{"id":"https://openalex.org/W3206895407","doi":"https://doi.org/10.1093/bioinformatics/btab699","title":"WikiNetworks: translating manually created biological pathways for topological analysis","display_name":"WikiNetworks: translating manually created biological pathways for topological analysis","publication_year":2021,"publication_date":"2021-10-11","ids":{"openalex":"https://openalex.org/W3206895407","doi":"https://doi.org/10.1093/bioinformatics/btab699","mag":"3206895407","pmid":"https://pubmed.ncbi.nlm.nih.gov/34636843"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab699","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab699","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8756176","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056509174","display_name":"Mukta G. Palshikar","orcid":"https://orcid.org/0000-0002-1179-7903"},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mukta G Palshikar","raw_affiliation_strings":["Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA"],"affiliations":[{"raw_affiliation_string":"Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008772684","display_name":"Shannon P. Hilchey","orcid":"https://orcid.org/0000-0003-1950-7381"},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shannon P Hilchey","raw_affiliation_strings":["Division of Nephrology, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA"],"affiliations":[{"raw_affiliation_string":"Division of Nephrology, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076140837","display_name":"Martin S. Zand","orcid":"https://orcid.org/0000-0002-7095-8682"},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin S Zand","raw_affiliation_strings":["Clinical and Translational Science Institute, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA","Division of Nephrology, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA"],"affiliations":[{"raw_affiliation_string":"Clinical and Translational Science Institute, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA","institution_ids":["https://openalex.org/I5388228"]},{"raw_affiliation_string":"Division of Nephrology, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039254521","display_name":"Juilee Thakar","orcid":"https://orcid.org/0000-0003-4479-4183"},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Juilee Thakar","raw_affiliation_strings":["Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA","Department of Microbiology and Immunology, Department of Biostatistics and Computational Biology, and Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA"],"affiliations":[{"raw_affiliation_string":"Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA","institution_ids":["https://openalex.org/I5388228"]},{"raw_affiliation_string":"Department of Microbiology and Immunology, Department of Biostatistics and Computational Biology, and Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA","institution_ids":["https://openalex.org/I5388228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5039254521"],"corresponding_institution_ids":["https://openalex.org/I5388228"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6436,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.6713478,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"38","issue":"3","first_page":"869","last_page":"871"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9940999746322632,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9914000034332275,"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/usable","display_name":"USable","score":0.8632383346557617},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8294921517372131},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5736403465270996},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.546423077583313},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.4732309579849243},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.457502156496048},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4151998460292816},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41193145513534546},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22373875975608826},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.18261432647705078},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14184719324111938},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08357736468315125}],"concepts":[{"id":"https://openalex.org/C2780615836","wikidata":"https://www.wikidata.org/wiki/Q2471869","display_name":"USable","level":2,"score":0.8632383346557617},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8294921517372131},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5736403465270996},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.546423077583313},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4732309579849243},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.457502156496048},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4151998460292816},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41193145513534546},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22373875975608826},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.18261432647705078},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14184719324111938},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08357736468315125},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab699","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab699","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34636843","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34636843","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8756176","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8756176","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8756176","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8756176","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5509502471","display_name":null,"funder_award_id":"R01 AI134058","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1999758530","https://openalex.org/W2069157810","https://openalex.org/W2106248311","https://openalex.org/W2132022337","https://openalex.org/W2138862823","https://openalex.org/W2157253968","https://openalex.org/W2159675211","https://openalex.org/W2165040702","https://openalex.org/W2165558283","https://openalex.org/W2931164250","https://openalex.org/W2971469637","https://openalex.org/W2981657561","https://openalex.org/W3003257820","https://openalex.org/W3025361835","https://openalex.org/W3033403590","https://openalex.org/W3102147110","https://openalex.org/W3103145119","https://openalex.org/W4230735861","https://openalex.org/W6769086666"],"related_works":["https://openalex.org/W2982321410","https://openalex.org/W2366107444","https://openalex.org/W2392004567","https://openalex.org/W2940029036","https://openalex.org/W4388292429","https://openalex.org/W2756595502","https://openalex.org/W2046296964","https://openalex.org/W2010789764","https://openalex.org/W2219281195","https://openalex.org/W2377717868"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
