Direct comparison
WormBase vs FlyBase vs MGI vs ZFIN Compared
Compare WormBase, FlyBase, MGI, and ZFIN: host institutions, funders, identifiers, and how the Alliance of Genome Resources links them.
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How do WormBase, FlyBase, MGI, ZFIN compare side by side?
The table below compares WormBase, FlyBase, MGI, ZFIN across 8 procurement-relevant dimensions, from organism covered through typical audience.
Side-by-side comparison
| Dimension | WormBase | FlyBase | MGI | ZFIN |
|---|---|---|---|---|
| Organism covered | Caenorhabditis elegans and related nematode species | Drosophila melanogaster and other Drosophila species | Mus musculus (laboratory mouse) | Danio rerio (zebrafish) |
| Host institution(s) | A distributed consortium historically anchored at Caltech, with curation partners including the European Bioinformatics Institute (EBI) and Ontario Institute for Cancer Research (OICR); WormBase data and infrastructure are transitioning onto the shared Alliance platform | A consortium led by Indiana University, with historical curation teams at Harvard University and the University of Cambridge (UK) | The Jackson Laboratory (JAX), Bar Harbor, Maine | University of Oregon, Eugene, Oregon |
| Primary funder | NIH National Human Genome Research Institute (NHGRI); historically also UK Medical Research Council co-funding for MRC-supported curation work | NIH NHGRI | NIH NHGRI (as the Mouse Genome Database, MGD, component of MGI) | NIH NHGRI |
| What it curates | Genome sequence and annotation, gene structure, expression, phenotype, RNAi, and strain data for C. elegans | Genome annotation, gene/allele records, expression, phenotype, and stock/strain data for Drosophila | Gene nomenclature, mouse strains, phenotype and disease-model data, gene expression (GXD), and orthology | Gene records, mutant and transgenic lines, expression patterns, phenotype, and anatomy ontology for zebrafish |
| Core identifier format | WBGene IDs (e.g., WBGene00006763) for genes; WBVar, WBStrain IDs for variants and strains | FBgn IDs (e.g., FBgn0000490) for genes; FBal, FBst for alleles and stocks | MGI accession IDs (e.g., MGI:96677) for genes, alleles, and strains | ZDB IDs (e.g., ZDB-GENE-...) for genes, lines, and other entities |
| Role in Alliance of Genome Resources | Founding Alliance member; core data increasingly served through shared Alliance infrastructure alongside the legacy WormBase site | Founding Alliance member, contributing gene/allele/phenotype curation to the shared portal | Founding Alliance member (as MGD); mouse remains the primary bridge organism linking model-organism data to human disease | Founding Alliance member, contributing zebrafish gene, phenotype, and expression data |
| RRID prefix (for citing in methods sections) | Species-specific strain/gene identifiers, typically cited directly by WBGene/WBStrain ID rather than a single RRID prefix | Cited by FBst (stock) or FBal (allele) identifiers; also indexed in the Antibody/Model Organism sections of the RRID system | MGI: prefix (e.g., RRID:MGI:3527935) is a recognized RRID format | ZDB (ZFIN ID) is a recognized RRID format for zebrafish lines |
| Typical audience | C. elegans developmental biology, neurobiology, and genetics labs | Drosophila genetics labs; also widely used for human disease-gene orthology screens | Mouse genetics, phenotyping, and disease-model labs; a major reference for human-disease orthology | Zebrafish developmental biology and disease/toxicology-model labs |
Common questions
Common questions about WormBase vs FlyBase vs MGI vs ZFIN
Do I need to cite WormBase, FlyBase, MGI, or ZFIN separately from the Alliance of Genome Resources?
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Cite whichever specific database record (gene, strain, or allele ID) you actually used -- e.g., a WBGene ID or an MGI accession number -- in your methods section, since that is the persistent, species-specific identifier reviewers and downstream researchers need to resolve. The Alliance of Genome Resources portal (alliancegenome.org) is useful for cross-species search and comparison, but it does not replace citing the underlying organism database's own identifier.
Are these four databases going to merge into one Alliance database?
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The Alliance of Genome Resources is a shared infrastructure and common-data-model consortium, not a single merged database. WormBase, FlyBase, MGI, and ZFIN (along with the Rat Genome Database, RGD, and Saccharomyces Genome Database, SGD) remain organism-specific curation groups with their own funding lines and identifier systems; the Alliance provides shared tooling, ontologies, and a unified search/comparison portal on top of that federated curation.
Which database should I use if my research spans more than one model organism?
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Start at the Alliance of Genome Resources portal, which lets you search a gene or phenotype across C. elegans, Drosophila, mouse, zebrafish, rat, and yeast simultaneously using shared orthology and disease-association data, then follow through to the organism-specific database for full curation detail, strain/stock ordering information, and the identifier to cite.
How do these databases relate to a data management plan (DMP)?
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For funder DMPs, model organism databases typically count as the designated repository for genetic/strain and phenotype data generated using that organism -- naming WormBase, FlyBase, MGI, or ZFIN (as applicable) in a DMP's repository section is generally accepted practice, since each is a long-standing, NIH-funded, community-endorsed resource for its respective species.
Going deeper
