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

• Type of Material: Article
• Authors: Bridget D Samuels, University of Southern California; Robert Aho, University of California San Francisco; James F Brinkley, University of Washington; Alejandro Bugacov, University of Southern California; Eleanor Feingold, University of Pittsburgh; Shannon Fisher, Boston University; Ana S Gonzalez-Reiche, Icahn School of Medicine at Mount Sinai; Joseph G Hacia, University of Southern California; Benedikt Hallgrimsson, University of Calgary; Karissa Hansen, University of California San Francisco; Matthew P Harris, Harvard Medical School; Thach-Vu Ho, University of Southern California; Greg Holmes, Icahn School of Medicine at Mount Sinai; Joan E Hooper, University of Colorado, Aurora; Ethylin W Jabs, Icahn School of Medicine at Mount Sinai; Kenneth L Jones, University of Colorado, Aurora; Carl Kesselman, University of Southern California; Ophir D Klein, University of California San Francisco; Elizabeth Leslie, Emory University; Hong Li, Univ Colorado; Eric C Liao, Massachusetts General Hospital; Hannah Long, Stanford University; Na Lu, Icahn School of Medicine at Mount Sinai; Richard L Maas, Harvard Medical School; Mary L Marazita, University of Pittsburgh; Jaaved Mohammed, Stanford University; Sara Prescott, Stanford University; Robert Schuler, University of Southern California; Licia Selleri, University of California San Francisco; Richard A Spritz, University of Colorado, Aurora; Tomek Swigut, Stanford University; Harm van Bakel, Icahn School of Medicine at Mount Sinai; Axel Visel, Lawrence Berkeley National Laboratory; Ian Welsh, University of California San Francisco; Cristina Williams, University of Southern California; Trevor J Williams, University of Colorado, Aurora; Joanna Wysocka, Stanford University; Yuan Yuan, University of Southern California; Yang Chai, University of Southern California
• Language: English
• Date: 2020-09-01
• Publisher: COMPANY BIOLOGISTS LTD
• Publication Version: Final Published Version
• Copyright Statement: © 2020. Published by The Company of Biologists Ltd
• Final Published Version (URL): http://dx.doi.org/10.1242/dev.191213
• Title of Journal or Parent Work: DEVELOPMENT
• Volume: 147
• Issue: 18
• Grant/Funding Information: 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.; 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.).; The FaceBase 3 Hub is supported by the National Institute of Dental and Craniofacial Research (U01-DE028729 to C.K. and Y.C.).
• Keywords: FaceBase Consortium; ZEBRAFISH; GENE-EXPRESSION; Craniofacial development; TOOTH; PALATE; GENOME; Data resource; Zebrafish; Human; Developmental Biology; DIVERSITY; Mouse; REGULATORS; Life Sciences & Biomedicine; EVOLUTION; CRANIAL NEURAL CREST; Science & Technology; FISH
• Research Categories: Chemistry, Biochemistry; Biology, Molecular; Health Sciences, Medicine and Surgery; Biology, Cell

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.