{"id":"https://openalex.org/W2126662543","doi":"https://doi.org/10.1109/bibe.2004.1317373","title":"Towards a proteomics meta-classification","display_name":"Towards a proteomics meta-classification","publication_year":2004,"publication_date":"2004-11-30","ids":{"openalex":"https://openalex.org/W2126662543","doi":"https://doi.org/10.1109/bibe.2004.1317373","mag":"2126662543"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2004.1317373","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317373","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://philpapers.org/archive/KUMTAP-2.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100673174","display_name":"Amit Kumar","orcid":"https://orcid.org/0000-0003-2775-6919"},"institutions":[{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE","IT"],"is_corresponding":false,"raw_author_name":"A. Kumar","raw_affiliation_strings":["Institute for Formal Ontology and Medical Science, University of Leipzig, Germany","Laboratory of Medical Informatics, University of Pavia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Formal Ontology and Medical Science, University of Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Laboratory of Medical Informatics, University of Pavia, Italy","institution_ids":["https://openalex.org/I25217355"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051216244","display_name":"Barry Smith","orcid":"https://orcid.org/0000-0003-1384-116X"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"B. Smith","raw_affiliation_strings":["Institute for Formal Ontology and Medical Science, University of Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Formal Ontology and Medical Science, University of Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"419","last_page":"426"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9970999956130981,"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":0.9901999831199646,"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":0.7654165029525757},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6410360336303711},{"id":"https://openalex.org/keywords/sort","display_name":"sort","score":0.6291146278381348},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.6161911487579346},{"id":"https://openalex.org/keywords/structural-classification-of-proteins-database","display_name":"Structural Classification of Proteins database","score":0.5911825895309448},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4853628873825073},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.48012709617614746},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.45613887906074524},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.4405912458896637},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4221498370170593},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3874802589416504},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36731594800949097},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.24028614163398743},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08389857411384583},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07647731900215149}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7654165029525757},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6410360336303711},{"id":"https://openalex.org/C88548561","wikidata":"https://www.wikidata.org/wiki/Q347599","display_name":"sort","level":2,"score":0.6291146278381348},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6161911487579346},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.5911825895309448},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4853628873825073},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.48012709617614746},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.45613887906074524},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.4405912458896637},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4221498370170593},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3874802589416504},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36731594800949097},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.24028614163398743},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08389857411384583},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07647731900215149},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/bibe.2004.1317373","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317373","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"},{"id":"pmh:oai:philarchive.org/rec/KUMTAP-2","is_oa":true,"landing_page_url":"https://philarchive.org/rec/KUMTAP-2","pdf_url":"https://philpapers.org/archive/KUMTAP-2.pdf","source":{"id":"https://openalex.org/S4306402130","display_name":"PhilPapers (PhilPapers Foundation)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.551.1861","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.551.1861","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.uni-leipzig.de/~akumar/Bibe2004.PDF","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.93.3303","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.93.3303","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://ontology.buffalo.edu/bio/BIBE2004Proteomics.pdf","raw_type":"text"},{"id":"pmh:oai:philpapers.org/rec/KUMTAP-2","is_oa":false,"landing_page_url":"https://philpapers.org/rec/KUMTAP-2","pdf_url":null,"source":{"id":"https://openalex.org/S4306402131","display_name":"PhilPapers (PhilPapers Foundation)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:philarchive.org/rec/KUMTAP-2","is_oa":true,"landing_page_url":"https://philarchive.org/rec/KUMTAP-2","pdf_url":"https://philpapers.org/archive/KUMTAP-2.pdf","source":{"id":"https://openalex.org/S4306402130","display_name":"PhilPapers (PhilPapers Foundation)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2126662543.pdf","grobid_xml":"https://content.openalex.org/works/W2126662543.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W159602724","https://openalex.org/W1548329420","https://openalex.org/W1666130637","https://openalex.org/W1836367264","https://openalex.org/W1970697508","https://openalex.org/W2002626038","https://openalex.org/W2041428546","https://openalex.org/W2047544230","https://openalex.org/W2133992441","https://openalex.org/W2142475479","https://openalex.org/W2155480785","https://openalex.org/W2159136327","https://openalex.org/W2162124237","https://openalex.org/W2167309441","https://openalex.org/W2477521491","https://openalex.org/W6606539241","https://openalex.org/W6679802932"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2487162673","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2063692638","https://openalex.org/W2981205093"],"abstract_inverted_index":{"There":[0],"is":[1,43],"a":[2,6,12,96,125],"recognized":[3],"need":[4],"for":[5,14],"meta-classification":[7,98,126],"that":[8],"can":[9],"serve":[10],"as":[11,45],"foundation":[13],"more":[15],"refined":[16],"ontologies":[17],"in":[18,28,87,120],"the":[19,49,58,88,100,116,132,140],"field":[20],"of":[21,30,41,51,60,64,90,99,142],"proteomics.":[22],"Standard":[23],"data":[24,70,118],"sources":[25,71,119],"classify":[26],"proteins":[27,47,56],"terms":[29],"just":[31],"one":[32],"or":[33],"two":[34],"specific":[35],"aspects.":[36],"Thus":[37],"SCOP":[38],"(structural":[39],"classification":[40],"proteins)":[42],"described":[44],"classifying":[46],"on":[48,57],"basis":[50,59],"structural":[52],"features;":[53],"SWlSS-PROT":[54],"annotates":[55],"their":[61],"structure":[62],"and":[63,136],"parameters":[65],"like":[66],"post-translational":[67],"modifications.":[68],"Such":[69],"are":[72,83],"connected":[73],"to":[74,94,122,139],"each":[75],"other":[76],"by":[77],"pairwise":[78],"term-to-term":[79],"mappings.":[80],"However,":[81],"there":[82],"obstacles":[84],"which":[85,109],"stand":[86],"way":[89],"combining":[91],"them":[92],"together":[93],"form":[95],"robust":[97],"needed":[101],"sort.":[102],"We":[103],"discuss":[104],"some":[105],"formal":[106],"ontological":[107],"principles":[108],"should":[110],"be":[111],"taken":[112],"into":[113,129],"account":[114,130],"within":[115],"existing":[117],"order":[121],"make":[123],"such":[124],"possible,":[127],"taking":[128],"also":[131],"gene":[133],"ontology":[134],"(GO)":[135],"its":[137],"application":[138],"annotation":[141],"proteins.":[143]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
