{"id":"https://openalex.org/W2114380686","doi":"https://doi.org/10.1093/bioinformatics/17.4.300","title":"A relational schema for both array-based and SAGE gene expression experiments","display_name":"A relational schema for both array-based and SAGE gene expression experiments","publication_year":2001,"publication_date":"2001-04-01","ids":{"openalex":"https://openalex.org/W2114380686","doi":"https://doi.org/10.1093/bioinformatics/17.4.300","mag":"2114380686","pmid":"https://pubmed.ncbi.nlm.nih.gov/11301298"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/17.4.300","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/17.4.300","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024151124","display_name":"C. J. Stoeckert","orcid":null},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C. Stoeckert","raw_affiliation_strings":["Computational Biology and Informatics Laboratory, Center for Bioinformatics, University of Pennsylvania, 1313 Blockley Hall, 418 Guardian Drive, Philadelphia, PA 19104-6021, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology and Informatics Laboratory, Center for Bioinformatics, University of Pennsylvania, 1313 Blockley Hall, 418 Guardian Drive, Philadelphia, PA 19104-6021, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026998349","display_name":"Angel Pizarro","orcid":"https://orcid.org/0000-0003-2263-2255"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Pizarro","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044878468","display_name":"Elisabetta Manduchi","orcid":"https://orcid.org/0000-0002-4110-3714"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E. Manduchi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020625661","display_name":"Molly K. Gibson","orcid":"https://orcid.org/0000-0003-1813-5037"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Gibson","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090491634","display_name":"Brian P. Brunk","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"B. Brunk","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073286805","display_name":"Jonathan Crabtree","orcid":"https://orcid.org/0000-0002-0139-7025"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Crabtree","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015126110","display_name":"Jonathan Schug","orcid":"https://orcid.org/0000-0001-6885-7869"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Schug","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063176243","display_name":"Shai S. Shen-Orr","orcid":"https://orcid.org/0000-0002-6991-7736"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. Shen-Orr","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5108447355","display_name":"G. Christian Overton","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"G. C. Overton","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.7808,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.90988415,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"4","first_page":"300","last_page":"308"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9997000098228455,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9997000098228455,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9922999739646912,"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":0.9879999756813049,"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/schema","display_name":"Schema (genetic algorithms)","score":0.7792335748672485},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7662277221679688},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5625515580177307},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5454457998275757},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.5350922346115112},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5288663506507874},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.46331357955932617},{"id":"https://openalex.org/keywords/database-schema","display_name":"Database schema","score":0.43784698843955994},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34150785207748413},{"id":"https://openalex.org/keywords/database-design","display_name":"Database design","score":0.18827921152114868},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1299874484539032}],"concepts":[{"id":"https://openalex.org/C52146309","wikidata":"https://www.wikidata.org/wiki/Q7431116","display_name":"Schema (genetic algorithms)","level":2,"score":0.7792335748672485},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7662277221679688},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5625515580177307},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5454457998275757},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.5350922346115112},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5288663506507874},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.46331357955932617},{"id":"https://openalex.org/C30775581","wikidata":"https://www.wikidata.org/wiki/Q632285","display_name":"Database schema","level":3,"score":0.43784698843955994},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34150785207748413},{"id":"https://openalex.org/C148840519","wikidata":"https://www.wikidata.org/wiki/Q1049878","display_name":"Database design","level":2,"score":0.18827921152114868},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1299874484539032}],"mesh":[{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/17.4.300","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/17.4.300","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:11301298","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11301298","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1841630786","display_name":null,"funder_award_id":"R01 RR04026","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1502713942","https://openalex.org/W1680359239","https://openalex.org/W1968766436","https://openalex.org/W1978393588","https://openalex.org/W1992427637","https://openalex.org/W2010888033","https://openalex.org/W2045512378","https://openalex.org/W2050163545","https://openalex.org/W2054774141","https://openalex.org/W2064737575","https://openalex.org/W2085969264","https://openalex.org/W2096525273","https://openalex.org/W2109970232","https://openalex.org/W2135187880","https://openalex.org/W2137786672","https://openalex.org/W2147246240","https://openalex.org/W2159482845"],"related_works":["https://openalex.org/W2031508292","https://openalex.org/W2079588361","https://openalex.org/W2460926837","https://openalex.org/W2354111411","https://openalex.org/W52829598","https://openalex.org/W2774489303","https://openalex.org/W2336519490","https://openalex.org/W2748090995","https://openalex.org/W223556604","https://openalex.org/W2356754926"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"and":[2,36,72,74,126,131,135,138,156,168,170],"Results:":[3],"A":[4],"relational":[5],"schema":[6,20,80,181],"is":[7,143,147,159,182],"described":[8],"for":[9,29,106,122,161,172],"capturing":[10],"highly":[11],"parallel":[12],"gene":[13,44,90],"expression":[14,45],"experiments":[15,46,115],"using":[16,37,88,95],"different":[17,33,38,50],"technologies.":[18],"This":[19],"grew":[21],"out":[22],"of":[23,40,52,64,78,175,199,205],"efforts":[24],"to":[25,101],"build":[26],"a":[27,89,102,148],"database":[28],"collaborators":[30],"working":[31],"on":[32,85],"biological":[34],"systems":[35],"types":[39,51],"platforms":[41],"in":[42],"their":[43],"as":[47,49],"well":[48],"image":[53,70],"quantification":[54],"software.":[55],"The":[56,76,145,180],"tables":[57],"are":[58,166],"conceptually":[59],"organized":[60],"into":[61],"three":[62],"categories":[63],"information:":[65],"Platform,":[66],"Experiment":[67],"(which":[68],"includes":[69],"scanning":[71],"quantification),":[73],"Data.":[75],"strengths":[77],"the":[79,112,118,123,141],"are:":[81],"(i)":[82],"integrating":[83],"information":[84],"array":[86,155],"elements":[87],"index;":[91],"(ii)":[92],"describing":[93],"samples":[94],"ontologies;":[96],"(iii)":[97],"reducing":[98],"an":[99],"experiment":[100],"single":[103],"RNA":[104],"source":[105],"precise":[107,167],"descriptions":[108,164],"yet":[109],"not":[110],"losing":[111],"relationships":[113],"between":[114,177],"done":[116],"at":[117,184],"same":[119,124],"time":[120],"or":[121],"project;":[125],"(iv)":[127],"maintaining":[128],"both":[129,154],"raw":[130],"processed":[132],"(e.g.":[133],"cleansed":[134],"normalized)":[136],"data":[137,142],"recording":[139],"how":[140],"processed.":[144],"result":[146],"novel":[149],"schema,":[150],"which":[151],"can":[152],"hold":[153],"non-array":[157],"data,":[158],"extensible":[160],"detailed":[162],"experimental":[163],"that":[165],"consistent,":[169],"allows":[171],"meaningful":[173],"comparisons":[174],"genes":[176],"experiments.":[178],"Availability:":[179],"available":[183],"http://www.cbil.upenn.edu/cgi-bin/RAD2/schemaBrowserRAD.pl.":[185],"Contact:":[186],"stoeckrt@pcbi.upenn.edu":[187],"*":[188],"To":[189],"whom":[190],"correspondence":[191],"should":[192],"be":[193],"addressed.":[194],"2":[195],"Present":[196],"address:":[197],"Department":[198],"Molecular":[200],"Cell":[201],"Biology,":[202],"Weizmann":[203],"Institute":[204],"Science,":[206],"Israel.":[207]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
