{"id":"https://openalex.org/W3007706128","doi":"https://doi.org/10.1109/bigdata47090.2019.9005648","title":"HDMF: Hierarchical Data Modeling Framework for Modern Science Data Standards","display_name":"HDMF: Hierarchical Data Modeling Framework for Modern Science Data Standards","publication_year":2019,"publication_date":"2019-12-01","ids":{"openalex":"https://openalex.org/W3007706128","doi":"https://doi.org/10.1109/bigdata47090.2019.9005648","mag":"3007706128","pmid":"https://pubmed.ncbi.nlm.nih.gov/34632466"},"language":"en","primary_location":{"id":"doi:10.1109/bigdata47090.2019.9005648","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bigdata47090.2019.9005648","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Big Data (Big Data)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8500680","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076792091","display_name":"Andrew Tritt","orcid":"https://orcid.org/0000-0002-1617-449X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrew J. Tritt","raw_affiliation_strings":["Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"],"affiliations":[{"raw_affiliation_string":"Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012378616","display_name":"Oliver R\u00fcbel","orcid":"https://orcid.org/0000-0001-9902-1984"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oliver Rubel","raw_affiliation_strings":["Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"],"affiliations":[{"raw_affiliation_string":"Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088656190","display_name":"Ben Dichter","orcid":"https://orcid.org/0000-0001-5725-6910"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin Dichter","raw_affiliation_strings":["Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"],"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026813861","display_name":"Ryan Ly","orcid":"https://orcid.org/0000-0001-9238-0642"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Ly","raw_affiliation_strings":["Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"],"affiliations":[{"raw_affiliation_string":"Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053151130","display_name":"Donghe Kang","orcid":null},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Donghe Kang","raw_affiliation_strings":["Computer Science and Engineering, Ohio State University, Columbus, OH, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091099837","display_name":"Edward F. Chang","orcid":"https://orcid.org/0000-0003-2480-4700"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I4210157890","display_name":"Neurological Surgery","ror":"https://ror.org/04r0gp612","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210157890"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward F. Chang","raw_affiliation_strings":["Department of Neurological Surgery and the Center for Integrative Neuroscience, University of California, San Francisco, San Francisco, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Neurological Surgery and the Center for Integrative Neuroscience, University of California, San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I4210157890","https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060193294","display_name":"Loren M. Frank","orcid":"https://orcid.org/0000-0002-1752-5677"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Loren M. Frank","raw_affiliation_strings":["Howard Hughes Medical Institute, Kavli Institute for Fundamental Neuroscience, Department of Physiology, University of California, San Francisco, San Francisco, CA","Department of Physiology, Howard Hughes Medical Institute, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA"],"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Kavli Institute for Fundamental Neuroscience, Department of Physiology, University of California, San Francisco, San Francisco, CA","institution_ids":[]},{"raw_affiliation_string":"Department of Physiology, Howard Hughes Medical Institute, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040319820","display_name":"Kristofer E. Bouchard","orcid":"https://orcid.org/0000-0002-1974-4603"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kristofer Bouchard","raw_affiliation_strings":["Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"],"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5076792091"],"corresponding_institution_ids":["https://openalex.org/I148283060"],"apc_list":null,"apc_paid":null,"fwci":1.3223,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.91180941,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"2019","issue":null,"first_page":"165","last_page":"179"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9995999932289124,"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"}},{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9939000010490417,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7840896844863892},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6754077672958374},{"id":"https://openalex.org/keywords/standardization","display_name":"Standardization","score":0.6395373344421387},{"id":"https://openalex.org/keywords/data-modeling","display_name":"Data modeling","score":0.6031278967857361},{"id":"https://openalex.org/keywords/data-mapping","display_name":"Data mapping","score":0.5994166731834412},{"id":"https://openalex.org/keywords/data-sharing","display_name":"Data sharing","score":0.4791400134563446},{"id":"https://openalex.org/keywords/data-warehouse","display_name":"Data warehouse","score":0.47582438588142395},{"id":"https://openalex.org/keywords/data-model","display_name":"Data model (GIS)","score":0.4679381251335144},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.45583298802375793},{"id":"https://openalex.org/keywords/data-element","display_name":"Data element","score":0.428450345993042},{"id":"https://openalex.org/keywords/computer-data-storage","display_name":"Computer data storage","score":0.4149002432823181},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3909521698951721},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.16274863481521606}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7840896844863892},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6754077672958374},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.6395373344421387},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.6031278967857361},{"id":"https://openalex.org/C137314826","wikidata":"https://www.wikidata.org/wiki/Q2330408","display_name":"Data mapping","level":2,"score":0.5994166731834412},{"id":"https://openalex.org/C2779965156","wikidata":"https://www.wikidata.org/wiki/Q5227350","display_name":"Data sharing","level":3,"score":0.4791400134563446},{"id":"https://openalex.org/C135572916","wikidata":"https://www.wikidata.org/wiki/Q193351","display_name":"Data warehouse","level":2,"score":0.47582438588142395},{"id":"https://openalex.org/C100463513","wikidata":"https://www.wikidata.org/wiki/Q5227322","display_name":"Data model (GIS)","level":2,"score":0.4679381251335144},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.45583298802375793},{"id":"https://openalex.org/C30872290","wikidata":"https://www.wikidata.org/wiki/Q1172389","display_name":"Data element","level":3,"score":0.428450345993042},{"id":"https://openalex.org/C194739806","wikidata":"https://www.wikidata.org/wiki/Q66221","display_name":"Computer data storage","level":2,"score":0.4149002432823181},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3909521698951721},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.16274863481521606},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/bigdata47090.2019.9005648","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bigdata47090.2019.9005648","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Big Data (Big Data)","raw_type":"proceedings-article"},{"id":"pmid:34632466","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34632466","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":"Proceedings : ... IEEE International Conference on Big Data. IEEE International Conference on Big Data","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7pw381dv","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/7pw381dv","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7393756","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8500680","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8500680","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8500680","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Int Conf Big Data","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8500680","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8500680","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Int Conf Big Data","raw_type":"Text"},"sustainable_development_goals":[{"score":0.46000000834465027,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1965014786","https://openalex.org/W1966180432","https://openalex.org/W1987822482","https://openalex.org/W1997412667","https://openalex.org/W2085573521","https://openalex.org/W2123799770","https://openalex.org/W2157219191","https://openalex.org/W2166661736","https://openalex.org/W2302501749","https://openalex.org/W2412428304","https://openalex.org/W2548277807","https://openalex.org/W2908833350","https://openalex.org/W2922457781","https://openalex.org/W4245444791"],"related_works":["https://openalex.org/W1810998667","https://openalex.org/W2585252724","https://openalex.org/W4293519456","https://openalex.org/W2369215403","https://openalex.org/W2161414465","https://openalex.org/W2183628870","https://openalex.org/W2390641883","https://openalex.org/W1976384368","https://openalex.org/W2369208597","https://openalex.org/W1575673652"],"abstract_inverted_index":{"A":[0],"ubiquitous":[1],"problem":[2],"in":[3,183],"aggregating":[4],"data":[5,11,26,38,44,53,60,65,71,74,90,112,120,129,147,152,155,165,175,192],"across":[6,197],"different":[7],"experimental":[8],"and":[9,22,27,62,67,69,73,84,100,114,119,157,173],"observational":[10],"sources":[12],"is":[13],"a":[14,36,190],"lack":[15],"of":[16,25,52,111,127,139,164,181],"software":[17],"infrastructure":[18,97],"that":[19],"enables":[20],"flexible":[21,109],"extensible":[23],"standardization":[24,54],"metadata.":[28],"To":[29,76,135],"address":[30],"this":[31],"challenge,":[32],"we":[33,48],"developed":[34],"HDMF,":[35,47],"hierarchical":[37],"modeling":[39,61],"framework":[40],"for":[41,150,169,194],"modern":[42,191],"science":[43,142,196],"standards.":[45],"With":[46],"separate":[49],"the":[50,81,89,108,124,128,137,179,198],"process":[51],"into":[55],"three":[56],"main":[57],"components:":[58],"(1)":[59],"specification,":[63],"(2)":[64],"I/O":[66,148],"storage,":[68],"(3)":[70],"interaction":[72],"APIs.":[75],"enable":[77],"standards":[78,113,130],"to":[79,98,132,185],"support":[80,168],"complex":[82],"requirements":[83],"varying":[85],"use":[86],"cases":[87],"throughout":[88],"life":[91],"cycle,":[92],"HDMF":[93,144,182],"provides":[94,145],"object":[95],"mapping":[96],"insulate":[99],"integrate":[101],"these":[102],"various":[103],"components.":[104],"This":[105],"approach":[106],"supports":[107,162],"development":[110],"extensions,":[115],"optimized":[116],"storage":[117,166],"backends,":[118],"APIs,":[121],"while":[122],"allowing":[123],"other":[125],"components":[126],"ecosystem":[131],"remain":[133],"stable.":[134],"meet":[136],"demands":[138],"modern,":[140],"large-scale":[141],"data,":[143],"advanced":[146],"functionality":[149],"iterative":[151],"write,":[153],"lazy":[154],"load,":[156],"parallel":[158],"I/O.":[159],"It":[160],"also":[161],"optimization":[163],"via":[167],"chunking,":[170],"compression,":[171],"linking,":[172],"modular":[174],"storage.":[176],"We":[177],"demonstrate":[178],"application":[180],"practice":[184],"design":[186],"NWB":[187],"2.0":[188],"[13],":[189],"standard":[193],"collaborative":[195],"neurophysiology":[199],"community.":[200]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
