{"id":"https://openalex.org/W4390988672","doi":"https://doi.org/10.1093/database/baad093","title":"An optimized relational database for querying structural patterns in proteins","display_name":"An optimized relational database for querying structural patterns in proteins","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4390988672","doi":"https://doi.org/10.1093/database/baad093","pmid":"https://pubmed.ncbi.nlm.nih.gov/38236197"},"language":"en","primary_location":{"id":"doi:10.1093/database/baad093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baad093","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baad093/56206892/baad093.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baad093/56206892/baad093.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010147021","display_name":"Renzo Angles","orcid":"https://orcid.org/0000-0002-6740-9711"},"institutions":[{"id":"https://openalex.org/I134695357","display_name":"University of Talca","ror":"https://ror.org/01s4gpq44","country_code":"CL","type":"education","lineage":["https://openalex.org/I134695357"]},{"id":"https://openalex.org/I4210167034","display_name":"Millennium Institute for Integrative Biology","ror":"https://ror.org/05xcmte05","country_code":"CL","type":"other","lineage":["https://openalex.org/I4210167034"]}],"countries":["CL"],"is_corresponding":false,"raw_author_name":"Renzo Angles","raw_affiliation_strings":["Department of Computer Science, Faculty of Engineering, Universidad de Talca , Camino a Los Niches Km. 1, Curic\u00f3, Regi\u00f3n del Maule 3340000, Chile","Millennium Institute for Foundational Research on Data (IMFD) , Vicu\u00f1a Mackenna 4860, Macul, Santiago, Regi\u00f3n Metropolitana 7810000, Chile"],"raw_orcid":"https://orcid.org/0000-0002-6740-9711","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Engineering, Universidad de Talca , Camino a Los Niches Km. 1, Curic\u00f3, Regi\u00f3n del Maule 3340000, Chile","institution_ids":["https://openalex.org/I134695357"]},{"raw_affiliation_string":"Millennium Institute for Foundational Research on Data (IMFD) , Vicu\u00f1a Mackenna 4860, Macul, Santiago, Regi\u00f3n Metropolitana 7810000, Chile","institution_ids":["https://openalex.org/I4210167034"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031521552","display_name":"Mauricio Arenas\u2010Salinas","orcid":"https://orcid.org/0000-0001-5143-1845"},"institutions":[{"id":"https://openalex.org/I134695357","display_name":"University of Talca","ror":"https://ror.org/01s4gpq44","country_code":"CL","type":"education","lineage":["https://openalex.org/I134695357"]}],"countries":["CL"],"is_corresponding":false,"raw_author_name":"Mauricio Arenas-Salinas","raw_affiliation_strings":["Centro de Bioinform\u00e1tica y Simulaci\u00f3n Molecular (CBSM), Faculty of Engineering, Universidad de Talca , Av. Lircay s/n, Talca Regi\u00f3n del Maule 34600000, Chile"],"raw_orcid":"https://orcid.org/0000-0001-5143-1845","affiliations":[{"raw_affiliation_string":"Centro de Bioinform\u00e1tica y Simulaci\u00f3n Molecular (CBSM), Faculty of Engineering, Universidad de Talca , Av. Lircay s/n, Talca Regi\u00f3n del Maule 34600000, Chile","institution_ids":["https://openalex.org/I134695357"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103076388","display_name":"Roberto Garc\u00eda","orcid":"https://orcid.org/0000-0001-6466-4541"},"institutions":[{"id":"https://openalex.org/I134695357","display_name":"University of Talca","ror":"https://ror.org/01s4gpq44","country_code":"CL","type":"education","lineage":["https://openalex.org/I134695357"]},{"id":"https://openalex.org/I4210167034","display_name":"Millennium Institute for Integrative Biology","ror":"https://ror.org/05xcmte05","country_code":"CL","type":"other","lineage":["https://openalex.org/I4210167034"]}],"countries":["CL"],"is_corresponding":false,"raw_author_name":"Roberto Garc\u00eda","raw_affiliation_strings":["Engineering Systems Doctoral Program, Faculty of Engineering, Universidad de Talca , Camino a Los Niches Km 1, Curic\u00f3, Regi\u00f3n del Maule 3340000, Chile","Millennium Institute for Foundational Research on Data (IMFD) , Vicu\u00f1a Mackenna 4860, Macul, Santiago, Regi\u00f3n Metropolitana 7810000, Chile"],"raw_orcid":"https://orcid.org/0000-0001-6466-4541","affiliations":[{"raw_affiliation_string":"Engineering Systems Doctoral Program, Faculty of Engineering, Universidad de Talca , Camino a Los Niches Km 1, Curic\u00f3, Regi\u00f3n del Maule 3340000, Chile","institution_ids":["https://openalex.org/I134695357"]},{"raw_affiliation_string":"Millennium Institute for Foundational Research on Data (IMFD) , Vicu\u00f1a Mackenna 4860, Macul, Santiago, Regi\u00f3n Metropolitana 7810000, Chile","institution_ids":["https://openalex.org/I4210167034"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003545971","display_name":"Ben Ingram","orcid":"https://orcid.org/0000-0003-4557-4342"},"institutions":[{"id":"https://openalex.org/I82284825","display_name":"Cranfield University","ror":"https://ror.org/05cncd958","country_code":"GB","type":"education","lineage":["https://openalex.org/I82284825"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ben Ingram","raw_affiliation_strings":["School of Water, Energy and Environment, Cranfield University , College Road, Cranfield, Bedfordshire MK43 0AL, England"],"raw_orcid":"https://orcid.org/0000-0003-4557-4342","affiliations":[{"raw_affiliation_string":"School of Water, Energy and Environment, Cranfield University , College Road, Cranfield, Bedfordshire MK43 0AL, England","institution_ids":["https://openalex.org/I82284825"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.7465,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.67814994,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"2024","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9966999888420105,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9966999888420105,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9829999804496765,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9819999933242798,"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":0.8392645716667175},{"id":"https://openalex.org/keywords/database-schema","display_name":"Database schema","score":0.6689797639846802},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.6395672559738159},{"id":"https://openalex.org/keywords/database-design","display_name":"Database design","score":0.6311523914337158},{"id":"https://openalex.org/keywords/relational-database-management-system","display_name":"Relational database management system","score":0.5605646371841431},{"id":"https://openalex.org/keywords/view","display_name":"View","score":0.5570427775382996},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5407441258430481},{"id":"https://openalex.org/keywords/database-model","display_name":"Database model","score":0.5375909805297852},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5148850679397583},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.49429917335510254},{"id":"https://openalex.org/keywords/schema","display_name":"Schema (genetic algorithms)","score":0.4826817810535431},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46078550815582275},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.43014290928840637},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.4136335253715515},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15262320637702942}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8392645716667175},{"id":"https://openalex.org/C30775581","wikidata":"https://www.wikidata.org/wiki/Q632285","display_name":"Database schema","level":3,"score":0.6689797639846802},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.6395672559738159},{"id":"https://openalex.org/C148840519","wikidata":"https://www.wikidata.org/wiki/Q1049878","display_name":"Database design","level":2,"score":0.6311523914337158},{"id":"https://openalex.org/C24394798","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database management system","level":3,"score":0.5605646371841431},{"id":"https://openalex.org/C54239708","wikidata":"https://www.wikidata.org/wiki/Q1329910","display_name":"View","level":3,"score":0.5570427775382996},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5407441258430481},{"id":"https://openalex.org/C5968703","wikidata":"https://www.wikidata.org/wiki/Q267136","display_name":"Database model","level":3,"score":0.5375909805297852},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5148850679397583},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49429917335510254},{"id":"https://openalex.org/C52146309","wikidata":"https://www.wikidata.org/wiki/Q7431116","display_name":"Schema (genetic algorithms)","level":2,"score":0.4826817810535431},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46078550815582275},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.43014290928840637},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.4136335253715515},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15262320637702942},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baad093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baad093","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baad093/56206892/baad093.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:38236197","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38236197","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10939390","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10939390","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10939390/pdf/baad093.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":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baad093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baad093","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baad093/56206892/baad093.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5027483003","display_name":"DEVELOPING THE FOUNDATIONS AND APPLICATIONS OF PATH MANIPULATION OPERATIONS","funder_award_id":"1221727","funder_id":"https://openalex.org/F4320331146","funder_display_name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo"},{"id":"https://openalex.org/G6016326127","display_name":null,"funder_award_id":"21192157","funder_id":"https://openalex.org/F4320334812","funder_display_name":"Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"}],"funders":[{"id":"https://openalex.org/F4320331146","display_name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo","ror":null},{"id":"https://openalex.org/F4320334812","display_name":"Comisi\u00f3n Nacional de Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","ror":"https://ror.org/02ap3w078"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390988672.pdf"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1480121071","https://openalex.org/W1536826708","https://openalex.org/W1568771894","https://openalex.org/W1971459549","https://openalex.org/W1975837734","https://openalex.org/W1989329332","https://openalex.org/W1991470077","https://openalex.org/W2000864931","https://openalex.org/W2015372451","https://openalex.org/W2053658804","https://openalex.org/W2077396040","https://openalex.org/W2093377893","https://openalex.org/W2110498021","https://openalex.org/W2113865463","https://openalex.org/W2123887743","https://openalex.org/W2129237258","https://openalex.org/W2130479394","https://openalex.org/W2130675570","https://openalex.org/W2132696400","https://openalex.org/W2160672469","https://openalex.org/W2167357284","https://openalex.org/W2251484078","https://openalex.org/W2288573127","https://openalex.org/W2288713920","https://openalex.org/W2296150852","https://openalex.org/W2322633051","https://openalex.org/W2380711945","https://openalex.org/W2544136853","https://openalex.org/W2770646498","https://openalex.org/W2782733505","https://openalex.org/W3011505309","https://openalex.org/W3046345744","https://openalex.org/W3111613574","https://openalex.org/W3188069612","https://openalex.org/W4388451167","https://openalex.org/W6696563654","https://openalex.org/W6710279331","https://openalex.org/W7075630220"],"related_works":["https://openalex.org/W3085968255","https://openalex.org/W279222092","https://openalex.org/W1502610062","https://openalex.org/W1588786827","https://openalex.org/W1016652228","https://openalex.org/W2188578519","https://openalex.org/W2153455914","https://openalex.org/W2591891926","https://openalex.org/W2955692919","https://openalex.org/W2477254085"],"abstract_inverted_index":{"A":[0],"database":[1,73,98],"is":[2,40],"an":[3],"essential":[4],"component":[5],"in":[6,46,85],"almost":[7],"any":[8],"software":[9],"system,":[10],"and":[11,20,28,79,103],"its":[12],"creation":[13],"involves":[14],"more":[15],"than":[16],"just":[17],"data":[18],"modeling":[19],"schema":[21],"design.":[22],"It":[23],"also":[24],"includes":[25],"query":[26],"optimization":[27,69],"tuning.":[29],"This":[30,65],"paper":[31],"focuses":[32],"on":[33],"a":[34,51],"web":[35],"system":[36,49],"called":[37],"GSP4PDB,":[38],"which":[39,55],"used":[41],"for":[42,62],"searching":[43],"structural":[44,106],"patterns":[45],"proteins.":[47],"The":[48,81],"utilizes":[50],"normalized":[52],"relational":[53],"database,":[54],"has":[56],"proven":[57],"to":[58],"be":[59],"inefficient":[60],"even":[61],"simple":[63],"queries.":[64],"article":[66,87],"discusses":[67],"the":[68,71,86,94,97],"of":[70,96],"GSP4PDB":[72],"by":[74],"implementing":[75],"two":[76],"techniques:":[77],"denormalization":[78],"indexing.":[80],"empirical":[82],"evaluation":[83],"described":[84],"shows":[88],"that":[89],"combining":[90],"these":[91],"techniques":[92],"enhances":[93],"efficiency":[95],"when":[99],"querying":[100],"both":[101],"real":[102],"artificial":[104],"graph-based":[105],"patterns.":[107]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
