{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,4,28]],"date-time":"2024-04-28T22:40:10Z","timestamp":1714344010041},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: The integration between BioDAS ProServer and Automated Sequence Annotation Pipeline (ASAP) provides an interface for querying diverse annotation sources, chaining and linking results, and standardizing the output using the Distributed Annotation System (DAS) protocol. This interface allows pipeline plans in ASAP to be integrated into any system using HTTP and also allows the information returned by ASAP to be included in the DAS registry for use in any DAS-aware system. Three example implementations have been developed: the first accesses TRANSFAC information to automatically create gene sets for the Coordinated Gene Activity in Pattern Sets (CoGAPS) algorithm; the second integrates annotations from multiple array platforms and provides unified annotations in an R environment; and the third wraps the UniProt database for integration with the SPICE DAS client.<\/jats:p><jats:p>Availability: Source code for ASAP 2.7 and the DAS 1.6 interface is available under the GNU public license. Proserver 2.20 is free software available from SourceForge. Scripts for installation and configuration on Linux are provided at our website: http:\/\/www.rits.onc.jhmi.edu\/dbb\/custom\/A6\/<\/jats:p><jats:p>Contact: Speier@mii.ucla.edu or mfo@jhu.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts530","type":"journal-article","created":{"date-parts":[[2012,9,4]],"date-time":"2012-09-04T00:49:26Z","timestamp":1346719766000},"page":"2858-2859","source":"Crossref","is-referenced-by-count":4,"title":["Updating annotations with the distributed annotation system and the automated sequence annotation pipeline"],"prefix":"10.1093","volume":"28","author":[{"given":"William","family":"Speier","sequence":"first","affiliation":[{"name":"1 Medical Imaging Informatics Group, University of California, Los Angeles, CA, 2Department of Bioengineering, University of California, Los Angeles, CA, and 3Department of Oncology and Division of Oncology Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA"},{"name":"1 Medical Imaging Informatics Group, University of California, Los Angeles, CA, 2Department of Bioengineering, University of California, Los Angeles, CA, and 3Department of Oncology and Division of Oncology Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA"},{"name":"1 Medical Imaging Informatics Group, University of California, Los Angeles, CA, 2Department of Bioengineering, University of California, Los Angeles, CA, and 3Department of Oncology and Division of Oncology Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael F.","family":"Ochs","sequence":"additional","affiliation":[{"name":"1 Medical Imaging Informatics Group, University of California, Los Angeles, CA, 2Department of Bioengineering, University of California, Los Angeles, CA, and 3Department of Oncology and Division of Oncology Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,9,3]]},"reference":[{"key":"2023012513151147800_bts530-B1","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":"2023012513151147800_bts530-B2","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-2-7","article-title":"The distributed annotation 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