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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. 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
more » ... rch (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:// 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.
doi:10.1093/nar/gkt376 pmid:23671338 pmcid:PMC3692137 fatcat:wb6vvm34dnfphcqexbxudruomq

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. These include sequence similarity search services (https://www.ebi. such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https: // such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools ( such as InterProScan. Through these services users can search
more » ... instream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces ( uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https: // and the dbfetch retrieval service ( further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, Inter-ProScan 5 and PfamScan, new categories such as RNA analysis tools ( rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.
doi:10.1093/nar/gkv279 pmid:25845596 pmcid:PMC4489272 fatcat:kgooeoagc5ailfjlzkwck2wgk4

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 nucleotide and protein sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures,
more » ... s well as the life science literature. 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.
doi:10.1093/nar/gkx359 pmid:28472374 pmcid:PMC5570174 fatcat:7vlgpmowhrgcvjhqn2sk7w4hse

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-- provides free and unrestricted access to data across all major areas of biology and biomedicine. Searching and extracting knowledge across these domains requires a fast and scalable solution that addresses the requirements of domain experts as well as casual users. 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
more » ... l capabilities. API integration provides access to analytical tools, allowing users to further investigate the results of their search. 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, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, together with relevant life science literature.
doi:10.1093/nar/gkv316 pmid:25855807 pmcid:PMC4489232 fatcat:m6wp7w7c4zdbrpsunzxlzqy4mi

Genotoxic effects of daily personal exposure to particle mass and number concentrations on buccal cells

Daniela S. de Almeida, Silvano César da Costa, Marcos Ribeiro, Camila A.B. Moreira, Alexandra Beal, Rafaela Squizzato, Anderson Paulo Rudke, Sameh Adib Abou Rafee, Jorge A. Martins, Graciana Freitas Palioto, Prashant Kumar, Leila D. Martins
2018 Atmospheric Environment  
Table 3 Squizzato et al. (2016) and Heal et al. (2005) show stationary source measurements of PM 2.5 in mid-size to large cities in Asia and Europe.  ... 
doi:10.1016/j.atmosenv.2017.12.021 fatcat:fpfjmv5jhre77pfohdd5nx3p2m

Omics Discovery Index - Discovering and Linking Public Omics Datasets [article]

Yasset Perez-Riverol, Mingze Bai, Felipe Leprevost, Silvano Squizzato, Young Mi Park, Ove Kenneth Haug, Adam J. Carroll, Dylan Spalding, Justin Paschall, Mingxun Wang, Noemi del-Toro, Tobias Ternent (+14 others)
2016 bioRxiv   pre-print
Biomedical data, in particular omics datasets are being generated at an unprecedented rate. This is due to the falling costs of generating experimental data, improved accuracy and better accessibility to different omics platforms such as genomics, proteomics and metabolomics. As a result, the number of deposited datasets in public repositories originating from various omics approaches has increased dramatically in recent years. This increase in public data deposition of omics results is a good
more » ... tarting point, but opens up a series of new challenges. For example the research community must now find more efficient ways for storing, organizing and providing access to biomedical data across platforms. These challenges range from achieving a common representation framework for the datasets and the associated metadata from different omics fields, to the availability of efficient methods, protocols and file formats for data exchange between multiple repositories. Therefore, there is a great need for development of new platforms and applications to make possible to search datasets across different omics fields, making such information accessible to the end-user. In this context, we introduce the Omics Discovery Index (OmicsDI -, an integrated and open source platform facilitating the access and dissemination of omics datasets. OmicsDI provides a unique infrastructure to integrate datasets coming from multiple omics studies, including at present proteomics, genomics and metabolomics, as a distributed resource.
doi:10.1101/049205 fatcat:2aj2k6of3rde5aumoqjgiv53lm

Assembly information services in the European Nucleotide Archive

Nima Pakseresht, Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Tamer Gur, Mikyung Jang, Simon Kay, Rasko Leinonen, Weizhong Li (+18 others)
2013 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www. is a repository for the world public domain nucleotide sequence data output. ENA content covers a spectrum of data types including raw reads, assembly data and functional annotation. ENA has faced a dramatic growth in genome assembly submission rates, data volumes and complexity of datasets. This has prompted a broad reworking of assembly submission services, for which we now reach the end of a major programme of work and many
more » ... ncements have already been made available over the year to components of the submission service. In this article, we briefly review ENA content and growth over 2013, describe our rapidly developing services for genome assembly information and outline further major developments over the last year.
doi:10.1093/nar/gkt1082 pmid:24214989 pmcid:PMC3965037 fatcat:sddhoeztgfdkhbyx3zrms3ajza

Discovering and linking public omics data sets using the Omics Discovery Index

Yasset Perez-Riverol, Mingze Bai, Felipe da Veiga Leprevost, Silvano Squizzato, Young Mi Park, Kenneth Haug, Adam J Carroll, Dylan Spalding, Justin Paschall, Mingxun Wang, Noemi del-Toro, Tobias Ternent (+22 others)
2017 Nature Biotechnology  
doi:10.1038/nbt.3790 pmid:28486464 pmcid:PMC5831141 fatcat:4g3yqqyngjgfbotez4oc7pth2a

InterPro in 2017—beyond protein family and domain annotations

Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft (+35 others)
2016 Nucleic Acids Research  
Please refer to any applicable terms of use of the publisher.
doi:10.1093/nar/gkw1107 pmid:27899635 pmcid:PMC5210578 fatcat:wa7z5pgpuffnrh5bf5ycimw7kq

BioModels: expanding horizons to include more modelling approaches and formats

Mihai Glont, Tung V N Nguyen, Martin Graesslin, Robert Hälke, Raza Ali, Jochen Schramm, Sarala M Wimalaratne, Varun B Kothamachu, Nicolas Rodriguez, Maciej J Swat, Jurgen Eils, Roland Eils (+5 others)
2017 Nucleic Acids Research  
We are grateful to OmicsDI developers Gaurhari Dass and Yasset Perez-Riverol, as well as EBI Search developers Silvano Squizzato and Nicola Buso for their support.  ... 
doi:10.1093/nar/gkx1023 pmid:29106614 pmcid:PMC5753244 fatcat:3e4bpcbu7bh2dklf7v4vxeduwu

The Tiny Instrument Element [chapter]

Francesco Lelli, Cesare Pautasso
2009 Lecture Notes in Computer Science  
Acknowledgements We would like to thank Pietro Molini, Eric Frizziero and Silvano Squizzato for their participation in the Case Study.  ... 
doi:10.1007/978-3-642-01671-4_27 fatcat:qvtyckf6mrcghnjoc73ue3lita

Transcriptional data: a new gateway to drug repositioning?

Francesco Iorio, Timothy Rittman, Hong Ge, Michael Menden, Julio Saez-Rodriguez
2013 Drug Discovery Today  
We thank Clare Pacini, Mathew Garnett, Silvano Squizzato, Pedro Ballester, Thomas Klabunde, Sonja Eidorn, Constantine Alifrangis, Aidan Macnamara, Niccolò Bolli, Annalisa Buniello and Annalisa Mupo for  ... 
doi:10.1016/j.drudis.2012.07.014 pmid:22897878 pmcid:PMC3625109 fatcat:jjr6vyqeordj5l4tae6ogegzku

The many faces of the integration of instruments and the grid

F. Lelli, E. Frizziero, M. Gulmini, G. Maron, S. Orlando, A. Petrucci, S. Squizzato
2007 International Journal of Web and Grid Services  
Silvano Squizzato is a Software Engineer at the National Laboratories of Legnaro -INFN, Italy.  ... 
doi:10.1504/ijwgs.2007.014953 fatcat:ua47r2hzkzg7jakinphchiuz6a


Silvano Montaldo, direttore del Museo di Antropologia criminale Cesare Lombroso di Torino, con la relazione "Giubileo, morte, celebrazione ed esecrazione di Cesare Lombroso", ha parlato dello strano e  ...  monaca induista (Dal cibo nascono le creature; dalla pioggia è generato il cibo), Elena Viviani Seichin, monaca Zen Soto (La cucina dei monasteri zen, ovvero come cucinare la propria vita), don Paolo Squizzato  ... 
doi:10.7340/anuac2239-625x-125 fatcat:2etnuk4oh5gg3bzxoavn3z5hee