{"id":"https://openalex.org/W2103613886","doi":"https://doi.org/10.1093/database/baq021","title":"PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan","display_name":"PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan","publication_year":2010,"publication_date":"2010-08-25","ids":{"openalex":"https://openalex.org/W2103613886","doi":"https://doi.org/10.1093/database/baq021","mag":"2103613886","pmid":"https://pubmed.ncbi.nlm.nih.gov/20798081"},"language":"en","primary_location":{"id":"doi:10.1093/database/baq021","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baq021","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baq021/1136369/baq021.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/baq021/1136369/baq021.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080613861","display_name":"Akira R. Kinjo","orcid":"https://orcid.org/0000-0002-4006-8208"},"institutions":[{"id":"https://openalex.org/I4210152009","display_name":"Protein Research Foundation","ror":"https://ror.org/03yzv7g36","country_code":"JP","type":"other","lineage":["https://openalex.org/I4210152009"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"A. R. Kinjo","raw_affiliation_strings":["Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. akinjo@protein.osaka-u.ac.jp","Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. akinjo@protein.osaka-u.ac.jp","institution_ids":["https://openalex.org/I4210152009"]},{"raw_affiliation_string":"Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101697566","display_name":"Riu Yamashita","orcid":"https://orcid.org/0000-0003-0068-6949"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"R. Yamashita","raw_affiliation_strings":["Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109030144","display_name":"H. Nakamura","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"H. Nakamura","raw_affiliation_strings":["Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"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":0.8055,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.71878456,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"2010","issue":"0","first_page":"baq021","last_page":"baq021"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9847999811172485,"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/xpath","display_name":"XPath","score":0.9035272598266602},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8408211469650269},{"id":"https://openalex.org/keywords/xml-database","display_name":"XML database","score":0.7369232177734375},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.642254114151001},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5925866961479187},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.5832911729812622},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5672917366027832},{"id":"https://openalex.org/keywords/sql","display_name":"SQL","score":0.5526106953620911},{"id":"https://openalex.org/keywords/view","display_name":"View","score":0.4598046839237213},{"id":"https://openalex.org/keywords/database-model","display_name":"Database model","score":0.4596843421459198},{"id":"https://openalex.org/keywords/xquery","display_name":"XQuery","score":0.4532237946987152},{"id":"https://openalex.org/keywords/streaming-xml","display_name":"Streaming XML","score":0.4469642639160156},{"id":"https://openalex.org/keywords/table","display_name":"Table (database)","score":0.43823176622390747},{"id":"https://openalex.org/keywords/semi-structured-data","display_name":"Semi-structured data","score":0.42438799142837524},{"id":"https://openalex.org/keywords/database-design","display_name":"Database design","score":0.40610432624816895},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2627202868461609}],"concepts":[{"id":"https://openalex.org/C2780213375","wikidata":"https://www.wikidata.org/wiki/Q16340","display_name":"XPath","level":4,"score":0.9035272598266602},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8408211469650269},{"id":"https://openalex.org/C183068750","wikidata":"https://www.wikidata.org/wiki/Q357393","display_name":"XML database","level":3,"score":0.7369232177734375},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.642254114151001},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5925866961479187},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.5832911729812622},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5672917366027832},{"id":"https://openalex.org/C510870499","wikidata":"https://www.wikidata.org/wiki/Q47607","display_name":"SQL","level":2,"score":0.5526106953620911},{"id":"https://openalex.org/C54239708","wikidata":"https://www.wikidata.org/wiki/Q1329910","display_name":"View","level":3,"score":0.4598046839237213},{"id":"https://openalex.org/C5968703","wikidata":"https://www.wikidata.org/wiki/Q267136","display_name":"Database model","level":3,"score":0.4596843421459198},{"id":"https://openalex.org/C2780512708","wikidata":"https://www.wikidata.org/wiki/Q850661","display_name":"XQuery","level":4,"score":0.4532237946987152},{"id":"https://openalex.org/C44883583","wikidata":"https://www.wikidata.org/wiki/Q7622687","display_name":"Streaming XML","level":3,"score":0.4469642639160156},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.43823176622390747},{"id":"https://openalex.org/C40077939","wikidata":"https://www.wikidata.org/wiki/Q2336004","display_name":"Semi-structured data","level":3,"score":0.42438799142837524},{"id":"https://openalex.org/C148840519","wikidata":"https://www.wikidata.org/wiki/Q1049878","display_name":"Database design","level":2,"score":0.40610432624816895},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2627202868461609}],"mesh":[{"descriptor_ui":"D007564","descriptor_name":"Japan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007564","descriptor_name":"Japan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007564","descriptor_name":"Japan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baq021","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baq021","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baq021/1136369/baq021.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:20798081","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20798081","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:2997606","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2997606","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baq021","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baq021","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baq021/1136369/baq021.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":[],"funders":[{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2103613886.pdf","grobid_xml":"https://content.openalex.org/works/W2103613886.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1964640688","https://openalex.org/W1977064288","https://openalex.org/W2013617281","https://openalex.org/W2061636126","https://openalex.org/W2109872885","https://openalex.org/W2119087770","https://openalex.org/W2139242647","https://openalex.org/W2150306348","https://openalex.org/W2150852650","https://openalex.org/W2158714788","https://openalex.org/W2161062388","https://openalex.org/W4243649771"],"related_works":["https://openalex.org/W2355446901","https://openalex.org/W2486756614","https://openalex.org/W4213327256","https://openalex.org/W2073024456","https://openalex.org/W2062115694","https://openalex.org/W4252166815","https://openalex.org/W1997305375","https://openalex.org/W214946328","https://openalex.org/W4253215314","https://openalex.org/W1517184773"],"abstract_inverted_index":{"This":[0],"article":[1],"is":[2,117,133],"a":[3,8,145,182,189],"tutorial":[4],"for":[5,14,47,105],"PDBj":[6,21,51,71,186],"Mine,":[7,22],"new":[9],"database":[10,65,173],"and":[11,67,84,87,156,197],"its":[12],"interface":[13],"Protein":[15],"Data":[16],"Bank":[17],"Japan":[18],"(PDBj).":[19],"In":[20],"data":[23,88,104],"are":[24,44,78,89,109,142],"loaded":[25],"from":[26,128],"files":[27,77],"in":[28,91,181],"the":[29,48,53,59,63,92,96,100,112,120,129,165,172,192,198,201],"PDBMLplus":[30,76,130],"format":[31],"(an":[32],"extension":[33],"of":[34,50,62,70,75,99,125,191,194,200],"PDBML,":[35],"PDB's":[36],"canonical":[37],"XML":[38,101,131,195],"format,":[39],"enriched":[40],"with":[41],"annotations),":[42],"which":[43,159,177],"then":[45],"served":[46],"user":[49],"via":[52],"worldwide":[54],"web":[55,68],"(WWW).":[56],"We":[57],"describe":[58],"basic":[60],"design":[61],"relational":[64,114],"(RDB)":[66],"interfaces":[69],"Mine.":[72],"The":[73,103,123],"contents":[74],"first":[79],"broken":[80],"into":[81,111,144],"XPath":[82,107,121],"entities,":[83],"these":[85],"paths":[86],"indexed":[90],"way":[93],"that":[94,116],"reflects":[95],"hierarchical":[97],"structure":[98],"files.":[102],"each":[106],"type":[108],"saved":[110],"corresponding":[113],"table":[115,126],"named":[118],"as":[119],"itself.":[122],"generation":[124],"definitions":[127],"schema":[132],"fully":[134],"automated.":[135],"For":[136],"efficient":[137],"search,":[138,155],"frequently":[139],"queried":[140],"terms":[141],"compiled":[143],"brief":[146],"summary":[147],"table.":[148],"Casual":[149],"users":[150,169],"can":[151,160,170,178],"perform":[152],"simple":[153],"keyword":[154],"'Advanced":[157],"Search'":[158],"specify":[161],"various":[162],"conditions":[163],"on":[164],"entries.":[166],"More":[167],"experienced":[168],"query":[171],"using":[174],"SQL":[175],"statements":[176],"be":[179],"constructed":[180],"uniform":[183],"manner.":[184],"Thus,":[185],"Mine":[187],"achieves":[188],"combination":[190],"flexibility":[193],"documents":[196],"robustness":[199],"RDB.":[202],"Database":[203],"URL:":[204],"http://www.pdbj.org/":[205]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
