{"id":"https://openalex.org/W2103707329","doi":"https://doi.org/10.1093/bioinformatics/bts030","title":"medpie: an information extraction package for medical message board posts","display_name":"medpie: an information extraction package for medical message board posts","publication_year":2012,"publication_date":"2012-01-19","ids":{"openalex":"https://openalex.org/W2103707329","doi":"https://doi.org/10.1093/bioinformatics/bts030","mag":"2103707329","pmid":"https://pubmed.ncbi.nlm.nih.gov/22262673"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts030","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts030","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/5/743/689838/bts030.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/28/5/743/689838/bts030.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015913526","display_name":"Allyson Lucinda Benton","orcid":"https://orcid.org/0000-0002-2685-4114"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. Benton","raw_affiliation_strings":["1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032708536","display_name":"John H. Holmes","orcid":"https://orcid.org/0000-0003-2167-3602"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. H. Holmes","raw_affiliation_strings":["1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079348469","display_name":"Steven Hill","orcid":"https://orcid.org/0000-0003-1840-3767"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Hill","raw_affiliation_strings":["1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030295784","display_name":"Annie Chung","orcid":"https://orcid.org/0000-0002-3072-7038"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Chung","raw_affiliation_strings":["1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044944954","display_name":"Lyle Ungar","orcid":"https://orcid.org/0000-0003-2047-1443"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"L. Ungar","raw_affiliation_strings":["1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, 2University of Pennsylvania, The Wharton School, Department of Operations and Information Management and 3University of Pennsylvania School of Engineering and Applied Science, Department of Computer and Information Science, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5015913526"],"corresponding_institution_ids":["https://openalex.org/I79576946"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2907,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.89778491,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"28","issue":"5","first_page":"743","last_page":"744"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9528999924659729,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9528999924659729,"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/T10737","display_name":"Health Literacy and Information Accessibility","score":0.9423999786376953,"subfield":{"id":"https://openalex.org/subfields/3600","display_name":"General Health Professions"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9315000176429749,"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":0.6797980070114136},{"id":"https://openalex.org/keywords/medical-information","display_name":"Medical information","score":0.5374188423156738},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.5330926775932312},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4261581003665924},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.41009607911109924},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3710131049156189},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35705769062042236},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3509123623371124},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1438838541507721}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6797980070114136},{"id":"https://openalex.org/C3019150057","wikidata":"https://www.wikidata.org/wiki/Q92779279","display_name":"Medical information","level":2,"score":0.5374188423156738},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.5330926775932312},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4261581003665924},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.41009607911109924},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3710131049156189},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35705769062042236},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3509123623371124},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1438838541507721},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004032","descriptor_name":"Diet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004032","descriptor_name":"Diet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004032","descriptor_name":"Diet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008490","descriptor_name":"Medical Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008490","descriptor_name":"Medical Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008490","descriptor_name":"Medical Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D016907","descriptor_name":"Adverse Drug Reaction Reporting Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016907","descriptor_name":"Adverse Drug Reaction Reporting Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016907","descriptor_name":"Adverse Drug Reaction Reporting Systems","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts030","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts030","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/5/743/689838/bts030.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:22262673","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22262673","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:europepmc.org:2581825","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3289922","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts030","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts030","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/5/743/689838/bts030.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/G765924629","display_name":null,"funder_award_id":"RC1 LM010342","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W257334765","https://openalex.org/W1732045928","https://openalex.org/W1987581851","https://openalex.org/W2069870853","https://openalex.org/W2147686623","https://openalex.org/W2160987310","https://openalex.org/W6609639407","https://openalex.org/W6637554045","https://openalex.org/W6681616754","https://openalex.org/W6683596099"],"related_works":["https://openalex.org/W2377297411","https://openalex.org/W3148217948","https://openalex.org/W2375788636","https://openalex.org/W2358561207","https://openalex.org/W2388704129","https://openalex.org/W2149263892","https://openalex.org/W4235496431","https://openalex.org/W2155302041","https://openalex.org/W1990412843","https://openalex.org/W3042945901"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"have":[2],"developed":[3],"medpie,":[4],"a":[5,44],"software":[6],"package":[7,30],"for":[8,20],"preparing":[9],"medical":[10],"message":[11],"board":[12],"corpora":[13],"and":[14,18,23,37,51],"extracting":[15],"patient":[16],"mentions":[17],"statistics":[19],"drugs,":[21,49],"herbs":[22,50],"adverse":[24,52],"effects":[25],"experienced":[26],"from":[27],"them.":[28],"The":[29],"is":[31],"divided":[32],"into":[33],"web-crawling,":[34],"HTML-cleaning,":[35],"de-identification":[36],"information":[38],"extraction":[39],"modules.":[40],"It":[41],"also":[42],"includes":[43],"sample":[45],"controlled":[46],"vocabulary":[47],"of":[48],"effect":[53],"terms.":[54],"AVAILABILITY:":[55],"http://www.cis.upenn.edu/~ungar/medpie.zip.":[56],"DEPENDENCIES:":[57],"Python":[58],"2.6":[59],"or":[60],"2.7.":[61]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
