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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  
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.  ...  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.  ...  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  
Another important component of CIEIPOS, which is not part of traditional biological data centers such as NCBI and EBI, is omics informatics.  ...  Implementation outlook of CIEIPOS in hardware and network is discussed. biological database services, omics informatics, information engineering infrastructure for pan-omics studies Citation: Zhu W M,  ...  The major issue of both search engines is the lack of a top level navigation mechanism for the ease of browsing.  ... 
doi:10.1007/s11427-013-4440-1 pmid:23526387 fatcat:mxamluxjdzbnfdgjdwncvixyxe

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  
marine shotgun metagenomics datasets developed. ● Cloud deployment of pipelines to increase compute capacity. ● New data analysis outputs that will feed the databases developed as part of this work package  ...  Language (CWL) to enable reproducibility, facilitate comparisons and enhance development agility. ● Benchmark datasets generated for evaluating amplicon analyses across a range of biomes and 6 different  ...  To this end, we have exposed all of the sample metadata and analysis summaries within the EBI search (36) , which provides a search infrastructure for enabling simple faceted searches, and implemented  ... 
doi:10.5281/zenodo.3228301 fatcat:nb2r64odubauno62doau6n5lr4

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  
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  ...  New technologies are revolutionising biological research and its applications by making it easier and cheaper to generate ever-greater volumes and types of data.  ...  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

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.  ...  Here we describe LAILAPS (, an IR system designed to link plant genomic data in the context of phenotypic attributes for a detailed forward genetic research.  ...  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

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  
In addition to the traditional web form based interfaces, APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpress.  ...  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

IntegromeDB: an integrated system and biological search engine

Michael Baitaluk, Sergey Kozhenkov, Yulia Dubinina, Julia Ponomarenko
2012 BMC Genomics  
However, general-purpose search engines are not specialized for the search of biological data.  ...  With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers.  ...  Acknowledgements This work was supported by the National Institute of Health grants R01GM084881 to MB and R01GM085325 to JP. Author details  ... 
doi:10.1186/1471-2164-13-35 pmid:22260095 pmcid:PMC3293773 fatcat:wrjk3un4urf2vd3psw4xpvozoe

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  
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 European Bioinformatics Institute ( archives, curates and analyses life sciences data produced by researchers throughout the world, and makes these data available for re-use  ...  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 European Bioinformatics Institute's data resources 2014

Catherine Brooksbank, Mary Todd Bergman, Rolf Apweiler, Ewan Birney, Janet Thornton
2013 Nucleic Acids Research  
Molecular Biology has been at the heart of the 'big data' revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of  ...  The authors are also indebted to hundreds of thousands of scientists who have submitted data and annotation to the shared data collections.  ...  ACKNOWLEDGEMENTS The EMBL-EBI is indebted to the support of its funders: EMBL's member states, the European Commission, the Wellcome Trust, the UK Research Councils, the US National Institutes of Health  ... 
doi:10.1093/nar/gkt1206 pmid:24271396 pmcid:PMC3964968 fatcat:7dgar73rqjhwzci6shbolfpvfq

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  
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.  ...  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  ...  Through the European Open Science Cloud, we are making our data services more accessible in external cloud services.  ... 
doi:10.1093/nar/gkx1154 pmid:29186510 pmcid:PMC5753251 fatcat:ubzlegb2kjcltbtdftwsh6mlja

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  ...  The HMMER website now provides a single point of entry for those wishing to access the profile HMM libraries supported by EMBL-EBI.  ... 
doi:10.1093/nar/gky448 pmid:29905871 pmcid:PMC6030962 fatcat:k3vsfblq5ba3tkdhcp57ufiq5q

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.  ...  The EB-eye can be accessed over the web or programmatically using a SOAP Web Services interface.  ...  As well as the integration of search capabilities the web service can also be used to provide access to the data network, for example in the EBI Sequence Similarity Search Services (  ... 
doi:10.1093/bib/bbp065 pmid:20150321 pmcid:PMC2905521 fatcat:qebowfm43fauvno5ncgtxe5dom

Information Retrieval in Life Sciences: The LAILAPS Search Engine

Matthias Lange, Jinbo Chen, Uwe Scholz
2012 Jahrestagung der Gesellschaft für Informatik  
Miehe as administrator of the project website, Tomcat engine, and Maven developer pipeline. This work was supported by the European Commission within its 7th Framework Program, contract number 283496.  ...  The LAILAPS Search Engine In this contribution we apply the LAILAPS search engine [LSB + 10] as a system that combines a range of well discriminating database relevance features within a probabilistic  ...  The system was designed to provide the look and feel of a web search engine. To support a platform independent implementation and scalable service, we decided to use a JAVA 3-tier web application.  ... 
dblp:conf/gi/LangeCS12 fatcat:ylex65ivf5ffhnhpcusybjkw5a

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.  ...  Finally, we would like to thank all the scientists, past, present and future, who deposit their data in the BioImage Archive.  ... 
doi:10.1101/2021.12.17.473169 fatcat:77atec3jszenhnnpy6tup65fne
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