{"id":"https://openalex.org/W2079135682","doi":"https://doi.org/10.1186/1471-2105-10-s5-s3","title":"TGF-beta signaling proteins and the Protein Ontology","display_name":"TGF-beta signaling proteins and the Protein Ontology","publication_year":2009,"publication_date":"2009-05-01","ids":{"openalex":"https://openalex.org/W2079135682","doi":"https://doi.org/10.1186/1471-2105-10-s5-s3","mag":"2079135682","pmid":"https://pubmed.ncbi.nlm.nih.gov/19426460"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-s5-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s5-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S5-S3","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/10.1186/1471-2105-10-S5-S3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001355963","display_name":"Cecilia N. Arighi","orcid":"https://orcid.org/0000-0002-0803-4817"},"institutions":[{"id":"https://openalex.org/I1312106833","display_name":"Biotechnology Institute","ror":"https://ror.org/00s1jty20","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312106833"]},{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cecilia N Arighi","raw_affiliation_strings":["Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA. arighi@dbi.udel.edu","Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA. arighi@dbi.udel.edu","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101585391","display_name":"Hongfang Liu","orcid":"https://orcid.org/0000-0003-2570-3741"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongfang Liu","raw_affiliation_strings":["Georgetown University Medical Center, Washington, DC, USA","Georgetown University Medical Center, Washington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Georgetown University Medical Center, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]},{"raw_affiliation_string":"Georgetown University Medical Center, Washington, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005555412","display_name":"Darren A. Natale","orcid":"https://orcid.org/0000-0001-5809-9523"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Darren A Natale","raw_affiliation_strings":["Georgetown University Medical Center, Washington, DC, USA","Georgetown University Medical Center, Washington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Georgetown University Medical Center, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]},{"raw_affiliation_string":"Georgetown University Medical Center, Washington, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059783115","display_name":"Winona C. Barker","orcid":null},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Winona C Barker","raw_affiliation_strings":["Georgetown University Medical Center, Washington, DC, USA","Georgetown University Medical Center, Washington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Georgetown University Medical Center, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]},{"raw_affiliation_string":"Georgetown University Medical Center, Washington, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006288716","display_name":"Harold Drabkin","orcid":"https://orcid.org/0000-0003-2689-5511"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harold Drabkin","raw_affiliation_strings":["The Jackson Laboratory, Bar Harbor, ME, USA","The Jackson Laboratory, Bar Harbor, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, ME, USA","institution_ids":["https://openalex.org/I4210115256"]},{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016349593","display_name":"Judith A. Blake","orcid":"https://orcid.org/0000-0001-8522-334X"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Judith A Blake","raw_affiliation_strings":["The Jackson Laboratory, Bar Harbor, ME, USA","The Jackson Laboratory, Bar Harbor, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, ME, USA","institution_ids":["https://openalex.org/I4210115256"]},{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051216244","display_name":"Barry Smith","orcid":"https://orcid.org/0000-0003-1384-116X"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Barry Smith","raw_affiliation_strings":["Center of Excellence in Bioinformatics and Life Sciences, and Department of Philosophy, University at Buffalo, NY, USA","Center of Excellence in Bioinformatics and Life Sciences, and Department of Philosophy, University at Buffalo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence in Bioinformatics and Life Sciences, and Department of Philosophy, University at Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Center of Excellence in Bioinformatics and Life Sciences, and Department of Philosophy, University at Buffalo, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053761444","display_name":"Cathy Wu","orcid":"https://orcid.org/0000-0001-6379-8601"},"institutions":[{"id":"https://openalex.org/I1312106833","display_name":"Biotechnology Institute","ror":"https://ror.org/00s1jty20","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312106833"]},{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]},{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cathy H Wu","raw_affiliation_strings":["Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA","Georgetown University Medical Center, Washington, DC, USA","Georgetown University Medical Center, Washington, USA","Delaware Biotechnology Institute, University of Delaware, Newark, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I86501945"]},{"raw_affiliation_string":"Georgetown University Medical Center, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]},{"raw_affiliation_string":"Georgetown University Medical Center, Washington, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]},{"raw_affiliation_string":"Delaware Biotechnology Institute, University of Delaware, Newark, USA","institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5053761444"],"corresponding_institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I184565670","https://openalex.org/I2799903593","https://openalex.org/I86501945"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.2592,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.78439964,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"S5","first_page":"S3","last_page":"S3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9628999829292297,"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":0.9628999829292297,"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":0.023600000888109207,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.004999999888241291,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.5773387551307678},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.571909487247467},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5257031917572021},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5079570412635803},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.5077815651893616},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.48002782464027405},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.4781644940376282},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.413940966129303},{"id":"https://openalex.org/keywords/process-ontology","display_name":"Process ontology","score":0.38206803798675537},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.38119012117385864},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3605616092681885},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33394598960876465},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26830869913101196},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.23868030309677124},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23139941692352295},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.14369967579841614},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14281335473060608}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5773387551307678},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.571909487247467},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5257031917572021},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5079570412635803},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.5077815651893616},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.48002782464027405},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.4781644940376282},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.413940966129303},{"id":"https://openalex.org/C137003198","wikidata":"https://www.wikidata.org/wiki/Q7247296","display_name":"Process ontology","level":3,"score":0.38206803798675537},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.38119012117385864},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3605616092681885},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33394598960876465},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26830869913101196},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.23868030309677124},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23139941692352295},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.14369967579841614},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14281335473060608},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016212","descriptor_name":"Transforming Growth Factor beta","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016212","descriptor_name":"Transforming Growth Factor beta","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016212","descriptor_name":"Transforming Growth Factor beta","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016212","descriptor_name":"Transforming Growth Factor beta","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016212","descriptor_name":"Transforming Growth Factor beta","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016212","descriptor_name":"Transforming Growth Factor beta","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047908","descriptor_name":"Intracellular Signaling Peptides and Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D047908","descriptor_name":"Intracellular Signaling Peptides and Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D047908","descriptor_name":"Intracellular Signaling Peptides and Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D047908","descriptor_name":"Intracellular Signaling Peptides and Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D047908","descriptor_name":"Intracellular Signaling Peptides and Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D047908","descriptor_name":"Intracellular Signaling Peptides and Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-10-s5-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s5-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S5-S3","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:19426460","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19426460","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:mouseion.jax.org:stfb2000_2009-2950","is_oa":true,"landing_page_url":"http://www.biomedcentral.com/1471-2105/10/S5/S3","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"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":"Faculty Research 2000 - 2009","raw_type":"text"},{"id":"pmh:oai:philarchive.org/rec/ARITSP-2","is_oa":false,"landing_page_url":"https://philarchive.org/rec/ARITSP-2","pdf_url":null,"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:philpapers.org/rec/ARITSP-2","is_oa":false,"landing_page_url":"https://philpapers.org/rec/ARITSP-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"},{"id":"pmh:oai:pubmedcentral.nih.gov:2679403","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2679403","pdf_url":null,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-s5-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s5-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S5-S3","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/G1293109142","display_name":null,"funder_award_id":"R01 GM080646","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2225135173","display_name":null,"funder_award_id":"U54 HG004028","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G2858025007","display_name":null,"funder_award_id":"R01 LM009959","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G627711816","display_name":null,"funder_award_id":"1 R01 GM080646-01","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2079135682.pdf","grobid_xml":"https://content.openalex.org/works/W2079135682.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1564162226","https://openalex.org/W1999773781","https://openalex.org/W2016602738","https://openalex.org/W2035933413","https://openalex.org/W2081245863","https://openalex.org/W2096704019","https://openalex.org/W2103260426","https://openalex.org/W2112797550","https://openalex.org/W2113142309","https://openalex.org/W2123171788","https://openalex.org/W2128549389","https://openalex.org/W2132992030","https://openalex.org/W2135252110","https://openalex.org/W2136514583","https://openalex.org/W2140000393","https://openalex.org/W2141885858","https://openalex.org/W2147323051","https://openalex.org/W2152521795","https://openalex.org/W2156918975","https://openalex.org/W2161062388","https://openalex.org/W2161241566","https://openalex.org/W2180180358","https://openalex.org/W2566511875","https://openalex.org/W2604823638","https://openalex.org/W2744744159","https://openalex.org/W4211054902"],"related_works":["https://openalex.org/W2102027645","https://openalex.org/W2116726748","https://openalex.org/W2107785922","https://openalex.org/W2035528219","https://openalex.org/W2098932404","https://openalex.org/W2402478170","https://openalex.org/W2946410450","https://openalex.org/W2999847357","https://openalex.org/W2901823680","https://openalex.org/W72173000"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,20,121,188],"Protein":[2],"Ontology":[3],"(PRO)":[4],"is":[5,80,126,156,313],"designed":[6,314],"as":[7,158,178,180,227],"a":[8,26,49,159,242,296],"formal":[9,300],"and":[10,74,110,113,133,185,214,220,241,259,265,305,319,321,338],"principled":[11],"Open":[12],"Biomedical":[13],"Ontologies":[14],"(OBO)":[15],"Foundry":[16],"ontology":[17],"for":[18,166,235,244,254,266,298],"proteins.":[19],"components":[21],"of":[22,28,33,43,48,76,86,106,124,153,195,238,268,277,285,302,328,341],"PRO":[23,79,119,125,149,154,161,169,233,251,294],"extend":[24],"from":[25,54,95,131,173],"classification":[27],"proteins":[29,135],"on":[30,63,83,289],"the":[31,37,41,44,64,70,84,104,107,111,118,148,151,174,181,193,230,236,246,278,283,299,309,325,339],"basis":[32,85],"evolutionary":[34],"relationships":[35,115],"at":[36,324],"homeomorphic":[38],"level":[39,327],"to":[40,117,147,197,209,274,315],"representation":[42,237,301],"multiple":[45],"protein":[46,97,108,138,222,239,291,303,306],"forms":[47,139,203,223,261,307],"gene,":[50],"including":[51],"those":[52],"resulting":[53],"alternative":[55],"splicing,":[56],"cleavage":[57],"and/or":[58],"post-translational":[59],"modifications.":[60,292],"Focusing":[61],"specifically":[62],"TGF-beta":[65],"signaling":[66],"proteins,":[67,329],"we":[68],"describe":[69],"building,":[71],"curation,":[72],"usage":[73],"dissemination":[75],"PRO.":[77],"RESULTS:":[78],"manually":[81],"curated":[82],"PrePRO,":[87],"an":[88,171],"automatically":[89],"generated":[90],"file":[91],"with":[92],"content":[93],"derived":[94],"standard":[96],"data":[98,130,317],"sources.":[99],"Manual":[100],"curation":[101],"ensures":[102],"that":[103],"treatment":[105],"classes":[109,304],"internal":[112],"external":[114],"conform":[116],"framework.":[120],"current":[122],"release":[123],"based":[127],"upon":[128],"experimental":[129],"mouse":[132],"human":[134],"wherein":[136],"equivalent":[137,202],"are":[140,190,207,224],"represented":[141,226],"by":[142],"single":[143],"terms.":[144],"In":[145],"addition":[146],"ontology,":[150],"annotation":[152,172],"terms":[155],"released":[157],"separate":[160],"association":[162],"file,":[163],"which":[164,282],"contains,":[165],"each":[167],"given":[168],"term,":[170],"experimentally":[175],"characterized":[176],"sub-types":[177],"well":[179],"corresponding":[182],"database":[183],"identifiers":[184],"sequence":[186],"coordinates.":[187],"annotations":[189],"added":[191],"in":[192,204,229,281,308],"form":[194],"relationship":[196],"other":[198,205],"ontologies.":[199],"Whenever":[200],"possible,":[201],"species":[206],"listed":[208],"facilitate":[210],"cross-species":[211,332],"comparison.":[212],"Splice":[213],"allelic":[215],"variants,":[216],"gene":[217],"fusion":[218],"products":[219],"modified":[221,260],"all":[225],"entities":[228,240],"ontology.":[231],"Therefore,":[232],"provides":[234,295],"resource":[243],"describing":[245],"associated":[247],"data.":[248],"This":[249],"makes":[250],"useful":[252],"both":[253],"proteomics":[255],"studies":[256,267],"where":[257,271],"isoforms":[258],"must":[262],"be":[263],"differentiated,":[264],"biological":[269],"pathways,":[270],"representations":[272],"need":[273],"take":[275],"account":[276],"different":[279],"ways":[280],"cascade":[284],"events":[286],"may":[287],"depend":[288],"specific":[290],"CONCLUSION:":[293],"framework":[297],"OBO":[310],"Foundry.":[311],"It":[312],"enable":[316],"retrieval":[318],"integration":[320],"machine":[322],"reasoning":[323],"molecular":[326],"thereby":[330],"facilitating":[331],"comparisons,":[333],"pathway":[334],"analysis,":[335],"disease":[336],"modeling":[337],"generation":[340],"new":[342],"hypotheses.":[343]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
