The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of

open-source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Op ...

components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States

National Institutes of Health The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...

National Science Foundation The National Science Foundation (NSF) is an independent agency of the United States government that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National I ...

and the USDA Agricultural Research Service.

History

The GMOD project was started in the early 2000s as a collaboration between several

model organism databases Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large set ...

(MODs) who shared a need to create similar

software Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work. At the lowest programming level, executable code consists ...

tools for processing data from sequencing projects. MODs, or organism-specific

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases sp ...

s, describe

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

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 Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary i ...

. Rather than each group designing their own software, four major MODs--

FlyBase FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, ''Drosophila melanogaster'', a wide range of ...

Saccharomyces Genome Database The ''Saccharomyces'' Genome Database (SGD) is a scientific database of the molecular biology and genetics of the yeast ''Saccharomyces cerevisiae'', which is commonly known as baker's or budding yeast. ''Saccharomyces'' Genome Database The SGD ...

Mouse Genome Database Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kenned ...

, and WormBase—worked together to create applications that provide functionality needed by all MODs, such as software to help manage the data within the MOD, and to help users access and query the data. The GMOD project works to keep software components interoperable. To this end, many of the tools use a common input/output file format or run off a Chado schema database.

Chado database schema

The Chado 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 The Sequence Ontology (SO) is an ontology In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality. Ontology addresses questions like how entities are grouped int ...

. 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. These components include:

Participating databases

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

Related projects

* Bioperl,

BioJava BioJava is an open-source software project dedicated to provide Java tools to process biological data.VS Matha and P Kangueane, 2009, ''Bioinformatics: a concept-based introduction'', 2009. p26 BioJava is a set of library functions written in the ...

, Biopython, BioRuby, etc. *

Ensembl Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other v ...

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...

*DAS *Genomics Unified Schema *Manatee: Manual Annotation Tool *Biocurator.org *

Open Biomedical Ontologies The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a s ...

*Sequence Ontology Project

References

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External links

GMOD website
Model organism databases Genomics Bioinformatics software