{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T07:50:54Z","timestamp":1777881054643,"version":"3.51.4"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,26]],"date-time":"2022-05-26T00:00:00Z","timestamp":1653523200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Genome Quebec"},{"DOI":"10.13039\/501100001804","name":"Canada Research Chairs","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001804","id-type":"DOI","asserted-by":"publisher"}]},{"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"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Researchers are increasingly seeking to interpret molecular data within a multi-omics context to gain a more comprehensive picture of their study system. OmicsNet (www.omicsnet.ca) is a web-based tool developed to allow users to easily build, visualize, and analyze multi-omics networks to study rich relationships among lists of \u2018omics features of interest. Three major improvements have been introduced in OmicsNet 2.0, which include: (i) enhanced network visual analytics with eleven 2D graph layout options and a novel 3D module layout; (ii) support for three new \u2018omics types: single nucleotide polymorphism (SNP) list from genetic variation studies; taxon list from microbiome profiling studies, as well as liquid chromatography\u2013mass spectrometry (LC\u2013MS) peaks from\u00a0untargeted metabolomics;\u00a0and (iii) measures to improve research reproducibility by coupling R command history with the release of the companion OmicsNetR package, and generation of persistent links to share interactive network views. We performed a case study using the multi-omics data obtained from a recent large-scale investigation\u00a0on inflammatory bowel disease (IBD) and demonstrated that OmicsNet was able to quickly create meaningful multi-omics context to facilitate hypothesis generation and mechanistic insights.<\/jats:p>","DOI":"10.1093\/nar\/gkac376","type":"journal-article","created":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T20:09:12Z","timestamp":1651781352000},"page":"W527-W533","source":"Crossref","is-referenced-by-count":164,"title":["OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics"],"prefix":"10.1093","volume":"50","author":[{"given":"Guangyan","family":"Zhou","sequence":"first","affiliation":[{"name":"Institute of Parasitology, McGill University ,\u00a0 Quebec ,\u00a0 Canada"}]},{"given":"Zhiqiang","family":"Pang","sequence":"additional","affiliation":[{"name":"Institute of Parasitology, McGill University ,\u00a0 Quebec ,\u00a0 Canada"}]},{"given":"Yao","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, McGill University ,\u00a0 Quebec ,\u00a0 Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7555-736X","authenticated-orcid":false,"given":"Jessica","family":"Ewald","sequence":"additional","affiliation":[{"name":"Department of Natural Resource Sciences, McGill University ,\u00a0 Quebec ,\u00a0 Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2040-2624","authenticated-orcid":false,"given":"Jianguo","family":"Xia","sequence":"additional","affiliation":[{"name":"Institute of Parasitology, McGill University ,\u00a0 Quebec ,\u00a0 Canada"},{"name":"Department of Microbiology and Immunology, McGill University ,\u00a0 Quebec ,\u00a0 Canada"}]}],"member":"286","published-online":{"date-parts":[[2022,5,26]]},"reference":[{"key":"2022070423570256500_B1","doi-asserted-by":"crossref","first-page":"e0154387","DOI":"10.1371\/journal.pone.0154387","article-title":"Genetic factors are not the major causes of chronic diseases","volume":"11","author":"Rappaport","year":"2016","journal-title":"PLoS One"},{"key":"2022070423570256500_B2","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1002\/bies.201600084","article-title":"Missing heritability of complex diseases: enlightenment by genetic variants from intermediate phenotypes","volume":"38","author":"Blanco-Gomez","year":"2016","journal-title":"Bioessays"},{"key":"2022070423570256500_B3","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/s41588-020-00751-5","article-title":"A cross-platform approach identifies genetic regulators of human metabolism and health","volume":"53","author":"Lotta","year":"2021","journal-title":"Nat. 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