{"id":"https://openalex.org/W2128031888","doi":"https://doi.org/10.1186/1758-2946-6-4","title":"Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing","display_name":"Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing","publication_year":2014,"publication_date":"2014-01-30","ids":{"openalex":"https://openalex.org/W2128031888","doi":"https://doi.org/10.1186/1758-2946-6-4","mag":"2128031888","pmid":"https://pubmed.ncbi.nlm.nih.gov/24484917"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-6-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110202807","display_name":"Julien Thibault","orcid":null},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Julien C Thibault","raw_affiliation_strings":["Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA","Department of Biomedical Informatics, University of Utah, Salt Lake City, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"Department of Biomedical Informatics, University of Utah, Salt Lake City, USA#TAB#","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062098434","display_name":"Daniel R. Roe","orcid":"https://orcid.org/0000-0002-5834-2447"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel R Roe","raw_affiliation_strings":["Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA","Department of Medicinal Chemistry, University of Utah,Salt Lake City,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"Department of Medicinal Chemistry, University of Utah,Salt Lake City,USA","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007190695","display_name":"Julio C. Facelli","orcid":"https://orcid.org/0000-0003-1449-477X"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julio C Facelli","raw_affiliation_strings":["Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA. julio.facelli@utah.edu","Department of Biomedical Informatics, University of Utah, Salt Lake City, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA. julio.facelli@utah.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Biomedical Informatics, University of Utah, Salt Lake City, USA#TAB#","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020579549","display_name":"Thomas E. Cheatham","orcid":"https://orcid.org/0000-0003-0298-3904"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas E Cheatham","raw_affiliation_strings":["Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA","Department of Medicinal Chemistry, University of Utah,Salt Lake City,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"Department of Medicinal Chemistry, University of Utah,Salt Lake City,USA","institution_ids":["https://openalex.org/I223532165"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5110202807"],"corresponding_institution_ids":["https://openalex.org/I223532165"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.8537,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.73450646,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"6","issue":"1","first_page":"4","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5641999840736389,"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":0.5641999840736389,"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":0.21729999780654907,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.031700000166893005,"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/computer-science","display_name":"Computer science","score":0.8647010326385498},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.5200223922729492},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.49513188004493713},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4914737939834595},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4886992275714874},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.45544055104255676},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4495396614074707},{"id":"https://openalex.org/keywords/logical-data-model","display_name":"Logical data model","score":0.4249315857887268},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.4232484996318817},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4077727794647217},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3994590640068054},{"id":"https://openalex.org/keywords/data-modeling","display_name":"Data modeling","score":0.3591892123222351},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3055099546909332},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17490819096565247},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.13860854506492615}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8647010326385498},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.5200223922729492},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.49513188004493713},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4914737939834595},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4886992275714874},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.45544055104255676},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4495396614074707},{"id":"https://openalex.org/C203702819","wikidata":"https://www.wikidata.org/wiki/Q17146953","display_name":"Logical data model","level":3,"score":0.4249315857887268},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.4232484996318817},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4077727794647217},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3994590640068054},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.3591892123222351},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3055099546909332},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17490819096565247},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.13860854506492615},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-6-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:24484917","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24484917","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 cheminformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2901478","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3915074","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"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-6-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.5199999809265137}],"awards":[{"id":"https://openalex.org/G1237383050","display_name":null,"funder_award_id":"1266307","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G1401553414","display_name":null,"funder_award_id":"NSF OCI 07-25070","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1690346126","display_name":null,"funder_award_id":"CHE-1266307","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2430488620","display_name":null,"funder_award_id":"CHE-1266307","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G399814938","display_name":null,"funder_award_id":"MCA01S027P","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6476835034","display_name":null,"funder_award_id":"OCI 07-25070","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6524269621","display_name":null,"funder_award_id":"OCI-1053575","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6778350887","display_name":null,"funder_award_id":"1053575","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6973747507","display_name":"CDS&E:  Tools to facilitate deeper data analysis, exploration, management, and sharing of ensembles of molecular dynamics trajectory data","funder_award_id":"1266307","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7516183200","display_name":"PRAC - Hierarchical molecular dynamics sampling for assessing pathways and free energies of RNA catalysis, ligand binding, and conformational change","funder_award_id":"1036208","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7579982596","display_name":null,"funder_award_id":"1053575","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310050","display_name":"University of Utah","ror":"https://ror.org/03r0ha626"},{"id":"https://openalex.org/F4320334105","display_name":"Center for High Performance Computing","ror":null},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128031888.pdf","grobid_xml":"https://content.openalex.org/works/W2128031888.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W47624896","https://openalex.org/W1516459493","https://openalex.org/W1527894967","https://openalex.org/W1535747019","https://openalex.org/W1965092590","https://openalex.org/W1966078827","https://openalex.org/W1968344479","https://openalex.org/W1975147762","https://openalex.org/W1993892970","https://openalex.org/W2006026068","https://openalex.org/W2016088798","https://openalex.org/W2026020661","https://openalex.org/W2029667189","https://openalex.org/W2033377040","https://openalex.org/W2037424046","https://openalex.org/W2043668344","https://openalex.org/W2049160854","https://openalex.org/W2049961577","https://openalex.org/W2054652150","https://openalex.org/W2055043387","https://openalex.org/W2058673890","https://openalex.org/W2074553281","https://openalex.org/W2079875740","https://openalex.org/W2081417077","https://openalex.org/W2091257550","https://openalex.org/W2100871034","https://openalex.org/W2108370395","https://openalex.org/W2108507420","https://openalex.org/W2110257394","https://openalex.org/W2118233996","https://openalex.org/W2121400889","https://openalex.org/W2127821584","https://openalex.org/W2130479394","https://openalex.org/W2140728823","https://openalex.org/W2148664936","https://openalex.org/W2151220474","https://openalex.org/W2152652376","https://openalex.org/W2159583324","https://openalex.org/W2170711116","https://openalex.org/W2171123303","https://openalex.org/W2237656138","https://openalex.org/W2332712348","https://openalex.org/W2399012521","https://openalex.org/W2620248835","https://openalex.org/W2780466810","https://openalex.org/W4234898958","https://openalex.org/W4285719527","https://openalex.org/W4298068285"],"related_works":["https://openalex.org/W3089353361","https://openalex.org/W81164209","https://openalex.org/W638142098","https://openalex.org/W2991945580","https://openalex.org/W1592030807","https://openalex.org/W2098136777","https://openalex.org/W846443833","https://openalex.org/W2050347474","https://openalex.org/W2148942320","https://openalex.org/W2547185650"],"abstract_inverted_index":{"BACKGROUND:":[0],"Few":[1],"environments":[2],"have":[3],"been":[4],"developed":[5],"or":[6,14,174],"deployed":[7],"to":[8,15,19,52,83,109,150,168,204],"widely":[9,45],"share":[10,55],"biomolecular":[11,91,205,251],"simulation":[12],"data":[13,21,31,57,80,100,122,142,260],"enable":[16],"collaborative":[17],"networks":[18],"facilitate":[20],"exploration":[22],"and":[23,28,39,54,106,118,136,157,190,214,218,233,236,263,268],"reuse.":[24],"As":[25],"the":[26,40,47,66,74,77,85,112,125,152,182,201,226,238,266],"amount":[27],"complexity":[29],"of":[30,68,76,87,98,130,154,164,200,212,228,240,245],"generated":[32],"by":[33,103],"these":[34],"simulations":[35,252],"is":[36],"dramatically":[37],"increasing":[38],"methods":[41],"are":[42,274],"being":[43],"more":[44,215],"applied,":[46],"need":[48],"for":[49,79,90,127,250,276],"new":[50,155],"tools":[51],"manage":[53],"this":[56,62,272],"has":[58],"become":[59],"obvious.":[60],"In":[61],"paper":[63,273],"we":[64],"present":[65],"results":[67],"a":[69,96,116,147,162,177,195,246],"process":[70],"aimed":[71],"at":[72,278],"assessing":[73],"needs":[75],"community":[78,113],"representation":[81,199],"standards":[82],"guide":[84,151,209],"implementation":[86],"future":[88,210],"repositories":[89,213],"simulations.":[92],"RESULTS:":[93],"We":[94],"introduce":[95],"list":[97],"common":[99,247],"elements,":[101],"inspired":[102],"previous":[104],"work,":[105],"updated":[107],"according":[108],"feedback":[110],"from":[111],"collected":[114],"through":[115,225,255],"survey":[117],"personal":[119],"interviews.":[120],"These":[121],"elements":[123,143],"integrate":[124],"concepts":[126,202],"multiple":[128],"types":[129],"computational":[131],"methods,":[132],"including":[133,259],"quantum":[134],"chemistry":[135],"molecular":[137],"dynamics.":[138],"The":[139,188,220,243],"identified":[140],"core":[141],"were":[144],"organized":[145],"into":[146,231],"logical":[148,248],"model":[149,189,221,249],"design":[153],"databases":[156],"application":[158],"programming":[159],"interfaces.":[160],"Finally":[161],"set":[163],"dictionaries":[165,193,269],"was":[166,253],"implemented":[167],"be":[169],"used":[170],"via":[171,176,237],"SQL":[172],"queries":[173],"locally":[175],"Java":[178],"API":[179],"built":[180],"upon":[181],"Apache":[183],"Lucene":[184],"text-search":[185],"engine.":[186],"CONCLUSIONS:":[187],"its":[191],"associated":[192],"provide":[194],"simple":[196],"yet":[197],"rich":[198],"related":[203],"simulations,":[206],"which":[207],"should":[208],"developments":[211],"complex":[216],"terminologies":[217],"ontologies.":[219],"still":[222],"remains":[223],"extensible":[224],"decomposition":[227],"virtual":[229],"experiments":[230],"tasks":[232],"parameter":[234],"sets,":[235],"use":[239,257],"extended":[241],"attributes.":[242],"benefits":[244],"illustrated":[254],"various":[256],"cases,":[258],"storage,":[261],"indexing,":[262],"presentation.":[264],"All":[265],"models":[267],"introduced":[270],"in":[271],"available":[275],"download":[277],"http://ibiomes.chpc.utah.edu/mediawiki/index.php/Downloads.":[279]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
