{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:24:10Z","timestamp":1763810650150,"version":"3.37.3"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,10,12]],"date-time":"2021-10-12T00:00:00Z","timestamp":1633996800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI134058"],"award-info":[{"award-number":["R01 AI134058"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>WikiPathways is a database of 2979 biological pathways across 31 species created using the drawing software PathVisio. Many of these pathways are not directly usable for network-based topological analyses due to differences in curation styles and drawings. We developed the WikiNetworks package to standardize and construct directed networks by combining geometric information and manual annotations from WikiPathways. WikiNetworks performs significantly better than existing tools. This enables the use of high-quality WikiPathways resource for network-based topological analysis of high-throughput data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>WikiNetworks is written in Python3 and is available on github.com\/Thakar-Lab\/wikinetworks and on PyPI.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab699","type":"journal-article","created":{"date-parts":[[2021,10,11]],"date-time":"2021-10-11T19:33:00Z","timestamp":1633980780000},"page":"869-871","source":"Crossref","is-referenced-by-count":7,"title":["WikiNetworks: translating manually created biological pathways for topological analysis"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1179-7903","authenticated-orcid":false,"given":"Mukta G","family":"Palshikar","sequence":"first","affiliation":[{"name":"Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA"}]},{"given":"Shannon P","family":"Hilchey","sequence":"additional","affiliation":[{"name":"Division of Nephrology, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA"}]},{"given":"Martin S","family":"Zand","sequence":"additional","affiliation":[{"name":"Division of Nephrology, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA"},{"name":"Clinical and Translational Science Institute, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4479-4183","authenticated-orcid":false,"given":"Juilee","family":"Thakar","sequence":"additional","affiliation":[{"name":"Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry , Rochester, NY 14642, USA"},{"name":"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"}]}],"member":"286","published-online":{"date-parts":[[2021,10,12]]},"reference":[{"key":"2023020108481104400_btab699-B1","doi-asserted-by":"crossref","first-page":"4473","DOI":"10.1093\/bioinformatics\/btaa484","article-title":"Automated inference of Boolean models from molecular interaction maps using CaSQ","volume":"36","author":"Aghamiri","year":"2020","journal-title":"Bioinformatics"},{"year":"2009","key":"2023020108481104400_btab699-B2"},{"key":"2023020108481104400_btab699-B3","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1145\/361002.361007","article-title":"Multidimensional binary search trees used for associative searching","volume":"18","author":"Bentley","year":"1975","journal-title":"Commun. 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