{"id":"https://openalex.org/W2158523138","doi":"https://doi.org/10.1093/bioinformatics/bts644","title":"ADAM: automated data management for research datasets","display_name":"ADAM: automated data management for research datasets","publication_year":2012,"publication_date":"2012-10-29","ids":{"openalex":"https://openalex.org/W2158523138","doi":"https://doi.org/10.1093/bioinformatics/bts644","mag":"2158523138","pmid":"https://pubmed.ncbi.nlm.nih.gov/23109181"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/146/763014/bts644.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/146/763014/bts644.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049341457","display_name":"Mark Woodbridge","orcid":"https://orcid.org/0000-0002-0650-9751"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Mark Woodbridge","raw_affiliation_strings":["Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067888810","display_name":"Christopher Tomlinson","orcid":"https://orcid.org/0000-0002-8634-6111"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christopher D. Tomlinson","raw_affiliation_strings":["Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001416834","display_name":"Sarah Butcher","orcid":"https://orcid.org/0000-0002-4494-5124"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sarah A. Butcher","raw_affiliation_strings":["Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5049341457"],"corresponding_institution_ids":["https://openalex.org/I47508984"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2912,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.78229376,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"29","issue":"1","first_page":"146","last_page":"147"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.548799991607666,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.548799991607666,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.35569998621940613,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.03869999945163727,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8345533609390259},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.6191447973251343},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6087548732757568},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5581331849098206},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5381743311882019},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.504001796245575},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4801977872848511},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.45143067836761475},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4420667290687561},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4394029378890991},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.41138356924057007},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3886266350746155},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3848516345024109},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3660278916358948},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2691233456134796}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8345533609390259},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.6191447973251343},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6087548732757568},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5581331849098206},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5381743311882019},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.504001796245575},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4801977872848511},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.45143067836761475},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4420667290687561},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4394029378890991},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.41138356924057007},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3886266350746155},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3848516345024109},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3660278916358948},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2691233456134796},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"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":"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/146/763014/bts644.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23109181","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23109181","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":null},{"id":"pmh:oai:europepmc.org:2527661","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3530912","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/10496","is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/10496","pdf_url":null,"source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"147","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/146/763014/bts644.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4099999964237213,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320283","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2158523138.pdf","grobid_xml":"https://content.openalex.org/works/W2158523138.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W1974694769","https://openalex.org/W2031502025","https://openalex.org/W2094261404","https://openalex.org/W2166934660"],"related_works":["https://openalex.org/W1873761914","https://openalex.org/W2999281421","https://openalex.org/W2753370921","https://openalex.org/W3089853590","https://openalex.org/W3005685668","https://openalex.org/W4286787790","https://openalex.org/W2315002870","https://openalex.org/W2126320151","https://openalex.org/W1878038826","https://openalex.org/W2145284006"],"abstract_inverted_index":{"UNLABELLED:":[0],"Existing":[1],"repositories":[2],"for":[3,30],"experimental":[4,15,75],"datasets":[5],"typically":[6],"capture":[7],"snapshots":[8],"of":[9,50,90],"data":[10,33,92],"acquired":[11],"using":[12,102],"a":[13,27,51,123],"single":[14],"technique":[16],"and":[17,22,44,68,84,88,104,126,130],"often":[18],"require":[19],"manual":[20],"population":[21],"continual":[23],"curation.":[24],"We":[25],"present":[26],"storage":[28],"system":[29,125],"heterogeneous":[31],"research":[32],"that":[34],"performs":[35],"dynamic":[36],"automated":[37],"indexing":[38],"to":[39,57,73],"provide":[40],"powerful":[41],"search,":[42],"discovery":[43],"collaboration":[45],"features":[46],"without":[47],"the":[48,74,113],"restrictions":[49],"structured":[52],"repository.":[53],"ADAM":[54,99],"is":[55,80,100,109],"able":[56],"index":[58],"many":[59],"commonly":[60],"used":[61],"file":[62],"formats":[63],"generated":[64],"by":[65],"laboratory":[66],"assays":[67],"therefore":[69],"offers":[70],"specific":[71,83],"advantages":[72],"biology":[76],"community.":[77],"However,":[78],"it":[79],"not":[81],"domain":[82],"can":[85],"promote":[86],"sharing":[87],"re-use":[89],"working":[91],"across":[93],"scientific":[94],"disciplines.":[95],"AVAILABILITY":[96],"AND":[97],"IMPLEMENTATION:":[98],"implemented":[101],"Java":[103],"supported":[105],"on":[106],"Linux.":[107],"It":[108],"open":[110],"source":[111],"under":[112],"GNU":[114],"General":[115],"Public":[116],"License":[117],"v3.0.":[118],"Installation":[119],"instructions,":[120],"binary":[121],"code,":[122],"demo":[124],"virtual":[127],"machine":[128],"image":[129],"are":[131],"available":[132],"at":[133],"http://www.imperial.ac.uk/bioinfsupport/resources/software/adam.":[134]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}