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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  
We present the EBI Search engine, referred to here as 'EBI Search', an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities.  ...  The European Bioinformatics Institute (EMBL-EBI-- provides free and unrestricted access to data across all major areas of biology and biomedicine.  ...  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 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  
We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities.  ...  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  ...  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

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

2019 Nucleic Acids Research  
The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities  ...  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

Information engineering infrastructure for life sciences and its implementation in China

WeiMin Zhu, YunPing Zhu, XiaoLing Yang
2013 Science China Life Sciences  
Biological data, represented by the data from omics platforms, are accumulating exponentially.  ...  The demand for such power in omics studies is argued as the fundamental function to meet for CIEIPOS.  ...  Both NCBI and EBI are continuously working at improving functions and usability of their search engines.  ... 
doi:10.1007/s11427-013-4440-1 pmid:23526387 fatcat:mxamluxjdzbnfdgjdwncvixyxe

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  
From the user's point of view, these Web Services provide the same functionality as the browser-based forms.  ...  The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997.  ...  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

LAILAPS: The Plant Science Search Engine

Maria Esch, Jinbo Chen, Christian Colmsee, Matthias Klapperstück, Eva Grafahrend-Belau, Uwe Scholz, Matthias Lange
2014 Plant and Cell Physiology  
The LAILAPS search engine allows fuzzy querying for candidate genes linked to specific traits over a loosely integrated system of indexed and interlinked genome databases.  ...  Information retrieval (IR) has become an all-encompassing bioinformatics methodology for extracting knowledge from complex, heterogeneous and distributed databases, and therefore can be a useful tool for  ...  Furthermore, we thank all transPLANT partners for fruitful discussions and providing mapping files to their plant genomic resources. Disclosures The authors declare no conflicts of interest.  ... 
doi:10.1093/pcp/pcu185 pmid:25480116 pmcid:PMC4301746 fatcat:7tlrxllcdzgsjgpmhxsnufelhu

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  
pdbe-kb), which collates functional annotations and predictions for structure data in the Protein Data Bank.  ...  EMBL-EBI maintains over 150 analytical bioinformatics tools that complement our data resources.  ...  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

ELIXIR-EXCELERATE D6.3: Report describing a set of tools, pipelines and search engine for interrogation of marine metagenomic data

Alex Mitchell, Maxim Scheremetjew, Gianluca De Moro, Bruno Fosso, Monica Santamaria, Graziano Pesole, Shriya Raj, Lars Ailo Bongo, Nils Peder Willassen, Robert D. Finn
2019 Zenodo  
. ● Examples generated for federating searches across resource programmatic interfaces. ● Wide range of different training activities and material developed. ● Major interaction with Compute (WP4) and  ...  ● Pipelines expanded to increase scope of analysis, tools updated and tailoring of analysis to meet the demands of the Marine Metagenomics community. ● Analysis pipelines described in the Common Workflow  ...  For example, " Retrieve all related sulfatase sequences sequences in all assembled marine samples stored in EMBL-EBI MGnify platform" .  ... 
doi:10.5281/zenodo.3228301 fatcat:nb2r64odubauno62doau6n5lr4

Fast and efficient searching of biological data resources--using EB-eye

F. Valentin, S. Squizzato, M. Goujon, H. McWilliam, J. Paern, R. Lopez
2010 Briefings in Bioinformatics  
The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI.  ...  This allows its search and retrieval capabilities to be exploited in workflows and analytical pipe-lines. The EB-eye is a novel alternative to existing biological search and retrieval engines.  ...  EB-eye improves the user's experience by providing a search engine that presents consistent result pages and navigation across all the data resources maintained by EMBL-EBI.  ... 
doi:10.1093/bib/bbp065 pmid:20150321 pmcid:PMC2905521 fatcat:qebowfm43fauvno5ncgtxe5dom

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  
Sequence searching and protein function analysis: WSFasta, WSWUBlast, WSInterProScan The EBI provides Web Services for sequence similarity tools such as Fasta (13) , WUBlast (14) and the protein function  ...  These include tools for sequence and literature data retrieval, sequence similarity search services, protein function analysis and structural analysis tools that access the Macromolecular Structure Database  ... 
doi:10.1093/nar/gki491 pmid:15980463 pmcid:PMC1160251 fatcat:2odbedc7xzfnnldtxk7spoqxry

The European Bioinformatics Institute's data resources

Catherine Brooksbank, Graham Cameron, Janet Thornton
2009 Nucleic Acids Research  
All of the resources described here can be accessed from the EMBL-EBI website:  ...  It has also put the need for unrestricted access to biological data at the centre of biology.  ...  of thousands of scientists who have submitted data and annotation to the shared data collections.  ... 
doi:10.1093/nar/gkp986 pmid:19934258 pmcid:PMC2808956 fatcat:lha7vmv3fnhipb7kunhmvunveu

The BioImage Archive - home of life-sciences microscopy data [article]

Matthew Hartley, Gerard Kleywegt, Ardan Patwardhan, Ugis Sarkans, Jason R Swedlow, Alvis Brazma
2021 bioRxiv   pre-print
Despite the importance of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities.  ...  The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap.  ...  We also thank the IDR, EMPIAR, BioStudies and BioImage Archive teams, EMBL-EBI's Bioimaging project team and the storage team within EMBL-EBI's Technical Services Cluster.  ... 
doi:10.1101/2021.12.17.473169 fatcat:77atec3jszenhnnpy6tup65fne

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.  ...  In Europe and worldwide, EMBL-EBI and other scientific data providers are addressing the challenges that arise from this growth through collaboration and cooperation (see Figure 2 ).  ... 
doi:10.1093/nar/gkx1154 pmid:29186510 pmcid:PMC5753251 fatcat:ubzlegb2kjcltbtdftwsh6mlja

Introduction on Several Popular Nucleic Acids Databases

Changmin Liao
2013 Journal of Computer Engineering and Informatics  
Nucleic acids are major biological molecules essential for life, and everyday, there are large number of nucleic acids sequences that are released and searched.  ...  Now, many nucleic acids databases were used to assembly and distribute structural information related nucleic acids on the internet.  ...  China) for his critical reading to my manuscript.  ... 
doi:10.5963/jcei0102005 fatcat:3uwyh5eakbdfriznaeuv2jnsdi

HMMER web server: 2018 update

Simon C Potter, Aurélien Luciani, Sean R Eddy, Youngmi Park, Rodrigo Lopez, Robert D Finn
2018 Nucleic Acids Research  
To help users explore the biological context of their results, and to discover new data resources, search results are now supplemented with cross references to other EMBL-EBI databases.  ...  The HMMER webserver [ hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using  ...  EBI-Search powers text searches from the EMBL-EBI website and many of the resources held at the institute via its API layer.  ... 
doi:10.1093/nar/gky448 pmid:29905871 pmcid:PMC6030962 fatcat:k3vsfblq5ba3tkdhcp57ufiq5q
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