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status[950]
GeNemo


https://www.genemo.org/

logo_2019/
GeNemo is a very special vertical search engine. It is aimed at scientists looking for information on functional genomic data. Genemo indexes data from online data repositories and creates metadata on the Genemo servers. Genemoo started in 2016 and was developed by Zhang, Y., Cao, X., & Zhong, S. of UC San Diego.

     
Language English



Launched 2016
Closed No



Developer Sheng Zhong bioengineering lab at UC San Diego



Country of Origin US America



Owner



Topic Academic, Scientific or Educational SeEn



Region No Limitation



Technical functionalities
and/or
Strategy
Crawler / robot based SeEn using a white list of selected sites
SeEn for special character



Used SeEn GeNemo






Older Version Internet Archive / WebCite



Phys.org (2016): »University of California San Diego bioengineers have created what they believe to be the first online search engine for functional genomics data. [...] The functions of an organism's genome, captured in functional genomic data, are directly relevant to health and disease. Functional genomics data record the diverse activities of every piece of an organism's genome. The new search system may lead researchers to uncover the functional aspects in specific parts of genomes that are associated with normal physiology or disease of specific organs and tissues.« Source

Zhang et al. (2016): »A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org.« Source




Name

»The name GeNemo is a combination of "Ge" from the word gene and Nemo from the movie "Finding Nemo."« Source



Critical points




Features & Functionality

Phys.org (2016): »GeNemo addresses a pressing challenge: effectively searching functional genomic data from online data repositories. GeNemo queries user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. Instead of just "searching by text," the new tool allows researchers to search inside the functional data. Searching for binding patterns that are similar to that of a novel transcription factor is just one example. "If you think of functional genomic data files as video files, then the 'text search' is like searching by keywords in the title or the description of a video file. The 'inside data search' is like searching for a video clip by pattern matching within the video itself," explained Zhong. « Source



More




References & further Publications

Wikipedia (EN): n.a.
Wikipedia (Others): n.a.
     

Other Sources

Phys.org (2016): Bioengineers create first online search engine for functional genomics data URL: https://phys.org/news/2016-05-bioengineers-online-functional-genomics.html
Zhang, Y., Cao, X., & Zhong, S. (2016). GeNemo: a search engine for web-based functional genomic data. Nucleic Acids Research, 44(W1), W122—-W127. URL: https://doi.org/10.1093/nar/gkw299
GeNemo Search Manual URL: http://www.genemo.org/genemo-assets/manual_genemo.html




Created: 2017-04-21