{"id":"https://openalex.org/W1973352244","doi":"https://doi.org/10.1186/1471-2105-14-12","title":"A detailed error analysis of 13 kernel methods for protein-protein interaction extraction","display_name":"A detailed error analysis of 13 kernel methods for protein-protein interaction extraction","publication_year":2013,"publication_date":"2013-01-16","ids":{"openalex":"https://openalex.org/W1973352244","doi":"https://doi.org/10.1186/1471-2105-14-12","mag":"1973352244","pmid":"https://pubmed.ncbi.nlm.nih.gov/23323857"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-12","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-12","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-12","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070226189","display_name":"Domonkos Tikk","orcid":null},"institutions":[{"id":"https://openalex.org/I114772536","display_name":"Software Engineering Institute","ror":"https://ror.org/01xqjjn94","country_code":"US","type":"facility","lineage":["https://openalex.org/I114772536","https://openalex.org/I74973139"]},{"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","US"],"is_corresponding":true,"raw_author_name":"Domonkos Tikk","raw_affiliation_strings":["Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, 10099 Berlin, Germany. tikk@informatik.hu-berlin.de","Software Engineering Institute, \u00d3buda University, Budapest, Hungary","Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, 10099 Berlin, Germany. tikk@informatik.hu-berlin.de","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Software Engineering Institute, \u00d3buda University, Budapest, Hungary","institution_ids":["https://openalex.org/I114772536"]},{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026073384","display_name":"Ill\u00e9s Solt","orcid":null},"institutions":[{"id":"https://openalex.org/I29770179","display_name":"Budapest University of Technology and Economics","ror":"https://ror.org/02w42ss30","country_code":"HU","type":"education","lineage":["https://openalex.org/I29770179"]},{"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","HU"],"is_corresponding":false,"raw_author_name":"Ill\u00e9s Solt","raw_affiliation_strings":["Department of Telecommunications and Telematics, Budapest University of Technology and Economics, 1117, Budapest, Hungary","Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, 10099, Berlin, Germany","Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","Department of Telecommunications and Telematics, Budapest University of Technology and Economics, Budapest, Hungary"],"affiliations":[{"raw_affiliation_string":"Department of Telecommunications and Telematics, Budapest University of Technology and Economics, 1117, Budapest, Hungary","institution_ids":["https://openalex.org/I29770179"]},{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, 10099, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Department of Telecommunications and Telematics, Budapest University of Technology and Economics, Budapest, Hungary","institution_ids":["https://openalex.org/I29770179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025893671","display_name":"Philippe Thomas","orcid":"https://orcid.org/0000-0001-9136-9660"},"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":"Philippe Thomas","raw_affiliation_strings":["Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, 10099, Berlin, Germany","Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, 10099, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"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":false,"raw_author_name":"Ulf Leser","raw_affiliation_strings":["Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, 10099, Berlin, Germany","Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, 10099, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5070226189"],"corresponding_institution_ids":["https://openalex.org/I114772536","https://openalex.org/I39343248"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.7432,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.93737984,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"14","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9901000261306763,"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":0.972100019454956,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5687145590782166},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5666886568069458},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.4534168839454651},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.4249304533004761},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3590107560157776},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3319970965385437},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3193846344947815},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26301613450050354},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21738797426223755},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1995246410369873},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.16929548978805542}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5687145590782166},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5666886568069458},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.4534168839454651},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.4249304533004761},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3590107560157776},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3319970965385437},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3193846344947815},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26301613450050354},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21738797426223755},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1995246410369873},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.16929548978805542},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-14-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-12","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-12","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23323857","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23323857","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2685172","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3680070","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-12","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-12","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5412250075","display_name":null,"funder_award_id":"B-10/1-2010-0009","funder_id":"https://openalex.org/F4320311358","funder_display_name":"Budapesti M\u0171szaki \u00e9s Gazdas\u00e1gtudom\u00e1nyi Egyetem"}],"funders":[{"id":"https://openalex.org/F4320308269","display_name":"Alexander von Humboldt-Stiftung","ror":"https://ror.org/012kf4317"},{"id":"https://openalex.org/F4320311358","display_name":"Budapesti M\u0171szaki \u00e9s Gazdas\u00e1gtudom\u00e1nyi Egyetem","ror":"https://ror.org/02w42ss30"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1973352244.pdf","grobid_xml":"https://content.openalex.org/works/W1973352244.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W28412257","https://openalex.org/W76749362","https://openalex.org/W1493270114","https://openalex.org/W1493490255","https://openalex.org/W1560724230","https://openalex.org/W1570448133","https://openalex.org/W1576213419","https://openalex.org/W1587871245","https://openalex.org/W1604685658","https://openalex.org/W1792818653","https://openalex.org/W1850865022","https://openalex.org/W1986704581","https://openalex.org/W1992770405","https://openalex.org/W1996787131","https://openalex.org/W2006566482","https://openalex.org/W2016928406","https://openalex.org/W2048059249","https://openalex.org/W2065656592","https://openalex.org/W2069377314","https://openalex.org/W2077997913","https://openalex.org/W2089933214","https://openalex.org/W2097960255","https://openalex.org/W2104768328","https://openalex.org/W2108604762","https://openalex.org/W2108706252","https://openalex.org/W2109070394","https://openalex.org/W2120736575","https://openalex.org/W2121844933","https://openalex.org/W2124225821","https://openalex.org/W2127224553","https://openalex.org/W2127603354","https://openalex.org/W2127713198","https://openalex.org/W2141605886","https://openalex.org/W2143954109","https://openalex.org/W2149803936","https://openalex.org/W2152398020","https://openalex.org/W2152698860","https://openalex.org/W2153635508","https://openalex.org/W2157628440","https://openalex.org/W2166111585","https://openalex.org/W2166474856","https://openalex.org/W2168905447","https://openalex.org/W2169974160","https://openalex.org/W2170953709","https://openalex.org/W2251450145","https://openalex.org/W2912934387","https://openalex.org/W2913389685","https://openalex.org/W3120421331","https://openalex.org/W3144619878","https://openalex.org/W4285719527"],"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/W2392827053","https://openalex.org/W2975617233","https://openalex.org/W2377877252","https://openalex.org/W2362914816","https://openalex.org/W2372644337"],"abstract_inverted_index":{"Our":[0,37],"experiments":[1],"show":[2],"that":[3,40],"current":[4],"methods":[5],"do":[6,10],"not":[7],"seem":[8],"to":[9,27],"very":[11,33],"well":[12],"in":[13,48,53],"capturing":[14],"the":[15,28,31],"shared":[16],"characteristics":[17],"of":[18,30],"positive":[19],"PPI":[20],"pairs,":[21],"which":[22],"must":[23],"also":[24],"be":[25,44],"attributed":[26],"heterogeneity":[29],"(still":[32],"few)":[34],"available":[35],"corpora.":[36],"analysis":[38],"suggests":[39],"performance":[41],"improvements":[42],"shall":[43],"sought":[45],"after":[46],"rather":[47],"novel":[49,54],"feature":[50],"sets":[51],"than":[52],"kernel":[55],"functions.":[56]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
