| RGD | | Rat Genome Database pathway resource | | http://rgd.mcw.edu/wg/home/pathway2/molecular-pathways2 | | March 4th, 2017 | The Pathway Portal at the Rat Genome Database (RGD) - http://rgd.mcw.edu/wg/home/pathway2?100, is a multi-tier approach offering dynamic graphic representations of pathways along with associated annotations, integration with other portals and navigational capabilities.
The Pathway Ontology, also developed at RGD, is the vehicle that connects the elements of the portal from pathway terms to ontology report pages and from there to interactive diagram or gene report pages, or from gene reports to ontology reports and associated links. Links are also available from genes in diagrams to gene report pages, or from pathway objects to either gene lists or other types of report pages, as applicable. Pathways triggered or directly associated and present in a diagram page, link to their ontology report pages and to diagram pages, where available . Those pathways more globally related or revolving around a central concept are captured within pathway suites, and suite networks when more than one suite is present. The ontology, via mapping, also allows for the building of automatic import pipelines to bring in pathway data from KEGG, PID and soon PharmGKB and SMPD.
At the portal site, the user has the choice of accessing the entire collection of interactive diagram pages by selecting Molecular Pathways? and the link at the homepage of Pathguide. In addition, publications are also available on the same page, and pathway annotation files are available for download from pathway ontology report pages and the RGD ftp site. The rat, human and mouse gene annotation files, by ontology, can be downloaded from the RGD ftp site as well.
The portal is a work in progress and new venues and options for tool development and data presentation are continuously considered.
The portal can also be accessed from the NCBO Bioportal site for the Pathway Ontology - http://bioportal.bioontology.org/ontologies/1035. | | | | Secondary | | Free to all users | The Rat Genome Database, update 2007--easing the path from disease to data and back again.
Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ; RGD Team.
Nucleic Acids Res. 2007 Jan;35(Database issue):D658-62.
The Rat Genome Database 2009: variation, ontologies and pathways.
Dwinell MR, Worthey EA, Shimoyama M, Bakir-Gungor B, DePons J, Laulederkind S, Lowry T, Nigram R, Petri V, Smith J, Stoddard A, Twigger SN, Jacob HJ; RGD Team.
Nucleic Acids Res. 2009 Jan;37(Database issue):D744-9.
The Rat Genome Database pathway portal.
Petri V, Shimoyama M, Hayman GT, Smith JR, Tutaj M, de Pons J, Dwinell MR, Munzenmaier DH, Twigger SN, Jacob HJ; RGD Team.
Database (Oxford). 2011 Apr 8;2011:bar010.
The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information.
Hayman GT, Jayaraman P, Petri V, Tutaj M, Liu W, De Pons J, Dwinell MR, Shimoyama M.
Hum Genomics. 2013 Feb 5;7:4.
The Rat Genome Database 2013--data, tools and users.
Laulederkind SJ, Hayman GT, Wang SJ, Smith JR, Lowry TF, Nigam R, Petri V, de Pons J, Dwinell MR, Shimoyama M, Munzenmaier DH, Worthey EA, Jacob HJ.
Brief Bioinform. 2013 Jul;14(4):520-6.
Analysis of disease-associated objects at the Rat Genome Database.
Wang SJ, Laulederkind SJ, Hayman GT, Smith JR, Petri V, Lowry TF, Nigam R, Dwinell MR, Worthey EA, Munzenmaier DH, Shimoyama M, Jacob HJ.
Database (Oxford). 2013 Jun 21;2013:bat046.
Rat Genome Database: a unique resource for rat, human, and mouse quantitative trait locus data.
Nigam R, Laulederkind SJ, Hayman GT, Smith JR, Wang SJ, Lowry TF, Petri V, De Pons J, Tutaj M, Liu W, Jayaraman P, Munzenmaier DH, Worthey EA, Dwinell MR, Shimoyama M, Jacob HJ.
Physiol Genomics. 2013 Sep 16;45(18):809-16.
Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.
Nigam R, Munzenmaier DH, Worthey EA, Dwinell MR, Shimoyama M, Jacob HJ.
J Biomed Semantics. 2013 Nov 22;4(1):36.
Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease.
Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind SJ, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR, Worthey EA, Jacob HJ.
Hum Genomics. 2014 Sep 30;8:17.
The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.
Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H.
Nucleic Acids Res. 2015 Jan;43(Database issue):D743-50.
OntoMate: a text-mining tool aiding curation at the Rat Genome Database.
Liu W, Laulederkind SJ, Hayman GT, Wang SJ, Nigam R, Smith JR, De Pons J, Dwinell MR, Shimoyama M.
Database (Oxford). 2015 Jan 25;2015. pii: bau129.
The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.
Hayman GT, Laulederkind SJ, Smith JR, Wang SJ, Petri V, Nigam R, Tutaj M, De Pons J, Dwinell MR, Shimoyama M.
Database (Oxford). 2016 Mar 23;2016. pii: baw034.
Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.
Wang SJ, Laulederkind SJ, Hayman GT, Petri V, Smith JR, Tutaj M, Nigam R, Dwinell MR, Shimoyama M.
Physiol Genomics. 2016 Aug 1;48(8):589-600.
Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass.
Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind S, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR.
Comput Struct Biotechnol J. 2015 Nov 26;14:35-48.
Exploring human disease using the Rat Genome Database.
Shimoyama M, Laulederkind SJ, De Pons J, Nigam R, Smith JR, Tutaj M, Petri V, Hayman GT, Wang SJ, Ghiasvand O, Thota J, Dwinell MR.
Dis Model Mech. 2016 Oct 1;9(10):1089-1095.
| | Protein-Protein Interactions, Metabolic Pathways, Signaling Pathways, Pathway Diagrams | | Pathway diagram tools | | Pathways: | 234 | | Last Content Update: | November 7th, 2016 |
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