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Analysis Tool Web Services from the EMBL-EBI

Hamish McWilliam, Weizhong Li, Mahmut Uludag, Silvano Squizzato, Young Mi Park, Nicola Buso, Andrew Peter Cowley, Rodrigo Lopez
2013 Nucleic Acids Research  
Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces.  ...  This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g.  ...  ACKNOWLEDGEMENTS The authors wish to acknowledge all software developers, database administrators, data curators and users at the EMBL-EBI and elsewhere, who have provided extremely valuable feedback and  ... 
doi:10.1093/nar/gkt376 pmid:23671338 pmcid:PMC3692137 fatcat:wb6vvm34dnfphcqexbxudruomq

The EMBL-EBI search and sequence analysis tools APIs in 2019

2019 Nucleic Acids Research  
Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+  ...  at the EMBL-EBI.  ...  We would like to also thank all EMBL-EBI teams for their invaluable help in providing biological data, applications and expertise.  ... 
doi:10.1093/nar/gkz268 pmid:30976793 pmcid:PMC6602479 fatcat:ojioxdg3pna2bdvgeea5zhj5sm

The EMBL-EBI bioinformatics web and programmatic tools framework

Weizhong Li, Andrew Cowley, Mahmut Uludag, Tamer Gur, Hamish McWilliam, Silvano Squizzato, Young Mi Park, Nicola Buso, Rodrigo Lopez
2015 Nucleic Acids Research  
Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications.  ...  Integration with EBI Search (https: //www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework.  ...  William Pearson from the University of Virginia for his support and feedback and the web administrators and Systems team at EMBL-EBI for their assistance in the provision of the tools framework service  ... 
doi:10.1093/nar/gkv279 pmid:25845596 pmcid:PMC4489272 fatcat:kgooeoagc5ailfjlzkwck2wgk4

Web services at the European Bioinformatics Institute-2009

H. Mcwilliam, F. Valentin, M. Goujon, W. Li, M. Narayanasamy, J. Martin, T. Miyar, R. Lopez
2009 Nucleic Acids Research  
The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997.  ...  From the user's point of view, these Web Services provide the same functionality as the browser-based forms.  ...  ACKNOWLEDGEMENTS The authors wish to acknowledge all software developers, database administrators, data curators and users at the EMBL-EBI and elsewhere, who have provided extremely valuable feedback and  ... 
doi:10.1093/nar/gkp302 pmid:19435877 pmcid:PMC2703973 fatcat:5kah2noaqjhjbd477rxenbrxvu

The EMBL Nucleotide Sequence Database

G. Stoesser
2002 Nucleic Acids Research  
Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces.  ...  EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK.  ...  are available from the EMBL-EBI World Wide Web site and from within Webin.  ... 
doi:10.1093/nar/30.1.21 pmid:11752244 pmcid:PMC99098 fatcat:d4m5pk36dvcvxivcuvskxwn3oe

The European Bioinformatics Institute in 2018: tools, infrastructure and training

Charles E Cook, Rodrigo Lopez, Oana Stroe, Guy Cochrane, Cath Brooksbank, Ewan Birney, Rolf Apweiler
2018 Nucleic Acids Research  
EMBL-EBI maintains over 150 analytical bioinformatics tools that complement our data resources.  ...  We make these tools available for users through a web interface as well as programmatically using application programming interfaces, whilst ensuring the latest versions are available for our users.  ...  ACKNOWLEDGEMENTS EMBL-EBI is indebted to its funders, including the EMBL member states, the European Commission, Wellcome, the UK Research Councils, the US National Institutes of Health, our Industry Programme  ... 
doi:10.1093/nar/gky1124 pmid:30445657 pmcid:PMC6323906 fatcat:ww5xqc5aorgone5pt43p43o6tu

Programmatic access to bioinformatics tools from EMBL-EBI update: 2017

Szymon Chojnacki, Andrew Cowley, Joon Lee, Anna Foix, Rodrigo Lopez
2017 Nucleic Acids Research  
Since 2009 the EMBL-EBI provides free and unrestricted access to several bioinformatics tools via the user's browser as well as programmatically via Web Services APIs.  ...  Programmatic access to these tools, which is fundamental to bioinformatics, is increasingly important as more high-throughput data is generated, e.g. from proteomics and metagenomic experiments.  ...  We also would like to thank all EMBL-EBI teams involved in providing sequence data.  ... 
doi:10.1093/nar/gkx273 pmid:28431173 pmcid:PMC5570243 fatcat:bvascotp75b3tbylkfuooizzz4

Public services from the European Bioinformatics Institute

R. Lopez
2003 Briefings in Bioinformatics  
include: ppsearch, access to the ClusTr database, PRATT 27 and RADAR. 28 Structural analysis A number of public tools for the analysis of structural data are available from the EBI.  ...  The following sections describe the various submission tools available on the web for depositing data in the EBI databases.  ... 
doi:10.1093/bib/4.4.332 pmid:14725346 fatcat:zm73usfw4jhnxm6xx5txwzamfm

The EMBL Nucleotide Sequence Database: major new developments

G. Stoesser
2003 Nucleic Acids Research  
The EMBL Nucleotide  ...  /genome_mot.html Database searching, browsing and analysis tools Access to searching, browsing and analysis tools www.ebi.ac.uk/Tools/ Title URL General EMBL-EBI Home Page www.ebi.ac.uk/ EMBL Nucleotide  ...  CON entries are available in the CON.dat file at ftp:// ftp.ebi.ac.uk/pub/databases/embl/release/, from the EBI Genome Web server at URL http://www.ebi.ac.uk/genomes/ and also in the FTP Genomes directory  ... 
doi:10.1093/nar/gkg021 pmid:12519939 pmcid:PMC165468 fatcat:wy5qtqialvgopgydjharwgb6yy

Public web-based services from the European Bioinformatics Institute

N. Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen, R. Lopez
2004 Nucleic Acids Research  
This paper provides a detailed introduction to the interactive analysis systemsthatare available from the EBI and a brief introduction to other, related services.  ...  The mission of the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL) in Heidelberg, is to ensure that the growing body of information from molecular  ...  Further information about EBI funding can be obtained at http://www.ebi.ac.uk/Information/funding/.  ... 
doi:10.1093/nar/gkh405 pmid:15215339 pmcid:PMC441543 fatcat:3q4of4kokrff7pyrexa6wxhx3u

SOAP-based services provided by the European Bioinformatics Institute

S. Pillai, V. Silventoinen, K. Kallio, M. Senger, S. Sobhany, J. Tate, S. Velankar, A. Golovin, K. Henrick, P. Rice, P. Stoehr, R. Lopez
2005 Nucleic Acids Research  
The results of jobs are stored at the EBI for 24 h after the job has completed. Structural Analysis The EBI provides a Web Services interface to tools that access the MSD.  ...  Web Services clients allow the programmer as well as the service provider to integrate and build more complex analysis workflows using existing EBI services.  ... 
doi:10.1093/nar/gki491 pmid:15980463 pmcid:PMC1160251 fatcat:2odbedc7xzfnnldtxk7spoqxry

The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences

2019 Nucleic Acids Research  
Data resources at the European Bioinformatics Institute (EMBL-EBI, https://www.ebi.ac.uk/) archive, organize and provide added-value analysis of research data produced around the world.  ...  Training is a core mission of EMBL-EBI and in 2018 our training team served more users, both in-person and through web-based programmes, than ever before.  ...  FUNDING EMBL-EBI is indebted to its funders, including the EMBL member states, the European Commission, Wellcome, UK Research and Innovation, the US National Institutes of Health, our Industry Programme  ... 
doi:10.1093/nar/gkz1033 pmid:31701143 pmcid:PMC6943058 fatcat:i2gcxbfkprb37etd37stq4t74a

A new Ontology Lookup Service at EMBL-EBI

Simon Jupp, Tony Burdett, Catherine Leroy, Helen E. Parkinson
2015 Workshop on Semantic Web Applications and Tools for Life Sciences  
The Ontology Lookup Service (OLS) hosted at the EMBL European Bioinformatics Institute has been providing ontology search and visualisation services for over ten years.  ...  One of the major shifts has been the increasing use of the W3C Web Ontology Language (OWL) for representing biomedical ontologies.  ...  The EMBL-EBI Ontology Lookup Service (OLS) 1 was one of the earliest public ontology browsers, offering searching and browsing services along with Web services for programmatic access to ontologies.  ... 
dblp:conf/swat4ls/JuppBLP15 fatcat:wmub2ck7xrcbzmzcl7djapy7g4

A new bioinformatics analysis tools framework at EMBL-EBI

M. Goujon, H. McWilliam, W. Li, F. Valentin, S. Squizzato, J. Paern, R. Lopez
2010 Nucleic Acids Research  
The EMBL-EBI provides access to various mainstream sequence analysis applications.  ...  These services are available over the web and via Web Services interfaces for users who require systematic access or want to interface with customized pipe-lines and workflows using common programming  ...  ACKNOWLEDGEMENTS We acknowledge valuable feedback from Prof. William Pearson from the University of Virginia, USA and the InterPro and UniProt teams at EMBL-EBI.  ... 
doi:10.1093/nar/gkq313 pmid:20439314 pmcid:PMC2896090 fatcat:f43hzuilk5aqdkq3etyowhh24a

The EBI search engine: EBI search as a service—making biological data accessible for all

Young M. Park, Silvano Squizzato, Nicola Buso, Tamer Gur, Rodrigo Lopez
2017 Nucleic Acids Research  
The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include  ...  EBI Search provides a powerful RESTful API that enables its integration into thirdparty portals, thus providing 'Search as a Service' capabilities, which are the main topic of this article.  ...  Finally, we would like to thank all EMBL-EBI teams involved in providing data to the EBI Search. FUNDING  ... 
doi:10.1093/nar/gkx359 pmid:28472374 pmcid:PMC5570174 fatcat:7vlgpmowhrgcvjhqn2sk7w4hse
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