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- ...ough GMOD uses the [[Chado]] [[Glossary#Schema|schema]] for its underlying database, each group has developed a separate interface to their databases. This mee ...ly, or create a relational schema and middleware automatically from a data model ([[InterMine]]). The second class involved hand-coding an API to create an40 KB (5,672 words) - 21:27, 15 August 2013
- ...ratory database of genome annotations, or a large web-accessible community database. GMOD tools are in use at [[MOD|many large and small community databases]]. [[File:ChadoLogo.png|250px|thumb|none|link=Chado|Chado: Biological database schema]]5 KB (651 words) - 18:22, 30 March 2021
- |full name=Generic Genome Browser |about=GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on ge11 KB (1,422 words) - 16:47, 10 April 2023
- ...ite analysis tool. It is a component of the Generic Model Organism Systems Database project.595 B (80 words) - 22:36, 11 September 2009
- ...se join the [http://www.mendeley.com/groups/2472261/generic-model-organism-database-gmod-project/ GMOD group] and contribute GMOD and GMOD-related papers to th ...ywidget src="http://www.mendeley.com/groups/2472261/generic-model-organism-database-gmod-project/" width="100%" height="400px" n_papers="50" />21 KB (3,298 words) - 22:22, 9 February 2015
- GMOD Generic Model Organism Database ...GMOD_presentation20060630.ppt]] - The Genomic Diversity and Phenotype Data Model (GDPDM)3 KB (426 words) - 19:30, 23 January 2008
- .../www.genome.gov/10006356 <br /> NIH/NIAID/Wellcome Trust Workshop on Model Organism Databases, April 2002<br />]''' ...report discusses and summarizes good practices for new and existing model organism/genome databases.26 KB (3,975 words) - 05:03, 28 January 2008
- ...ecting a varied audience of bioinformaticians and biologists who work with organism/genome databases, or who are learning how to start one. There may well be s ...ne, searching with broader concepts, extracting focused answers, and cross-database facilitation. We hope most presenters can touch on these to give the audien4 KB (599 words) - 01:32, 29 March 2007
- ...l is to produce reusable components which would allow a new Model Organism Database (MOD) to be assembled by mixing components from GMOD [4]. Clearly, to meet6 KB (855 words) - 23:50, 25 January 2008
- ===Chado - Generic module organism database schema=== ===Chado - generic model organism database schema===1 KB (143 words) - 05:33, 28 January 2008
- ...databases can use the GMODWeb skin as a starting point for creating a new organism website. See [http://radius.genomics.ctrl.ucla.edu/turnkey/pmwiki.php?n=Mai [[Turnkey]] takes a relational schema of a given database as input and transforms it into a fully-functional and customizable website2 KB (288 words) - 19:30, 4 April 2011
- Generic Model Organism Database Construction Set886 B (116 words) - 17:43, 26 May 2008
- Generic Model Organism Database Construction Set790 B (110 words) - 14:02, 6 April 2007
- Generic Model Organism Database Construction Set * Generic Schema (generic_pub)28 KB (4,338 words) - 22:06, 29 October 2010
- Generic Model Organism Database Construction Set 1:50 Shannon Schlueter (Arabidopsis thaliana Plant Genome Database, Iowa State University)<br>42 KB (6,309 words) - 20:37, 30 November 2010
- Generic Model Organism Database Construction Set3 KB (355 words) - 15:30, 6 April 2007
- Generic Model Organism Database Construction Set7 KB (915 words) - 17:07, 14 March 2008
- Generic Model Organism Database Construction Set5 KB (752 words) - 22:15, 28 July 2010
- GMOD Generic Model Organism Database | Candida Genome Database4 KB (601 words) - 22:33, 10 September 2009
- ...s ''given the data I have, what database should I use?", "do I even need a database?'', or ''how hard is this going to be?''. ...o appear and many of the first genome databases used GMOD components. GMOD database and software components have developed and expanded with the massive growth34 KB (5,526 words) - 19:56, 7 October 2013
- The Generic Model Organism Database project ([http://gmod.org GMOD]) is a collection of open source software to ...er science or related field; three or more years of experience with genome database administration or curation, preferably in a GMOD environment; at least one2 KB (359 words) - 16:42, 22 August 2012
- mechanism, which is absent from the standard relational model. For example, SO tells us that sequence of other features in the database. For example, exon sequences are generally not stored,64 KB (9,963 words) - 22:17, 18 December 2013
- * At first, a database for FlyBase: incredibly interesting dataset * A database for '''very''' deep curation14 KB (2,071 words) - 22:45, 11 January 2019
- ...se these elements ALWAYS correspond to a table or column in the relational database, where the meaning of this element is (hopefully) documented. ...e documentation. Until that time it is best to also consult the relational database documentation.10 KB (1,539 words) - 21:16, 9 October 2012
- The following is a selection of the websites (including organism databases, research groups, and software) using [[GBrowse]], [[JBrowse]], [ | http://amborella.org || Amborella Genome Database || Amborella || GBrowse, Tripal || 201431 KB (3,762 words) - 10:43, 12 August 2014
- 'Generic-Genome-Browser' directory ...of annotated features), you can skip installing MySQL and use an in-memory database instead.35 KB (5,565 words) - 22:39, 8 August 2012
- * Relational Database Management System [officially supported: PostgreSQL] * User database helper scripts77 KB (11,812 words) - 00:39, 21 May 2014
- This document provides information on configuring version 1 of the [[GBrowse|Generic Genome Browser (GBrowse)]], part of the [[Main Page|GMOD Project]]. For ver ...WTO|installing GBrowse]] is to get the genomic data you want to see into a database that GBrowse can read.79 KB (12,563 words) - 16:45, 15 August 2011
- ParameciumDB (http://paramecium.cgm.cnrs-gif.fr) is a model organism database for the unicellular eukaryote ''Paramecium tetraurelia''. ParameciumDB con ...mecium tetraurelia genome sequence with genetic data], in the January 2007 Database Issue of [http://nar.oxfordjournals.org/ ''Nucleic Acids Research''].10 KB (1,362 words) - 08:29, 6 April 2013
- ...set of modules for [http://drupal.org Drupal] to interact with a [[Chado]] database. * Modules for [[Chado Organism Module|organism]], [[Chado Library Module|library]], [[Chado Sequence Module|sequence]]59 KB (8,741 words) - 19:37, 4 September 2013
- Model organism/genome databases (MODs) produce gene pages of similar ...nyms; Map locations; Sequences and Reagents; Gene ontology; Similar Genes; Database cross-refs and external links; Alleles and Transcripts; Proteins, Structur7 KB (1,051 words) - 19:24, 4 September 2013
- ...ngoproject.com/ Django] (Python based) framework for accessing a [[Chado]] database. The Django framework can be used to create web interfaces and command line ...nice choice for data disclosure projects like a website on top of a Chado database. There are other such frameworks like [http://turbogears.org/ Turbogears] (16 KB (2,412 words) - 18:11, 9 October 2012
- |Metadata Input and Submission Tool and GIS linked metagenomic database ...df|PDF]], [[#Metadata Input and Submission Tool and GIS linked metagenomic database|Summary]]50 KB (7,612 words) - 18:53, 8 October 2012
- ...]". The main idea is to increase interoperability among the various model organism databases by creating an easy to use high level RESTful [[Glossary#API|API] * Data model agnostic25 KB (3,166 words) - 23:02, 15 August 2013
- ...addressed critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that limited its utility for evolutionary research. Specific :Worked on establishing a common database backend and {{GlossaryLink|JSON|JSON}}-based API for comparative genomics d17 KB (2,407 words) - 13:22, 13 November 2015
- ...ates their output to produce what MAKER finds to be the best possible gene model for a given location based on evidence alignments. ...gene models but should include a documented evidence trail supporting the model in addition to quality control metrics.80 KB (12,961 words) - 23:47, 29 July 2013
- ! [http://www.intl-pag.org/18/abstracts/W26_PAGXVIII_192.html Database Resources at the EBI: Ensembl And Ensembl Genomes - Access To Genome-Scale ! [[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Y13 KB (1,711 words) - 18:17, 2 October 2012
- ...nomics Information Management and Marker Discovery Toolkit For A Non-Model Organism | Bovine Genome Database; BeeBase; NasoniaBase; Hymenoptera Genome Database26 KB (3,722 words) - 19:17, 4 September 2013
- ...e EST contigs sequenced from a novel genome align to the genome of a model organism. ...elements/features, choices to make them permanently or privately part of a database26 KB (3,948 words) - 17:18, 6 October 2009
- ...on to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. ...by many large and small, collaborative and single-investigator biological database projects for the dissemination of experimental results and curated knowledg12 KB (1,744 words) - 18:53, 8 October 2012
- * Can also provide GUI to database tables * Potential to give wiki access to a Chado database100 KB (14,725 words) - 17:31, 30 November 2012
- : Generic Model Organism Database (GMOD), http://gmod.org ....g., [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 Database tools for evolutionary genomics] at [http://ccg.biology.uiowa.edu/smbe/inde7 KB (1,003 words) - 18:14, 8 January 2013
- ...wse_syn]], a comparative genomics viewer; [[Chado]], a generic and modular database schema; [[CMap]], a comparative map viewer; as well as many other component ...on to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research.6 KB (906 words) - 18:53, 8 October 2012
- '''GMOD''' is the Generic Model Organism Database project, a collection of interoperable open-source [[GMOD Components|softwa10 KB (1,435 words) - 00:41, 15 September 2012
- '''GMOD''' is the Generic Model Organism Database project, a collection of interoperable open-source [[GMOD Components|softwa | Mimosa: Miniature Model Organism Sequence Aligner18 KB (2,659 words) - 19:19, 4 September 2013
- '''GMOD''' is the Generic Model Organism Database project, a collection of interoperable open-source [[GMOD Components|softwa4 KB (576 words) - 18:55, 8 October 2012
- ...amene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database. Links: [http://www.gmod.org Website], [http://blog.gmod.org GMOD Blog] ;'''[http://gmod.org/wiki/GBrowse GBrowse]''': The Generic Genome Browser (GBrowse) is a web application for searching and displaying4 KB (561 words) - 18:02, 19 February 2016
- The Generic Model Organism Database project (GMOD, http://gmod.org) is a collection of open source software too ...database management systems; three or more years of experience with genome database administration or curation, preferably in a GMOD environment; at least one3 KB (378 words) - 00:01, 5 March 2011
- ...ce" will depend on how you are using JBrowse. For a model organism genome database, each reference sequence would typically represent a chromosome or a [http: ...ces from a gff file or a database. In order to read fasta sequences from a database, a config file must be used.185 KB (26,536 words) - 02:48, 30 September 2020
- ...mation resource and as a mode to publish and distribute their results. The database is constantly updated and new versions are released on a monthly basis. Wor ...atform compatibility and wide usability in mind. Data is stored in a MySQL database, the web site is implemented in Perl and data entry tool in Java programmin20 KB (2,895 words) - 23:51, 25 July 2012
