FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research

Author:

Samuels Bridget D.1ORCID,Aho Robert2,Brinkley James F.3,Bugacov Alejandro4,Feingold Eleanor5,Fisher Shannon6,Gonzalez-Reiche Ana S.7,Hacia Joseph G.8,Hallgrimsson Benedikt9ORCID,Hansen Karissa2ORCID,Harris Matthew P.10,Ho Thach-Vu1,Holmes Greg7,Hooper Joan E.11,Jabs Ethylin Wang7,Jones Kenneth L.12,Kesselman Carl4,Klein Ophir D.13,Leslie Elizabeth J.14,Li Hong15,Liao Eric C.16,Long Hannah17,Lu Na7,Maas Richard L.18,Marazita Mary L.51920,Mohammed Jaaved17,Prescott Sara17,Schuler Robert4,Selleri Licia2,Spritz Richard A.21,Swigut Tomek17,van Bakel Harm7ORCID,Visel Axel222324,Welsh Ian2,Williams Cristina4,Williams Trevor J.15,Wysocka Joanna17,Yuan Yuan1,Chai Yang1ORCID

Affiliation:

1. Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA

2. Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA

3. Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA 98195, USA

4. Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA

5. Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA

6. Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA

7. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA

8. Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA

9. Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, and McCaig Bone and Joint Institute, University of Calgary, Alberta, Canada

10. Department of Orthopedic Research, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA

11. Department of Cell and Developmental Biology, School of Medicine, University of Colorado, Aurora, CO 80045, USA

12. Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA

13. Program in Craniofacial Biology, Departments of Orofacial Sciences and Pediatrics, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA

14. Department of Human Genetics, Emory University, Atlanta, GA 30322, USA

15. Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA

16. Massachusetts General Hospital, Plastic and Reconstructive Surgery, Boston, MA 02114, USA

17. Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA

18. Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA

19. Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA

20. Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA

21. Human Medical Genetics and Genomics Program, School of Medicine, University of Colorado, Aurora, CO 80045, USA

22. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

23. U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

24. School of Natural Sciences, University of California Merced, Merced, CA 95343, USA

Abstract

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.

Funder

National Institute of Dental and Craniofacial Research

Lawrence Berkeley National Laboratory

Publisher

The Company of Biologists

Subject

Developmental Biology,Molecular Biology

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