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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1295 Scopus citations

Abstract

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. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Original languageEnglish (US)
Pages (from-to)W597-600
JournalUnknown Journal
Volume41
Issue numberWeb Server issue
DOIs
StatePublished - Jul 2013
Externally publishedYes

Bibliographical note

Funding Information:
Brooke Heidenga, Joelle Nadle, Susan Brooks, Alison Ryan, California Emerging Infections Program; Tessa Carter, Paula Clogher, Maria Correa, Daewi Kim, Carol Lyons, Amber Maslar, Adam Misiorski, Connecticut Emerging Infections Program, Yale School of Public Health; Jeremiah Williams, Siyeh Gretzinger, Jana Manning, Asmith Joseph, Allison Roebling, Chandler Surell, Stephanie Lehman, Taylor Eisenstein, Gracie Chambers, Grayson Kallas, Annabel Patterson, Georgia Emerging Infections Program, Georgia Department of Health; Foundation for Atlanta Veterans Education and Research, Atlanta Veterans Affairs Medical Center; Maya L. Monroe, Patricia A. Ryan, Alicia Brooks, Elisabeth Vaeth, Cindy Zerrlaut, David Blythe, Maryland Department of Health; Rachel Park, Michelle Wilson, Maryland Emerging Infections Program - The Johns Hopkins Bloomberg School of Public Health; Jim Collins, Shannon Johnson, Justin Henderson, Libby Reeg, Alexander Kohrman, Val Tellez Nunez, Sierra Peguies-Khan, Chloe Brown, Michigan Department of Health and Human Services; Austin Bell, Kayla Bilski, Emma Contestabile, Claire Henrichsen, Amanda Gordon, Cynthia Kenyon, Melissa McMahon, Katherine Schleiss, Samantha Siebman, Emily Holodnick, Lisa Nguyen, Kristen Ehresmann, Minnesota Department of Health; Emily B. Hancock, Yadira Salazar-Sanchez, Nancy Eisenberg, Melissa Christian, Mayvilynne Poblete, Wickliffe Omondi, New Mexico Emerging Infections Program; Suzanne McGuire, Katarina Manzi, Grant Barney, New York State Department of Health; Virginia Cafferky, Christine Long, RaeAnne Kurtz, Maria Gaitan, University of Rochester School of Medicine and Dentistry; Nicholas Fisher, Krista Lung, Maya Sculllin, Ohio Department of Health; Ama Owusu-Dommey, Breanna McArdle, Emily Youngers, Sam Hawkins, Public Health Division, Oregon Health Authority; Kylie Seeley, Oregon Health & Science University School of Medicine; Katie Dyer, Karen Leib, Terri McMinn, Danielle Ndi, John Ujwok, Gail Hughett, Emmanuel Sackey, Kathy Billings, Anise Elie, Manideepthi Pemmaraju, Vanderbilt University Medical Center; Amanda Carter, Andrea Price, Andrew Haraghey, Ashley Swain, Caitlin Shaw, Ian Buchta, Jake Ortega, Laine McCullough, Ryan Chatelain, Tyler Riedesel, Salt Lake County Health Department; Alvin Shultz, Robert W. Pinner, Rainy Henry, Sonja Mali Nti-Berko, Susan Gantt, CDC; Mimi Huynh, Council of State and Territorial Epidemiologists.

Funding Information:
All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. William Schaffner reports consultant fees from VBI Vaccines, outside the submitted work. Eli Shiltz and Laurie M. Billing report grant funding from the Council of State and Territorial Epidemiologists (CSTE) for the population-based Influenza Hospitalization Surveillance Project (IHSP) and COVID-NET activities. Lauren Leegwater and Sue Kim report grant support from CSTE through the Michigan Department of Health and Human Services. Andy Weigel and Kenzie Teno report grant support from CSTE for data collection and participation in ongoing meetings related to COVID-19 hospitalization surveillance. Evan J. Anderson reports grants for clinical trials from Pfizer, Merck, PaxVax, Micron, Sanofi-Pasteur, Janssen, MedImmune, and GSK; consulting fees from Sanofi-Pasteur, Pfizer, Janssen, and Medscape; personal fees for data safety monitoring board participation from Kentucky Bioprocessing, Inc. and Sanofi-Pasteur; and institutional funding from the National Institutes of Health to conduct clinical trials of Moderna and Janssen COVID-19 vaccines. No other potential conflicts of interest were disclosed.

ASJC Scopus subject areas

  • Genetics

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