Generic Model Organism Database

{{Infobox software

| name = Generic Model Organism Database (GMOD)

| logo = GMOD project logo.png

| screenshot =

| caption = Generic Model Organism Database project logo

| developer =

| latest release version =

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| operating system = Windows, Mac OS X

| genre = Bioinformatics

| license = GPL v3

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The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States National Institutes of Health, National Science Foundation and the USDA Agricultural Research Service.

History

The GMOD project was started in the early 2000s as a collaboration between several model organism databases (MODs) who shared a need to create similar software tools for processing data from sequencing projects. MODs, or organism-specific databases, describe genome and other information about important experimental organisms in the life sciences and capture the large volumes of data and information being generated by modern biology. Rather than each group designing their own software, four major MODs--FlyBase, Saccharomyces Genome Database, Mouse Genome Database, and at or run off a Chado schema database.

Chado database schema

The Chado{{Cite journal

|author1=Christopher J. Mungall |author2=David B. Emmert |author3=The FlyBase Consortium | title= A Chado case study: an ontology-based modular schema for representing genome-associated biological information

| journal=Bioinformatics

| year= 2007

| volume= 23

| pages= i337–i346

| doi= 10.1093/bioinformatics/btm189

| pmid= 17646315

| issue= 13

| doi-access=free}} schema aims to cover many of the classes of data frequently used by modern biologists, from genetic data to phylogenetic trees to publications to organisms to microarray data to IDs to RNA/protein expression. Chado makes extensive use of controlled vocabularies to type all entities in the database; for example: genes, transcripts, exons, transposable elements, etc., are stored in a feature table, with the type provided by Sequence Ontology. When a new type is added to the Sequence Ontology, the feature table requires no modification, only an update of the data in the database. The same is largely true of analysis data that can be stored in Chado as well.

The existing core modules of Chado are:

sequence - for sequences/features
cv - for controlled-vocabs/ontologies
general - currently just dbxrefs
organism - taxonomic data
pub - publication and references
companalysis - augments sequence module with computational analysis data
map - non-sequence maps
genetic - genetic and phenotypic data
expression - gene expression
natural diversity - population data

Software

The full list of GMOD software components is found on the GMOD Components page.{{cite web |title=GMOD Components - GMOD |url=http://gmod.org/wiki/GMOD_Components |website=gmod.org}} These components include:

* GMOD Core (Chado database and tools)

Chado: the Chado schema and tools to install it.{{cite web |title=Chado - Getting Started - GMOD |url=http://gmod.org/wiki/Chado |website=gmod.org}}
XORT: a tool for loading and dumping chado-xml{{cite web |title=XORT - GMOD |url=http://gmod.org/wiki/XORT |website=gmod.org}}
GMODTools: extracts data from a Chado database into common genome bulk formats (GFF, Fasta, etc.){{cite web |title=GMODTools - GMOD |url=http://gmod.org/wiki/GMODTools |website=gmod.org}}
MOD website
Tripal: a web front end based on Drupal.{{cite web |title=Tripal |url=http://gmod.org/wiki/Tripal |publisher=gmod.org}}
Genome Editing and Visualization
Apollo: a Java application for viewing and editing genome annotations{{cite web |title=Apollo - GMOD |url=http://gmod.org/wiki/Apollo |website=gmod.org}}{{cite web |title=Apollo — Apollo 2.7.0 documentation |url=https://genomearchitect.readthedocs.io/en/latest/ |website=genomearchitect.readthedocs.io |language=en}}
GBrowse: a CGI application for displaying genome annotations{{cite web |title=GBrowse - GMOD |url=http://gmod.org/wiki/GBrowse |website=gmod.org}}{{cite journal

| journal=Genome Res.

| year= 2002

| volume= 12

| pages= 1599–610

| doi= 10.1101/gr.403602

| pmid= 12368253

| issue= 10

| pmc= 187535

}}

JBrowse: a JavaScript application for displaying genome annotations{{cite web |title=JBrowse - GMOD |url=http://gmod.org/wiki/JBrowse |website=gmod.org}}
Pathway Tools: a genome browser with a comparative mode
Comparative Genomics
GBrowse_syn: a GBrowse based synteny viewer{{cite web |title=GBrowse syn - GMOD |url=http://gmod.org/wiki/GBrowse_syn |website=gmod.org}}
CMap: a CGI application for displaying comparative maps{{cite web |title=CMap - GMOD |url=http://gmod.org/wiki/CMap |website=gmod.org}}
Literature curation
Textpresso: a text mining system for scientific literature {{cite web |title=Textpresso |url=http://gmod.org/wiki/Textpresso |publisher=gmod.org}}
Database querying tools
BioMart: a query-oriented data management system
InterMine: open source data warehouse system
Biological Pathways
Pathway Tools: tools for metabolic pathway information, and analysis of high-throughput functional genomics data
Regulatory Networks
Pathway Tools: supports definition of regulatory interactions and browsing of regulatory networks
Analysis
Galaxy{{Cite journal

| last1 = Afgan | first1 = E.

| last2 = Baker | first2 =D.

| last3 = van den Beek | first3 = M.

| last4 = Blankenberg | first4 = D.

| last5 = Bouvier | first5 = D.

| last6 = Čech | first6 = M.

| last7 = Chilton | first7 = J.

| last8 = Clements | first8 = D.

| last9 = Coraor | first9 = N.

| last10 = Eberhard | first10 = C.

| last11 = Grüning | first11 = B.

| last12 = Guerler | first12 = A.

| last13 = Hillman-Jackson | first13 = J.

| last14 = Von Kuster | first14 = G.

| last15 = Rasche | first15 = E.

| last16 = Soranzo | first16 = N.

| last17 = Turaga | first17 = N.

| last18 = Taylor | first18 = J.

| last19 = Nekrutenko | first19 = A.

| last20 = Goecks | first20 = J.

| title = The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

| doi = 10.1093/nar/gkw343

| journal = Nucleic Acids Research

| volume = 44

| issue = W1

| pages = W3–W10

| date = 8 July 2016

| pmid = 27137889

| pmc = 4987906

}}

MAKER{{cite journal |last1=Cantarel |first1=Brandi L. |last2=Korf |first2=Ian |last3=Robb |first3=Sofia M. C. |last4=Parra |first4=Genis |last5=Ross |first5=Eric |last6=Moore |first6=Barry |last7=Holt |first7=Carson |last8=Sánchez Alvarado |first8=Alejandro |last9=Yandell |first9=Mark |title=MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes |url=http://gmod.org/wiki/MAKER |journal=Genome Research |pages=188–196 |doi=10.1101/gr.6743907 |date=January 2008|volume=18 |pmc=2134774 }}

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Participating databases

The following organism databases are contributing to and/or adopting GMOD components for model organism databases.

NISEED{{cite journal |last1=Tassy |first1=Olivier |last2=Dauga |first2=Delphine |last3=Daian |first3=Fabrice |last4=Sobral |first4=Daniel |last5=Robin |first5=François |last6=Khoueiry |first6=Pierre |last7=Salgado |first7=David |last8=Fox |first8=Vanessa |last9=Caillol |first9=Danièle |last10=Schiappa |first10=Renaud |last11=Laporte |first11=Baptiste |last12=Rios |first12=Anne |last13=Luxardi |first13=Guillaume |last14=Kusakabe |first14=Takehiro |last15=Joly |first15=Jean-Stéphane |last16=Darras |first16=Sébastien |last17=Christiaen |first17=Lionel |last18=Contensin |first18=Magali |last19=Auger |first19=Hélène |last20=Lamy |first20=Clément |last21=Hudson |first21=Clare |last22=Rothbächer |first22=Ute |last23=Gilchrist |first23=Michael J. |last24=Makabe |first24=Kazuhiro W. |last25=Hotta |first25=Kohji |last26=Fujiwara |first26=Shigeki |last27=Satoh |first27=Nori |last28=Satou |first28=Yutaka |last29=Lemaire |first29=Patrick |title=The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program |journal=Genome Research |date=1 October 2010 |volume=20 |issue=10 |pages=1459–1468 |doi=10.1101/gr.108175.110 |pmid=20647237 |url=https://genome.cshlp.org/content/20/10/1459.short |language=en |issn=1088-9051|pmc=2945195 }}

| AntonosporaDB{{cn|date=January 2024}}

| Arabidopsis{{cite journal |last1=Weems |first1=Danforth |last2=Miller |first2=Neil |last3=Garcia-Hernandez |first3=Margarita |last4=Huala |first4=Eva |last5=Rhee |first5=Seung Y. |title=Design, Implementation and Maintenance of a Model Organism Database for Arabidopsis thaliana |journal=Comparative and Functional Genomics |date=2004 |volume=5 |issue=4 |pages=362–369 |doi=10.1002/cfg.408 |pmid=18629167 |language=en |issn=1531-6912|pmc=2447457 }}

BeeBase

| BeetleBase{{cite journal

| journal=Nucleic Acids Res.

| year= 2007

| volume= 35

| pages= D476–9

| doi= 10.1093/nar/gkl776

| pmid= 17090595

| issue= Database issue

| pmc= 1669707

}}{{cite web |title=BeetleBase |url=http://www.bioinformatics.ksu.edu/BeetleBase/ |website=www.bioinformatics.ksu.edu/Be |archiveurl=https://web.archive.org/web/20060713200536/http://www.bioinformatics.ksu.edu/BeetleBase/ |archivedate=13 July 2006}}

|Bovine genome database (BGD)

BioHealthBase{{cite book |last1=Noronha |first1=Antonio |last2=Cui |first2=Changhai |last3=Harris |first3=Robert Adron |last4=Crabbe |first4=John C. |title=Neurobiology of Alcohol Dependence |date=2014 |publisher=Elsevier |isbn=978-0-12-407155-1 |url=https://books.google.com/books?id=TbNZAwAAQBAJ&dq=Generic+Model+Organism+Database+BioHealth+Base&pg=PA533 |language=en}}

|Bovine QTL Viewer

|Cattle EST Gene Family Database

CGD

|CGL

|ChromDB

Chromosome 7 Annotation Project

|CSHLmpd

|Database of Genomic Variants

DictyBase{{cite journal

| journal=Nucleic Acids Res.

| year= 2006

| volume= 34