{"id":"https://openalex.org/W2100899895","doi":"https://doi.org/10.1186/1471-2105-10-s11-s5","title":"HPD: an online integrated human pathway database enabling systems biology studies","display_name":"HPD: an online integrated human pathway database enabling systems biology studies","publication_year":2009,"publication_date":"2009-10-01","ids":{"openalex":"https://openalex.org/W2100899895","doi":"https://doi.org/10.1186/1471-2105-10-s11-s5","mag":"2100899895","pmid":"https://pubmed.ncbi.nlm.nih.gov/19811689"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-s11-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s11-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S11-S5","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-S11-S5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091850433","display_name":"Sudhir Chowbina","orcid":null},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sudhir R Chowbina","raw_affiliation_strings":["Indiana University School of Informatics, Indianapolis, IN 46202, USA","Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA","Indiana University School of Informatics, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045121596","display_name":"Xiaogang Wu","orcid":"https://orcid.org/0000-0003-4373-6926"},"institutions":[{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaogang Wu","raw_affiliation_strings":["Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, IN, 46202, USA","Indiana University School of Informatics, Indianapolis, IN, 46202, USA","Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA","Indiana University School of Informatics, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100403504","display_name":"Fan Zhang","orcid":"https://orcid.org/0000-0002-8038-7916"},"institutions":[{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fan Zhang","raw_affiliation_strings":["Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, IN, 46202, USA","Indiana University School of Informatics, Indianapolis, IN, 46202, USA","Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA","Indiana University School of Informatics, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085568229","display_name":"Peter M Li","orcid":null},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter M Li","raw_affiliation_strings":["Indiana University School of Informatics, Indianapolis, IN, 46202, USA","Indiana University School of Informatics, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071816838","display_name":"Ragini Pandey","orcid":null},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ragini Pandey","raw_affiliation_strings":["Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, IN, 46202, USA","Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006382427","display_name":"Harini N Kasamsetty","orcid":null},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harini N Kasamsetty","raw_affiliation_strings":["Indiana University School of Informatics, Indianapolis, IN, 46202, USA","Indiana University School of Informatics, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058469124","display_name":"Jake Y. Chen","orcid":"https://orcid.org/0000-0001-8829-7504"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I135191193","display_name":"University of Indianapolis","ror":"https://ror.org/052133d12","country_code":"US","type":"education","lineage":["https://openalex.org/I135191193"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jake Y Chen","raw_affiliation_strings":["Department of Computer and Information Science, Purdue University School of Science, Indianapolis, IN, 46202, USA","Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, IN, 46202, USA","Indiana University School of Informatics, Indianapolis, IN, 46202, USA","Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA","Indiana University School of Informatics, Indianapolis, USA","Department of Computer and Information Science, Purdue University School of Science, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, Purdue University School of Science, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I135191193","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University \u2013 Purdue University, Indianapolis, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Informatics, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"Department of Computer and Information Science, Purdue University School of Science, Indianapolis, USA","institution_ids":["https://openalex.org/I135191193","https://openalex.org/I55769427"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5091850433"],"corresponding_institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.5135,"has_fulltext":true,"cited_by_count":58,"citation_normalized_percentile":{"value":0.93287274,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"S11","first_page":"S5","last_page":"S5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9545000195503235,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9545000195503235,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.02319999970495701,"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":0.00139999995008111,"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/computational-biology","display_name":"Computational biology","score":0.59012770652771},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5442240238189697},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5437085032463074},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.48141881823539734},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4550853371620178},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3380884528160095},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3376980423927307},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1966170370578766},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14080402255058289},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10515934228897095}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.59012770652771},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5442240238189697},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5437085032463074},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48141881823539734},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4550853371620178},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3380884528160095},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3376980423927307},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1966170370578766},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14080402255058289},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10515934228897095}],"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-10-s11-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s11-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S11-S5","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:19811689","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19811689","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:pubmedcentral.nih.gov:3226194","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3226194","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"},{"id":"pmh:oai:scholarworks.indianapolis.iu.edu:1805/52313","is_oa":true,"landing_page_url":"https://hdl.handle.net/1805/52313","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"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":"PMC","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-s11-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s11-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S11-S5","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/G4119534169","display_name":null,"funder_award_id":"W81XWH","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"}],"funders":[{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100899895.pdf","grobid_xml":"https://content.openalex.org/works/W2100899895.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W68599619","https://openalex.org/W1597403892","https://openalex.org/W1871698357","https://openalex.org/W1969040600","https://openalex.org/W1970594207","https://openalex.org/W1973813521","https://openalex.org/W1980034972","https://openalex.org/W1983943352","https://openalex.org/W1986767070","https://openalex.org/W1988319444","https://openalex.org/W1991395379","https://openalex.org/W1992688520","https://openalex.org/W1993614561","https://openalex.org/W1994664175","https://openalex.org/W1996695017","https://openalex.org/W1999895438","https://openalex.org/W2005937921","https://openalex.org/W2008001403","https://openalex.org/W2010502047","https://openalex.org/W2020556380","https://openalex.org/W2027224357","https://openalex.org/W2031176449","https://openalex.org/W2031498118","https://openalex.org/W2034032177","https://openalex.org/W2041345281","https://openalex.org/W2049483248","https://openalex.org/W2060798669","https://openalex.org/W2061755061","https://openalex.org/W2073131340","https://openalex.org/W2075556692","https://openalex.org/W2083901790","https://openalex.org/W2090863707","https://openalex.org/W2096766502","https://openalex.org/W2097847183","https://openalex.org/W2098425296","https://openalex.org/W2101825119","https://openalex.org/W2104858809","https://openalex.org/W2108739303","https://openalex.org/W2117121924","https://openalex.org/W2119284420","https://openalex.org/W2120377931","https://openalex.org/W2121071871","https://openalex.org/W2123500593","https://openalex.org/W2132899427","https://openalex.org/W2134394193","https://openalex.org/W2137028370","https://openalex.org/W2137141752","https://openalex.org/W2137687319","https://openalex.org/W2138906045","https://openalex.org/W2140326317","https://openalex.org/W2142890842","https://openalex.org/W2142945974","https://openalex.org/W2155723007","https://openalex.org/W2159482845","https://openalex.org/W2161441225","https://openalex.org/W2161732286","https://openalex.org/W2171018484","https://openalex.org/W2182122766","https://openalex.org/W2507720777","https://openalex.org/W2764474601","https://openalex.org/W3187515181","https://openalex.org/W4212771095","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W1802639773","https://openalex.org/W2118505788","https://openalex.org/W4254166511","https://openalex.org/W2150084125","https://openalex.org/W1542823905","https://openalex.org/W5284979","https://openalex.org/W4245853730"],"abstract_inverted_index":{"BACKGROUND:":[0],"Pathway-oriented":[1],"experimental":[2],"and":[3,29,51,80,88,135,146,170,185,204,249,259,281,301,306],"computational":[4],"studies":[5],"have":[6,74],"led":[7],"to":[8,65,83,86,219],"a":[9,37,141,153,197,205,275,321],"significant":[10],"accumulation":[11],"of":[12,19,36,39,61,129,177,261,287,294,324],"biological":[13,20,57,284,296],"knowledge":[14],"concerning":[15],"three":[16,266],"major":[17],"types":[18],"pathway":[21,34,41,58,71,104,130,143,212,215,239,253,311],"events:":[22],"molecular":[23,40,45,190,303],"signaling":[24,165],"events,":[25,28,166,169],"gene":[26,171],"regulation":[27],"metabolic":[30,167],"reaction":[31,168],"events.":[32,173],"A":[33],"consists":[35],"series":[38],"events":[42],"that":[43,106,157],"link":[44],"entities":[46],"such":[47],"as":[48,60],"proteins,":[49,160],"genes,":[50,161],"metabolites.":[52],"There":[53],"are":[54,81,107],"approximately":[55],"300":[56],"resources":[59,227],"April":[62],"2009":[63],"according":[64],"the":[66,95,111,123,175,257,262],"Pathguide":[67],"database;":[68],"however,":[69],"these":[70],"databases":[72],"generally":[73],"poor":[75,78],"coverage":[76],"or":[77,120,235],"quality,":[79],"difficult":[82],"integrate,":[84],"due":[85],"syntactic-level":[87],"semantic-level":[89],"data":[90,105,131,144,147],"incompatibilities.":[91],"RESULTS:":[92],"We":[93,255],"developed":[94],"Human":[96],"Pathway":[97,113],"Database":[98,115],"(HPD)":[99],"by":[100,228],"integrating":[101],"heterogeneous":[102],"human":[103,159,183,189,223,283,295,328],"either":[108],"curated":[109],"at":[110,132],"NCI":[112],"Interaction":[114],"(PID),":[116],"Reactome,":[117],"BioCarta,":[118],"KEGG":[119],"indexed":[121],"from":[122,225],"Protein":[124],"Lounge":[125],"Web":[126,199],"sites.":[127],"Integration":[128],"syntactic,":[133],"semantic,":[134],"schematic":[136],"levels":[137],"was":[138],"based":[139],"on":[140],"unified":[142],"model":[145],"warehousing-based":[148],"integration":[149],"techniques.":[150],"HPD":[151,180,193,264,272,288,315],"provides":[152,195],"comprehensive":[154],"online":[155,202],"view":[156],"connects":[158],"RNA":[162],"transcripts,":[163],"enzymes,":[164],"regulatory":[172],"At":[174],"time":[176],"this":[178],"writing":[179],"includes":[181],"999":[182],"pathways":[184,224,234,300],"more":[186],"than":[187],"59,341":[188],"entities.":[191],"The":[192,313],"software":[194,316],"both":[196],"user-friendly":[198],"interface":[200],"for":[201,210,222,278],"use":[203],"robust":[206],"relational":[207],"database":[208],"backend":[209],"advanced":[211],"querying.":[213],"This":[214],"tool":[216],"enables":[217],"users":[218,319],"1)":[220],"search":[221,290],"different":[226],"simply":[229],"entering":[230],"genes/proteins":[231],"involved":[232],"in":[233,238,327],"words":[236],"appearing":[237],"names,":[240],"2)":[241],"analyze":[242],"pathway-protein":[243],"association,":[244],"3)":[245],"study":[246],"pathway-pathway":[247],"similarity,":[248],"4)":[250],"build":[251,307],"integrated":[252],"networks.":[254],"demonstrated":[256],"usage":[258],"characteristics":[260],"new":[263,276],"through":[265],"breast":[267],"cancer":[268],"case":[269],"studies.":[270,331],"CONCLUSION:":[271],"http://bio.informatics.iupui.edu/HPD":[273],"is":[274],"resource":[277],"searching,":[279],"managing,":[280],"studying":[282],"pathways.":[285],"Users":[286],"can":[289,317],"against":[291],"large":[292],"collections":[293],"pathways,":[297],"compare":[298],"related":[299],"their":[302],"entity":[304],"compositions,":[305],"high-quality,":[308],"expanded-scope":[309],"disease":[310,329],"models.":[312],"current":[314],"help":[318],"address":[320],"wide":[322],"range":[323],"pathway-related":[325],"questions":[326],"biology":[330]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":8}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
