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TECHNIQUES AND RESOURCES
FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research
Bridget D. Samuels, Robert Aho, James F. Brinkley, Alejandro Bugacov, Eleanor Feingold, Shannon Fisher, Ana S. Gonzalez-Reiche, Joseph G. Hacia, Benedikt Hallgrimsson, Karissa Hansen, Matthew P. Harris, Thach-Vu Ho, Greg Holmes, Joan E. Hooper, Ethylin Wang Jabs, Kenneth L. Jones, Carl Kesselman, Ophir D. Klein, Elizabeth J. Leslie, Hong Li, Eric C. Liao, Hannah Long, Na Lu, Richard L. Maas, Mary L. Marazita, Jaaved Mohammed, Sara Prescott, Robert Schuler, Licia Selleri, Richard A. Spritz, Tomek Swigut, Harm van Bakel, Axel Visel, Ian Welsh, Cristina Williams, Trevor J. Williams, Joanna Wysocka, Yuan Yuan, Yang Chai
Development 2020 147: dev191213 doi: 10.1242/dev.191213 Published 21 September 2020
Bridget D. Samuels
1Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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  • ORCID record for Bridget D. Samuels
Robert Aho
2Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
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James F. Brinkley
3Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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Alejandro Bugacov
4Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
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Eleanor Feingold
5Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
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Shannon Fisher
6Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
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Ana S. Gonzalez-Reiche
7Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Joseph G. Hacia
8Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Benedikt Hallgrimsson
9Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, and McCaig Bone and Joint Institute, University of Calgary, Alberta, Canada
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  • ORCID record for Benedikt Hallgrimsson
Karissa Hansen
2Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
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  • ORCID record for Karissa Hansen
Matthew P. Harris
10Department of Orthopedic Research, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Thach-Vu Ho
1Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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Greg Holmes
7Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Joan E. Hooper
11Department of Cell and Developmental Biology, School of Medicine, University of Colorado, Aurora, CO 80045, USA
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Ethylin Wang Jabs
7Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Kenneth L. Jones
12Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
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Carl Kesselman
4Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
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Ophir D. Klein
13Program in Craniofacial Biology, Departments of Orofacial Sciences and Pediatrics, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
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Elizabeth J. Leslie
14Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
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Hong Li
15Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA
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Eric C. Liao
16Massachusetts General Hospital, Plastic and Reconstructive Surgery, Boston, MA 02114, USA
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Hannah Long
17Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
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Na Lu
7Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Richard L. Maas
18Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Mary L. Marazita
5Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
19Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
20Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
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Jaaved Mohammed
17Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
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Sara Prescott
17Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
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Robert Schuler
4Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
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Licia Selleri
2Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
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Richard A. Spritz
21Human Medical Genetics and Genomics Program, School of Medicine, University of Colorado, Aurora, CO 80045, USA
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Tomek Swigut
17Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
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Harm van Bakel
7Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Axel Visel
22Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
23U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
24School of Natural Sciences, University of California Merced, Merced, CA 95343, USA
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Ian Welsh
2Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
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Cristina Williams
4Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
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Trevor J. Williams
15Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA
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Joanna Wysocka
17Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
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Yuan Yuan
1Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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Yang Chai
1Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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  • For correspondence: ychai@usc.edu

Handling Editor: James Briscoe

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ABSTRACT

The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a ‘big data’ resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.

Footnotes

  • Competing interests

    The authors declare no competing or financial interests.

  • Author contributions

    Conceptualization: C.K., Y.C.; Methodology: C.K., R.S.; Software: A.B., M.L.M., R.S., A.V., C.W.; Validation: A.V., T.J.W.; Formal analysis: R.A., J.F.B., E.F., S.F., A.S.G.-R., B.H., K.H., M.P.H., T.H., G.H., J.E.H., E.W.J., K.L.J., O.D.K., E.J.L., H. Li, E.C.L., H. Long, N.L., R.L.M., M.L.M., J.M., S.P., L.S., R.A.S., T.S., H.v.B., A.V., I.W., T.J.W., J.W., Y.Y.; Investigation: R.A., J.F.B., E.F., S.F., A.S.G.-R., B.H., K.H., M.P.H., T.H., G.H., J.E.H., E.W.J., K.L.J., O.D.K., E.J.L., H. Li, E.C.L., H. Long, N.L., R.L.M., M.L.M., J.M., S.P., L.S., R.A.S., T.S., H.v.B., A.V., I.W., T.J.W., J.W., Y.Y.; Data curation: B.D.S., A.B., J.G.H., B.H., T.H., M.L.M., R.S., T.S., A.V., C.W., Y.C.; Writing - original draft: B.D.S., R.A., J.F.B., E.F., S.F., A.S.G.-R., B.H., K.H., M.P.H., T.H., G.H., J.E.H., E.W.J., K.L.J., C.K., O.D.K., E.J.L., H. Li, E.C.L., H. Long, N.L., R.L.M., M.L.M., J.M., S.P., R.S., L.S., R.A.S., T.S., H.v.B, A.V., I.W., C.W., T.J.W., J.W., Y.Y., Y.C.; Writing - review & editing: B.D.S., J.F.B., S.F., J.G.H., B.H., M.P.H., T.H., G.H., J.E.H., E.W.J., K.L.J., C.K., O.D.K., E.C.L., R.L.M., M.L.M., R.S., L.S., R.A.S., H.v.B., A.V., C.W., T.J.W., J.W., Y.C.; Visualization: B.D.S., R.S., C.W.; Supervision: E.F., B.H., M.P.H., G.H., J.E.H., E.W.J., K.L.J., R.L.M., L.S., R.A.S., H.v.B., A.V., T.J.W., J.W., Y.C.; Project administration: B.D.S., S.F., C.K., C.W., Y.C.; Funding acquisition: J.F.B., S.F., B.H., M.P.H., G.H., J.E.H., E.W.J., K.L.J., C.K., O.D.K., E.C.L., R.L.M., M.L.M., L.S., R.A.S., H.v.B., A.V., T.J.W., J.W., Y.C.

  • Funding

    The FaceBase 3 Hub is supported by the National Institute of Dental and Craniofacial Research (U01-DE028729 to C.K. and Y.C.). The FaceBase 2 Consortium projects were supported by the following awards from the National Institute of Dental and Craniofacial Research: U01-DE024449 (C.K.), U01-DE024434 (S.F. and M.P.H.), U01-DE024440 (R.S. and O.D.K.), U01-DE024430 (J.W. and L.S.), U01-DE024427 (A.V.), U01-DE024425 (M.L.M.), U01-DE024421 (Y.C.), U01-DE024417 (J.F.B.), U01-DE024443 (R.M.), U01-DE024429 (T.J.W., J.G.H. and K.L.J.) and U01-DE024448 (E.W.J., G.H. and H.v.B.). Research conducted at the E.O. Lawrence Berkeley National Laboratory was performed under Department of Energy Contract DE-AC02-05CH11231, University of California. Deposited in PMC for release after 12 months.

  • Data availability

    The datasets referenced in this article are available through the FaceBase Hub (facebase.org)

  • Supplementary information

    Supplementary information available online at https://dev.biologists.org/lookup/doi/10.1242/dev.191213.supplemental

  • Received April 2, 2020.
  • Accepted August 13, 2020.
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Keywords

  • FaceBase Consortium
  • Craniofacial development
  • Data resource
  • Human
  • Mouse
  • Zebrafish

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TECHNIQUES AND RESOURCES
FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research
Bridget D. Samuels, Robert Aho, James F. Brinkley, Alejandro Bugacov, Eleanor Feingold, Shannon Fisher, Ana S. Gonzalez-Reiche, Joseph G. Hacia, Benedikt Hallgrimsson, Karissa Hansen, Matthew P. Harris, Thach-Vu Ho, Greg Holmes, Joan E. Hooper, Ethylin Wang Jabs, Kenneth L. Jones, Carl Kesselman, Ophir D. Klein, Elizabeth J. Leslie, Hong Li, Eric C. Liao, Hannah Long, Na Lu, Richard L. Maas, Mary L. Marazita, Jaaved Mohammed, Sara Prescott, Robert Schuler, Licia Selleri, Richard A. Spritz, Tomek Swigut, Harm van Bakel, Axel Visel, Ian Welsh, Cristina Williams, Trevor J. Williams, Joanna Wysocka, Yuan Yuan, Yang Chai
Development 2020 147: dev191213 doi: 10.1242/dev.191213 Published 21 September 2020
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TECHNIQUES AND RESOURCES
FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research
Bridget D. Samuels, Robert Aho, James F. Brinkley, Alejandro Bugacov, Eleanor Feingold, Shannon Fisher, Ana S. Gonzalez-Reiche, Joseph G. Hacia, Benedikt Hallgrimsson, Karissa Hansen, Matthew P. Harris, Thach-Vu Ho, Greg Holmes, Joan E. Hooper, Ethylin Wang Jabs, Kenneth L. Jones, Carl Kesselman, Ophir D. Klein, Elizabeth J. Leslie, Hong Li, Eric C. Liao, Hannah Long, Na Lu, Richard L. Maas, Mary L. Marazita, Jaaved Mohammed, Sara Prescott, Robert Schuler, Licia Selleri, Richard A. Spritz, Tomek Swigut, Harm van Bakel, Axel Visel, Ian Welsh, Cristina Williams, Trevor J. Williams, Joanna Wysocka, Yuan Yuan, Yang Chai
Development 2020 147: dev191213 doi: 10.1242/dev.191213 Published 21 September 2020

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  • Top
  • Article
    • ABSTRACT
    • Introduction
    • FaceBase 2 spoke projects
    • Anatomical atlas and transgenic tools for late skull formation in the zebrafish (https://doi.org/10.25550/1WW2)
    • Transcriptome atlases of the craniofacial sutures (https://doi.org/10.25550/1WW8)
    • Genomic and transgenic resources for craniofacial enhancer studies (https://doi.org/10.25550/1WW4)
    • Integrated research of functional genomics and craniofacial morphogenesis (https://doi.org/10.25550/1WWE)
    • RNA dynamics in the developing mouse face (https://doi.org/10.25550/1WW6)
    • Epigenetic landscapes and regulatory divergence of human craniofacial traits (https://doi.org/10.25550/1WWG)
    • Rapid identification and validation of human craniofacial development genes (https://doi.org/10.25550/1WWA)
    • Developing 3D craniofacial morphometry data and tools to transform dysmorphology (https://doi.org/10.25550/1WWC)
    • Ontology of craniofacial development and malformation (OCDM) (https://doi.org/10.25550/1WX2)
    • Human genomics analysis interface (https://doi.org/10.25550/1WX0)
    • The FaceBase Hub: a FAIR data resource for complex, diverse, evolving research data to advance craniofacial research
    • Technical overview
    • Technical innovations
    • The future of FaceBase
    • Acknowledgements
    • Footnotes
    • Peer review history
    • References
  • Figures & tables
  • Supp info
  • Info & metrics
  • PDF + SI
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