{"id":"https://openalex.org/W2163385116","doi":"https://doi.org/10.1093/bioinformatics/btq715","title":"A Java API for working with PubChem datasets","display_name":"A Java API for working with PubChem datasets","publication_year":2011,"publication_date":"2011-01-06","ids":{"openalex":"https://openalex.org/W2163385116","doi":"https://doi.org/10.1093/bioinformatics/btq715","mag":"2163385116","pmid":"https://pubmed.ncbi.nlm.nih.gov/21216779"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq715","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq715","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/741/48867340/bioinformatics_27_5_741.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/741/48867340/bioinformatics_27_5_741.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110013943","display_name":"Mark R. Southern","orcid":null},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark R. Southern","raw_affiliation_strings":["Translational Research Institute and Molecular Therapeutics, The Scripps Research Institute, , Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Research Institute and Molecular Therapeutics, The Scripps Research Institute, , Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000139914","display_name":"Patrick R. Griffin","orcid":"https://orcid.org/0000-0002-3404-690X"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick R. Griffin","raw_affiliation_strings":["Translational Research Institute and Molecular Therapeutics, The Scripps Research Institute, , Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Research Institute and Molecular Therapeutics, The Scripps Research Institute, , Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA","institution_ids":["https://openalex.org/I123431417"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5110013943"],"corresponding_institution_ids":["https://openalex.org/I123431417"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9787,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.77568725,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"27","issue":"5","first_page":"741","last_page":"742"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6345000267028809,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.6345000267028809,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.07169999927282333,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.03240000084042549,"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/pubchem","display_name":"PubChem","score":0.9827022552490234},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7030901908874512},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5468981266021729},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5296936631202698},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5161494016647339},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.44349780678749084},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44201990962028503},{"id":"https://openalex.org/keywords/java-applet","display_name":"Java applet","score":0.42726579308509827},{"id":"https://openalex.org/keywords/web-resource","display_name":"Web resource","score":0.41165655851364136},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.20216432213783264},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09789887070655823},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.09017768502235413}],"concepts":[{"id":"https://openalex.org/C158180186","wikidata":"https://www.wikidata.org/wiki/Q278487","display_name":"PubChem","level":2,"score":0.9827022552490234},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7030901908874512},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5468981266021729},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5296936631202698},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5161494016647339},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.44349780678749084},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44201990962028503},{"id":"https://openalex.org/C15524039","wikidata":"https://www.wikidata.org/wiki/Q865817","display_name":"Java applet","level":3,"score":0.42726579308509827},{"id":"https://openalex.org/C65603577","wikidata":"https://www.wikidata.org/wiki/Q3427877","display_name":"Web resource","level":2,"score":0.41165655851364136},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.20216432213783264},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09789887070655823},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.09017768502235413}],"mesh":[{"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":"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":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq715","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq715","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/741/48867340/bioinformatics_27_5_741.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21216779","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21216779","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3105478","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3105478","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq715","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq715","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/741/48867340/bioinformatics_27_5_741.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1846198318","display_name":null,"funder_award_id":"U19 DA026838","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G414296946","display_name":null,"funder_award_id":"U54 MH084512","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G6814112452","display_name":null,"funder_award_id":"5 U54 MH084512-02","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"}],"funders":[{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W1496826797","https://openalex.org/W1601495365","https://openalex.org/W2016017240","https://openalex.org/W2080886752","https://openalex.org/W2127553917"],"related_works":["https://openalex.org/W2363664451","https://openalex.org/W2362572990","https://openalex.org/W1566439789","https://openalex.org/W2087788498","https://openalex.org/W1529272169","https://openalex.org/W2035527068","https://openalex.org/W2378903629","https://openalex.org/W2584926276","https://openalex.org/W2235564429","https://openalex.org/W2358098929"],"abstract_inverted_index":{"UNLABELLED:":[0],"PubChem":[1,14,37,95,107,111,151,170],"is":[2,146,155,178],"a":[3,76,86,124,160,173,189],"public":[4],"repository":[5],"of":[6,137],"chemical":[7,115,130],"structures":[8],"and":[9,21,23,40,54,97,106,113,121,133,135,194],"associated":[10,114],"biological":[11,24],"activities.":[12],"The":[13,36,153],"BioAssay":[15],"database":[16,174],"contains":[17],"assay":[18],"descriptions,":[19],"conditions":[20],"readouts":[22],"screening":[25],"results":[26],"that":[27,145],"have":[28],"been":[29],"submitted":[30],"by":[31,74],"the":[32,52,81,94,103],"biomedical":[33],"research":[34],"community.":[35],"web":[38,45,109],"site":[39],"Power":[41],"User":[42],"Gateway":[43],"(PUG)":[44],"service":[46],"allow":[47],"users":[48],"to":[49,65,79,93,156,168,187],"interact":[50],"with":[51,89,98,159],"data":[53],"raw":[55],"files":[56],"are":[57,63],"available":[58,149],"via":[59],"FTP.":[60],"These":[61],"resources":[62],"helpful":[64],"many":[66],"but":[67,186],"there":[68],"can":[69,117],"also":[70],"be":[71,119],"great":[72],"benefit":[73],"using":[75],"software":[77],"API":[78,88],"manipulate":[80,169],"data.":[82],"Here,":[83],"we":[84],"describe":[85],"Java":[87],"entity":[90],"objects":[91],"mapped":[92],"Schema":[96],"wrapper":[99],"functions":[100],"for":[101,191],"calling":[102],"NCBI":[104],"eUtilities":[105],"PUG":[108],"services.":[110],"BioAssays":[112,171],"compounds":[116],"then":[118],"queried":[120],"manipulated":[122],"in":[123,172],"local":[125,164],"relational":[126],"database.":[127],"Features":[128],"include":[129],"structure":[131],"searching":[132],"generation":[134],"display":[136],"curve":[138],"fits":[139],"from":[140,166],"stored":[141],"dose-response":[142],"experiments,":[143],"something":[144],"not":[147,179],"yet":[148],"within":[150],"itself.":[152],"aim":[154],"provide":[157,188],"researchers":[158],"fast,":[161],"consistent,":[162],"queryable":[163],"resource":[165],"which":[167],"agnostic":[175],"manner.":[176],"It":[177],"intended":[180],"as":[181],"an":[182],"end":[183],"user":[184],"tool":[185],"platform":[190],"further":[192],"automation":[193],"tools":[195],"development.":[196],"AVAILABILITY:":[197],"http://code.google.com/p/pubchemdb.":[198]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
