{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T05:26:44Z","timestamp":1674624404156},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Taverna workbench is an environment for construction, visualization and execution of bioinformatic workflows that integrate specialized tools available through the internet. It is gaining popularity fast, because of supporting the most important bioinformatic services and its simple, yet robust graphical notation. Here we present XQTav\u2014an extension of Taverna that provides full integration with XQuery (the query language for XML) engine. XQTav allows execution of XQuery scripts in Taverna workflow diagrams. All existing Taverna processors can be accessed in the XQuery scripts. This provides an alternative way of specifying subworkflows in Taverna and is useful when one deals with query-like algorithms (e.g. filters and inner joins). Moreover, XQtav may be used to automatically generate an XQuery script that is equivalent to Taverna's workflow. This constitutes another way of creating and enacting bioinformatic workflows: overall structure of a diagram is drawn in Taverna environment, XQuery code is generated and possibly adjusted by hand. It can be executed by XQuery engines or incorporated into other software environments.<\/jats:p>\n               <jats:p>Availability: XQtav is an open source software. It may be downloaded from . The page also contains various tutorials and examples, including the one described in this report.<\/jats:p>\n               <jats:p>Contact: \u00a0sroka@mimuw.edu.pl, a.kierzek@surrey.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl101","type":"journal-article","created":{"date-parts":[[2006,3,22]],"date-time":"2006-03-22T02:33:29Z","timestamp":1142994809000},"page":"1280-1281","source":"Crossref","is-referenced-by-count":1,"title":["XQTav: an XQuery processor for Taverna environment"],"prefix":"10.1093","volume":"22","author":[{"given":"Jacek","family":"Sroka","sequence":"first","affiliation":[{"name":"Warsaw University 1 \u00a0 1 \u00a0 \u00a0 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grzegorz","family":"Kaczor","sequence":"additional","affiliation":[{"name":"Warsaw University 1 \u00a0 1 \u00a0 \u00a0 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jerzy","family":"Tyszkiewicz","sequence":"additional","affiliation":[{"name":"Warsaw University 1 \u00a0 1 \u00a0 \u00a0 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrzej M.","family":"Kierzek","sequence":"additional","affiliation":[{"name":"SBMS, University of Surrey 2 \u00a0 2 \u00a0 \u00a0 Guildford, GU2 7XH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,3,21]]},"reference":[{"key":"2023012408302425800_b1","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1093\/bioinformatics\/17.2.115","article-title":"XML, bioinformatics and data integration","volume":"17","author":"Achard","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012408302425800_b2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023012408302425800_b3","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gki070","article-title":"The Universal Protein Resource (UniProt)","volume":"33","author":"Bairoch","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408302425800_b4","article-title":"XQuery 1.0: An XML Query Language","author":"Boag","year":"2005"},{"key":"2023012408302425800_b5","article-title":"XML for molecular biology as compiled by Paul Gordon","author":"Gordon","year":"2003"},{"key":"2023012408302425800_b6","article-title":"Interactive web applications with Xquery","author":"Ivanov","year":"2003"},{"key":"2023012408302425800_b7","doi-asserted-by":"crossref","first-page":"3045","DOI":"10.1093\/bioinformatics\/bth361","article-title":"Taverna: a tool for the composition and enactment of bioinformatics workflows","volume":"20","author":"Oinn","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012408302425800_b8","article-title":"XQTav Reference Guide","author":"Sroka","year":"2006"},{"key":"2023012408302425800_b9","doi-asserted-by":"crossref","first-page":"i303","DOI":"10.1093\/bioinformatics\/bth944","article-title":"Exploring Williams\u2013Beuren syndrome using myGrid","volume":"20","author":"Stevens","year":"2003","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/10\/1280\/48838233\/bioinformatics_22_10_1280.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/10\/1280\/48838233\/bioinformatics_22_10_1280.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T08:32:29Z","timestamp":1674549149000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/10\/1280\/237400"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,3,21]]},"references-count":9,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2006,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl101","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,5,15]]},"published":{"date-parts":[[2006,3,21]]}}}