{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T00:14:54Z","timestamp":1772583294173,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2019,6,25]],"date-time":"2019-06-25T00:00:00Z","timestamp":1561420800000},"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\/100012596","name":"Nuclear Waste Management Organization","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100012596","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>A critical step in comparative genomics is the identification of differences in the presence\/absence of encoded biochemical pathways among organisms. Our library, Pygenprop, facilitates these comparisons using data from the Genome Properties database. Pygenprop is written in Python and, unlike existing libraries, it is compatible with a variety of tools in the Python data science ecosystem, such as Jupyter Notebooks for interactive analyses and scikit-learn for machine learning. Pygenprop assigns YES, NO, or PARTIAL support for each property based on InterProScan annotations of open reading frames from an organism\u2019s genome. The library contains classes for representing the Genome Properties database as a whole and methods for detecting differences in property assignments between organisms. As the Genome Properties database grows, we anticipate widespread adoption of Pygenprop for routine genome analyses and integration within third-party bioinformatics software.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Pygenprop is written in Python and is compatible with versions 3.6 or higher. Source code is available under Apache Licence Version 2 at https:\/\/github.com\/Micromeda\/pygenprop. The package can be installed from both PyPi (https:\/\/pypi.org\/project\/pygenprop) and Anaconda (https:\/\/anaconda.org\/lbergstrand\/pygenprop). Documentation is available on Read the Docs (http:\/\/pygenprop.rtfd.io\/).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz522","type":"journal-article","created":{"date-parts":[[2019,6,20]],"date-time":"2019-06-20T21:38:40Z","timestamp":1561066720000},"page":"5063-5065","source":"Crossref","is-referenced-by-count":4,"title":["Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties"],"prefix":"10.1093","volume":"35","author":[{"given":"Lee H","family":"Bergstrand","sequence":"first","affiliation":[{"name":"Department of Biology, University of Waterloo , Waterloo, Canada"}]},{"given":"Josh D","family":"Neufeld","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Waterloo , Waterloo, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2015-099X","authenticated-orcid":false,"given":"Andrew C","family":"Doxey","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Waterloo , Waterloo, Canada"}]}],"member":"286","published-online":{"date-parts":[[2019,6,25]]},"reference":[{"key":"2023013108320830100_btz522-B1","doi-asserted-by":"crossref","first-page":"D623","DOI":"10.1093\/nar\/gkm900","article-title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway\/genome databases","volume":"36","author":"Caspi","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023013108320830100_btz522-B2","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gks1234","article-title":"TIGRFAMs and genome properties in 2013","volume":"41","author":"Haft","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023013108320830100_btz522-B3","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023013108320830100_btz522-B4","first-page":"87","author":"Kluyver","year":"2016"},{"key":"2023013108320830100_btz522-B5","first-page":"51","volume-title":"Proceedings of the 9th Python in Science Conference","author":"McKinney","year":"2010"},{"key":"2023013108320830100_btz522-B6","doi-asserted-by":"crossref","first-page":"D351","DOI":"10.1093\/nar\/gky1100","article-title":"InterPro in 2019: improving coverage, classification and access to protein sequence annotations","volume":"47","author":"Mitchell","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023013108320830100_btz522-B7","doi-asserted-by":"crossref","first-page":"D206","DOI":"10.1093\/nar\/gkt1226","article-title":"The seed and the rapid annotation of microbial genomes using subsystems technology (RAST)","volume":"42","author":"Overbeek","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023013108320830100_btz522-B8","article-title":"Automatic differentiation in pytorch","volume-title":"Proceedings of the 31st Conference on Neural Information Processing Systems Workshop on Automatic Differentiation","author":"Paszke","year":"2017"},{"key":"2023013108320830100_btz522-B9","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J. Mach. Learn. Res"},{"key":"2023013108320830100_btz522-B10","doi-asserted-by":"crossref","first-page":"D564","DOI":"10.1093\/nar\/gky1013","article-title":"Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes","volume":"47","author":"Richardson","year":"2019","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz522\/28934924\/btz522.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/23\/5063\/48978141\/bioinformatics_35_23_5063.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/23\/5063\/48978141\/bioinformatics_35_23_5063.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T17:37:31Z","timestamp":1675186651000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/23\/5063\/5522910"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,6,25]]},"references-count":10,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2019,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz522","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,12,1]]},"published":{"date-parts":[[2019,6,25]]}}}