{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T05:40:42Z","timestamp":1710481242057},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2641,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The work presented here describes the \u2018anatomical Gene-Expression Mapping (aGEM)\u2019 Platform, a development conceived to integrate phenotypic information with the spatial and temporal distributions of genes expressed in the mouse. The aGEM Platform has been built by extending the Distributed Annotation System (DAS) protocol, which was originally designed to share genome annotations over the WWW. DAS is a client-server system in which a single client integrates information from multiple distributed servers.<\/jats:p><jats:p>Results: The aGEM Platform provides information to answer three main questions. (i) Which genes are expressed in a given mouse anatomical component? (ii) In which mouse anatomical structures are a given gene or set of genes expressed? And (iii) is there any correlation among these findings? Currently, this Platform includes several well-known mouse resources (EMAGE, GXD and GENSAT), hosting gene-expression data mostly obtained from in situ techniques together with a broad set of image-derived annotations.<\/jats:p><jats:p>Availability: The Platform is optimized for Firefox 3.0 and it is accessed through a friendly and intuitive display: http:\/\/agem.cnb.csic.es<\/jats:p><jats:p>Contact: \u00a0natalia@cnb.csic.es<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at http:\/\/bioweb.cnb.csic.es\/VisualOmics\/aGEM\/home.html and http:\/\/bioweb.cnb.csic.es\/VisualOmics\/index_VO.html and Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp422","type":"journal-article","created":{"date-parts":[[2009,7,11]],"date-time":"2009-07-11T00:13:56Z","timestamp":1247271236000},"page":"2566-2572","source":"Crossref","is-referenced-by-count":3,"title":["aGEM: an integrative system for analyzing spatial-temporal gene-expression information"],"prefix":"10.1093","volume":"25","author":[{"given":"Natalia","family":"Jim\u00e9nez-Lozano","sequence":"first","affiliation":[{"name":"GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit of the National Centre for Biotechnology (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain"}]},{"given":"Joan","family":"Segura","sequence":"additional","affiliation":[{"name":"GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit of the National Centre for Biotechnology (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain"}]},{"given":"Jos\u00e9 Ram\u00f3n","family":"Mac\u00edas","sequence":"additional","affiliation":[{"name":"GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit of the National Centre for Biotechnology (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain"}]},{"given":"Juanjo","family":"Vega","sequence":"additional","affiliation":[{"name":"GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit of the National Centre for Biotechnology (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain"}]},{"given":"Jos\u00e9 Mar\u00eda","family":"Carazo","sequence":"additional","affiliation":[{"name":"GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit of the National Centre for Biotechnology (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2009,7,9]]},"reference":[{"key":"2023013112124639400_B1","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1385\/NI:1:4:309","article-title":"EMAP and EMAGE: a framework for understanding spatially organized data","volume":"1","author":"Baldock","year":"2003","journal-title":"Neuroinformatics"},{"key":"2023013112124639400_B2","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1186\/gb-2005-6-4-108","article-title":"Anatomical ontologies: names and places in biology","volume":"6","author":"Baldock","year":"2005","journal-title":"Genome Biol."},{"key":"2023013112124639400_B3","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkl983","article-title":"Mouse Tumor Biology Database (MTB): status update and future directions","volume":"35","author":"Begley","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112124639400_B4","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1093\/bioinformatics\/btg400","article-title":"Formalization of mouse embryo anatomy","volume":"20","author":"Burger","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013112124639400_B5","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1002\/(SICI)1098-1004(200001)15:1<62::AID-HUMU13>3.0.CO;2-R","article-title":"Future vision of the GDB human genome database","volume":"15","author":"Cuticchia","year":"2000","journal-title":"Hum. Mutant."},{"key":"2023013112124639400_B6","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-2-7","article-title":"The distributed annotation system","volume":"2","author":"Dowell","year":"2001","journal-title":"BMC Bioinformatics 2001"},{"key":"2023013112124639400_B7","doi-asserted-by":"crossref","first-page":"1568","DOI":"10.1093\/bioinformatics\/btl650","article-title":"ProServer: a simple, extensible Perl DAS server","volume":"23","author":"Finn","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112124639400_B8","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2023013112124639400_B9","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1038\/ng0894-463","article-title":"PAX6 gene dosage effect in a family with congenital cataracts, aniridia, anophthalmia and central nervous system defects","volume":"7","author":"Glaser","year":"1994","journal-title":"Nat. Genet."},{"key":"2023013112124639400_B10","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/372045a0","article-title":"Alzheimer's disease. Risky apolipoprotein in brain","volume":"373","author":"Goedert","year":"1994","journal-title":"Nature"},{"key":"2023013112124639400_B11","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1038\/nature02033","article-title":"A gene expression atlas of the central nervous system based on bacterial artificial chromosomes","volume":"425","author":"Gong","year":"2003","journal-title":"Nature"},{"key":"2023013112124639400_B12","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1093\/nar\/30.1.52","article-title":"Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders","volume":"30","author":"Hamosh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023013112124639400_B13","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2005-6-3-r29","article-title":"The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data","volume":"6","author":"Hayamizu","year":"2005","journal-title":"Genome Biol."},{"key":"2023013112124639400_B14","doi-asserted-by":"crossref","first-page":"D847","DOI":"10.1093\/nar\/gkm797","article-title":"4DXpress: a database for cross-species expression pattern comparisons","volume":"36","author":"Haudry","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112124639400_B15","doi-asserted-by":"crossref","first-page":"D610","DOI":"10.1093\/nar\/gkl996","article-title":"Ensembl 2007","volume":"35","author":"Hubbard","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112124639400_B16","doi-asserted-by":"crossref","first-page":"3198","DOI":"10.1093\/bioinformatics\/bti506","article-title":"a perfect pair for protein feature visualization","volume":"21","author":"Jones","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013112124639400_B17","doi-asserted-by":"crossref","first-page":"R229","DOI":"10.1186\/gb-2007-8-10-r229","article-title":"Simplified ontologies allowing comparison of developmental mammalian gene expression","volume":"8","author":"Kruger","year":"2007","journal-title":"Genome Biol."},{"key":"2023013112124639400_B18","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1093\/nar\/26.1.94","article-title":"GDB: the human genome database","volume":"26","author":"Letovsky","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"2023013112124639400_B19","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/372092a0","article-title":"Amyloid-associated proteins alpha 1-antichymotrypsin and apolipoprotein E promote assembly of Alzheimer beta-protein into filaments","volume":"372","author":"Ma","year":"1994","journal-title":"Nature"},{"key":"2023013112124639400_B20","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/j.jsb.2007.02.004","article-title":"Integrating electron microscopy information into existing Distributed Annotation Systems","volume":"158","author":"Macias","year":"2007","journal-title":"J. Struct. Biol."},{"key":"2023013112124639400_B21","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1093\/bioinformatics\/bti1106","article-title":"Adding some SPICE to DAS","volume":"2","author":"Prlic","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013112124639400_B22","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1126\/science.8091224","article-title":"A database for mouse development","volume":"265","author":"Ringwald","year":"1994","journal-title":"Science"},{"key":"2023013112124639400_B23","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1093\/nar\/27.1.106","article-title":"GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group","volume":"27","author":"Ringwald","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023013112124639400_B24","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/S0091-679X(08)61406-5","article-title":"The Worm Community System, release 2.0 (WCSr2)","volume":"48","author":"Shoman","year":"1995","journal-title":"Methods Cell Biol."},{"key":"2023013112124639400_B25","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1093\/nar\/27.1.35","article-title":"The Genome Sequence DataBase: towards an integrated functional genomics resource","volume":"27","author":"Skupski","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023013112124639400_B26","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1006\/dbio.1998.8921","article-title":"Mouse Alx3: an aristaless-like homeobox gene expressed during embryogenesis in ectomesenchyme and lateral plate mesoderm","volume":"199","author":"ten Berge","year":"1998","journal-title":"Dev. Biol."},{"key":"2023013112124639400_B27","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1186\/gb-2006-7-5-402","article-title":"The success (or not) of HUGO nomenclature","volume":"7","author":"Tamames","year":"2006","journal-title":"Genome Biol."},{"key":"2023013112124639400_B28","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-88418-4","volume-title":"The House Mouse: Atlas of Embryonic Development.","author":"Theiler","year":"1989"},{"key":"2023013112124639400_B29","doi-asserted-by":"crossref","first-page":"D169","DOI":"10.1093\/nar\/gkn664","article-title":"The Universal Protein Resource (UniProt) 2009","volume":"37","author":"The UniProt Consortium","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023013112124639400_B30","doi-asserted-by":"crossref","first-page":"D860","DOI":"10.1093\/nar\/gkm938","article-title":"EMAGE: Edinburgh Mouse Atlas of Gene Expression: 2008 update","volume":"36","author":"Venkataraman","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112124639400_B31","doi-asserted-by":"crossref","first-page":"D552","DOI":"10.1093\/nar\/gkh029","article-title":"GenePaint.org: an atlas of gene expression patterns in the mouse embryo","volume":"32","author":"Visel","year":"2004","journal-title":"Nucleic Acid Res."},{"key":"2023013112124639400_B32","doi-asserted-by":"crossref","first-page":"D13","DOI":"10.1093\/nar\/gkm1000","article-title":"Database resources of the National Center for Biotechnology Information","volume":"36","author":"Wheeler","year":"2008","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/19\/2566\/48995175\/bioinformatics_25_19_2566.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/19\/2566\/48995175\/bioinformatics_25_19_2566.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T05:07:16Z","timestamp":1710479236000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/19\/2566\/179846"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,7,9]]},"references-count":32,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2009,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp422","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,10,1]]},"published":{"date-parts":[[2009,7,9]]}}}