{"id":"https://openalex.org/W4381337638","doi":"https://doi.org/10.1186/s13321-023-00729-5","title":"A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL","display_name":"A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL","publication_year":2023,"publication_date":"2023-06-20","ids":{"openalex":"https://openalex.org/W4381337638","doi":"https://doi.org/10.1186/s13321-023-00729-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/37340506"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00729-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00729-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00729-5","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00729-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079524677","display_name":"Jakub Galgonek","orcid":"https://orcid.org/0000-0002-7038-544X"},"institutions":[{"id":"https://openalex.org/I4210145889","display_name":"Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry","ror":"https://ror.org/04nfjn472","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210145889"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Jakub Galgonek","raw_affiliation_strings":["Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo n\u00e1m\u011bst\u00ed 2, 166 10, Prague 6, Czech Republic. jakub.galgonek@uochb.cas.cz","Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo n\u00e1m\u011bst\u00ed 2, 166 10, Prague 6, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo n\u00e1m\u011bst\u00ed 2, 166 10, Prague 6, Czech Republic. jakub.galgonek@uochb.cas.cz","institution_ids":[]},{"raw_affiliation_string":"Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo n\u00e1m\u011bst\u00ed 2, 166 10, Prague 6, Czech Republic","institution_ids":["https://openalex.org/I4210145889"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031688867","display_name":"Ji\u0159\u0131\u0301 Vondr\u00e1\u0161ek","orcid":"https://orcid.org/0000-0002-6066-973X"},"institutions":[{"id":"https://openalex.org/I4210145889","display_name":"Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry","ror":"https://ror.org/04nfjn472","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210145889"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ji\u0159\u00ed Vondr\u00e1\u0161ek","raw_affiliation_strings":["Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo n\u00e1m\u011bst\u00ed 2, 166 10, Prague 6, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo n\u00e1m\u011bst\u00ed 2, 166 10, Prague 6, Czech Republic","institution_ids":["https://openalex.org/I4210145889"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079524677"],"corresponding_institution_ids":["https://openalex.org/I4210145889"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.8565,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.78264823,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"15","issue":"1","first_page":"61","last_page":"61"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9965999722480774,"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"}},"topics":[{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9965999722480774,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9944999814033508,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9904000163078308,"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/sparql","display_name":"SPARQL","score":0.9479336738586426},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.8364500999450684},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8206504583358765},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6867377758026123},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.6564077138900757},{"id":"https://openalex.org/keywords/sql","display_name":"SQL","score":0.6535236835479736},{"id":"https://openalex.org/keywords/relational-database-management-system","display_name":"Relational database management system","score":0.5870010256767273},{"id":"https://openalex.org/keywords/rdf-schema","display_name":"RDF Schema","score":0.5532285571098328},{"id":"https://openalex.org/keywords/database-model","display_name":"Database model","score":0.5188645124435425},{"id":"https://openalex.org/keywords/named-graph","display_name":"Named graph","score":0.5036024451255798},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4642311930656433},{"id":"https://openalex.org/keywords/database-design","display_name":"Database design","score":0.4587251842021942},{"id":"https://openalex.org/keywords/linked-data","display_name":"Linked data","score":0.4258129596710205},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.345151424407959}],"concepts":[{"id":"https://openalex.org/C41009113","wikidata":"https://www.wikidata.org/wiki/Q54871","display_name":"SPARQL","level":4,"score":0.9479336738586426},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.8364500999450684},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8206504583358765},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6867377758026123},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.6564077138900757},{"id":"https://openalex.org/C510870499","wikidata":"https://www.wikidata.org/wiki/Q47607","display_name":"SQL","level":2,"score":0.6535236835479736},{"id":"https://openalex.org/C24394798","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database management system","level":3,"score":0.5870010256767273},{"id":"https://openalex.org/C15657843","wikidata":"https://www.wikidata.org/wiki/Q1751819","display_name":"RDF Schema","level":5,"score":0.5532285571098328},{"id":"https://openalex.org/C5968703","wikidata":"https://www.wikidata.org/wiki/Q267136","display_name":"Database model","level":3,"score":0.5188645124435425},{"id":"https://openalex.org/C110893760","wikidata":"https://www.wikidata.org/wiki/Q3115590","display_name":"Named graph","level":5,"score":0.5036024451255798},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4642311930656433},{"id":"https://openalex.org/C148840519","wikidata":"https://www.wikidata.org/wiki/Q1049878","display_name":"Database design","level":2,"score":0.4587251842021942},{"id":"https://openalex.org/C69075417","wikidata":"https://www.wikidata.org/wiki/Q515701","display_name":"Linked data","level":3,"score":0.4258129596710205},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.345151424407959}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-023-00729-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00729-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00729-5","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:37340506","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37340506","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:pubmedcentral.nih.gov:10280967","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10280967","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10280967/pdf/13321_2023_Article_729.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:564d8cb6e9214647a637fa5ef7ff9ff7","is_oa":true,"landing_page_url":"https://doaj.org/article/564d8cb6e9214647a637fa5ef7ff9ff7","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-14 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00729-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00729-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00729-5","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2808607119","display_name":null,"funder_award_id":"61388963","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G7762211927","display_name":null,"funder_award_id":"RVO:61388963","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G954903593","display_name":null,"funder_award_id":"LM2018131","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"}],"funders":[{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4381337638.pdf"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W142231902","https://openalex.org/W2077004593","https://openalex.org/W2108723491","https://openalex.org/W2185907055","https://openalex.org/W2302501749","https://openalex.org/W2761148806","https://openalex.org/W2802734758","https://openalex.org/W2807294144","https://openalex.org/W2900090807","https://openalex.org/W2954428948","https://openalex.org/W2982975240","https://openalex.org/W2983166786","https://openalex.org/W3112376646","https://openalex.org/W3160452578","https://openalex.org/W3211718555","https://openalex.org/W4281658583","https://openalex.org/W4282926473"],"related_works":["https://openalex.org/W4299413097","https://openalex.org/W2952880872","https://openalex.org/W1935612762","https://openalex.org/W2294139181","https://openalex.org/W3033347047","https://openalex.org/W2416869599","https://openalex.org/W2615202182","https://openalex.org/W1651036378","https://openalex.org/W3086848874","https://openalex.org/W1596232896"],"abstract_inverted_index":{"Current":[0],"biological":[1,81],"and":[2,30,69,82,103,129,167,233],"chemical":[3,83],"research":[4],"is":[5,23,50,229],"increasingly":[6],"dependent":[7],"on":[8,55,60,70,194,231],"the":[9,43,61,71,77,88,100,125,134,150,154,237],"reusability":[10],"of":[11,42,90,133,201],"previously":[12],"acquired":[13],"data,":[14],"which":[15,176],"typically":[16],"come":[17],"from":[18,236],"various":[19],"sources.":[20],"Consequently,":[21],"there":[22],"a":[24,91,96,107,147,158,180,191,220],"growing":[25],"need":[26],"for":[27],"database":[28,93,98,110,127,152],"systems":[29,53,189,218],"databases":[31,84],"stored":[32,86],"in":[33,87,106,116,162],"them":[34],"to":[35,46,51,66,75,123,145,153,172,209],"be":[36,114,121,139,144,198],"interoperable":[37],"with":[38,190],"each":[39],"other.":[40],"One":[41],"possible":[44],"solutions":[45],"address":[47],"this":[48],"issue":[49],"use":[52,146],"based":[54],"Semantic":[56],"Web":[57],"technologies,":[58],"namely":[59],"Resource":[62],"Description":[63],"Framework":[64],"(RDF)":[65],"express":[67],"data":[68,136,161,232],"SPARQL":[72,170],"query":[73],"language":[74],"retrieve":[76],"data.":[78],"Many":[79],"existing":[80],"are":[85,177],"form":[89,102,166],"relational":[92,97,151,165],"(RDB).":[94],"Converting":[95],"into":[99],"RDF":[101,109,155],"storing":[104],"it":[105,205],"native":[108],"system":[111,148,159],"may":[112,120,137,143],"not":[113,138],"desirable":[115],"many":[117],"cases.":[118],"It":[119],"necessary":[122],"preserve":[124],"original":[126,164],"form,":[128],"having":[130],"two":[131],"versions":[132],"same":[135],"convenient.":[140],"A":[141],"solution":[142],"mapping":[149,188],"form.":[156],"Such":[157],"keeps":[160],"their":[163],"translates":[168],"incoming":[169],"queries":[171,234],"equivalent":[173],"SQL":[174],"queries,":[175],"evaluated":[178],"by":[179],"relational-database":[181],"system.":[182],"This":[183],"review":[184,214],"compares":[185,206],"different":[186,207],"RDB-to-RDF":[187,211],"primary":[192],"focus":[193],"those":[195],"that":[196,216],"can":[197],"used":[199],"free":[200],"charge.":[202],"In":[203],"addition,":[204],"approaches":[208],"expressing":[210],"mappings.":[212],"The":[213],"shows":[215],"these":[217],"represent":[219],"viable":[221],"method":[222],"providing":[223],"sufficient":[224],"performance.":[225],"Their":[226],"real-life":[227],"performance":[228],"demonstrated":[230],"coming":[235],"neXtProt":[238],"project.":[239]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
