{"id":"https://openalex.org/W2041966896","doi":"https://doi.org/10.1109/tcbb.2014.2344681","title":"iPFPi: A System for Improving Protein Function Prediction through Cumulative Iterations","display_name":"iPFPi: A System for Improving Protein Function Prediction through Cumulative Iterations","publication_year":2014,"publication_date":"2014-08-05","ids":{"openalex":"https://openalex.org/W2041966896","doi":"https://doi.org/10.1109/tcbb.2014.2344681","mag":"2041966896","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357323"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2344681","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2344681","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/7180481/06871330.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://ieeexplore.ieee.org/ielx7/8857/7180481/06871330.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074032096","display_name":"Kamal Taha","orcid":"https://orcid.org/0000-0002-6674-4614"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Kamal Taha","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Khalifa University, Abu Dhabi, UAE","Department of Electrical and Computer Engineering Khalifa University Abu Dhabi UAE"],"raw_orcid":"https://orcid.org/0000-0002-6674-4614","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Khalifa University, Abu Dhabi, UAE","institution_ids":["https://openalex.org/I176601375"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering Khalifa University Abu Dhabi UAE","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014443986","display_name":"Paul D. Yoo","orcid":"https://orcid.org/0000-0001-7665-8616"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Paul D. Yoo","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Khalifa University, Abu Dhabi, UAE","Department of Electrical and Computer Engineering Khalifa University Abu Dhabi UAE"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Khalifa University, Abu Dhabi, UAE","institution_ids":["https://openalex.org/I176601375"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering Khalifa University Abu Dhabi UAE","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036756021","display_name":"Mohammed Alzaabi","orcid":"https://orcid.org/0000-0003-0847-1459"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Mohammed Alzaabi","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Khalifa University, Abu Dhabi, UAE","Department of Electrical and Computer Engineering Khalifa University Abu Dhabi UAE"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Khalifa University, Abu Dhabi, UAE","institution_ids":["https://openalex.org/I176601375"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering Khalifa University Abu Dhabi UAE","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I176601375"],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":0.3896,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.60261509,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"4","first_page":"825","last_page":"836"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9990000128746033,"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":0.9990000128746033,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.995199978351593,"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":0.9868999719619751,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.6698482036590576},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.636765718460083},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5441348552703857},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5045164823532104},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.42950087785720825},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.42781734466552734},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3775343894958496},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35573339462280273},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18452098965644836},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08242720365524292}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6698482036590576},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.636765718460083},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5441348552703857},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5045164823532104},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.42950087785720825},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42781734466552734},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3775343894958496},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35573339462280273},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18452098965644836},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08242720365524292},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2014.2344681","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2344681","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/7180481/06871330.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26357323","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357323","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1109/tcbb.2014.2344681","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2344681","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/7180481/06871330.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2041966896.pdf","grobid_xml":"https://content.openalex.org/works/W2041966896.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1504124766","https://openalex.org/W1755219215","https://openalex.org/W1991570251","https://openalex.org/W2015574703","https://openalex.org/W2017380119","https://openalex.org/W2032584931","https://openalex.org/W2042252652","https://openalex.org/W2049346142","https://openalex.org/W2064820767","https://openalex.org/W2073867161","https://openalex.org/W2074156599","https://openalex.org/W2083654996","https://openalex.org/W2101263862","https://openalex.org/W2109886974","https://openalex.org/W2111577229","https://openalex.org/W2117486996","https://openalex.org/W2124649441","https://openalex.org/W2128049108","https://openalex.org/W2132784310","https://openalex.org/W2136940180","https://openalex.org/W2138842411","https://openalex.org/W2140735973","https://openalex.org/W2148722247","https://openalex.org/W2160356737","https://openalex.org/W2161062388","https://openalex.org/W2162891889","https://openalex.org/W2164154943","https://openalex.org/W2167318540","https://openalex.org/W6637723064"],"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/W2358755282","https://openalex.org/W2383918176"],"abstract_inverted_index":{"We":[0,120,256],"propose":[1],"a":[2,37,122,152,174],"classifier":[3],"system":[4],"called":[5],"iPFPi":[6,14,104,184,261],"that":[7,26,127,154,247],"predicts":[8],"the":[9,20,56,72,79,83,92,109,135,156,180,188,192,199,202,214,218,223,238,242,252,258],"functions":[10,21],"of":[11,22,49,58,66,74,85,96,111,138,159,182,191,201,216,220,225,241,254,260],"un-annotated":[12,17,33],"proteins.":[13],"assigns":[15],"an":[16],"protein":[18,34,175,269],"P":[19,35,50,107,176],"GO":[23,38,52,68],"annotation":[24,39],"terms":[25,53,69,98,194,204,244],"are":[27,42,51,117,248],"semantically":[28,118],"similar":[29],"to":[30,162],"P.":[31,63,206],"An":[32],"and":[36,89,101,115,169,186],"term":[40,141],"T":[41,100,196,221],"represented":[43],"by":[44,262],"their":[45],"characteristics.":[46],"The":[47,64],"characteristics":[48,65],"found":[54,70],"within":[55,71],"abstracts":[57,73],"biomedical":[59,75],"literature":[60,76],"associated":[61,77],"with":[62,78,82,108,179,251,266],"Tare":[67],"proteins":[80,227,246],"annotated":[81,178,250],"function":[84,110,181,219,224,253,270],"T.":[86,255],"Let":[87],"F":[88,114,145,208],"F/":[90,116],"be":[91,210],"important":[93],"(dominant)":[94],"sets":[95],"characteristic":[97,140,164,193,203,243],"representing":[99,245],"P,":[102],"respectively.":[103],"would":[105],"annotate":[106],"T,":[112,183],"if":[113],"similar.":[119],"constructed":[121],"novel":[123],"semantic":[124],"similarity":[125],"measure":[126],"takes":[128],"into":[129],"consideration":[130],"several":[131],"factors,":[132],"such":[133],"as":[134,222],"dominance":[136,157],"degree":[137],"each":[139],"t":[142,160],"in":[143],"set":[144],"based":[146,197],"on":[147,198],"its":[148],"score,":[149],"which":[150],"is":[151,177],"value":[153],"reflects":[155],"status":[158],"relative":[161],"other":[163],"terms,":[165],"using":[166],"pairwise":[167],"beats":[168],"looses":[170],"procedure.":[171],"Every":[172],"time":[173,235],"updates":[185],"optimizes":[187],"current":[189],"scores":[190],"for":[195,205],"weights":[200,240],"Set":[207],"will":[209],"updated":[211],"accordingly.":[212],"Thus,":[213],"accuracy":[215,231],"predicting":[217],"subsequent":[226],"improves.":[228],"This":[229],"prediction":[230,271],"keeps":[232],"improving":[233],"over":[234],"iteratively":[236],"through":[237],"cumulative":[239],"successively":[249],"evaluated":[257],"quality":[259],"comparing":[263],"it":[264],"experimentally":[265],"two":[267],"recent":[268],"systems.":[272],"Results":[273],"showed":[274],"marked":[275],"improvement.":[276]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}