{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:52:23Z","timestamp":1778226743368,"version":"3.51.4"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2019,3,23]],"date-time":"2019-03-23T00:00:00Z","timestamp":1553299200000},"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\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007917","name":"Agricultural Research Service","doi-asserted-by":"publisher","award":["5030-21000-068-00D"],"award-info":[{"award-number":["5030-21000-068-00D"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007917","name":"Agricultural Research Service","doi-asserted-by":"publisher","award":["2030-21000-024-00D"],"award-info":[{"award-number":["2030-21000-024-00D"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Plant breeding aims to improve current germplasm that can tolerate a wide range of biotic and abiotic stresses. To accomplish this goal, breeders rely on developing a deeper understanding of genetic makeup and relationships between plant varieties to make informed plant selections. Although rapid advances in genotyping technology generated a large amount of data for breeders, tools that facilitate pedigree analysis and visualization are scant, leaving breeders to use classical, but inherently limited, hierarchical pedigree diagrams for a handful of plant varieties. To answer this need, we developed a simple web-based tool that can be easily implemented at biological databases, called PedigreeNet, to create and visualize customizable pedigree relationships in a network context, displaying pre- and user-uploaded data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>As a proof-of-concept, we implemented PedigreeNet at the maize model organism database, MaizeGDB. The PedigreeNet viewer at MaizeGDB has a dynamically-generated pedigree network of 4706 maize lines and 5487 relationships that are currently available as both a stand-alone web-based tool and integrated directly on the MaizeGDB Stock Pages. The tool allows the user to apply a number of filters, select or upload their own breeding relationships, center a pedigree network on a plant variety, identify the common ancestor between two varieties, and display the shortest path(s) between two varieties on the pedigree network. The PedigreeNet code layer is written as a JavaScript wrapper around Cytoscape Web. PedigreeNet fills a great need for breeders to have access to an online tool to represent and visually customize pedigree relationships.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>PedigreeNet is accessible at https:\/\/www.maizegdb.org\/breeders_toolbox. The open source code is publically and freely available at GitHub: https:\/\/github.com\/Maize-Genetics-and-Genomics-Database\/PedigreeNet.<\/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\/btz208","type":"journal-article","created":{"date-parts":[[2019,3,20]],"date-time":"2019-03-20T20:23:04Z","timestamp":1553113384000},"page":"4184-4186","source":"Crossref","is-referenced-by-count":5,"title":["PedigreeNet: a web-based pedigree viewer for biological databases"],"prefix":"10.1093","volume":"35","author":[{"given":"Bremen L","family":"Braun","sequence":"first","affiliation":[{"name":"U.S. Department of Agriculture, Agricultural Research Service , Corn Insects and Crop Genetics Research Unit, Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David A","family":"Schott","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture, Agricultural Research Service , Corn Insects and Crop Genetics Research Unit, Ames, IA, USA"},{"name":"Department of Computer Science, Iowa State University , Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John L","family":"Portwood","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture, Agricultural Research Service , Corn Insects and Crop Genetics Research Unit, Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carson M","family":"Andorf","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture, Agricultural Research Service , Corn Insects and Crop Genetics Research Unit, Ames, IA, USA"},{"name":"Department of Computer Science, Iowa State University , Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taner Z","family":"Sen","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture, Agricultural Research Service , Crop Improvement and Genetics Research Unit, Albany, CA, USA"},{"name":"Department of Genetics, Development, and Cell Biology, Iowa State University , Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,3,23]]},"reference":[{"key":"2023020108351076400_btz208-B1","doi-asserted-by":"crossref","first-page":"D1195","DOI":"10.1093\/nar\/gkv1007","article-title":"MaizeGDB update: new tools, data and interface for the maize model organism database","volume":"44","author":"Andorf","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020108351076400_btz208-B2","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1109\/TVCG.2010.159","article-title":"GeneaQuilts: a system for exploring large genealogies","volume":"16","author":"Bezerianos","year":"2010","journal-title":"IEEE Trans. Vis. Comput. Graph"},{"key":"2023020108351076400_btz208-B3","doi-asserted-by":"crossref","first-page":"6191","DOI":"10.1093\/jxb\/eru064","article-title":"Breeding drought-tolerant maize hybrids for the US corn-belt: discovery to product","volume":"65","author":"Cooper","year":"2014","journal-title":"J. Exp. Bot"},{"key":"2023020108351076400_btz208-B4","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1093\/bioinformatics\/btv557","article-title":"Cytoscape.js: a graph theory library for visualisation and analysis","volume":"32","author":"Franz","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020108351076400_btz208-B5","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1007\/978-981-10-6056-4_7","volume-title":"Breeding Insect Resistant Crops for Sustainable Agriculture","author":"Karjagi","year":"2017"},{"key":"2023020108351076400_btz208-B6","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1038\/sj.ejhg.5201430","article-title":"High-throughput pedigree drawing","volume":"13","author":"Makinen","year":"2005","journal-title":"Eur. J. Hum. Genet"},{"key":"2023020108351076400_btz208-B7","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.cpb.2017.11.001","article-title":"The art of curation at a biological database: principles and application","volume":"11-12","author":"Odell","year":"2017","journal-title":"Curr. Plant Biol"},{"key":"2023020108351076400_btz208-B8","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bay037","article-title":"SNPversity: a web-based tool for visualizing diversity","volume":"2018","author":"Schott","year":"2018","journal-title":"Database (Oxford)"},{"key":"2023020108351076400_btz208-B9","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bax031","article-title":"Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation","volume":"2017","author":"Sen","year":"2017","journal-title":"Database (Oxford)"},{"key":"2023020108351076400_btz208-B10","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1186\/1471-2105-15-259","article-title":"Helium: visualization of large scale plant pedigrees","volume":"15","author":"Shaw","year":"2014","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz208\/28492150\/btz208.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/20\/4184\/48977361\/bioinformatics_35_20_4184.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/20\/4184\/48977361\/bioinformatics_35_20_4184.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,14]],"date-time":"2023-09-14T18:26:09Z","timestamp":1694715969000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/20\/4184\/5418795"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,3,23]]},"references-count":10,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2019,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz208","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,10,15]]},"published":{"date-parts":[[2019,3,23]]}}}