{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T07:34:18Z","timestamp":1769499258552,"version":"3.49.0"},"reference-count":6,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Source Code Biol Med"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and\/or biomedical content for various applications.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Methods<\/jats:title>\n            <jats:p>Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.maayanlab.net\/G2W\" ext-link-type=\"uri\">http:\/\/www.maayanlab.net\/G2W<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1751-0473-6-15","type":"journal-article","created":{"date-parts":[[2011,11,9]],"date-time":"2011-11-09T20:18:12Z","timestamp":1320869892000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Genes2WordCloud: a quick way to identify biological themes from gene lists and free text"],"prefix":"10.1186","volume":"6","author":[{"given":"Caroline","family":"Baroukh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sherry L","family":"Jenkins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruth","family":"Dannenfelser","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Avi","family":"Ma'ayan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,10,13]]},"reference":[{"key":"68_CR1","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1145\/1242572.1242766","volume-title":"Proceedings of the 16th international conference on World Wide Web:","author":"BYL Kuo","year":"2007","unstructured":"Kuo BYL, Hentrich T, Good BM, Wilkinson MD: Tag clouds for summarizing web search results. Proceedings of the 16th international conference on World Wide Web:. 2007, ACM, 1203-1204. ; New York, New York, USA"},{"issue":"7","key":"68_CR2","first-page":"709","volume":"680","author":"J Desai","year":"2011","unstructured":"Desai J, Flatow JM, Song J, Zhu LJ, Du P, Huang C-C, Lu H, Lin SM, Kibbe WA: Visual Presentation as a Welcome Alternative to Textual Presentation of Gene Annotation Information. Advances in Experimental Medicine and Biology. 2011, 680 (7): 709-715.","journal-title":"Advances in Experimental Medicine and Biology"},{"issue":"1","key":"68_CR3","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1751-0473-6-7","volume":"6","author":"L Oesper","year":"2011","unstructured":"Oesper L, Merico D, Isserlin R, Bader G: WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code for Biology and Medicine. 2011, 6 (1): 7-10.1186\/1751-0473-6-7.","journal-title":"Source Code for Biology and Medicine"},{"key":"68_CR4","first-page":"563","volume":"2009","author":"IN Sarkar","year":"2009","unstructured":"Sarkar IN, Schenk R, Miller H, Norton CN: LigerCat: Using \"MeSH Clouds\" from Journal, Article, or Gene Citations to Facilitate the Identification of Relevant Biomedical Literature. AMIA Annu Symp Proc. 2009, 2009: 563-567.","journal-title":"AMIA Annu Symp Proc"},{"key":"68_CR5","doi-asserted-by":"crossref","unstructured":"Consortium GO: The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010, D331-335. 38 Database","DOI":"10.1093\/nar\/gkp1018"},{"issue":"3","key":"68_CR6","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1002\/wsbm.44","volume":"1","author":"CL Smith","year":"2009","unstructured":"Smith CL, Eppig JT: The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med. 2009, 1 (3): 390-399. 10.1002\/wsbm.44.","journal-title":"Wiley Interdiscip Rev Syst Biol Med"}],"container-title":["Source Code for Biology and Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1751-0473-6-15.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:20:18Z","timestamp":1630495218000},"score":1,"resource":{"primary":{"URL":"https:\/\/scfbm.biomedcentral.com\/articles\/10.1186\/1751-0473-6-15"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,10,13]]},"references-count":6,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["68"],"URL":"https:\/\/doi.org\/10.1186\/1751-0473-6-15","relation":{},"ISSN":["1751-0473"],"issn-type":[{"value":"1751-0473","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,13]]},"assertion":[{"value":"11 September 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 October 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 October 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"15"}}