Presentation is loading. Please wait.

Presentation is loading. Please wait.

Generic model/many/my organism database Oct/Nov 2007 Don Gilbert Genome Informatics Lab, Biology Dept., Indiana University GMOD.

Published by Modified over 9 years ago

Similar presentations

Presentation on theme: "Generic model/many/my organism database Oct/Nov 2007 Don Gilbert Genome Informatics Lab, Biology Dept., Indiana University GMOD."— Presentation transcript:

1 generic model/many/my organism database Oct/Nov 2007 Don Gilbert Genome Informatics Lab, Biology Dept., Indiana University gilbertd@indiana.edu GMOD

2 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Indiana GMOD Potpourri Recent Updates for GMOD-CSHL-0711 Genome Grid GMODTools update Gene Summary Pages in XML

3 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Genome Grid Middleware to easily use TeraGrid (& other Grid) for genome analyses Give me your genomes to Gridalyze Collaborators wanted ! Apply BioMart, Ergatis, LuceGene, Galaxy Science gateway to use TeraGrid for genome analyses Blast: proteome x non-redudant; organisms x genome gene finders, interproscan, others gmod.org/Genome_grid

4 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf GMODTools update Update: config for new genome chado dbs (sea urchin, paramecium) loaded via GMOD gff2chado New: GO gene-association output Please publish your Chado DB gmod.org/Public_Chado_Databases each project chado has variations Cleans database contents for public use Todo: add gene page xml, others? gmod.org/GMODTools

5 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Gene Summary Pages Simple, readable XML summarizes gene info. In use at Daphnia (wFleaBase.org) base wfleabase.org/lucegene/lookup?id=NCBI_GNO_ 149114 wfleabase.org/lucegene/lookup?id=NCBI_GNO_ 149114 Created from Chado DB or overloaded GFF Software is simple Perl lib, XML DTD eugenes.org/gmod/gene-report-examples/

6 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Gene Page XML Gene Summary 2007-Sep-02 NCBI_GNO_200214 Daphnia pulex C:integral to membrane F:rhodopsin-like receptor activity P:G-protein coupled receptor protein signalin... P:phototransduction Rh3-PA Drosophila virilis UniProt:Q8I138 Bacterial infection Pfam:PF00001 7tm_1 WFes0143594

7 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf.. on to Introduction to GMOD..

8 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Generic Model Organism Database Built by and for many contributing projects Loosely coupled tool kit Work as separate parts and together Complex and simple No more complex than necessary; complexity is part of this territory. GMOD Introduction

9 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf New Genome? Draft assembly in parts; many computed annotations; little literature; Known Genome? Large literature base; rich and complex biology knowledge; Lab integration? Support and integrate with focused lab research project Your project needs?

10 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf gmod.org/Getting Started Documentation is now rich and improving Installation options: distribution tar-ball Virtual Machine-Ware for demo YUM Unix packages Getting Started w/ GMOD

11 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Chado – database schema and middleware GBrowse – Web-based genome annotation viewing Apollo – Desktop-based genome annotation editing CMap – Web-based comparative map viewing BioMart – Genome data mining from Ensembl/GMOD GMOD Components

12 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Chado - Getting Started gmod.org/Chado_Manual modules, conventions, design principles Worked examples @ gmod.org Load_RefSeq_Into_Chado Load_BLAST_Into_Chado Sample_Chado_SQL Chado Database How-To

13 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Modularity: inherent Chado schema, core module, biology groupings, with common structure. Ontologies: standard biology vocabularies a core of Chado design. Associated software: Perl and Java middleware, stand-alone programs with Chado adaptors. Chado Design

14 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Complexity and Detail: inherent in genome data, Chado embraces with room to grow, plus long-term stability. Data Integration: key component of Chado, public and lab data sets can be combined. Support: shared responsibility among the GMOD community. Chado Design [2]

15 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf CV: Controlled vocabularies and ontologies Sequence: Biological sequences and objects which can be localized on them Companalysis: Adjunct to sequence module for in- silico analysis Map: Adjunct to sequence module for non-sequence localization Organism: Taxonomy / species information Pub: Publication / Biblio. / Reference information General: General information / database cross- references Chado Schema: Core

16 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Expression: Transcript and protein expression events Mage: for microarray data Genetics: Genetic/phenotypic interactions in genotypic/environmental context Phenotype: for phenotypic data Library: for descriptions of molecular libraries Phylogeny: for organisms and phylogenetic trees Stock: for specimens and biological collections Contact: for people, groups, and organizations Chado Schema: More

17 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf GFF to Chado data loader, with BioPerl extensions (GenBank2GFF -> Chado, …) GMODTools - Output Bulk genome data XORT - Chado XML input and output Modware - OO-Perl Chado access package (in/out) Java middleware (Hibernate; others) Chado Middleware

18 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf

19 Sybil – Web-based synteny viewing at gene & chromosome level Turnkey – “Skinable” Chado-based web site Pathway Tools – metabolic pathways PubFetch – Literature management Textpresso – Automatic paper classification LuceGene - Genome object/text/web search system GMOD Components [2]

20 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Wikipedia Community Annotation (in development; EcoliWiki ++) Comparative visualization - SynBrowse & SynView Genome grid - Teragrid methods for genome computations (in dev.) GMOD Components [3]

21 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf WikiGenomes (ecoliwiki.net)

22 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Database Frameworks: VMWare: virtual machine package with basic GMOD components for demo YUM distribution package ARGOS : replication framework for genome databases GMOD Components [4]

23 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Core: PostgreSQL database; Chado Schema; Sequence & OBO Ontologies System: Apache web server; Unix; BioPerl; … Load data: GFF to Chado View: Gbrowse (Chado; MySql;..) Edit/Update: Apollo, Wiki (coming), bulk-file updates Output: BulkFiles; BioMart; Putting GMOD together

24 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Example new MOD

25 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf New Genome? Known? Lab integration? Assess your customer needs Full database/toolset is overkill for some Loosely coupled tools; complex and simple Pick the parts you need Learn tools with examples first Recap:Your project needs?

26 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Genome Annotations Proteome annotations, EST/cDNA, gene predictions, RNA, transposon, promotor, etc. Database cross-refs: UniProt, Gene Ontology, KEGG, KOG, etc. Web-Database Gbrowse maps, Blast server with Chado output, Gene detail reports, BioMart data mining; Wikipedia community editing Chado-centric Genome

27 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf Current components Need adopters to share effort Re-use rather than re-invent Describe : GMOD.org Wiki needs more examples New components Discuss with other projects: common need? Shared specifications, use cases GMOD recommended practices Contributing to GMOD

28 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf https://lists.sourceforge.net/lists/listinfo/ gmod-announce gmod-schema All Chado schema issues gmod-gbrowse GBrowse mailing list gmod-devel General development Related: Ontologies (SO, OBO); BioPerl; Apollo; Biomart; Active GMOD Mailing Lists

29 http://eugenes.org/gmod/docs/gmod-intro-07oct.pdf

Download ppt "Generic model/many/my organism database Oct/Nov 2007 Don Gilbert Genome Informatics Lab, Biology Dept., Indiana University GMOD."

Similar presentations

May 16, 2005Scott Cain, CSHL. May 16, 2005Scott Cain, CSHL gmod update Gmod-0.003-RC2 last week New for 0.003: –Generic triggers for Apollo –Greatly enhanced.

May 16, 2005Scott Cain, CSHL. May 16, 2005Scott Cain, CSHL gmod update Gmod RC2 last week New for 0.003: –Generic triggers for Apollo –Greatly enhanced.
Generic model/many/my organism database toolkit Dec 2007 Don Gilbert Genome Informatics Lab, Biology Dept., Indiana University GMOD.

Generic model/many/my organism database toolkit Dec 2007 Don Gilbert Genome Informatics Lab, Biology Dept., Indiana University GMOD.
Integrating Genome and Transcriptome Resources into TreeGenes Jill Wegrzyn David Neale Doreen Main Keithanne Mockaitis.

Integrating Genome and Transcriptome Resources into TreeGenes Jill Wegrzyn David Neale Doreen Main Keithanne Mockaitis.
Chado Generic model organism database schema Presented at the NESCent GMOD Meeting 20 January, 2005 David Emmert

Chado Generic model organism database schema Presented at the NESCent GMOD Meeting 20 January, 2005 David Emmert
GMODTools, Argos & cetera A Replicable Genome infOrmation System of Common Components GMOD Meeting, Oct. 2004 Don Gilbert,

GMODTools, Argos & cetera A Replicable Genome infOrmation System of Common Components GMOD Meeting, Oct Don Gilbert,
Gene Ontology John Pinney

Gene Ontology John Pinney
Biopackages.net Operating System Packages for Bioinformatics Allen Day 2005.05.17.

Biopackages.net Operating System Packages for Bioinformatics Allen Day
Systems Biology Existing and future genome sequencing projects and the follow-on structural and functional analysis of complete genomes will produce an.

Systems Biology Existing and future genome sequencing projects and the follow-on structural and functional analysis of complete genomes will produce an.
1 genSpace: Community- Driven Knowledge Sharing for Biological Scientists Gail Kaiser’s Programming Systems Lab Columbia University Computer Science.

1 genSpace: Community- Driven Knowledge Sharing for Biological Scientists Gail Kaiser’s Programming Systems Lab Columbia University Computer Science.
Subsystem Approach to Genome Annotation National Microbial Pathogen Data Resource www.nmpdr.org Claudia Reich NCSA, University of Illinois, Urbana.

Subsystem Approach to Genome Annotation National Microbial Pathogen Data Resource Claudia Reich NCSA, University of Illinois, Urbana.
Using the Drupal Content Management Software (CMS) as a framework for OMICS/Imaging-based collaboration.

Using the Drupal Content Management Software (CMS) as a framework for OMICS/Imaging-based collaboration.
Login: BITseminar Pass: BITseminar2011 Login: BITseminar Pass: BITseminar2011.

Login: BITseminar Pass: BITseminar2011 Login: BITseminar Pass: BITseminar2011.
Genome database & information system for Daphnia Don Gilbert, October 2002 Talk doc at

Genome database & information system for Daphnia Don Gilbert, October 2002 Talk doc at
>>> Korean BioInformation Center >>> KRIBB Korea Research institute of Bioscience and Biotechnology GS2PATH: Linking Gene Ontology and Pathways Jin Ok.

>>> Korean BioInformation Center >>> KRIBB Korea Research institute of Bioscience and Biotechnology GS2PATH: Linking Gene Ontology and Pathways Jin Ok.
GMOD: Building Blocks for a Model Organism System Database Lincoln Stein, CSHL.

GMOD: Building Blocks for a Model Organism System Database Lincoln Stein, CSHL.
WormBase: A Resource for the Biology & Genome of C. elegans Lincoln D. Stein.

WormBase: A Resource for the Biology & Genome of C. elegans Lincoln D. Stein.
Argos & Genome Directories & Lucegene (‘Lucy Jean’) A Replicable Genome infOrmation System of Common Components GMOD Meeting, Sept. 2003 Don Gilbert,

Argos & Genome Directories & Lucegene (‘Lucy Jean’) A Replicable Genome infOrmation System of Common Components GMOD Meeting, Sept Don Gilbert,
GMOD in the Cloud Genome Informatics November 3, 2011 Scott Cain GMOD Project Coordinator Ontario Institute for Cancer Research

GMOD in the Cloud Genome Informatics November 3, 2011 Scott Cain GMOD Project Coordinator Ontario Institute for Cancer Research
WFleaBase Daphnia Genome Database from Common Components Daphnia Genomic Consortium Meeting, Sept. 2003 Don Gilbert,

WFleaBase Daphnia Genome Database from Common Components Daphnia Genomic Consortium Meeting, Sept Don Gilbert,
Gramene Objectives Develop a database and tools to store, visualize and analyze data on genetics, genomics, proteomics, and biochemistry of grass plants.

Gramene Objectives Develop a database and tools to store, visualize and analyze data on genetics, genomics, proteomics, and biochemistry of grass plants.

Similar presentations

Ads by Google