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1.  NETTAB 2013: Semantic, social, and mobile applications for bioinformatics and biomedical laboratories 
BMC Bioinformatics  2014;15(Suppl 14):S1.
The thirteenth NETTAB workshop, NETTAB 2013, was devoted to semantic, social, and mobile applications for bioinformatics and biomedical laboratories.
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 activities carried out in a biomedical laboratory.
About 30 scientific contributions were presentedat NETTAB 2013, including keynote and tutorial talks, oral communications, and posters. 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.
PMCID: PMC4255736  PMID: 25471662
2.  Combining ontologies and workflows to design formal protocols for biological laboratories 
Laboratory protocols in life sciences tend to be written in natural language, with negative consequences on repeatability, distribution and automation of scientific experiments. Formalization of knowledge is becoming popular in science. In the case of laboratory protocols two levels of formalization are needed: one for the entities and individuals operations involved in protocols and another one for the procedures, which can be manually or automatically executed. This study aims to combine ontologies and workflows for protocol formalization.
A laboratory domain specific ontology and the COW (Combining Ontologies with Workflows) software tool were developed to formalize workflows built on ontologies. A method was specifically set up to support the design of structured protocols for biological laboratory experiments. The workflows were enhanced with ontological concepts taken from the developed domain specific ontology.
The experimental protocols represented as workflows are saved in two linked files using two standard interchange languages (i.e. XPDL for workflows and OWL for ontologies). A distribution package of COW including installation procedure, ontology and workflow examples, is freely available from
Using COW, a laboratory protocol may be directly defined by wet-lab scientists without writing code, which will keep the resulting protocol's specifications clear and easy to read and maintain.
PMCID: PMC2873243  PMID: 20416048
3.  A Semantic Web for bioinformatics: goals, tools, systems, applications 
BMC Bioinformatics  2008;9(Suppl 4):S1.
PMCID: PMC2367628  PMID: 18460170
5.  Time to Organize the Bioinformatics Resourceome 
PLoS Computational Biology  2005;1(7):e76.
PMCID: PMC1323464  PMID: 16738704

Results 1-5 (5)