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

doi:10.1242/dev.191213

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

Development. 2020 Sep 21;147(18):dev191213. doi: 10.1242/dev.191213.

Authors

Bridget D Samuels¹, Robert Aho², James F Brinkley³, Alejandro Bugacov⁴, Eleanor Feingold⁵, Shannon Fisher⁶, Ana S Gonzalez-Reiche⁷, Joseph G Hacia⁸, Benedikt Hallgrimsson⁹, Karissa Hansen², Matthew P Harris¹⁰, Thach-Vu Ho¹, Greg Holmes⁷, Joan E Hooper¹¹, Ethylin Wang Jabs⁷, Kenneth L Jones¹², Carl Kesselman⁴, Ophir D Klein¹³, Elizabeth J Leslie¹⁴, Hong Li¹⁵, Eric C Liao¹⁶, Hannah Long¹⁷, Na Lu⁷, Richard L Maas¹⁸, Mary L Marazita^{5

19

20}, Jaaved Mohammed¹⁷, Sara Prescott¹⁷, Robert Schuler⁴, Licia Selleri², Richard A Spritz²¹, Tomek Swigut¹⁷, Harm van Bakel⁷, Axel Visel^{22

23

24}, Ian Welsh², Cristina Williams⁴, Trevor J Williams¹⁵, Joanna Wysocka¹⁷, Yuan Yuan¹, Yang Chai²⁵

Affiliations

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.
²⁵ Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA ychai@usc.edu.

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.

Keywords: Craniofacial development; Data resource; FaceBase Consortium; Human; Mouse; Zebrafish.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Animals
Databases, Factual
Dental Research / methods*
Facial Bones / physiology*
Humans
Reproducibility of Results
Research Personnel
Skull / physiology*

Abstract

Publication types

MeSH terms

Grants and funding