rassinoux
2010 IMIA Yearbook of Medical Informatics  
- 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

Duojiao Wu, Catherine M Rice, Xiangdong Wang
2012 BMC Bioinformatics  
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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