model organism database

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 sets of genes, efficiently plan experiments, integrate their data with existing knowledge, and formulate new hypotheses .{{cite journal | vauthors = Oliver SG, Lock A, Harris MA, Nurse P, Wood V | title = Model organism databases: essential resources that need the support of both funders and users | journal = BMC Biology | volume = 14 | issue = 1 | pages = 49 | date = June 2016 | pmid = 27334346 | pmc = 4918006 | doi = 10.1186/s12915-016-0276-z | doi-access = free }}{{cite journal | vauthors = Bond M, Holthaus SM, Tammen I, Tear G, Russell C | title = Use of model organisms for the study of neuronal ceroid lipofuscinosis | journal = Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease | volume = 1832 | issue = 11 | pages = 1842–65 | date = November 2013 | pmid = 23338040 | doi = 10.1016/j.bbadis.2013.01.009 | doi-access = free }} They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO){{cite journal | vauthors = Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G | display-authors = 6 | title = Gene ontology: tool for the unification of biology. The Gene Ontology Consortium | journal = Nature Genetics | volume = 25 | issue = 1 | pages = 25–9 | date = May 2000 | pmid = 10802651 | pmc = 3037419 | doi = 10.1038/75556 }}{{cite journal | author = Gene Ontology Consortium | title = Gene Ontology Consortium: going forward | journal = Nucleic Acids Research | volume = 43 | issue = Database issue | pages = D1049-56 | date = January 2015 | pmid = 25428369 | pmc = 4383973 | doi = 10.1093/nar/gku1179 }} to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs.{{cite journal | vauthors = O'Connor BD, Day A, Cain S, Arnaiz O, Sperling L, Stein LD | title = GMODWeb: a web framework for the Generic Model Organism Database | journal = Genome Biology | volume = 9 | issue = 6 | pages = R102 | year = 2008 | pmid = 18570664 | pmc = 2481422 | doi = 10.1186/gb-2008-9-6-r102 | doi-access = free }} Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.

Types of data and services

Model organism databases generate, source and collate species-specific information integratively by combining expert knowledge with literature curation and bioinformatics.

Services provided to biological research communities include:

Genome sequence annotations
Location of genes and regulatory regions in the genome
Functional curation of gene products
Discern functions fulfilled by the gene product by looking at a variety of data including Gene Ontology (GO) annotations, phenotypes, gene expression, pathway information
Protein/RNA sequence annotations
Anatomical information
Stock centres
Orthology

List of model organism databases

class="wikitable sortable"
Common name ! Scientific name ! Wikipedia page ! Database link-out
Baker's yeast \| Saccharomyces cerevisiae \| Saccharomyces Genome Database \| [http://www.yeastgenome.org SGD]{{cite journal \| vauthors = Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED \| display-authors = 6 \| title = Saccharomyces Genome Database: the genomics resource of budding yeast \| journal = Nucleic Acids Research \| volume = 40 \| issue = Database issue \| pages = D700-5 \| date = January 2012 \| pmid = 22110037 \| pmc = 3245034 \| doi = 10.1093/nar/gkr1029 }}
Fission yeast \| Schizosaccharomyces pombe \| PomBase \| [http://www.pombase.org PomBase]{{cite journal \| vauthors = Rutherford KM, Lera-Ramírez M, Wood V \| title = PomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability \| journal = Genetics \| volume = 227 \| issue = 1 \| date = May 2024 \| pmid = 38376816 \| pmc = 11075564 \| doi = 10.1093/genetics/iyae007 }}{{cite journal \| vauthors = Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG \| display-authors = 6 \| title = PomBase: a comprehensive online resource for fission yeast \| journal = Nucleic Acids Research \| volume = 40 \| issue = Database issue \| pages = D695-9 \| date = January 2012 \| pmid = 22039153 \| pmc = 3245111 \| doi = 10.1093/nar/gkr853 }}{{Cite book \| vauthors = Lock A, Rutherford K, Harris MA, Wood V \|title=Eukaryotic Genomic Databases \|chapter=PomBase: The Scientific Resource for Fission Yeast \|date=2018 \|volume=1757 \|pages=49–68 \|doi=10.1007/978-1-4939-7737-6_4 \|pmid=29761456\|series=Methods in Molecular Biology \|pmc=6440643 \|isbn=978-1-4939-7736-9 }}
Clawed frog \| Xenopus \| Xenbase \| [http://www.xenbase.org/entry/ Xenbase]{{cite journal \| vauthors = Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, Pells TJ, James-Zorn C, Wang Y, Ponferrada VG, Chu S, Chaturvedi P, Zorn AM, Vize PD \| display-authors = 6 \| title = Xenbase: a genomic, epigenomic and transcriptomic model organism database \| journal = Nucleic Acids Research \| volume = 46 \| issue = D1 \| pages = D861–D868 \| date = January 2018 \| pmid = 29059324 \| pmc = 5753396 \| doi = 10.1093/nar/gkx936 }}{{Cite book \| vauthors = James-Zorn C, Ponferrada VG, Fisher ME, Burns KA, Fortriede JD, Segerdell E, Karimi K, Lotay VS, Wang DZ, Chu S, Pells TJ, Wang Y, Vize PD, Zorn AM \| title = Eukaryotic Genomic Databases \| chapter = Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database \| journal = Eukaryotic Genomic Databases: Methods and Protocols \| volume = 1757 \| pages = 251–305 \| date = May 2018 \| pmid = 29761462 \| doi = 10.1007/978-1-4939-7737-6_10 \| series = Methods in Molecular Biology \| pmc = 6853059 \| isbn = 978-1-4939-7736-9 }}
Sea urchins, starfish, etc. \| Echinodermata \| Echinobase \| [http://www.echinobase.org/entry/ Echinobase]{{cite journal \| url=https://doi.org/10.1093/genetics/iyae002 \| doi=10.1093/genetics/iyae002 \| title=Echinobase: A resource to support the echinoderm research community \| date=2024 \| last1=Telmer \| first1=Cheryl A. \| last2=Karimi \| first2=Kamran \| last3=Chess \| first3=Macie M. \| last4=Agalakov \| first4=Sergei \| last5=Arshinoff \| first5=Bradley I. \| last6=Lotay \| first6=Vaneet \| last7=Wang \| first7=Dong Zhuo \| last8=Chu \| first8=Stanley \| last9=Pells \| first9=Troy J. \| last10=Vize \| first10=Peter D. \| last11=Hinman \| first11=Veronica F. \| last12=Ettensohn \| first12=Charles A. \| journal=Genetics \| volume=227 \| pmc=11075573 }}
Fruitfly \| Drosophila melanogaster \| FlyBase \| [http://flybase.org/ FlyBase]{{cite journal \| vauthors = Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ \| title = FlyBase: establishing a Gene Group resource for Drosophila melanogaster \| journal = Nucleic Acids Research \| volume = 44 \| issue = D1 \| pages = D786-92 \| date = January 2016 \| pmid = 26467478 \| pmc = 4702782 \| doi = 10.1093/nar/gkv1046 }}
Bees, wasps, ants \|Hymenoptera \|Hymenoptera Genome Database \|[https://hymenoptera.elsiklab.missouri.edu/ HGD]{{cite book \| vauthors = Elsik CG, Tayal A, Unni DR, Burns GW, Hagen DE \| chapter = Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects\|date=2018 \| title = Eukaryotic Genomic Databases\| series = Methods in Molecular Biology\|volume=1757\|pages=513–556\| veditors = Kollmar M \|place=New York, NY \|publisher=Springer New York \|doi=10.1007/978-1-4939-7737-6_17 \| pmid = 29761469\|isbn=978-1-4939-7736-9 }}
Mouse \| Mus musculus \| Mouse Genome Informatics \| [http://www.informatics.jax.org/ MGI]{{cite journal \| vauthors = Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE \| title = The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease \| journal = Nucleic Acids Research \| volume = 43 \| issue = Database issue \| pages = D726-36 \| date = January 2015 \| pmid = 25348401 \| pmc = 4384027 \| doi = 10.1093/nar/gku967 }}
Nematode \| Caenorhabditis elegans \| WormBase \| [https://wormbase.org/ WormBase]{{cite journal \| vauthors = Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW \| display-authors = 6 \| title = WormBase 2014: new views of curated biology \| journal = Nucleic Acids Research \| volume = 42 \| issue = Database issue \| pages = D789-93 \| date = January 2014 \| pmid = 24194605 \| pmc = 3965043 \| doi = 10.1093/nar/gkt1063 }}
Rat \| Rattus norvegicus \| Rat Genome Database \| [http://rgd.mcw.edu/ RGD]{{cite journal \| vauthors = Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H \| display-authors = 6 \| title = The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease \| journal = Nucleic Acids Research \| volume = 43 \| issue = Database issue \| pages = D743-50 \| date = January 2015 \| pmid = 25355511 \| pmc = 4383884 \| doi = 10.1093/nar/gku1026 }}
Social amoeba \| Dictyostelium discoideum \| DictyBase \| [https://dictycr.org dictyBase]{{cite journal \| vauthors = Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, Kimmel AR \| title = dictyBase: a new Dictyostelium discoideum genome database \| journal = Nucleic Acids Research \| volume = 32 \| issue = Database issue \| pages = D332-3 \| date = January 2004 \| pmid = 14681427 \| pmc = 308872 \| doi = 10.1093/nar/gkh138 }}
Ciliate \| Tetrahymena thermophila \| Tetrahymena Genome Database \| [http://ciliate.org/index.php/home/welcome TGD]
Thale cress \| Arabidopsis thaliana \| The Arabidopsis Information Resource \| [https://www.arabidopsis.org/ TAIR]{{cite journal \| vauthors = Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E \| display-authors = 6 \| title = The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools \| journal = Nucleic Acids Research \| volume = 40 \| issue = Database issue \| pages = D1202-10 \| date = January 2012 \| pmid = 22140109 \| pmc = 3245047 \| doi = 10.1093/nar/gkr1090 }}
Maize \| Zea mays ssp. mays \| - \| [http://www.maizegdb.org/ MaizeGDB]{{cite journal \| vauthors = Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V \| title = MaizeGDB, the community database for maize genetics and genomics \| journal = Nucleic Acids Research \| volume = 32 \| issue = Database issue \| pages = D393-7 \| date = January 2004 \| pmid = 14681441 \| pmc = 308746 \| doi = 10.1093/nar/gkh011 }}{{cite journal \| vauthors = Andorf CM, Cannon EK, Portwood JL, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Sen TZ, Lawrence-Dill CJ \| display-authors = 6 \| title = MaizeGDB update: new tools, data and interface for the maize model organism database \| journal = Nucleic Acids Research \| volume = 44 \| issue = D1 \| pages = D1195-201 \| date = January 2016 \| pmid = 26432828 \| pmc = 4702771 \| doi = 10.1093/nar/gkv1007 }}
Soybean \|Glycine soja \|SoyBase \|[https://soybase.org/ SoyBase]{{cite journal \| vauthors = Grant D, Nelson RT, Cannon SB, Shoemaker RC \| title = SoyBase, the USDA-ARS soybean genetics and genomics database \| journal = Nucleic Acids Research \| volume = 38 \| issue = Database issue \| pages = D843-6 \| date = January 2010 \| pmid = 20008513 \| pmc = 2808871 \| doi = 10.1093/nar/gkp798 }}
Zebrafish \| Danio rerio \| Zebrafish Information Network \| [http://zfin.org/ ZFIN]{{cite journal \| vauthors = Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Schaper K, Shao X, Singer A, Sprunger B, Van Slyke CE, Westerfield M \| display-authors = 6 \| title = ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics \| journal = Nucleic Acids Research \| volume = 41 \| issue = Database issue \| pages = D854-60 \| date = January 2013 \| pmid = 23074187 \| pmc = 3531097 \| doi = 10.1093/nar/gks938 }}
- \| Candida albicans \| - \| [http://www.candidagenome.org/ CGD]{{cite journal \| vauthors = Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G \| display-authors = 6 \| title = The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata \| journal = Nucleic Acids Research \| volume = 40 \| issue = Database issue \| pages = D667-74 \| date = January 2012 \| pmid = 22064862 \| pmc = 3245171 \| doi = 10.1093/nar/gkr945 }}
- \| Escherichia coli \| EcoCyc \| [http://ecocyc.org/ EcoCyc]{{cite journal \| vauthors = Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD \| display-authors = 6 \| title = EcoCyc: fusing model organism databases with systems biology \| journal = Nucleic Acids Research \| volume = 41 \| issue = Database issue \| pages = D605-12 \| date = January 2013 \| pmid = 23143106 \| pmc = 3531154 \| doi = 10.1093/nar/gks1027 }}
Hay bacillus \|Bacillus subtilis \| - \|[http://subtiwiki.uni-goettingen.de/ SubtiWiki]{{cite journal \| vauthors = Zhu B, Stülke J \| title = SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis \| journal = Nucleic Acids Research \| volume = 46 \| issue = D1 \| pages = D743–D748 \| date = January 2018 \| pmid = 29788229 \| pmc = 5753275 \| doi = 10.1093/nar/gkx908 }}

class="wikitable sortable"

Common name

! Scientific name

! Wikipedia page

! Database link-out

Baker's yeast

| Saccharomyces cerevisiae

| Saccharomyces Genome Database

| [http://www.yeastgenome.org SGD]{{cite journal | vauthors = Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED | display-authors = 6 | title = Saccharomyces Genome Database: the genomics resource of budding yeast | journal = Nucleic Acids Research | volume = 40 | issue = Database issue | pages = D700-5 | date = January 2012 | pmid = 22110037 | pmc = 3245034 | doi = 10.1093/nar/gkr1029 }}

Fission yeast

| Schizosaccharomyces pombe

| PomBase

| [http://www.pombase.org PomBase]{{cite journal | vauthors = Rutherford KM, Lera-Ramírez M, Wood V | title = PomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability | journal = Genetics | volume = 227 | issue = 1 | date = May 2024 | pmid = 38376816 | pmc = 11075564 | doi = 10.1093/genetics/iyae007 }}{{cite journal | vauthors = Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG | display-authors = 6 | title = PomBase: a comprehensive online resource for fission yeast | journal = Nucleic Acids Research | volume = 40 | issue = Database issue | pages = D695-9 | date = January 2012 | pmid = 22039153 | pmc = 3245111 | doi = 10.1093/nar/gkr853 }}{{Cite book | vauthors = Lock A, Rutherford K, Harris MA, Wood V |title=Eukaryotic Genomic Databases |chapter=PomBase: The Scientific Resource for Fission Yeast |date=2018 |volume=1757 |pages=49–68 |doi=10.1007/978-1-4939-7737-6_4 |pmid=29761456|series=Methods in Molecular Biology |pmc=6440643 |isbn=978-1-4939-7736-9 }}

Clawed frog

| Xenopus

| Xenbase

| [http://www.xenbase.org/entry/ Xenbase]{{cite journal | vauthors = Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, Pells TJ, James-Zorn C, Wang Y, Ponferrada VG, Chu S, Chaturvedi P, Zorn AM, Vize PD | display-authors = 6 | title = Xenbase: a genomic, epigenomic and transcriptomic model organism database | journal = Nucleic Acids Research | volume = 46 | issue = D1 | pages = D861–D868 | date = January 2018 | pmid = 29059324 | pmc = 5753396 | doi = 10.1093/nar/gkx936 }}{{Cite book | vauthors = James-Zorn C, Ponferrada VG, Fisher ME, Burns KA, Fortriede JD, Segerdell E, Karimi K, Lotay VS, Wang DZ, Chu S, Pells TJ, Wang Y, Vize PD, Zorn AM | title = Eukaryotic Genomic Databases | chapter = Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database | journal = Eukaryotic Genomic Databases: Methods and Protocols | volume = 1757 | pages = 251–305 | date = May 2018 | pmid = 29761462 | doi = 10.1007/978-1-4939-7737-6_10 | series = Methods in Molecular Biology | pmc = 6853059 | isbn = 978-1-4939-7736-9 }}

Sea urchins, starfish, etc.

| Echinodermata

| Echinobase

| [http://www.echinobase.org/entry/ Echinobase]{{cite journal | url=https://doi.org/10.1093/genetics/iyae002 | doi=10.1093/genetics/iyae002 | title=Echinobase: A resource to support the echinoderm research community | date=2024 | last1=Telmer | first1=Cheryl A. | last2=Karimi | first2=Kamran | last3=Chess | first3=Macie M. | last4=Agalakov | first4=Sergei | last5=Arshinoff | first5=Bradley I. | last6=Lotay | first6=Vaneet | last7=Wang | first7=Dong Zhuo | last8=Chu | first8=Stanley | last9=Pells | first9=Troy J. | last10=Vize | first10=Peter D. | last11=Hinman | first11=Veronica F. | last12=Ettensohn | first12=Charles A. | journal=Genetics | volume=227 | pmc=11075573 }}

Fruitfly

| Drosophila melanogaster

| FlyBase

| [http://flybase.org/ FlyBase]{{cite journal | vauthors = Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ | title = FlyBase: establishing a Gene Group resource for Drosophila melanogaster | journal = Nucleic Acids Research | volume = 44 | issue = D1 | pages = D786-92 | date = January 2016 | pmid = 26467478 | pmc = 4702782 | doi = 10.1093/nar/gkv1046 }}

Bees, wasps, ants

|Hymenoptera

|Hymenoptera Genome Database

|[https://hymenoptera.elsiklab.missouri.edu/ HGD]{{cite book | vauthors = Elsik CG, Tayal A, Unni DR, Burns GW, Hagen DE | chapter = Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects|date=2018 | title = Eukaryotic Genomic Databases| series = Methods in Molecular Biology|volume=1757|pages=513–556| veditors = Kollmar M |place=New York, NY |publisher=Springer New York |doi=10.1007/978-1-4939-7737-6_17 | pmid = 29761469|isbn=978-1-4939-7736-9 }}

Mouse

| Mus musculus

| Mouse Genome Informatics

| [http://www.informatics.jax.org/ MGI]{{cite journal | vauthors = Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE | title = The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease | journal = Nucleic Acids Research | volume = 43 | issue = Database issue | pages = D726-36 | date = January 2015 | pmid = 25348401 | pmc = 4384027 | doi = 10.1093/nar/gku967 }}

Nematode

| Caenorhabditis elegans

| WormBase

| [https://wormbase.org/ WormBase]{{cite journal | vauthors = Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW | display-authors = 6 | title = WormBase 2014: new views of curated biology | journal = Nucleic Acids Research | volume = 42 | issue = Database issue | pages = D789-93 | date = January 2014 | pmid = 24194605 | pmc = 3965043 | doi = 10.1093/nar/gkt1063 }}

Rat

| Rattus norvegicus

| Rat Genome Database

| [http://rgd.mcw.edu/ RGD]{{cite journal | vauthors = Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H | display-authors = 6 | title = The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease | journal = Nucleic Acids Research | volume = 43 | issue = Database issue | pages = D743-50 | date = January 2015 | pmid = 25355511 | pmc = 4383884 | doi = 10.1093/nar/gku1026 }}

Social amoeba

| Dictyostelium discoideum

| DictyBase

| [https://dictycr.org dictyBase]{{cite journal | vauthors = Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, Kimmel AR | title = dictyBase: a new Dictyostelium discoideum genome database | journal = Nucleic Acids Research | volume = 32 | issue = Database issue | pages = D332-3 | date = January 2004 | pmid = 14681427 | pmc = 308872 | doi = 10.1093/nar/gkh138 }}

Ciliate

| Tetrahymena thermophila

| Tetrahymena Genome Database

| [http://ciliate.org/index.php/home/welcome TGD]

Thale cress

| Arabidopsis thaliana

| The Arabidopsis Information Resource

| [https://www.arabidopsis.org/ TAIR]{{cite journal | vauthors = Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E | display-authors = 6 | title = The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools | journal = Nucleic Acids Research | volume = 40 | issue = Database issue | pages = D1202-10 | date = January 2012 | pmid = 22140109 | pmc = 3245047 | doi = 10.1093/nar/gkr1090 }}

Maize

| Zea mays ssp. mays

| -

| [http://www.maizegdb.org/ MaizeGDB]{{cite journal | vauthors = Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V | title = MaizeGDB, the community database for maize genetics and genomics | journal = Nucleic Acids Research | volume = 32 | issue = Database issue | pages = D393-7 | date = January 2004 | pmid = 14681441 | pmc = 308746 | doi = 10.1093/nar/gkh011 }}{{cite journal | vauthors = Andorf CM, Cannon EK, Portwood JL, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Sen TZ, Lawrence-Dill CJ | display-authors = 6 | title = MaizeGDB update: new tools, data and interface for the maize model organism database | journal = Nucleic Acids Research | volume = 44 | issue = D1 | pages = D1195-201 | date = January 2016 | pmid = 26432828 | pmc = 4702771 | doi = 10.1093/nar/gkv1007 }}

Soybean

|Glycine soja

|SoyBase

|[https://soybase.org/ SoyBase]{{cite journal | vauthors = Grant D, Nelson RT, Cannon SB, Shoemaker RC | title = SoyBase, the USDA-ARS soybean genetics and genomics database | journal = Nucleic Acids Research | volume = 38 | issue = Database issue | pages = D843-6 | date = January 2010 | pmid = 20008513 | pmc = 2808871 | doi = 10.1093/nar/gkp798 }}

Zebrafish

| Danio rerio

| Zebrafish Information Network

| [http://zfin.org/ ZFIN]{{cite journal | vauthors = Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Schaper K, Shao X, Singer A, Sprunger B, Van Slyke CE, Westerfield M | display-authors = 6 | title = ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D854-60 | date = January 2013 | pmid = 23074187 | pmc = 3531097 | doi = 10.1093/nar/gks938 }}

| Candida albicans

| -

| [http://www.candidagenome.org/ CGD]{{cite journal | vauthors = Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G | display-authors = 6 | title = The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata | journal = Nucleic Acids Research | volume = 40 | issue = Database issue | pages = D667-74 | date = January 2012 | pmid = 22064862 | pmc = 3245171 | doi = 10.1093/nar/gkr945 }}

| Escherichia coli

| EcoCyc

| [http://ecocyc.org/ EcoCyc]{{cite journal | vauthors = Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD | display-authors = 6 | title = EcoCyc: fusing model organism databases with systems biology | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D605-12 | date = January 2013 | pmid = 23143106 | pmc = 3531154 | doi = 10.1093/nar/gks1027 }}

Hay bacillus

|Bacillus subtilis

| -

|[http://subtiwiki.uni-goettingen.de/ SubtiWiki]{{cite journal | vauthors = Zhu B, Stülke J | title = SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis | journal = Nucleic Acids Research | volume = 46 | issue = D1 | pages = D743–D748 | date = January 2018 | pmid = 29788229 | pmc = 5753275 | doi = 10.1093/nar/gkx908 }}

References

Category:Model organism databases