Since 2009, FaceBase has developed a broad and deep base of data, first through integration of multidisciplinary research teams into a consortium with the idea being that not every research problem will be or even can be solved with a single approach. Most will require a range of tools and expertise, allowing a more powerful research synergy to peel away the many layers of biological complexity and reach the essence of the question.
In its first two phases, FaceBase focused on data from specific groups of targeted projects (known as spoke projects). This provided a large foundation of data from a range of tools and expertise, and allowed projects to focus on specific efforts within a theme: FaceBase 1 focused on midface structure and development, and FaceBase 2 expanded to include the whole face. Beginning with FaceBase 3, the consortium moved away from this "hub and spoke" model and opened the repository to community data submission — a shift that has continued and expanded in the current phase, FaceBase 4, as the resource evolves into a data-science hub serving the full translational spectrum of dental, oral, and craniofacial research.
FaceBase 1 (2009 - 2014)
FaceBase was initially launched in 2009 with eleven research and technology grants. The first phase from 2009 through 2014 focused on the middle region of the human face and the genetics related to developmental disorders such as cleft lip and palate. The data from this first band of projects created a huge database for the head and skull and craniofacial development available free to the public.
FB1 Spoke projects:
- FaceBase Management and Coordination Hub (Marazita/Murray)
- 3D Facial Norms Database (Marazita/Weinberg)
- Algum (Satyanarayanan)
- Functional Analysis of Neural Crest and Palate: Imaging Craniofacial Development (Fraser)
- Genetic Determinants of Orofacial Shape and Relationship to Cleft Lip/Palate (Hallgrimsson/Klein/Spritz)
- Genetic Tools and Resources for Orofacial Clefting Research (Donahue/Murray)
- Genome-Wide Atlas of Craniofacial Transcriptional Enhancers (Visel)
- Global Gene Expression Atlas of Craniofacial Development (Potter)
- Identification of miRNAs Involved in Midfacial Development and Clefting (Artinger/Clouthier/Postlethwait)
- Oral Clefts: Moving from Genome-Wide Studies Toward Functional Genomics (Beaty)
- Research on Functional Genomics, Image Analysis and Rescue of Cleft Palate (Chai)
- Shape-Based Retrieval of 3D Craniofacial Data (Shapiro)
FaceBase 2 (2014 - 2019)
In 2014, the second 5-year phase of FaceBase launched with ISI's Informatics Division manning the Coordinating Center (known as the Hub) and ten new projects expanding FaceBase's domain to include more regions. The Hub also developed new systems and tools including more complex yet intuitive search capabilities and greater detail and analysis in viewing data.
FB2 Spoke projects:
- FaceBase 2 Coordinating Center (Kesselman)
- Anatomical Atlas and Transgenic Toolkit for Late Skull Formation in Zebrafish (Fisher/Harris)
- Developing 3D Craniofacial Morphometry Data and Tools to Transform Dysmorphology (Hallgrimsson/Klein/Spritz)
- Epigenetic Landscapes and Regulatory Divergence of Human Craniofacial Traits (Selleri/Wysocka)
- Genomic and Transgenic Resources for Craniofacial Enhancer Studies (Visel)
- Human Genomics Analysis Interface for FaceBase 2 (Marazita)
- Integrated Research of Functional Genomics and Craniofacial Morphogenesis (Chai)
- The Ontology of Craniofacial Development and Malformation (Brinkley)
- Rapid Identification and Validation of Human Craniofacial Development Genes (Maas/Liao)
- RNA Dynamics in the Developing Mouse Face (Hooper/Jones/Williams)
- Transcriptome Atlases of the Craniofacial Sutures (Holmes/Jabs/Van Bakel)
FB2 Scientific Leadership Group:
- J. Michael Cherry, Stanford University
- Melissa Haendel, Oregon Heath & Sciences University
- Max Muenke, NIH/NHGRI
- Phil Soriano, Icahn School of Medicine at Mt Sinai
- Raimond Winslow, Johns Hopkins University
FB2 NIH/NIDCR staff:
- Steven Scholnick
- Jeannine Helm
- Nadya Lumelsky
- Lillian Shum
- Martha Somerman
- Lu Wang
FaceBase 3 (2019 - 2024)
FaceBase 3 marked a turning point for the consortium. Building on the foundation laid by the first two phases, this phase moved away from the "hub and spoke" model of funded data contributors and opened FaceBase to an open, community-based model in which researchers anywhere could submit data to the repository. This change proved highly successful, onboarding over 40 new data-contributing projects spanning roughly 50 experiment types — including genetic, imaging, anatomical, public health, and single-cell data from both humans and animal models.
During this period FaceBase broadened its range of data to fill gaps and flesh out its offerings across additional anatomical areas (such as teeth and gums), diseases, species, and tools, adapting to the ever-changing technologies reshaping the modern research landscape. By the close of the phase, FaceBase had become an exemplar of the FAIR data principles and adhered to the TRUST principles for digital repositories, serving a worldwide research community.
FaceBase 4 (2024 - present)
In its current phase, which began in 2024, FaceBase continues the open, community-based submission model established in FaceBase 3 and evolves the resource into a data-science hub for the full translational spectrum of dental, oral, and craniofacial (DOC) and related disciplines. The goal is to provide the biomedical research community with the means to create high-quality, data-driven results from basic science through clinical and translational application.
FaceBase 4 also expands the resource beyond its longtime home in craniofacial research into additional NIH institutional domains — for example, the inner ear and hearing research supported through our collaboration with the National Institute on Deafness and Other Communication Disorders (NIDCD), reflected in the launch of EarBase — and emphasizes federating data across complementary resources. Work in this phase is organized around three aims:
- Community needs and engagement. Recruit and publicly share data across the full translational spectrum of DOC and related disciplines, and support researchers through training opportunities — online and in-person boot camps, interactive notebook-based tutorials, videos, online courseware, and our annual Community Forum — while helping the community comply with the NIH Data Management and Sharing Policy.
- Quality of services and efficiency of operations. Provide flexible, cost-effective cloud hosting and sharing throughout the data lifecycle; maintain and extend compliance with the FAIR and TRUST principles; make shared data AI/ML/DL-ready; and ensure interoperability with complementary resources used in data-intensive research, such as large language models, notebooks, virtual computing environments, and computational frameworks.
- Governance. Implement best-practice policies for data access, privacy, and ethics; convene an external advisory committee representing the full translational spectrum of DOC and related communities; and continually assess and ensure the trustworthiness of the resource for its users.
To view the current personnel, go to the About page.
To view the current list of data we are most interested in to improve our repository, go to the Data Priorities page.