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Type of biological database
Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied
Model_organism_database
The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing
Generic Model Organism Database
Generic_Model_Organism_Database
Organisms used to study biology across species
that discoveries made in the model organism will provide insight into the workings of other organisms. Model organisms are widely used to research human
Model_organism
Species of amphibian
transcriptomic model organism database". Nucleic Acids Research. 46 (D1): D861–8. doi:10.1093/nar/gkx936. PMC 5753396. PMID 29059324. "Xenopus model organism database"
African_clawed_frog
Species of sea urchin
Lytechinus williamsi which has purple pedicellaria. Echinobase is the model organism database for the painted urchin and a number of other echinoderms. The green
Lytechinus_variegatus
Species of amphibian
significant model organism for genetics that complements the related species Xenopus laevis (the African clawed frog), a widely used vertebrate model for developmental
Western_clawed_frog
Species of starfish
more normal size is 10 to 30 cm (4 to 12 in). Echinobase is the model organism database for the painted urchin and a number of other echinoderms. The common
Common_starfish
Species of amphibian
Nanorana parkeri (common names: High Himalaya frog, Xizang Plateau frog, Parker's slow frog, mountain slow frog) is a species of frogs in the family Dicroglossidae
Nanorana_parkeri
Species of salamander
gills and parts of their eyes and brains. The species is also used as a model organism. As aquarium technology has developed, axolotls have become a common
Axolotl
Species of sea urchin
Juvenile urchins sometimes have banded spines. Echinobase is the model organism database for the painted urchin and a number of other echinoderms. Lytechinus
Lytechinus_pictus
Species of frog
247094 Observation.org: 203009 Open Tree of Life: 104971 Paleobiology Database: 401246 Xeno-canto: Hymenochirus-boettgeri Xenopus boettgeri Wikidata:
Hymenochirus_boettgeri
Species of amphibian
(genus Rana): A historical framework for a widely studied group of model organisms". Systematic Biology. 65 (5): 824–42. doi:10.1093/sysbio/syw055. hdl:2292/43460
American_bullfrog
Topics referred to by the same term
formats Modchip, a chip modifying an electronic system Model organism database, a biological database Moving object detection, a computing technology related
Mod
MolBio Available Software Databases A-Z Model organism databases provide in-depth biological data for intensively studied organisms. PomBase: the knowledgebase
List_of_biological_databases
Genus of amphibians
are commonly studied as model organisms for developmental biology, cell biology, toxicology, neuroscience and for modelling human disease and birth defects
Xenopus
bioinformatics database for the model organism Dictyostelium discoideum. dictyBase offers many ways of searching and retrieving data from the database: dictyMart
DictyBase
Biology journal
biological databases such as WormBase and PubMed. C. elegans was the first multicellular organism to have its genome sequenced and is a model organism for studying
WormBook
Science collective
National Center for Biotechnology Information Zebrafish Model Organism Database Rat Genome Database The goal of the Consortium is to correct the small number
Genome_Reference_Consortium
Topics referred to by the same term
to: Generic Model Organism Database (GMOD), a software project for model organism databases .GMOD, file extension for Golgotha 3D models; See List of
Gmod
transcriptomics and proteomics information from publicly available studies on model organisms and humans. As to date (2021) it has ceased activities and is unaccessible
Multi-Omics Profiling Expression Database
Multi-Omics_Profiling_Expression_Database
Model organism database on zebrafish
is an online biological database of information about the zebrafish (Danio rerio). The zebrafish is a widely used model organism for genetic, genomic, and
Zebrafish_Information_Network
Echinoderm genomic database
Echinobase is a Model Organism Database (MOD). It supports the international research community by providing a centralized, integrated web based resource
Echinobase
Species of starfish
hard coral communities occur in the region. Echinobase is the model organism database for A. planci and a number of other echinoderms. The body form
Crown-of-thorns_starfish
Database of soybean genetics
Results display soybean genetic (and genomic) data using Generic Model Organism Database (GMOD) open-source software. In addition to SoyBase, objects identified
SoyBase_Database
Database of nematode genomics
WormBase is an online biological database about the biology and genome of the nematode model organism Caenorhabditis elegans and contains information about
WormBase
American bioinformatician
resources, including the Generic Model Organism Database project, BioPerl, WormBase, and the Reactome pathway database. His work has also contributed to
Lincoln_Stein
Database of biological information
Other popular model organism databases include Mouse Genome Informatics for the laboratory mouse, Mus musculus, the Rat Genome Database for Rattus, ZFIN
Biological_database
Database on Schizosaccharomyces pombe
PomBase is a model organism database that provides online access to the fission yeast Schizosaccharomyces pombe genome sequence and annotated features
PomBase
Model organism database on Xenopus frogs
Xenbase is a Model Organism Database (MOD), providing informatics resources, as well as genomic and biological data on Xenopus frogs. Xenbase has been
Xenbase
Database for yeast metabolomics
The Yeast Metabolome Database (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced
Yeast_Metabolome_Database
exploring the genome and transcriptome of the model plant system Populus. PopGenie is a model organism database which brings together the increasingly extensive
Popgenie
Database on Drosophilidae genetics
family Drosophilidae. For the most extensively studied species and model organism, Drosophila melanogaster, a wide range of data are presented in different
FlyBase
Database on Arabidopsis thaliana
(TAIR) is a community resource and online model organism database of genetic and molecular biology data for the model plant Arabidopsis thaliana, commonly
The Arabidopsis Information Resource
The_Arabidopsis_Information_Resource
Free, online database and bioinformatics resource
Eppig, Janan T.; The Mouse Genome Database Group (Jan 2011). "The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and
Mouse_Genome_Informatics
Database of rat genomics
data. The rat continues to be extensively used by researchers as a model organism for investigating pharmacology, toxicology, general physiology and the
Rat_Genome_Database
This is a list of model organisms used in scientific research. Phages (infecting prokaryotes): Escherichia virus Lambda (Phage lambda) Phi X 174, the
List_of_model_organisms
Marine animals, subphylum of chordates
Web Portal Dutch Ascidians: Extensive database of images from around the world Aniseed: A model organism database for ascidians including Ciona intestinalis
Tunicate
Cmap-based comparative map viewer, both modules of the Generic Model Organism Database (GMOD) project. The genome viewer included tracks for known honey
BeeBase
mouse production and phenotyping programme aimed at identifying new model organisms of disease. Based at the Wellcome Trust Sanger Institute, the project
Mouse_Genetics_Project
Scientific naming of genes
typically created by abbreviating). For some nonhuman species, model organism databases serve as central repositories of guidelines and help resources
Gene_nomenclature
Marine phylum of animals often with radial symmetries
Veronica F. (7 January 2022). "Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and
Echinoderm
Database
about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their
Yeastract
Species of sea urchin
Veronica F (7 January 2022). "Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and
Strongylocentrotus_purpuratus
Genetically modified mouse used in gene research
KOMP project Mouse Genome Informatics (MGI) website – community model organism database for the laboratory mouse Homologous Recombination Method (and Knockout
Knockout_mouse
Database of transcription factors
YeTFaSCo (The Yeast Transcription Factor Specificity Compendium) is a database of transcription factors for Saccharomyces cerevisiae. Transcription factor
YeTFaSCo
Species of yeast
yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose
Schizosaccharomyces_pombe
preclinical databases. The IMPC uses the laboratory mouse (Mus musculus), primarily on the C57BL/6N genetic background, as a mammalian model organism to systematically
International Mouse Phenotyping Consortium
International_Mouse_Phenotyping_Consortium
promoter features in Saccharomyces cerevisiae". Nucleic Acids Res. 39 (Database issue). England: D647-52. doi:10.1093/nar/gkq1086. PMC 3013683. PMID 21045055
Yeast_Promoter_Atlas
Database
ARTADE (ARabidopsis Tiling Array-based Detection of Exons) is a database for the annotation of genome-wide tiling-array data in Arabidopsis DNA microarray
Artade
Scientific database
FlyExpress is a free database that collects the expression patterns of Drosophila melanogaster in embryogenesis via a series of images submitted from BDGP
FlyExpress
The Hymenoptera Genome Database (HGD) is a comprehensive resource supporting genomics of Hymenoptera. BeeBase Munoz-Torres, Monica C; Reese Justin T; Childers
Hymenoptera_Genome_Database
Scientific project organization
from the International Knockout Mouse Consortium". Nucleic Acids Res. 39 (Database issue). England: D849-55. doi:10.1093/nar/gkq879. PMC 3013768. PMID 20929875
International Knockout Mouse Consortium
International_Knockout_Mouse_Consortium
Scientific project at the European Bioinformatics Institute
vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information. Similar databases and browsers
Ensembl genome database project
Ensembl_genome_database_project
Organism altered by genetic engineering
A genetically modified organism (GMO) is any organism whose genetic material has been altered using genetic engineering techniques. The exact definition
Genetically_modified_organism
Species of tunicate
in the surface waters of most of the world's oceans. It is used as a model organism in research into developmental biology. Oikopleura dioica is a bioluminescent
Oikopleura_dioica
Online biodatabase of proteins
multicellular organisms. The database provides information about the individual proteins including computationally generated three-dimensional models of their
Membranome_database
Topics referred to by the same term
Science, in Fort Lauderdale, Florida, US Model Organism Databases, databases that house and disseminate organism-specific biological knowledge Search for
MODS
University of Missouri at St. Louis Missouri Botanical Garden Generic Model Organism Database Open Biomedical Ontologies OBO Foundry Walls, R. L.; Athreya, B
Plant_ontology
Public university in Eugene, Oregon, US
home of the Zebrafish Information Network (ZFIN), the zebrafish model organism database. Controversy stems from the lack of citizen involvement in the
University_of_Oregon
Slime bacterium
1128/JB.00608-08. ISSN 0021-9193. PMC 2620817. PMID 18996994. Model Organism Database John Kirby at the University of Iowa Dale Kaiser Lab at Stanford
Myxococcus_xanthus
Study of genes and heredity in plants
"MaizeGDB update: new tools, data and interface for the maize model organism database". Nucleic Acids Research. 44 (D1): D1195–D1201. doi:10.1093/nar/gkv1007
Plant_genetics
Database of E. coli metabolites
and metabolome of E. coli. ECMDB is part of a suite of organism-specific metabolomics databases that includes DrugBank, HMDB, YMDB and SMPDB. As a metabolomics
E._Coli_Metabolome_Database
Bioinformatics initiative
Saccharomyces cerevisiae (brewer's or baker's yeast). Many other Model Organism Databases have joined the Gene Ontology Consortium, contributing not only
Gene_Ontology
Online catalog of human genes
website that uses OMIM as one of the six human genetic databases and seven model organism databases to integrate information. "OMIM Entry Statistics". Online
Online Mendelian Inheritance in Man
Online_Mendelian_Inheritance_in_Man
Scientific research center in Durham, North Carolina
software, database development, IT support, and analytical tools in evolutionary biology. Major initiatives include the Generic Model Organism Database project
National Evolutionary Synthesis Center
National_Evolutionary_Synthesis_Center
analysis toolkit. List of open-source bioinformatics software Generic Model Organism Database "Open Bioinformatics Foundation". Retrieved 1 September 2014. "BOSC
Open Bioinformatics Foundation
Open_Bioinformatics_Foundation
Species of sea squirt
Ciona robusta - Hoshino & Tokioka, 1967, DORIS [fr] ANISEED, the Tunicate model organism database Ghost: genomic and cDNA resources from Kyoto University
Ciona_robusta
Form of biological modelling
in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction
Metabolic_network_modelling
Comparative genomics database for plant genomes
Genome Institute List of biological databases Model organism databases The Arabidopsis Information Resource PLAZA (database) Goodstein DM, Shu S, Howson R
Phytozome
This is a list of the longest-living biological organisms: the individuals or clones of a species with the longest natural maximum life spans. For a given
List of longest-living organisms
List_of_longest-living_organisms
Online biological database
The Mouse Phenome Database (MPD) is a web-accessible database of strain characterization data for the laboratory mouse, to facilitate translational research
Mouse_Phenome_Database
Research on the model organism Drosophila melanogaster has been facilitated by the development of a number of online databases for the storage and curation
List_of_Drosophila_databases
Informative representation of an entity
Ford Model T, an early car model) Model (organism) a non-human species that is studied to understand biological phenomena in other organisms, e.g. a
Model
Field dedicated to organizing and structuring biomedical data
and validates information that is disseminated by biological and model organism databases. It is a new profession, with the first mentions in the scientific
Biocuration
The BioCyc database collection is an assortment of organism specific Pathway/Genome Databases (PGDBs) that provide reference to genome and metabolic pathway
BioCyc_database_collection
Species of ascidian
intestinalis. MarLIN, detailed species review ANISEED, the Tunicate model organism database Ghost: genomic and cDNA resources from Kyoto University Four-dimensional
Ciona_intestinalis
Informal group of fungi
functional gene annotation of the two major yeast models can be accessed via their respective model organism databases: SGD and PomBase. Various yeast species have
Yeast
Biological database
extends the single species curation tool developed for PomBase, the model organism database for fission yeast. The first complete release of PHI-base 5, version
PHI-base
Content specialist charged with managing an institution's collections
validates information that is disseminated by biological databases and model organism databases. Education and outreach play an important role in some institutions
Curator
used; and degree of pain. Medical research Animal testing Generic Model Organism Database History of animal testing Comparative psychology Veterinary ethics
Comparative_medicine
Branch of biology that studies biological systems at the molecular level
facilitating the development of novel genetic manipulation methods in new non-model organisms. Likewise, synthetic molecular biologists will drive the industrial
Molecular_biology
list of projects can be viewed at the InterMine Registry Generic Model Organism Database modENCODE Archived 2010-12-27 at the Wayback Machine FlyMine HumanMine
InterMine
American plant biologist
the USDA-ARS. She served as the director of MaizeGDB, the maize model organism database through 2013. In 2014 she joined the faculty of Iowa State University
Carolyn_Lawrence-Dill
Web-based database of marine species
(WoRMS) is a taxonomic database that aims to provide an authoritative and comprehensive catalogue and list of names of marine organisms. The content of the
World Register of Marine Species
World_Register_of_Marine_Species
Medical condition
(2006-01-01). "The Zebrafish Information Network: the zebrafish model organism database". Nucleic Acids Research. 34 (90001): D581–D585. doi:10.1093/nar/gkj086
Halperin–Birk_syndrome
biocuration workflow for Ag Base, a non-model organism database". Database. 2012 bas038. doi:10.1093/database/bas038. PMC 3500517. PMID 23160411. McCarthy
AgBase
Biological database
BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats
BioGRID
PMID 19668247. Yang JH, Li JH, Jiang S, Zhou H, Qu LH (January 2013). "ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and
Transcription factor binding site databases
Transcription_factor_binding_site_databases
researcher. GMOD: GMOD (Generic Model Organism Database) is a collection of open-source tools for building and sharing genome databases. It provides a framework
Genome_browser
Database of Saccharomyces genomics
The Saccharomyces Genome Database (SGD) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is
Saccharomyces_Genome_Database
Collection of bioinformatics databases
other omics studies, modeling and simulation in systems biology, and translational research in drug development. The KEGG database project was initiated
KEGG
Database of biological reactions
the models in the curated section of BioModels Database have been described in peer-reviewed scientific literature. The models stored in BioModels' curated
BioModels
American immunologist
Retrieved 5 August 2016. "Zfin Lab: Steiner Lab". The Zebrafish Model Organism Database. Retrieved 5 August 2016. Eisenberg, David S. (June 2018). "How
Lisa_Steiner
Biological database
January 2006). "The Zebrafish Information Network: the zebrafish model organism database". Nucleic Acids Research. 34 (90001): D581–D585. doi:10.1093/nar/gkj086
Vertebrate Genome Annotation Project
Vertebrate_Genome_Annotation_Project
Database containing reference sequences of genes, proteins and transcripts
e. DNA, RNA or protein) for major organisms ranging from viruses to bacteria to eukaryotes. For each model organism, RefSeq aims to provide separate and
RefSeq
Species of slime mold, model organism
to the original mischaracterization of the organism as a fungus. P. polycephalum is used as a model organism for research into motility, cellular differentiation
Physarum_polycephalum
were added in this version. The sources of gene sets included model organism databases, Ensembl genome annotation and Entrez Gene. Since this version
PANTHER
Species of bacterium
bacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology.
Thermus_thermophilus
This is a compilation of databases, web portals, and servers used for cataloging microRNAs and their targets. MicroRNAs (miRNAs) represent an important
MicroRNA and microRNA target database
MicroRNA_and_microRNA_target_database
Species of cnidarian
flipping over itself. H. vulgaris is often used, like many hydra, as a model organism for morphallactic regeneration because they are easy to care for, requiring
Hydra_vulgaris
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MODEL ORGANISM-DATABASE
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MODEL ORGANISM-DATABASE
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MODEL ORGANISM-DATABASE
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