{"id":"https://openalex.org/W4388592618","doi":"https://doi.org/10.1093/bioinformatics/btad603","title":"PEDL+: protein-centered relation extraction from PubMed at your fingertip","display_name":"PEDL+: protein-centered relation extraction from PubMed at your fingertip","publication_year":2023,"publication_date":"2023-11-01","ids":{"openalex":"https://openalex.org/W4388592618","doi":"https://doi.org/10.1093/bioinformatics/btad603","pmid":"https://pubmed.ncbi.nlm.nih.gov/37950510"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad603","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad603","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad603/53180165/btad603.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad603/53180165/btad603.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041680406","display_name":"Leon Weber","orcid":"https://orcid.org/0000-0002-2499-472X"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Leon Weber","raw_affiliation_strings":["Center for Information and Language Processing, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen , Geschwister-Scholl-Platz 1 , M\u00fcnchen 80539, Germany"],"raw_orcid":"https://orcid.org/0000-0002-2499-472X","affiliations":[{"raw_affiliation_string":"Center for Information and Language Processing, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen , Geschwister-Scholl-Platz 1 , M\u00fcnchen 80539, Germany","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039156783","display_name":"Fabio Barth","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fabio Barth","raw_affiliation_strings":["Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Unter den Linden 6 , Berlin 10099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Unter den Linden 6 , Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012206987","display_name":"L. J. Lorenz","orcid":"https://orcid.org/0000-0002-1471-5782"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Leonie Lorenz","raw_affiliation_strings":["Pathogen Informatics and Modelling, EMBL-EBI , Hinxton, Cambridgeshire CB10 1SD, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pathogen Informatics and Modelling, EMBL-EBI , Hinxton, Cambridgeshire CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083286814","display_name":"Fabian Konrath","orcid":"https://orcid.org/0000-0002-6843-6252"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fabian Konrath","raw_affiliation_strings":["Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine , Robert-R\u00f6ssle-Str. 10 , Berlin 13125, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine , Robert-R\u00f6ssle-Str. 10 , Berlin 13125, Germany","institution_ids":["https://openalex.org/I205582932"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093243294","display_name":"Kirsten Huska","orcid":null},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kirsten Huska","raw_affiliation_strings":["Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine , Robert-R\u00f6ssle-Str. 10 , Berlin 13125, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine , Robert-R\u00f6ssle-Str. 10 , Berlin 13125, Germany","institution_ids":["https://openalex.org/I205582932"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011931952","display_name":"Jana Wolf","orcid":"https://orcid.org/0000-0003-3254-5868"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jana Wolf","raw_affiliation_strings":["Department of Mathematics and Computer Science, Free University Berlin , Berlin, 14195, Germany","Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine , Robert-R\u00f6ssle-Str. 10 , Berlin 13125, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, Free University Berlin , Berlin, 14195, Germany","institution_ids":["https://openalex.org/I75951250"]},{"raw_affiliation_string":"Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine , Robert-R\u00f6ssle-Str. 10 , Berlin 13125, Germany","institution_ids":["https://openalex.org/I205582932"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055236937","display_name":"Ulf Leser","orcid":"https://orcid.org/0000-0003-2166-9582"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ulf Leser","raw_affiliation_strings":["Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Unter den Linden 6 , Berlin 10099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Unter den Linden 6 , Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5011931952","https://openalex.org/A5055236937"],"corresponding_institution_ids":["https://openalex.org/I205582932","https://openalex.org/I39343248","https://openalex.org/I75951250"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6727,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.71569238,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":"39","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9905999898910522,"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":0.9905999898910522,"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":0.0019000000320374966,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.00139999995008111,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7959862947463989},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7580132484436035},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.6872836947441101},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.6648153066635132},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.6294047236442566},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5104066729545593},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5002772808074951},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4731995761394501},{"id":"https://openalex.org/keywords/data-extraction","display_name":"Data extraction","score":0.43837612867355347},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4319302439689636},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41741758584976196},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3822188973426819},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13946732878684998},{"id":"https://openalex.org/keywords/medline","display_name":"MEDLINE","score":0.12341922521591187},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09668087959289551}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7959862947463989},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7580132484436035},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.6872836947441101},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.6648153066635132},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.6294047236442566},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5104066729545593},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5002772808074951},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4731995761394501},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.43837612867355347},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4319302439689636},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41741758584976196},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3822188973426819},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13946732878684998},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.12341922521591187},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09668087959289551},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"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":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/btad603","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad603","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad603/53180165/btad603.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37950510","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37950510","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:edoc.mdc-berlin.de:23862","is_oa":true,"landing_page_url":null,"pdf_url":"http://edoc.mdc-berlin.de/23862/1/23862oa.pdf","source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:edoc.mdc-berlin.de:23862","is_oa":true,"landing_page_url":"https://orcid.org/0000-0002-2499-472X","pdf_url":"https://edoc.mdc-berlin.de/id/eprint/23862/7/23862suppl.pdf","source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"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":"Article"},{"id":"pmh:oai:epub.ub.uni-muenchen.de:130032","is_oa":true,"landing_page_url":"http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-130032-5","pdf_url":"https://epub.ub.uni-muenchen.de/130032/1/btad603.pdf","source":{"id":"https://openalex.org/S4306401845","display_name":"Open access LMU (Ludwid Maxmilian's Universitat Munchen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I8204097","host_organization_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","host_organization_lineage":["https://openalex.org/I8204097"],"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":"Bioinformatics","raw_type":"doc-type:article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10660277","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10660277","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10660277/pdf/btad603.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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:refubium.fu-berlin.de:fub188/42098","is_oa":true,"landing_page_url":"https://refubium.fu-berlin.de/handle/fub188/42098","pdf_url":"https://refubium.fu-berlin.de/bitstream/fub188/42098/1/btad603.pdf","source":{"id":"https://openalex.org/S4306402444","display_name":"Refubium (Universit\u00e4tsbibliothek der Freien Universit\u00e4t Berlin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I75951250","host_organization_name":"Freie Universit\u00e4t Berlin","host_organization_lineage":["https://openalex.org/I75951250"],"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":"","raw_type":"doc-type:article"},{"id":"doi:10.17169/refubium-41823","is_oa":true,"landing_page_url":"https://doi.org/10.17169/refubium-41823","pdf_url":null,"source":{"id":"https://openalex.org/S7407052913","display_name":"Universit\u00e4tsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad603","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad603","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad603/53180165/btad603.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.41999998688697815,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G7215454324","display_name":null,"funder_award_id":"CRC 1404 FONDA","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320306903","display_name":"Chesapeake Research Consortium","ror":"https://ror.org/00f2ymb10"},{"id":"https://openalex.org/F4320308022","display_name":"California Department of Fish and Game","ror":"https://ror.org/02v6w2r95"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388592618.pdf"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2031966872","https://openalex.org/W2911489562","https://openalex.org/W2915895751","https://openalex.org/W2946690328","https://openalex.org/W2952755768","https://openalex.org/W3040936192","https://openalex.org/W3214227002","https://openalex.org/W4309659061","https://openalex.org/W6759105839"],"related_works":["https://openalex.org/W4387688064","https://openalex.org/W2188500270","https://openalex.org/W2303858293","https://openalex.org/W3037187668","https://openalex.org/W2976808399","https://openalex.org/W2915512527","https://openalex.org/W51364034","https://openalex.org/W2798997222","https://openalex.org/W4226439756","https://openalex.org/W2798198862"],"abstract_inverted_index":{"SUMMARY:":[0],"Relation":[1],"extraction":[2],"(RE)":[3],"from":[4,77],"large":[5],"text":[6],"collections":[7],"is":[8,26,122],"an":[9],"important":[10],"tool":[11,70],"for":[12,71],"database":[13],"curation,":[14],"pathway":[15,104],"reconstruction,":[16],"or":[17,43,59],"functional":[18],"omics":[19],"data":[20,31],"analysis.":[21],"In":[22],"practice,":[23],"RE":[24],"often":[25],"part":[27],"of":[28,41,46,113],"a":[29,68],"complex":[30],"analysis":[32,97],"pipeline":[33],"requiring":[34],"specific":[35],"adaptations":[36],"like":[37],"restricting":[38],"the":[39,44],"types":[40],"relations":[42],"set":[45],"proteins":[47],"to":[48,111],"be":[49,94],"considered.":[50],"However,":[51],"current":[52],"systems":[53],"are":[54],"either":[55],"non-programmable":[56],"web":[57],"sites":[58],"research":[60],"code":[61],"with":[62,85],"fixed":[63],"functionality.":[64],"We":[65,99],"present":[66],"PEDL+,":[67],"user-friendly":[69],"extracting":[72],"protein-protein":[73],"and":[74,88,91,107],"protein-chemical":[75],"associations":[76],"PubMed":[78],"articles.":[79],"PEDL+":[80,101,121],"combines":[81],"state-of-the-art":[82],"NLP":[83],"technology":[84],"adaptable":[86],"ranking":[87],"filtering":[89],"options":[90],"can":[92],"easily":[93],"integrated":[95],"into":[96],"pipelines.":[98],"evaluated":[100],"in":[102],"two":[103],"curation":[105],"projects":[106],"found":[108],"that":[109],"59%":[110],"80%":[112],"its":[114],"extractions":[115],"were":[116],"helpful.":[117],"AVAILABILITY":[118],"AND":[119],"IMPLEMENTATION:":[120],"freely":[123],"available":[124],"at":[125],"https://github.com/leonweber/pedl.":[126]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}