Cargando…
ToxReporter: viewing the genome through the eyes of a toxicologist
One of the many roles of a toxicologist is to determine if an observed adverse event (AE) is related to a previously unrecognized function of a given gene/protein. Towards that end, he or she will search a variety of public and propriety databases for information linking that protein to the observed...
Autor principal: | |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199150/ https://www.ncbi.nlm.nih.gov/pubmed/27888230 http://dx.doi.org/10.1093/database/baw141 |
_version_ | 1782488956631252992 |
---|---|
author | Gosink, Mark |
author_facet | Gosink, Mark |
author_sort | Gosink, Mark |
collection | PubMed |
description | One of the many roles of a toxicologist is to determine if an observed adverse event (AE) is related to a previously unrecognized function of a given gene/protein. Towards that end, he or she will search a variety of public and propriety databases for information linking that protein to the observed AE. However, these databases tend to present all available information about a protein, which can be overwhelming, limiting the ability to find information about the specific toxicity being investigated. ToxReporter compiles information from a broad selection of resources and limits display of the information to user-selected areas of interest. ToxReporter is a PERL-based web-application which utilizes a MySQL database to streamline this process by categorizing public and proprietary domain-derived information into predefined safety categories according to a customizable lexicon. Users can view gene information that is ‘red-flagged’ according to the safety issue under investigation. ToxReporter also uses a scoring system based on relative counts of the red-flags to rank all genes for the amount of information pertaining to each safety issue and to display their scored ranking as an easily interpretable ‘Tox-At-A-Glance’ chart. Although ToxReporter was originally developed to display safety information, its flexible design could easily be adapted to display disease information as well. Database URL: ToxReporter is freely available at https://github.com/mgosink/ToxReporter. |
format | Online Article Text |
id | pubmed-5199150 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-51991502017-01-06 ToxReporter: viewing the genome through the eyes of a toxicologist Gosink, Mark Database (Oxford) Database Tool One of the many roles of a toxicologist is to determine if an observed adverse event (AE) is related to a previously unrecognized function of a given gene/protein. Towards that end, he or she will search a variety of public and propriety databases for information linking that protein to the observed AE. However, these databases tend to present all available information about a protein, which can be overwhelming, limiting the ability to find information about the specific toxicity being investigated. ToxReporter compiles information from a broad selection of resources and limits display of the information to user-selected areas of interest. ToxReporter is a PERL-based web-application which utilizes a MySQL database to streamline this process by categorizing public and proprietary domain-derived information into predefined safety categories according to a customizable lexicon. Users can view gene information that is ‘red-flagged’ according to the safety issue under investigation. ToxReporter also uses a scoring system based on relative counts of the red-flags to rank all genes for the amount of information pertaining to each safety issue and to display their scored ranking as an easily interpretable ‘Tox-At-A-Glance’ chart. Although ToxReporter was originally developed to display safety information, its flexible design could easily be adapted to display disease information as well. Database URL: ToxReporter is freely available at https://github.com/mgosink/ToxReporter. Oxford University Press 2016-10-02 /pmc/articles/PMC5199150/ /pubmed/27888230 http://dx.doi.org/10.1093/database/baw141 Text en © The Author(s) 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Tool Gosink, Mark ToxReporter: viewing the genome through the eyes of a toxicologist |
title | ToxReporter: viewing the genome through the eyes of a toxicologist |
title_full | ToxReporter: viewing the genome through the eyes of a toxicologist |
title_fullStr | ToxReporter: viewing the genome through the eyes of a toxicologist |
title_full_unstemmed | ToxReporter: viewing the genome through the eyes of a toxicologist |
title_short | ToxReporter: viewing the genome through the eyes of a toxicologist |
title_sort | toxreporter: viewing the genome through the eyes of a toxicologist |
topic | Database Tool |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199150/ https://www.ncbi.nlm.nih.gov/pubmed/27888230 http://dx.doi.org/10.1093/database/baw141 |
work_keys_str_mv | AT gosinkmark toxreporterviewingthegenomethroughtheeyesofatoxicologist |