Literature DB >> 35912790

FaceBase: A Community-Driven Hub for Data-Intensive Research.

R E Schuler1, A Bugacov1, J G Hacia2, T V Ho3, J Iwata4, L Pearlman1, B D Samuels3, C Williams1, Z Zhao5, C Kesselman1, Y Chai3.   

Abstract

The FaceBase Consortium, funded by the National Institute of Dental and Craniofacial Research of the National Institutes of Health, was established in 2009 with the recognition that dental and craniofacial research are increasingly data-intensive disciplines. Data sharing is critical for the validation and reproducibility of results as well as to enable reuse of data. In service of these goals, data ought to be FAIR: Findable, Accessible, Interoperable, and Reusable. The FaceBase data repository and educational resources exemplify the FAIR principles and support a broad user community including researchers in craniofacial development, molecular genetics, and genomics. FaceBase demonstrates that a model in which researchers "self-curate" their data can be successful and scalable. We present the results of the first 2.5 y of FaceBase's operations as an open community and summarize the data sets published during this period. We then describe a research highlight from work on the identification of regulatory networks and noncoding RNAs involved in cleft lip with/without cleft palate that both used and in turn contributed new findings to publicly available FaceBase resources. Collectively, FaceBase serves as a dynamic and continuously evolving resource to facilitate data-intensive research, enhance data reproducibility, and perform deep phenotyping across multiple species in dental and craniofacial research.

Entities:  

Keywords:  craniofacial abnormalities; data curation; developmental biology; genomics; molecular genetics; morphogenesis

Mesh:

Year:  2022        PMID: 35912790      PMCID: PMC9516628          DOI: 10.1177/00220345221107905

Source DB:  PubMed          Journal:  J Dent Res        ISSN: 0022-0345            Impact factor:   8.924


  27 in total

1.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

Review 2.  RNA epigenetics--chemical messages for posttranscriptional gene regulation.

Authors:  Ian A Roundtree; Chuan He
Journal:  Curr Opin Chem Biol       Date:  2015-11-26       Impact factor: 8.822

Review 3.  Single-Cell Non-coding RNA in Embryonic Development.

Authors:  Qiang Fu; Chuan-Jiang Liu; Zhen-Sheng Zhai; Xu Zhang; Tao Qin; Hong-Wei Zhang
Journal:  Adv Exp Med Biol       Date:  2018       Impact factor: 2.622

4.  Experiences with Deriva: An Asset Management Platform for Accelerating eScience.

Authors:  Alejandro Bugacov; Karl Czajkowski; Carl Kesselman; Anoop Kumar; Robert E Schuler; Hongsuda Tangmunarunkit
Journal:  Proc IEEE Int Conf Escience       Date:  2017-11-16

5.  Biocuration: Distilling data into knowledge.

Authors: 
Journal:  PLoS Biol       Date:  2018-04-16       Impact factor: 8.029

6.  Network-based identification of critical regulators as putative drivers of human cleft lip.

Authors:  Aimin Li; Guimin Qin; Akiko Suzuki; Mona Gajera; Junichi Iwata; Peilin Jia; Zhongming Zhao
Journal:  BMC Med Genomics       Date:  2019-01-31       Impact factor: 3.063

7.  MicroRNA-374a, -4680, and -133b suppress cell proliferation through the regulation of genes associated with human cleft palate in cultured human palate cells.

Authors:  Akiko Suzuki; Aimin Li; Mona Gajera; Nada Abdallah; Musi Zhang; Zhongming Zhao; Junichi Iwata
Journal:  BMC Med Genomics       Date:  2019-07-01       Impact factor: 3.063

8.  Excessive All-Trans Retinoic Acid Inhibits Cell Proliferation Through Upregulated MicroRNA-4680-3p in Cultured Human Palate Cells.

Authors:  Hiroki Yoshioka; Sai Shankar Ramakrishnan; Junbo Shim; Akiko Suzuki; Junichi Iwata
Journal:  Front Cell Dev Biol       Date:  2021-01-28

9.  UCSC Cell Browser: Visualize Your Single-Cell Data.

Authors:  Matthew L Speir; Aparna Bhaduri; Nikolay S Markov; Pablo Moreno; Tomasz J Nowakowski; Irene Papatheodorou; Alex A Pollen; Brian J Raney; Lucas Seninge; W James Kent; Maximilian Haeussler
Journal:  Bioinformatics       Date:  2021-07-09       Impact factor: 6.931

10.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

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  2 in total

1.  Sharing Begins at Home: How Continuous and Ubiquitous FAIRness Can Enhance Research Productivity and Data Reuse.

Authors:  William Dempsey; Ian Foster; Scott Fraser; Carl Kesselman
Journal:  Harv Data Sci Rev       Date:  2022-07-28

2.  Data-Driven Dental, Oral, and Craniofacial Analytics: Here to Stay.

Authors:  F Schwendicke; M L Marazita
Journal:  J Dent Res       Date:  2022-10       Impact factor: 8.924

  2 in total

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