{"id":"https://openalex.org/W2119100163","doi":"https://doi.org/10.2390/biecoll-jib-2008-92","title":"Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database","display_name":"Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database","publication_year":2008,"publication_date":"2008-01-01","ids":{"openalex":"https://openalex.org/W2119100163","doi":"https://doi.org/10.2390/biecoll-jib-2008-92","mag":"2119100163","pmid":"https://pubmed.ncbi.nlm.nih.gov/20134060"},"language":"en","primary_location":{"id":"pmid:20134060","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20134060","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.2390/biecoll-jib-2008-92","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074172886","display_name":"Mounia Belmamoune","orcid":null},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Belmamoune, Mounia","raw_affiliation_strings":["Section Imaging and Bioinformatics, Leiden Institute of Computer Science (LIACS), Niels Bohrweg 1, 2333 CA Leiden, The Netherlands. mounia@liacs.nl"],"affiliations":[{"raw_affiliation_string":"Section Imaging and Bioinformatics, Leiden Institute of Computer Science (LIACS), Niels Bohrweg 1, 2333 CA Leiden, The Netherlands. mounia@liacs.nl","institution_ids":["https://openalex.org/I121797337"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022631255","display_name":"Fons J. Verbeek","orcid":"https://orcid.org/0000-0003-2445-8158"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Verbeek, Fons J.","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074172886"],"corresponding_institution_ids":["https://openalex.org/I121797337"],"apc_list":null,"apc_paid":null,"fwci":0.4149,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.64659314,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"5","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9782999753952026,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9746000170707703,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/zebrafish","display_name":"Zebrafish","score":0.880081295967102},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5307856798171997},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4656091034412384},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.4628884196281433},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4563766419887543},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.43190404772758484},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.42970675230026245},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.4275834560394287},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41945844888687134},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3926883935928345},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1713389754295349}],"concepts":[{"id":"https://openalex.org/C2776878037","wikidata":"https://www.wikidata.org/wiki/Q169444","display_name":"Zebrafish","level":3,"score":0.880081295967102},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5307856798171997},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4656091034412384},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.4628884196281433},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4563766419887543},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.43190404772758484},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.42970675230026245},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.4275834560394287},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41945844888687134},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3926883935928345},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1713389754295349},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004625","descriptor_name":"Embryo, Nonmammalian","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004625","descriptor_name":"Embryo, Nonmammalian","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004625","descriptor_name":"Embryo, Nonmammalian","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"pmid:20134060","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20134060","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.453.7682","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.453.7682","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.imbio.de/journal/articles/pdf/jib-92.pdf","raw_type":"text"},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:286","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2008/286/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/index.php?paper_id=92","raw_type":"Journal Article"},{"id":"doi:10.2390/biecoll-jib-2008-92","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2008-92","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.2390/biecoll-jib-2008-92","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2008-92","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W202831144","https://openalex.org/W1580714437","https://openalex.org/W2008215988","https://openalex.org/W2017224321","https://openalex.org/W2028418089","https://openalex.org/W2053334540","https://openalex.org/W2088468751","https://openalex.org/W2102370826","https://openalex.org/W2106223061","https://openalex.org/W2114766990","https://openalex.org/W2124991490","https://openalex.org/W2136887407","https://openalex.org/W2150233912","https://openalex.org/W2150706940","https://openalex.org/W2915642007"],"related_works":["https://openalex.org/W2153691589","https://openalex.org/W1886336325","https://openalex.org/W1565145757","https://openalex.org/W2201744334","https://openalex.org/W2133045719","https://openalex.org/W2751953166","https://openalex.org/W2163109444","https://openalex.org/W2094108329","https://openalex.org/W1816540963","https://openalex.org/W2121403037","https://openalex.org/W2033311794","https://openalex.org/W2106238914","https://openalex.org/W2163707150","https://openalex.org/W2111530986","https://openalex.org/W2059579236","https://openalex.org/W1573673122","https://openalex.org/W2143811987","https://openalex.org/W2915391685","https://openalex.org/W2026022604","https://openalex.org/W2102370826"],"abstract_inverted_index":{"The":[0,94,125,202],"Gene":[1,180],"Expression":[2],"Management":[3],"System":[4],"(GEMS)":[5],"is":[6,30,144],"a":[7,100,103,155,261],"database":[8,101],"system":[9,60],"for":[10,198,207],"patterns":[11,16,73,188,210,258],"of":[12,37,41,74,92,106,112,122,131,134,164,189,209,211,246,264],"gene":[13,75,190,212,231],"expression.":[14],"These":[15,150],"result":[17],"from":[18,154,172,178],"systematic":[19],"whole-mount":[20],"fluorescent":[21],"in":[22,97,137,139,193,214,219,242],"situ":[23],"hybridization":[24],"studies":[25],"on":[26],"zebrafish":[27,107,113,135,227,247],"embryos.":[28],"GEMS":[29,95,215,235,256],"an":[31,147],"integrative":[32],"platform":[33],"that":[34,49],"addresses":[35],"one":[36,225],"the":[38,63,120,123,160,168,179,205,224,243,250],"important":[39],"challenges":[40],"developmental":[42,83],"biology:":[43],"how":[44],"to":[45,57,65,68,119,186,236,260],"integrate":[46],"genetic":[47],"data":[48,233,241],"underpin":[50],"morphological":[51],"changes":[52],"during":[53],"embryogenesis.":[54],"Our":[55],"motivation":[56],"build":[58],"this":[59,109,173,194],"was":[61],"by":[62],"need":[64],"be":[66,237],"able":[67],"organize":[69],"and":[70,84,192,200],"compare":[71],"multiple":[72],"expression":[76,191,213,232,257],"at":[77],"tissue":[78],"level.":[79],"Integration":[80],"with":[81,99,146,176,239],"other":[82,220,251],"biomolecular":[85,221],"databases":[86],"will":[87],"further":[88],"support":[89],"our":[90],"understanding":[91],"development.":[93,248],"operates":[96],"concert":[98],"containing":[102],"digital":[104,110],"atlas":[105,111,126,245],"embryo;":[108],"development":[114,136],"has":[115],"been":[116],"conceived":[117],"prior":[118],"expansion":[121],"GEMS.":[124],"contains":[127],"3D":[128,244],"volume":[129,141],"models":[130],"canonical":[132],"stages":[133],"which":[138],"each":[140],"model":[142],"element":[143],"annotated":[145],"anatomical":[148,157,170],"term.":[149],"terms":[151,171,177,254],"are":[152,183,204],"extracted":[153],"formal":[156],"ontology,":[158],"i.e.":[159],"Developmental":[161],"Anatomy":[162],"Ontology":[163,181],"Zebrafish":[165],"(DAOZ).":[166],"In":[167],"GEMS,":[169],"ontology":[174],"together":[175],"(GO)":[182],"also":[184],"used":[185],"annotate":[187],"manner":[195],"providing":[196],"mechanisms":[197],"integration":[199,208,259],"retrieval.":[201],"annotations":[203],"glue":[206],"as":[216,218],"well":[217],"databases.":[222],"At":[223,249],"hand,":[226,252],"anatomy":[228],"terminology":[229],"allows":[230],"within":[234],"integrated":[238],"phenotypical":[240],"GO":[253],"extend":[255],"wide":[262],"range":[263],"bioinformatics":[265],"resources.":[266]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}