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FaceBase is a collaborative data resource for craniofacial research, funded primarily by the National Institute of Dental and Craniofacial Research (NIDCR). It curates datasets contributed by the research community and shares them through the website facebase.org. This page is general information for researchers, lab staff and research administrators; it is not medical advice.
Short answer
FaceBase is both a long-running NIDCR-funded consortium and the data repository that consortium built. As a repository it holds genetic, molecular, biological, imaging and computational data on craniofacial development and malformation, managed under the FAIR principles. Researchers deposit data there, often as part of an NIH Data Management and Sharing Plan, and anyone using or downloading the data agrees to its Terms of Use.
Definition and scope
Two things share the name, and separating them avoids most confusion.
- The consortium. According to the FaceBase Consortium’s 2016 paper in Development (PMC4958338, read 2026-11-08), FaceBase 1 launched in 2009 with a data coordination Hub and ten “spoke” research projects focused on the midface. FaceBase 2 launched in 2014 with a new Hub and ten new spokes that extended beyond the midface and palate. The aim, in the paper’s words, was to accelerate understanding of craniofacial developmental biology. The FaceBase about page (read 2026-11-08) now refers to a “FaceBase phase 4”.
- The repository. The FaceBase website states its goal as being “the trusted primary data resource for craniofacial researchers worldwide”. Its listed funders are NIDCR, the National Institute on Deafness and Other Communication Disorders (NIDCD) and the NIH Office of Data Science Strategy (ODSS).
The resource covers high-throughput genetic, molecular, biological, imaging and computational data. The 2016 paper describes species including mouse, zebrafish, human and chimpanzee, and data types including microCT and optical projection tomography imaging, GWAS, RNA-seq and microarray data, ChIP-seq and enhancer assays, anatomical and molecular atlases, 3D facial photographs and software tools. Those descriptions reflect the paper’s date; the site does not publish current dataset counts on its about page, so this page gives none.
How it is used in practice
The 2016 paper describes the Hub’s features: faceted search, data curation, a 3D viewer, user-defined collections, a data model based on ISA-TAB, a RESTful API, and links to NCBI GEO and the UCSC Genome Browser. Data are described with the Ontology of Craniofacial Development and Malformation (OCDM), which the paper links to the Monarch Initiative and Uberon ontologies. For human genomic data, the paper says the interface returns pre-calculated results without releasing individual-level data.
The FaceBase “Contributing” page (read 2026-11-08) sets out four steps for depositors:
- Before the award, include FaceBase in the NIH Data Management and Sharing (DMS) Plan.
- After the award, submit the data for review.
- Prepare the data during collection.
- After approval, enter metadata and upload (“Upload early and often!”).
The page adds that contribution is open to the dental, oral and craniofacial research community at no cost, that FaceBase is an NIH-designated genomic data repository, that metadata are ontology-driven, that datasets can be embargoed until publication, and that each dataset receives a DOI. Questions go to [email protected].
Checklist: FaceBase and NIH data management planning
This table cross-walks the contributing steps to the planning documents research offices already handle. The left column is from FaceBase’s contributing page; the right column points to CASRAI pages on the general requirement.
| FaceBase step or feature | Planning question it answers | Related CASRAI page |
|---|---|---|
| Name FaceBase in the DMS Plan before award | Which repository will hold the data? | NIH Data Management and Sharing Plan |
| Submit data for review after award | Who must approve deposit, and when? | NIH DMS Policy |
| Ontology-driven metadata | How will the data be findable and reusable? | FAIR data principles |
| Embargo until publication | When does the data become public? | Embargo |
| Genomic data repository designation | Do genomic data sharing rules apply? | NIH Genomic Data Sharing Policy |
Where it matters for labs and research offices
Trust signals on the FaceBase about page (read 2026-11-08) include a re3data registry entry (DOI 10.17616/R31NJMQ7), a CoreTrustSeal certification record (DOI 10.34894/YSGDJU), and badges stating that the repository is approved for NIH DMS and NIH HEAL use. Research offices can use these identifiers to check the repository’s entry in the re3data registry and its CoreTrustSeal status directly, rather than relying on this page. The grant number listed for the current phase is U24DE034163. For background on how repositories differ, see Data Repository. For the wider field, see what dental research is.
Common misunderstandings
- “FaceBase is only about faces.” The 2016 paper describes craniofacial developmental biology broadly, with data on anatomy, gene expression and regulatory elements as well as 3D facial photographs.
- “The 2009 and 2016 numbers are current.” “Nearly 600 datasets” and “more than 100 publications” are figures from the 2016 paper about FaceBase 1; they are not present-day counts.
- “Using the data is unrestricted.” The site states that using or downloading data means agreeing to its Terms of Use.
FAQ
What is FaceBase?
A collaborative, NIDCR-funded data resource for craniofacial research that curates community-contributed datasets and shares them at facebase.org.
Who can contribute data?
The contributing page says contribution is open to the dental, oral and craniofacial research community at no cost.
Can data be embargoed?
Yes. The contributing page says datasets can be embargoed until publication, and each dataset gets a DOI.
Is FaceBase a trusted repository?
The site lists re3data and CoreTrustSeal identifiers and states NIH DMS and NIH HEAL approval. Check those records at the registries themselves.
Sources
- FaceBase, About: facebase.org/about (read 2026-11-08).
- FaceBase, Contributing: facebase.org/contributing (read 2026-11-08).
- FaceBase Consortium. Development, 2016: PMC4958338 (read 2026-11-08).
