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toxoMine: an integrated omics data warehouse forToxoplasma gondiisystems biology research

David B. Rhee, Matthew McKnight Croken, Kevin R. Shieh, Julie Sullivan, Gos Micklem, Kami Kim, Aaron Golden
<span title="">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
., Shieh,K.R. et al. toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research.  ...  As a data warehouse, toxoMine allows integration of high-throughput data sets with public T. gondii data. toxoMine is also able to execute complex queries involving multiple data sets with straightforward  ...  The authors also thank Ms Stacie Schwartz for editing and comments on the article. Toxoplasma gondii genomic sequence data and annotations were accessed via http://toxodb.org.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bav066">doi:10.1093/database/bav066</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26130662">pmid:26130662</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4485433/">pmcid:PMC4485433</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lmhs4bis7zhzvhr6py6kb4y6hi">fatcat:lmhs4bis7zhzvhr6py6kb4y6hi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170707192336/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/database/2015/10.1093_database_bav066/5/bav066.pdf?Expires=1499495116&amp;Signature=ejY5IZ9DeX1xrNRTcOXGJxN~PfiSgWOIJJvznnI7uGERFTaDmBmtFA0lCPR5vQRcJf7LK8V-fjPpGpS-j2m0ZwGE-4Jtoiz3eC7JqPt0oO9Hecj2CLTNLfuuKLuVTWVvTJ~hjuX~~BQvdYoFGP9Sapd8r7QJ6EVfJCHs9~EI-VOmr~dnxSlBwJY~~bE0nPJeQ-MkEeRpfgzfuafEaDd8ekNDypc3kY~KI2GssGvWl8vz23YDGLBluOyS1chVRSRTLIhMmKZh2iimaM6oHLNBi-KRDnCs~sAGwJqBuIVjrjl8hnAow3xe6iztwf4SRGvy2QElSWq~0st6wtIlCJjPuw__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/98/c1/98c1133f048af5aaf1381e0f3471f0fab2db3f90.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bav066"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4485433" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Understanding the Systems Biology of Pathogen Virulence Using Semantic Methodologies

David Rhee, Kevin Shieh, Julie Sullivan, Gos Micklem, Kami Kim, Aaron Golden
<span title="">2016</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wckytungwvfnhotxmw56y6k3q4" style="color: black;">2016 IEEE Tenth International Conference on Semantic Computing (ICSC)</a> </i> &nbsp;
In this paper we describe how we have applied one such solution, based around the InterMine data warehouse platform which uses as its basis the Sequence Ontology, to facilitate a systems biology analysis  ...  The central problem remains empowering the scientific community to actually implement such an integration, across seemingly diverse data types and measurements.  ...  Micklem) and National Human Genome Research Institute (Grant Number: R01HG004834 to Dr. G. Micklem).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/icsc.2016.33">doi:10.1109/icsc.2016.33</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/semco/RheeSSMKG16.html">dblp:conf/semco/RheeSSMKG16</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qgwc3e53wvd4bhgusjrmmgbyfm">fatcat:qgwc3e53wvd4bhgusjrmmgbyfm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191023044955/https://arxiv.org/pdf/1604.05189v1.pdf" title="fulltext PDF download [not primary version]" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <span style="color: #f43e3e;">&#10033;</span> <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c4/b1/c4b1d2393e7d7c11c112374055a17601ed198b01.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/icsc.2016.33"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>