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BioCatalogue: a universal catalogue of web services for the life sciences

J. Bhagat, F. Tanoh, E. Nzuobontane, T. Laurent, J. Orlowski, M. Roos, K. Wolstencroft, S. Aleksejevs, R. Stevens, S. Pettifer, R. Lopez, C. A. Goble
2010 Nucleic Acids Research  
Drawing together the experience of these existing initiatives, the BioCatalogue provides a universal catalogue of Web Services for the Life Sciences.  ...  The BioCatalogue has five key properties: (1) It provides a single up-to-date port-of-call for finding Life Science Web Services, regardless of their technology or provenance.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkq394 pmid:20484378 pmcid:PMC2896129 fatcat:z6hzdqyj65ecflk3pyue3pvdtm

Biological Web Service Repositories Review

David Urdidiales-Nieto, Ismael Navas-Delgado, José F. Aldana-Montes
2016 Molecular Informatics  
BioCatalogue pro-vides an interface for registering, browsing and annotating Web services for the life science community,a ggregating life science-specific content from others ources and classifying it  ...  Capabilities and features of each Webservice of the Web service repositories in the life sciences.  ... 
doi:10.1002/minf.201600035 pmid:27783459 pmcid:PMC5434852 fatcat:vt3uf2dewvakdmyvin5mtd4d74

A semantic approach for the requirement-driven discovery of web resources in the Life Sciences

María Pérez-Catalán, Rafael Berlanga, Ismael Sanz, María José Aramburu
2012 Knowledge and Information Systems  
Research in the Life Sciences depends on the integration of large, distributed and heterogeneous web resources (e.g. data sources and web services).  ...  In this paper we contribute with a semi-automatic approach, based on semantic techniques, to assist researchers in the discovery of the most appropriate web resources to fulfill a set of requirements.  ...  We thank the BioCatalogue team for providing us with statistical information about their queries, and also the reviewers for their constructive and detailed comments.  ... 
doi:10.1007/s10115-012-0498-5 fatcat:us7flpuwzzh4ld7b7meg6sexm4

Tools and data services registry: a community effort to document bioinformatics resources

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau (+57 others)
2015 Nucleic Acids Research  
BINF.KU.DK Services and Software http://www.binf.ku.dk/services A collection of over 20 web services, databases and software packages from The Bioinformatics Centre at The University of Copenhagen.  ...  The list includes a cross-section of bioinformatics service providers including other catalogues such as SEQwiki and BioCatalogue Name, URL, Short description CBS Prediction Servers http://www.cbs.dtu.dk  ...  ACKNOWLEDGEMENTS The authors would like to thank Steve Pettifer and Dave Thorne for the initial discussions and ideas founding the registry effort.  ... 
doi:10.1093/nar/gkv1116 pmid:26538599 pmcid:PMC4702812 fatcat:npzer6xh7fezlbcamfmdvv552m

Network Analysis of Scientific Workflows: A Gateway to Reuse

Wei Tan, Jia Zhang, Ian Foster
2010 Computer  
We thank Carole Goble and David De Roure for supporting our assessment of Taverna, myExperiment, and BioCatalogue. We also thank Ravi Madduri for constructive discussions on workflow reuse in caBIG.  ...  The work described in this article is partially supported by the National Cancer Institute, the National Institutes of Health under contract N01-CO-12400, and the National Science Foundation under grant  ...  For example, BioCatalogue, 5 a sister project to myExperiment, has catalogued more than 1,600 life-science Web services. Such online repositories have opened a gateway to scientific workflow reuse.  ... 
doi:10.1109/mc.2010.262 fatcat:a3unojgw3bdcndoqt23xouhqoe

BioUSeR: a semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements

María Pérez, Rafael Berlanga, Ismael Sanz, María Aramburu
2013 Journal of Biomedical Semantics  
Open metadata registries are a fundamental tool for researchers in the Life Sciences trying to locate resources.  ...  This reality must be taken into account in order to develop effective techniques for resource discovery in Life Sciences.  ...  Acknowledgements This work has been partially funded by the "Ministerio de Economía y Competitividad" with contract number TIN2011-24147, and the Fundació Caixa Castelló project P1-1B2010-49.  ... 
doi:10.1186/2041-1480-4-12 pmid:23635042 pmcid:PMC3698192 fatcat:4q4gkykd6fedziwh4gze24enwu

mORCA: ubiquitous access to life science web services

Sergio Diaz-del-Pino, Oswaldo Trelles, Juan Falgueras
2018 BMC Genomics  
Furthermore, in the life sciences world there has been a vast proliferation of data types and services that finish as Web Services.  ...  This suggests the need for research into mobile clients to deal with life sciences applications for effective usage and exploitation.  ...  We would also like to thank Simon Coxon, our language quality reviewer, for proof-reading of the document.  ... 
doi:10.1186/s12864-018-4439-x pmid:29338691 pmcid:PMC5771032 fatcat:j4amjkyksvdulhjhzhipwzptlq

Duomenų tyrybos sistemos, pagrįstos saityno paslaugomis

Olga Kurasova, Virginijus Marcinkevičius, Viktor Medvedev, Aurimas Rapečka
2013 Informacijos mokslai  
According to the criteria, a comparative analysis of the popular data mining systems, based on web services, is made.  ...  An analytical review of the data mining systems, based on web services, is provided. Some comparison criteria are selected.  ...  BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Research, W689-W694. BOINC (2013) [interaktyvus] [žiūrėta 2013 m. liepos 8 d.].  ... 
doi:10.15388/im.2013.0.2054 fatcat:mtj74jeoaja6xdev7xjrzoz45q

D8.4_Mirri_Report On Comparison Of Various Integration Software Operating In Life Sciences

B. Bunk, DP Colobraro, P. Dawyndt, P. De Vos, F.O. Glöckner, A. Kopf, V. Robert, P. Romano, D. Smith, C. Söhngen, F. Van Hauwenhuyse, A. Vasilenko
2015 Zenodo  
The objective of this deliverable is the analysis of some data integration architectures and tools in Life Sciences to determine their respective advantages and disadvantages in meeting the objectives  ...  of the MIRRI infrastructure.  ...  BioCatalogue is a public curated registry of Life Science Web services developed by implementing some of the typical features of social networks (18) .  ... 
doi:10.5281/zenodo.49968 fatcat:72fy55qtjfgbrecrkslp25s5he

Cross-Language Semantic Web Service Discovery to Improve the Selection Mechanism by using Data Mining Techniques

Ahmed SharafEldin, Ayman E. Khedr, Fahad Kamal Al-Sharif
2015 International Journal of Computer Applications  
Text mining techniques were applied on SWSDL content and user's query to be ready for CLIR methods, this sub model was tested on a curated catalogue of Life Science Web Services http://www.biocatalogue.org  ...  Web service became one of the important methods for communication through the internet and its usage increased in the levels of users and developers.  ...  BioCatalogue A Curated Web Service Registry BioCatalogue is a web service registry dedicated to the life science community.  ... 
doi:10.5120/19289-0713 fatcat:w47ex3t5k5en3h3bj27a5x7zyy

Mining Semantic Descriptions of Bioinformatics Web Resources from the Literature [chapter]

Hammad Afzal, Robert Stevens, Goran Nenadic
2009 Lecture Notes in Computer Science  
We illustrate the potential of natural language processing not only for mining descriptions of known services, but also for discovering new services that have been described in the literature.  ...  They can be used to facilitate subsequent manual description of services, but also for providing a semantic synopsis of a service that can be used to locate related services.  ...  We are thankful to the National University of Sciences & Technology Pakistan's Higher Education Program for additional support.  ... 
doi:10.1007/978-3-642-02121-3_40 fatcat:dtpm6iflsrcgbdn74lt2rnu6py

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Alex R. Hardisty, Finn Bacall, Niall Beard, Maria-Paula Balcázar-Vargas, Bachir Balech, Zoltán Barcza, Sarah J. Bourlat, Renato De Giovanni, Yde de Jong, Francesca De Leo, Laura Dobor, Giacinto Donvito (+40 others)
2016 BMC Ecology  
Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry  ...  We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services  ...  Without the contributions of each of them we would not have arrived at the position of being able to offer a pilot service to the scientific community for in silico digital biodiversity and ecosystems  ... 
doi:10.1186/s12898-016-0103-y pmid:27765035 pmcid:PMC5073428 fatcat:kphzgb67bzh4tdnwchbkvf2nvq

Management and provision of computational models

Camille Laibe, Camille Laibe
2012 Nature Precedings  
Bioinformatics (2010) BioCatalogue: a universal catalogue of web services for the life sciences.  ...  Provided by other people curating models out of interest Models provenance MIRIAM The Minimum Information Required In the Annotation of a Model http://biomodels.net/miriam/ set of guidelines for the curation  ... 
doi:10.1038/npre.2012.7013.1 fatcat:cg7ucvvnzrb53ioacds3mecnjq

Management and provision of computational models

Camille Laibe, Camille Laibe
2012 Nature Precedings  
Bioinformatics (2010) BioCatalogue: a universal catalogue of web services for the life sciences.  ...  Provided by other people curating models out of interest Models provenance MIRIAM The Minimum Information Required In the Annotation of a Model http://biomodels.net/miriam/ set of guidelines for the curation  ... 
doi:10.1038/npre.2012.7013 fatcat:qbr6rknqxrfq3ao2xj7jzlmhfe

Cross Language Information Retrieval Model for Discovering WSDL Documents Using Arabic Language Query

Prof. Dr., Dr. Ayman, Fahad Kamal
2013 International Journal of Advanced Computer Science and Applications  
The proposed model was tested on a curated catalogue of Life Science Web Services http://www.biocatalogue.org/ and used for solving the research problem with 99.87 % accuracy and 95.06 precision  ...  Web service discovery is the process of finding a suitable Web service for a given user's query through analyzing the web service's WSDL content and finding the best match for the user's query.  ...  And we found the BioCatalogue, it is a centralized registry of curated Life Science Web Services and it has the following functions: 1) Search (by Keywords): User or agent could search using any part  ... 
doi:10.14569/ijacsa.2013.040817 fatcat:mnfb5gyvtjdm7gcttascygdf3e
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