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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

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.  ...  ACKNOWLEDGEMENTS The authors wish to acknowledge the following: Simone Badoer, Andrea Cristofori and Philip Lewis for web adminis-tration support.  ... 
doi:10.1093/nar/gkx273 pmid:28431173 pmcid:PMC5570243 fatcat:bvascotp75b3tbylkfuooizzz4

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

2019 Nucleic Acids Research  
at the EMBL-EBI.  ...  Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility  ...  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

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.  ...  Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes.  ...  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 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.  ...  The authors and staff of EMBL-EBI are also indebted to the hundreds of thousands of scientists who have submitted data and annotation to the shared data collections.  ... 
doi:10.1093/nar/gky1124 pmid:30445657 pmcid:PMC6323906 fatcat:ww5xqc5aorgone5pt43p43o6tu

The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI

Silvano Squizzato, Young Mi Park, Nicola Buso, Tamer Gur, Andrew Cowley, Weizhong Li, Mahmut Uludag, Sangya Pundir, Jennifer A. Cham, Hamish McWilliam, Rodrigo Lopez
2015 Nucleic Acids Research  
The European Bioinformatics Institute (EMBL-EBI--https://www.ebi.ac.uk) provides free and unrestricted access to data across all major areas of biology and biomedicine.  ...  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 including sequences  ...  ACKNOWLEDGEMENTS We would like to thank the following staff and collaborators for their support: Anton Petrov, Dietmar Sturmayr, Francis Rowland, Philip Lewis, Andrea Cristofori and Simone Badoer.  ... 
doi:10.1093/nar/gkv316 pmid:25855807 pmcid:PMC4489232 fatcat:m6wp7w7c4zdbrpsunzxlzqy4mi

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.  ...  The authors and staff of EMBL-EBI are also indebted to the hundreds of thousands of scientists who have submitted data and annotation to the shared data collections.  ... 
doi:10.1093/nar/gkz1033 pmid:31701143 pmcid:PMC6943058 fatcat:i2gcxbfkprb37etd37stq4t74a

Web Services at the European Bioinformatics Institute

A. Labarga, F. Valentin, M. Anderson, R. Lopez
2007 Nucleic Acids Research  
All available information about EBI web services can be accessed from the web page http://www.ebi.ac.uk/Tools/webservices.  ...  Sequence and Literature data retrieval WSDbfetch provides programmatic access to the popular sequence and literature data retrieval tool dbfetch (http://www.ebi.ac.uk/Tools/dbfetch).  ... 
doi:10.1093/nar/gkm291 pmid:17576686 pmcid:PMC1933145 fatcat:tc6mwelg3rbnpgqjfqr26v3y5i

The European Bioinformatics Institute in 2016: Data growth and integration

Charles E. Cook, Mary Todd Bergman, Robert D. Finn, Guy Cochrane, Ewan Birney, Rolf Apweiler
2015 Nucleic Acids Research  
In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.uk) are continually expanding: total disk capacity increases significantly every year to keep  ...  Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework  ...  The authors and staff of EMBL-EBI are indebted to the hundreds of thousands of scientists who have submitted data and annotation to the shared data collections.  ... 
doi:10.1093/nar/gkv1352 pmid:26673705 pmcid:PMC4702932 fatcat:2oonfh72mrbpfi2ywith6updti

The European Nucleotide Archive in 2018

Peter W Harrison, Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Sam Holt, Abdulrahman Hussein, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu (+12 others)
2018 Nucleic Acids Research  
The European Nucleotide Archive (ENA; https://www. ebi.ac.uk/ena), provided from EMBL-EBI, has for more than three decades been responsible for archiving the world's public sequencing data and presenting  ...  template expansion, early pre-submission validation tools and our move towards a new browser and retrieval infrastructure.  ...  Content is distributed under the EMBL-EBI Terms of Use available at (https://www.ebi.ac.uk/about/terms-ofuse).  ... 
doi:10.1093/nar/gky1078 pmid:30395270 fatcat:kmr4vyojundfzabhv3dwdciamu

The European Bioinformatics Institute in 2017: data coordination and integration

Charles E Cook, Mary T Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney
2017 Nucleic Acids Research  
The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https  ...  This update gives a birds-eye view of EMBL-EBI's approach to data integration and service development as genomics begins to enter the clinic.  ...  of standards, tools, frameworks and best practice.  ... 
doi:10.1093/nar/gkx1154 pmid:29186510 pmcid:PMC5753251 fatcat:ubzlegb2kjcltbtdftwsh6mlja

EOSC-Life Enhanced COVID-19 Portal and data mobilisation reporting

Guy Cochrane, Marianna Ventouratou
2021 Zenodo  
Objective 1: over 5 million records from across EMBL-EBI resources are displayed on the portal, with many options for search and retrieval Objective 2: consensus sequence data from 101 countries, and raw  ...  More specifically the objectives of WP13 are to: Mobilise open biomolecular data relevant to COVID-19 research from structured bioinformatics databases and prioritised life science RI resources via the  ...  databases and furnished with web and programmatic interfaces appropriate to support diverse and extensive research upon the data served.The COVID-19 Data Portal displays the following useful features  ... 
doi:10.5281/zenodo.5642936 fatcat:5jyttuq3nfeerhtrvtwjgzwjry

D8.6_Mirri_Report On Human And Programmatic Access

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  
This report outlines the optimal approach following technology produced in the World Wide Web Consortium (W3C), as well as in the ELIXIR system and in the BioMedBriges project.  ...  It intends to get the maximum compliance with databases, ontologies and the standards for applications like human health, veterinary science, pharma, agriculture, food production, winemaking, brewing and  ...  Programmatic access The main technology for programmatic access in ELIXIR, EMBL-EBI and BioMedBridges is Semantic WEB, general description in http://www.w3.org/2001/sw/.  ... 
doi:10.5281/zenodo.49970 fatcat:xjddke3a7zaivn5x3zqmu2htuy

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
We contribute substantially to training in transcriptomics and other EMBL-EBI bioinformatics tools.  ...  We are responsible for the global EBI search engine, which indexes more than 1 billion entries from all the EMBL-EBI data resources, and for the Job Dispatcher framework and corresponding SOAP/REST web  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

Sarah Hunter, Matthew Corbett, Hubert Denise, Matthew Fraser, Alejandra Gonzalez-Beltran, Christopher Hunter, Philip Jones, Rasko Leinonen, Craig McAnulla, Eamonn Maguire, John Maslen, Alex Mitchell (+11 others)
2013 Nucleic Acids Research  
analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive.  ...  Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data.  ...  ACKNOWLEDGEMENTS The authors would like to thank users from the metagenomics community who have volunteered in usability studies and/or provided feedback to us via surveys and emails; they are too numerous  ... 
doi:10.1093/nar/gkt961 pmid:24165880 pmcid:PMC3965009 fatcat:omjatsv6lrhklc5qhkldkhejl4
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