{"id":"https://openalex.org/W4414661559","doi":"https://doi.org/10.5334/dsj-2025-028","title":"Enhancing Multiscale Simulation Data Management with Domain Ontologies and an ELN: Addressing Challenges and Implementing Strategies","display_name":"Enhancing Multiscale Simulation Data Management with Domain Ontologies and an ELN: Addressing Challenges and Implementing Strategies","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4414661559","doi":"https://doi.org/10.5334/dsj-2025-028"},"language":"en","primary_location":{"id":"doi:10.5334/dsj-2025-028","is_oa":true,"landing_page_url":"https://doi.org/10.5334/dsj-2025-028","pdf_url":"https://datascience.codata.org/articles/1859/files/68dbcfdca68c4.pdf","source":{"id":"https://openalex.org/S62969111","display_name":"Data Science Journal","issn_l":"1683-1470","issn":["1683-1470"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320511","host_organization_name":"Ubiquity Press","host_organization_lineage":["https://openalex.org/P4310320511"],"host_organization_lineage_names":["Ubiquity Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data Science Journal","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://datascience.codata.org/articles/1859/files/68dbcfdca68c4.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119780957","display_name":"Hafiz Muhammad Noman","orcid":"https://orcid.org/0009-0001-6710-6681"},"institutions":[{"id":"https://openalex.org/I4210123207","display_name":"Institute of Nanotechnology","ror":"https://ror.org/02ma7yv75","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210123207"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Hafiz Muhammad Noman","raw_affiliation_strings":["Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , Hermann- von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany"],"raw_orcid":"https://orcid.org/0009-0001-6710-6681","affiliations":[{"raw_affiliation_string":"Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , Hermann- von-Helmholtz-Platz 1 , 76344 Eggenstein-Leopoldshafen , Germany","institution_ids":["https://openalex.org/I4210123207"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037815782","display_name":"Michael Selzer","orcid":"https://orcid.org/0000-0002-9756-646X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michael Selzer","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-9756-646X","affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5119780957"],"corresponding_institution_ids":["https://openalex.org/I4210123207"],"apc_list":{"value":350,"currency":"GBP","value_usd":429},"apc_paid":{"value":350,"currency":"GBP","value_usd":429},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.25063979,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"24","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9983999729156494,"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":0.9983999729156494,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9909999966621399,"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/ontology","display_name":"Ontology","score":0.8443999886512756},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.6837000250816345},{"id":"https://openalex.org/keywords/process-ontology","display_name":"Process ontology","score":0.6553000211715698},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.6134999990463257},{"id":"https://openalex.org/keywords/multidisciplinary-approach","display_name":"Multidisciplinary approach","score":0.5633000135421753},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.5393000245094299},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.536300003528595},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.46950000524520874},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.43209999799728394}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.8443999886512756},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8281000256538391},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.6837000250816345},{"id":"https://openalex.org/C137003198","wikidata":"https://www.wikidata.org/wiki/Q7247296","display_name":"Process ontology","level":3,"score":0.6553000211715698},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.6134999990463257},{"id":"https://openalex.org/C22467394","wikidata":"https://www.wikidata.org/wiki/Q849359","display_name":"Multidisciplinary approach","level":2,"score":0.5633000135421753},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.5393000245094299},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.536300003528595},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5177000164985657},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.46950000524520874},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.43209999799728394},{"id":"https://openalex.org/C1668388","wikidata":"https://www.wikidata.org/wiki/Q1149776","display_name":"Data management","level":2,"score":0.42890000343322754},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.4207000136375427},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4115999937057495},{"id":"https://openalex.org/C50382505","wikidata":"https://www.wikidata.org/wiki/Q2553356","display_name":"OWL-S","level":4,"score":0.3869999945163727},{"id":"https://openalex.org/C101230327","wikidata":"https://www.wikidata.org/wiki/Q826165","display_name":"Web Ontology Language","level":3,"score":0.36570000648498535},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3540000021457672},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.3540000021457672},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.32600000500679016},{"id":"https://openalex.org/C61673122","wikidata":"https://www.wikidata.org/wiki/Q7095059","display_name":"Ontology language","level":3,"score":0.3095000088214874},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3077999949455261},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.30709999799728394},{"id":"https://openalex.org/C2778820784","wikidata":"https://www.wikidata.org/wiki/Q1027508","display_name":"Ontology engineering","level":4,"score":0.3068000078201294},{"id":"https://openalex.org/C56739046","wikidata":"https://www.wikidata.org/wiki/Q192060","display_name":"Knowledge management","level":1,"score":0.3028999865055084},{"id":"https://openalex.org/C115408247","wikidata":"https://www.wikidata.org/wiki/Q3882789","display_name":"Ontology Inference Layer","level":5,"score":0.302700012922287},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.2939000129699707},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.29120001196861267},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2802000045776367},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.25999999046325684},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.25699999928474426},{"id":"https://openalex.org/C69075417","wikidata":"https://www.wikidata.org/wiki/Q515701","display_name":"Linked data","level":3,"score":0.2567000091075897},{"id":"https://openalex.org/C2777002027","wikidata":"https://www.wikidata.org/wiki/Q3620938","display_name":"Ontology learning","level":5,"score":0.2522999942302704},{"id":"https://openalex.org/C154210476","wikidata":"https://www.wikidata.org/wiki/Q7095057","display_name":"Ontology components","level":5,"score":0.25060001015663147}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5334/dsj-2025-028","is_oa":true,"landing_page_url":"https://doi.org/10.5334/dsj-2025-028","pdf_url":"https://datascience.codata.org/articles/1859/files/68dbcfdca68c4.pdf","source":{"id":"https://openalex.org/S62969111","display_name":"Data Science Journal","issn_l":"1683-1470","issn":["1683-1470"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320511","host_organization_name":"Ubiquity Press","host_organization_lineage":["https://openalex.org/P4310320511"],"host_organization_lineage_names":["Ubiquity Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data Science Journal","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:3027bc38402e463e97c7b8338445980d","is_oa":true,"landing_page_url":"https://doaj.org/article/3027bc38402e463e97c7b8338445980d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Data Science Journal, Vol 24, Pp 28-28 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.5334/dsj-2025-028","is_oa":true,"landing_page_url":"https://doi.org/10.5334/dsj-2025-028","pdf_url":"https://datascience.codata.org/articles/1859/files/68dbcfdca68c4.pdf","source":{"id":"https://openalex.org/S62969111","display_name":"Data Science Journal","issn_l":"1683-1470","issn":["1683-1470"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320511","host_organization_name":"Ubiquity Press","host_organization_lineage":["https://openalex.org/P4310320511"],"host_organization_lineage_names":["Ubiquity Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data Science Journal","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6365342299","display_name":null,"funder_award_id":"442146713","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7902395741","display_name":null,"funder_award_id":"390874152","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414661559.pdf","grobid_xml":"https://content.openalex.org/works/W4414661559.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2000397925","https://openalex.org/W2103017472","https://openalex.org/W2130466936","https://openalex.org/W2144427809","https://openalex.org/W2770044072","https://openalex.org/W2897561926","https://openalex.org/W2916124791","https://openalex.org/W2963328453","https://openalex.org/W3128701936","https://openalex.org/W4210611011","https://openalex.org/W4387951959","https://openalex.org/W4390331596"],"related_works":[],"abstract_inverted_index":{"Data":[0,154],"plays":[1],"a":[2,51,96,202],"fundamental":[3,192],"role":[4],"in":[5,98,104,129,194,210],"advancing":[6],"knowledge":[7,177],"and":[8,45,81,93,179,207,240,246],"driving":[9],"research":[10,150,188],"across":[11],"all":[12],"fields.":[13],"Despite":[14],"the":[15,71,77,110,120,123,142,152,164,173,185,191,235],"abundance":[16],"of":[17,34,65,176],"data,":[18,32],"several":[19,46],"challenges":[20,27,57],"still":[21],"need":[22],"to":[23,54,162,184],"be":[24],"addressed.":[25],"These":[26],"include":[28],"limited":[29],"accessibility,":[30],"heterogeneous":[31],"lack":[33],"interconnections":[35],"between":[36],"associated":[37],"topics,":[38],"difficulty":[39],"retrieving":[40],"required":[41],"information,":[42],"semantic":[43],"mismatches,":[44],"other":[47,138],"challenges.":[48],"Ontologies":[49],"provide":[50],"structured":[52],"method":[53],"address":[55],"these":[56],"effectively.":[58],"This":[59,187],"study":[60],"addresses":[61],"two":[62],"central":[63],"aspects":[64],"ontology":[66,73,105,165,198,218,231],"research.":[67],"First,":[68],"it":[69,108],"details":[70],"multidisciplinary":[72],"development":[74,232],"process,":[75],"highlighting":[76],"challenges,":[78],"mitigation":[79],"strategies,":[80],"impacts":[82],"on":[83,101],"domain":[84],"data":[85,99,181,209,227],"management.":[86],"It":[87],"then":[88],"offers":[89],"guidelines":[90,121],"for":[91,112,205],"beginners":[92],"individuals":[94],"with":[95,137,151,243],"background":[97],"management":[100,228],"effective":[102],"engagement":[103],"creation.":[106],"Second,":[107],"introduces":[109],"Ontology":[111,131,146],"Multiscale":[113],"Simulation":[114],"methods":[115],"(Onto-MS),":[116],"constructed":[117],"by":[118],"following":[119],"from":[122],"first":[124],"part.":[125],"The":[126],"ontology,":[127],"developed":[128],"Web":[130],"Language":[132],"(OWL)":[133],"using":[134],"Prot\u00e9g\u00e9,":[135],"integrates":[136],"ontologies,":[139],"such":[140],"as":[141],"Elementary":[143],"Multiperspective":[144],"Material":[145],"(EMMO),":[147],"aligning":[148],"this":[149],"Linked":[153],"concept.":[155],"A":[156],"custom":[157],"Python":[158],"script":[159],"was":[160],"used":[161],"incorporate":[163],"into":[166,220,226],"an":[167,221],"Electronic":[168],"Laboratory":[169],"Notebook":[170],"(ELN),":[171],"enabling":[172],"automatic":[174],"creation":[175],"graphs":[178],"systematic":[180],"organization":[182],"conforming":[183],"ontology.":[186],"successfully":[189],"answers":[190],"questions":[193],"interdisciplinary":[195],"or":[196],"domain-level":[197],"development.":[199],"Onto-MS":[200],"provides":[201],"robust":[203],"framework":[204],"organizing":[206],"linking":[208],"multiscale":[211],"simulations":[212],"within":[213],"computational":[214],"materials":[215],"science.":[216],"Furthermore,":[217],"incorporation":[219],"ELN":[222],"simplifies":[223],"its":[224],"integration":[225],"practices.":[229],"While":[230],"is":[233,238],"ongoing,":[234],"current":[236],"version":[237],"functional":[239],"continuously":[241],"refined":[242],"new":[244],"insights":[245],"feedback.":[247]},"counts_by_year":[],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
