FlyBase
FlyBase is a non-profit, NIH-funded model organism database consortium founded in 1992 that provides curated Drosophila gene and genome data to the global academic, biomedical, and educational research community via web portal, API, and bulk downloads.
- Company typePrivate
- Founded1992
- HeadquartersCambridge, United States
- Headcount1–10
- GTM typeB2B
- OfferingSoftware
What FlyBase does
FlyBase is a non-profit Model Organism Database (MOD) consortium founded in 1992 that provides the authoritative, curated reference resource for Drosophila (fruit fly) genes and genomes to the global research community. The organization serves academic researchers, biomedical scientists using Drosophila as a human disease model, and educators across universities worldwide, with primary funding flowing through NIH/NHGRI grants. Its core product is the FlyBase Database — a comprehensive knowledge base covering genes, alleles, expression patterns, phenotypes, genetic interactions, disease models, Gene Ontology annotations, sequences, and publications, accessible via a web portal with QuickSearch, programmatic API endpoints, a public PostgreSQL Chado database (chado.flybase.org), and bulk data downloads including over 4TB of archive releases from FB2006_01 through FB2026_02.
The underlying technology stack is built on a PostgreSQL Chado database architecture and integrates JBrowse for genome visualization, local BLAST for sequence similarity, and standardized ontologies (Gene Ontology, anatomy, developmental, disease, sequence). Data is distributed in multiple formats (Chado XML, TSV, JSON, FASTA, GFF, GTF) through the web portal, S3 FTP (hosted under the AWS Open Data Sponsorship Program), and wget-accessible bulk downloads. FlyBase is a founding member of the Alliance of Genome Resources consortium linking it to SGD, WormBase, MGI, ZFIN, and other model organism databases, and maintains deep integrations with InterPro, DIOPT, UniProtKB, modENCODE RNA-Seq, FlyAtlas2, EBI Single Cell Expression Atlas, and the Fly Cell Atlas Consortium. Community-driven curation is enabled through the Fast-Track Your Paper system and Gene Snapshots authored by FlyBase curators.
The business model is publicly funded non-profit operations with no commercial pricing tiers. Primary revenue flows from NHGRI grants, with US-based team funding restored in March 2026 and the Cambridge UK curation team's foreign subaward terminated, prompting a transition toward soliciting annual contributions from fly laboratories. AWS provides in-kind sponsorship of storage and data transfer costs. The resource is provided free of charge worldwide, with no subscription fees. The go-to-market motion is community-led via Fly Board governance, the FlyBase Community Advisory Group, newsletter, Slack channels, Bluesky/Mastodon/X social presence, and YouTube tutorials, targeting engagement with the Drosophila research community rather than commercial customer acquisition.
FlyBase firmographics
Firmographics- Name
- FlyBase
- Legal name
- FlyBase
- Website
- https://flybase.org
- Company type
- Private
- Founded year
- 1992
- Operating status
- Operating
- Headcount range
- 1–10 employees
- Short description
- FlyBase is a non-profit, NIH-funded model organism database consortium founded in 1992 that provides curated Drosophila gene and genome data to the global academic, biomedical, and educational research community via web portal, API, and bulk downloads.
- Ownership category
- akta.pro rank
Where FlyBase is headquartered
LocationHeadquarters
- HQ city
- Cambridge
- HQ country
- United States
- HQ region
- North America
Offices1 record
Markets served
FlyBase business model
Business model- GTM type
- B2B
- Offering type
- Software
- Cost components
- Personnel, Technology or R&D, Infrastructure, Operations
Revenue model
- Public Funding (NHGRI): FlyBase is primarily funded by the National Human Genome Research Institute (NHGRI) of the NIH. The funding was restored for US-based FlyBase teams in March 2026. Foreign subaward to Cambridge UK team was terminated, requiring the Cambridge team to seek annual contributions from fly labs.
- Community Contributions: Following termination of foreign subaward, the Cambridge UK curation team requests annual contributions from fly labs to support ongoing data curation. Without contributions, FlyBase will become frozen in its current state.
Go-to-market motion1 record
Distribution channels4 records
Marketing channels6 records
FlyBase product offering
Product offeringCore offering
FlyBase is a comprehensive, curated Model Organism Database (MOD) for Drosophila (fruit fly) genes and genomes, providing searchable data on genes, alleles, expression patterns, phenotypes, genetic and molecular interactions, disease models, orthology, GO annotations, sequences, and publications. It is accessed globally through a web portal (QuickSearch, QueryBuilder, JBrowse, BLAST), a public PostgreSQL Chado SQL database, and bulk data downloads (over 4 terabytes) via AWS S3. The resource is free and openly available to the research community.
Product overview
FlyBase is a comprehensive Model Organism Database (MOD) for Drosophila genes and genomes. The core product is the FlyBase Database—a curated knowledge base providing searchable access to genes, alleles, expression patterns, phenotypes, genetic and molecular interactions, disease models, GO annotations, sequences, and publications. The primary access methods are the web interface (QuickSearch, QueryBuilder, Vocabularies), programmatic API (PostgreSQL Chado database, S3 bulk downloads, wget), and community tools (Fast-Track Your Paper, Gene Snapshots). Supporting tools include JBrowse (genome browser), BLAST (sequence alignment), Batch Download (tabular data retrieval), Sequence Downloader, ID Validator, Interactions Browser, ImageBrowse, and CytoSearch. Data integrations connect FlyBase to Alliance of Genome Resources, DIOPT, FlyAtlas2, InterPro, UniProtKB, modENCODE RNA-Seq, EBI Single Cell Expression Atlas, Fly Cell Atlas, and AWS S3 Open Data storage.
Differentiator
Problem solved
Functional benefit
Products and services
- FlyBase Database
- Bulk Data Downloads
- Chado PostgreSQL Database
Companies that use FlyBase
Customer profileSegments3 records
Ideal customer profiles3 records
FlyBase technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- Yes
- API docs
- API detail
Core technology
AI maturity
App detail
Integration11 records
AI capability3 records
Feature7 records
FlyBase partnerships and signals
Strategic signalPartnerships
Six partnerships are on record, tiered core and major.
- Amazon Web Services (AWS)coreAWS sponsors storage and data transfer costs for the FlyBase bulk data repository through the AWS Open Data Sponsorship Program. This enables FlyBase to preserve and provide broader access to nearly two decades of archive releases. The S3 bucket (s3ftp.flybase.org) hosts over 4 terabytes of data.
- Alliance of Genome ResourcescoreFlyBase is a founding member of the Alliance of Genome Resources, a consortium of model organism databases (including SGD, WormBase, MGI, ZFIN, Xenbase, RGD, dictyBase, PomBase) that collaborates on shared infrastructure, standards, and cross-species data integration for biomedical research.
- Bloomington Drosophila Stock Center (BDSC)coreLong-standing partnership with the BDSC at Indiana University. FlyBase provides integrated access to stock information and links to BDSC resources. Dr. Kathy Matthews, co-founder of FlyBase, was also instrumental in establishing BDSC. Partnership includes Kathy Matthews BDSC Endowment established in her honor.
- EBI Single Cell Expression AtlasmajorFlyBase has an ongoing collaboration with EBI's Single Cell Expression Atlas, integrating single-cell RNA-seq data into FlyBase resources and contributing to the broader single-cell genomics community.
- Stock Centers (FlyORF, VDRC, KDRC, Kyoto, NIG-FLY, THFC)majorFlyBase provides links to multiple Drosophila stock centers worldwide for researcher access to strains and reagents referenced in the database.
- Fly Cell Atlas ConsortiummajorCollaboration with the Fly Cell Atlas (FCA) consortium to integrate single-cell RNA-seq data from the adult fly cell atlas project, including data from 15+ tissues, into FlyBase resources.
Scale indicators7 records
Recent moves6 records
Expansion highlights5 records
FlyBase competitors and assessment
Company assessmentDirect peers
- Xenbase: Model organism database for Xenopus (frog) species. Alliance of Genome Resources partner with FlyBase, sharing curation workflows, Chado architecture, and the same NIH-funded non-profit operating model for an analogous developmental biology research community.
- WormBase: Model organism database for C. elegans and related nematodes. Co-founding member of the Alliance of Genome Resources alongside FlyBase, using the same Chado/PostgreSQL architecture and serving the same academic researcher persona with curated gene, allele, expression, and phenotype data.
- Saccharomyces Genome Database (SGD): Model organism database for budding yeast (S. cerevisiae). Founding member of the Alliance of Genome Resources with FlyBase, providing curated gene/genome annotations and tools for an analogous academic community, with the same community-curation and grant-funded operating model.
- Mouse Genome Informatics (MGI): Model organism database for the laboratory mouse maintained by The Jackson Laboratory. Alliance of Genome Resources co-founding partner with FlyBase, focused on mammalian genetics but offering the same class of curated nomenclature, orthology, and phenotype data to the research community.
- Zebrafish Information Network (ZFIN): Model organism database for zebrafish. Alliance of Genome Resources partner alongside FlyBase, providing gene, expression, phenotype, and disease annotation for an analogous vertebrate model organism research community.
- Rat Genome Database (RGD): Model organism database for Rattus norvegicus. Alliance of Genome Resources partner with FlyBase, delivering curated genetic and physiological data to biomedical researchers using a comparable grant-funded MOD structure and ontology integration.
- PomBase: Model organism database for fission yeast (S. pombe). Alliance of Genome Resources partner with FlyBase, providing gene and genome curation to a specialized research community using a similar Chado-based architecture and release cadence.
- dictyBase: Model organism database for Dictyostelium discoideum (social amoeba). Alliance of Genome Resources partner alongside FlyBase, sharing the Chado schema and the same NIH-funded MOD operating model for a smaller but analogous research community.
- Alliance of Genome Resources: Consortium that FlyBase co-founded, integrating data from SGD, WormBase, MGI, ZFIN, Xenbase, RGD, dictyBase and PomBase. Operates shared BLAST, orthology (DIOPT), and cross-MOD search infrastructure that directly competes with/extends FlyBase-native capabilities.
Broad incumbents
- NCBI / National Center for Biotechnology Information: Broader NIH-funded biomedical information infrastructure hosting GenBank, RefSeq, PubMed, and Taxonomy — sources FlyBase integrates with. NCBI provides overlapping reference sequence and literature services, functioning as the federal incumbent against which all MODs position themselves.
Market position
Strengths5 records
Weaknesses5 records
Competitive moat5 records
Key risks5 records
Key highlights7 records
Customer concentration
FlyBase social profiles
Digital presenceFlyBase financial estimates
Financial estimateRevenue estimate
Valuation estimate
FlyBase leadership team
Management profileNumber of profiles
FlyBase funding detail
Funding detailFunding overview
Funding rounds
Investors
Funding detail is available on the Subscription and Enterprise plan.Contact sales →
FlyBase M&A and investment
M&A and investmentM&A
Investments
M&A and investment is available on the Subscription and Enterprise plan.Contact sales →
Frequently asked questions about FlyBase
What does FlyBase do?
FlyBase is a comprehensive, curated Model Organism Database (MOD) for Drosophila (fruit fly) genes and genomes, providing searchable data on genes, alleles, expression patterns, phenotypes, genetic and molecular interactions, disease models, orthology, GO annotations, sequences, and publications. It is accessed globally through a web portal (QuickSearch, QueryBuilder, JBrowse, BLAST), a public PostgreSQL Chado SQL database, and bulk data downloads (over 4 terabytes) via AWS S3. The resource is free and openly available to the research community.
Is FlyBase a public or private company?
FlyBase is a private company. It is classified as nonprofit foundation owned and is currently operating.
When was FlyBase founded?
FlyBase was founded in 1992. It employs 1 to 10 people.
Where is FlyBase based?
FlyBase is headquartered in Cambridge, United States, in the North America region.
How does FlyBase make money?
Two revenue lines are on record. Public Funding (NHGRI) is the primary driver. The others are community Contributions.
Who are FlyBase's main competitors?
Direct peers on record are Xenbase, WormBase, Saccharomyces Genome Database (SGD), Mouse Genome Informatics (MGI), Zebrafish Information Network (ZFIN), Rat Genome Database (RGD), PomBase, dictyBase and Alliance of Genome Resources. NCBI / National Center for Biotechnology Information is listed as a broad incumbent.
Does FlyBase have an API?
Yes. FlyBase provides programmatic access via a public PostgreSQL Chado database (chado.flybase.org) for direct SQL queries, S3 FTP and HTTPS bulk downloads of precomputed files (current and archived releases from FB2006_01 onward), and Chado XML data dumps. Bulk data is accessible via wget using standard URLs (e.g., wget https://s3ftp.flybase.org/releases/current/precomputed_files/). Current release FB2026_02 (June 18, 2026) is available via the /releases/current/ path. A psql database dump of FB2026_02 is 16GB in compressed form. Developer documentation is at flybase.github.io.