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

Cannata, Nicola; Schröder, Michael; Marangoni, Roberto; Romano, Paolo

doi:10.1186/1471-2105-9-s4-s1

Cited by 29 publications

(14 citation statements)

References 19 publications

(18 reference statements)

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“…Various topics have therefore been focused and discussed, some of which have been very timely, including, among others, XML-based data integration in 2001, scientific workflows in 2005, Web Services in 2006 [2], the Semantic Web in 2007 [3], biological Wikis in 2010, and mobile applications (apps) for Life Sciences in 2013 [4]. A full list of topics and access to web sites is available on the web [1].…”

Section: Nettab Workhopsmentioning

confidence: 99%

NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology

Romano

Cordero

2016

BMC Bioinformatics

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The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology. The topics of the workshop were centred around bioinformatics methods, tools, applications, and perspectives for models, standards and management of high-throughput biological data, structural bioinformatics, functional proteomics, mass spectrometry, drug discovery, and systems biology. 43 scientific contributions were presented at NETTAB 2014, including keynote, special guest and tutorial talks, oral communications, and posters. Full papers from some of the best contributions presented at the workshop were later submitted to a special Call for this Supplement. Here, we provide an overview of the workshop and introduce manuscripts that have been accepted for publication in this Supplement.

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Section: Nettab Workhopsmentioning

confidence: 99%

NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology

Romano

Cordero

2016

BMC Bioinformatics

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“…We also anticipate improving the amount, quality, and accessibility of metadata. Semantic Web representations and reasoning methods hold the promise of more automated analysis and will be incorporated into future work [32]; Semantic Web approaches have already been adopted in a number of life sciences applications [4, 13, 33–39]. For subsequent releases of the PATRIC website, we will be soliciting user feedback through a number of new mechanisms, including bi-annual users workshops (to support user-based evaluation), as well as online surveys to gather feedback from online users as they experience usability problems or think of website enhancements.…”

Section: Discussionmentioning

confidence: 99%

Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned

Sullivan

Gabbard

Shukla

et al. 2010

Chemistry & Biodiversity

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Systems-biology and infectious-disease (host -pathogen -environment) research and development is becoming increasingly dependent on integrating data from diverse and dynamic sources. Maintaining integrated resources over long periods of time presents distinct challenges. This review describes experiences and lessons learned from integrating data in two five-year projects focused on pathosystems biology: the Pathosystems Resource Integration Center (PATRIC, http://patric.vbi.vt.edu/), with a goal of developing bioinformatics resources for the research and countermeasures-development communities based on genomics data, and the Resource Center for Biodefense Proteomics Research (RCBPR, http:// www.proteomicsresource.org/), with a goal of developing resources based on the experiment data such as microarray and proteomics data from diverse sources and technologies. Some challenges include integrating genomic sequence and experiment data, data synchronization, data quality control, and usability engineering. We present examples of a variety of data-integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long-term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include 1) an approach for addressing discrepancies between experiment results and interpreted results, and 2) expanding the range of data-integration techniques to include usability engineering at the presentation level.

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“…Slater [9] and Kozhenkov [10] research underlines drawbacks intrinsic to current strategies and recognize the need for novel approaches, based on distinct skills and ideals. For this, Semantic Web methodologies arise as the desired resolution in spite of their projected slow adoption [11]. Next, a discussion on the various challenges for this slower adoption is detailed.…”

Section: Motivationmentioning

confidence: 99%

Towards knowledge federation in biomedical applications

Lopes

Oliveira

2011

Proceedings of the 7th International Conference on Semantic Systems

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Knowledge federation is a particular matter of concern in the life sciences domain. The magnitude of data generated by biomedical software and hardware since the initial discovery of the human genome is tremendous in quantity and diversity. Consequently, state-of-the-art software solutions have always lagged behind researchers' demands, even more so with recent developments in high-throughput sequencing technology and open access to digital disease records. The maturity of Semantic Web technologies brought with it new strategies to tackle life sciences challenges. In spite of the increased awareness regarding these technologies' advantages, its adoption has been slow paced. With a steep learning curve and lacking turnkey solutions, bioinformatics developers are faced with many roadblocks, resulting in a low number of purely semantic solutions. Our research springs new life to knowledge federation in the life sciences with a new application deployment framework, which includes a native federation layer connecting and federating deployed instances by default. This feature is integrated in a complete software stack for creating new applications, easing the troubled development cycle associated with Semantic Web tools. As a result, the door is opened for harnessing more insightful knowledge from the aggregated network of relationships amongst biological data.

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

Cited by 29 publications

References 19 publications

NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology

NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology

Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned

Towards knowledge federation in biomedical applications

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