{"id":"https://openalex.org/W7128808092","doi":"https://doi.org/10.21105/joss.09950","title":"dbparser: An R Package for Parsing and Integrating Pharmacological Databases","display_name":"dbparser: An R Package for Parsing and Integrating Pharmacological Databases","publication_year":2026,"publication_date":"2026-02-13","ids":{"openalex":"https://openalex.org/W7128808092","doi":"https://doi.org/10.21105/joss.09950"},"language":null,"primary_location":{"id":"doi:10.21105/joss.09950","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.09950","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.09950.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"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 Open Source Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.09950.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5125951111","display_name":"Mohammed Y. Ali","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Mohammed Ali","raw_affiliation_strings":["Independent Researcher"],"affiliations":[{"raw_affiliation_string":"Independent Researcher","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003922274","display_name":"Ali Ezzat","orcid":"https://orcid.org/0000-0002-7426-3888"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ali Ezzat","raw_affiliation_strings":["Independent Researcher"],"affiliations":[{"raw_affiliation_string":"Independent Researcher","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5125951111"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.49393073,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"11","issue":"118","first_page":"9950","last_page":"9950"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.3319999873638153,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.3319999873638153,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.19189999997615814,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.12349999696016312,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/parsing","display_name":"Parsing","score":0.8190000057220459},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6043000221252441},{"id":"https://openalex.org/keywords/bottom-up-parsing","display_name":"Bottom-up parsing","score":0.3095000088214874}],"concepts":[{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.8190000057220459},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8159999847412109},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6043000221252441},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5523999929428101},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4683000147342682},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.45179998874664307},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4016999900341034},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3303000032901764},{"id":"https://openalex.org/C60690694","wikidata":"https://www.wikidata.org/wiki/Q894902","display_name":"Bottom-up parsing","level":4,"score":0.3095000088214874},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.25}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21105/joss.09950","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.09950","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.09950.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"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 Open Source Software","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.21105/joss.09950","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.09950","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.09950.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"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 Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320313996","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7128808092.pdf","grobid_xml":"https://content.openalex.org/works/W7128808092.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W2054730686","https://openalex.org/W2119002393","https://openalex.org/W2160697532","https://openalex.org/W2767891136","https://openalex.org/W2990427812","https://openalex.org/W3117618393","https://openalex.org/W3128009357","https://openalex.org/W3144103640","https://openalex.org/W4235243453","https://openalex.org/W4296394314","https://openalex.org/W4308630679","https://openalex.org/W4313526385","https://openalex.org/W4386859869","https://openalex.org/W4389158587","https://openalex.org/W4390012867","https://openalex.org/W4393156180","https://openalex.org/W4403599112"],"related_works":[],"abstract_inverted_index":{"dbparser":[0,82],"is":[1,50],"an":[2],"rOpenSci":[3],"peer-reviewed":[4],"R":[5,24],"package":[6,26],"that":[7],"provides":[8],"a":[9,53,59,84],"unified":[10],"framework":[11],"for":[12],"parsing":[13,73],"and":[14,18,43,78,91],"integrating":[15],"major":[16],"pharmacological":[17],"pharmacovigilance":[19],"databases":[20],"into":[21,52],"standardized,":[22],"analysis-ready":[23],"objects.The":[25],"supports":[27],"three":[28],"essential":[29],"drug":[30,95],"information":[31],"resources:":[32],"DrugBank":[33],"(Wishart":[34],"et":[35,40,46],"al.,":[36,41,47],"2018),":[37],"OnSIDES":[38],"(Galeano":[39],"2022)":[42],"TWOSIDES":[44],"(Tatonetti":[45],"2012).Each":[48],"database":[49],"parsed":[51],"consistent":[54],"nested":[55],"list":[56],"structure":[57],"called":[58],"dvobject,":[60],"which":[61],"preserves":[62],"complex":[63],"relational":[64],"hierarchies":[65],"while":[66],"enabling":[67],"seamless":[68],"crossdatabase":[69],"integration.By":[70],"providing":[71],"high-performance":[72],"functions,":[74],"chainable":[75],"merge":[76],"operations,":[77],"comprehensive":[79],"metadata":[80],"tracking,":[81],"eliminates":[83],"significant":[85],"bottleneck":[86],"in":[87],"computational":[88],"pharmacology":[89],"research":[90],"enables":[92],"reproducible,":[93],"large-scale":[94],"safety":[96],"analyses.":[97]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2026-02-13T00:00:00"}