FaceBase 3

Translational Genomics Research Branch, DER, NIDCR

Objective

Continued support and development of the FaceBase online resource to better serve the craniofacial research community by facilitating computational, bioinformatic, and systems biological studies of craniofacial development through advances in data sharing, integration, and accessibility.

Background

The FaceBase consortium was created to advance craniofacial research through the generation and wide dissemination of a variety of datasets that have traditionally not resulted from R01-funded projects but whose availability would facilitate hypothesis- driven research. FaceBase’s ultimate goal is managing and integrating those data in such a way that they can be readily searched and used as the basis of projects conducted by researchers outside of the consortium, especially those using systems biology approaches.

Since its inception in 2009, the FaceBase consortium has consisted of two rounds of 10 dataset-generating spoke projects coupled to a data management/integration hub responsible for the development of the FaceBase website through which the datasets are disseminated. The awards supporting the current round of projects will expire in April of 2019.

The utility of the site has continued to improve and there are now ~280 users from around the world who have registered for accounts. The hub holds 705 individually downloadable datasets as well as being the sole host for reference sources such as craniofacial development atlases of the mouse (Mouse Anatomy) and zebrafish (FishFace), a 3D atlas of normal human face shape (3D Facial Norms Database), and the Human Genomics Analysis Interface for viewing the findings of genome-wide genetic studies of craniofacial morphology and disorders. Between October 2016 and January 2017 there were over 940 dataset downloads and 1,675 images viewed by logged-in users.

Gaps and Opportunities

Although still relatively underutilized, systems biological and bioinformatic/big data approaches to craniofacial biology are being employed by an increasing number of research labs. As the number of labs pursuing those goals increases so does the number of datasets relevant to FaceBase. While NIH data/resource sharing policies mandate that datasets resulting from NIH-funded research be made available to the wider research community, depositing these datasets in large and generic data repositories does not bring them together in an integrated, easily findable and accessible platform. While the NIH’s Big Data 2 Knowledge program’s efforts to develop a prototype data discovery index (DataMED) have helped, there is still much to be gained by bringing together and integrating craniofacial data within one community resource.

The goal of this initiative is therefore to enhance the utility of FaceBase by bringing together FaceBase 1 and 2 datasets and datasets now being generated outside of the consortium. It could also increase the impact of datasets created with NIDCR R01 funds through advanced annotation and curation of datasets. This can be accomplished through a change in FaceBase’s structure and emphasis, with the current hub and spoke model replaced by a hub-only model. The new hub would be responsible for maintenance and continued development of the website and data repository as well as acquisition of relevant datasets now being produced by the wider craniofacial research community.

These responsibilities would include:

The scope of this initiative includes but is not limited to:

  1. improved curation, integration, and dissemination of existing datasets, with a significant emphasis on development/adoption of new methods of data display that allow users to conduct searches and analyses across multiple datasets using user- defined parameters (as opposed to fixed presentations of data).
  2. extension of curation/annotation efforts to datasets produced by relevant R01- funded projects. The hub would be charged with working with investigators from these projects to make their data conform to the Ontology of Craniofacial Development and Malformation (OCDM), the FaceBase data models, and community data standards so that these new data can be integrated with other datasets held by FaceBase and disseminated to the wider community through the hub website. These R01-funded projects could come from any FOA and any IC as long as they are relevant to craniofacial biology and potentially useful to our research community. Projects funded by the NIDCR would be encouraged to satisfy their data sharing requirements through FaceBase. Researchers from outside of the consortium have offered their data to FaceBase over the years, evidence that wider community is willing to participate in this way.
  3. outreach to members of the craniofacial research community that are not proficient in bioinformatics/data science. This could include creation of publicly available tutorials, “How to use FaceBase” tables at relevant scientific meetings, etc.
  4. identification of resources outside of FaceBase that could either be integrated into FaceBase’s website or linked to from a “resources” page (e.g., the Deciphering the Mechanisms of Developmental Disorders resource supported by the Welcome Trust).

Current Portfolio Overview

Since the issuance of the last FaceBase RFA in 2013, the number of projects generating large datasets in the Translational Genomics Research Branch’s portfolio has grown considerably. However, there has not been a proportionate growth in the number of computational biology/bioinformatics/biostatistics groups analyzing those data. While some researchers in those fields have been drawn to craniofacial research through the availability of FaceBase datasets and the FaceBase secondary analysis PAR (PAR-16-362), there is clearly room for improvement in this area. This is particularly true for the integration of diverse datasets that together can yield a more complete understanding of craniofacial development.

Individuals And Groups Whose Input Was Solicited For This Initiative

Other NIDCR program and executive staff were consulted during the planning of this concept. Public comments were solicited by NIDCR from August 4 - September 5, 2017.

Alignment With Institute Goals And Strategic Plan:

This initiative is aligned with Goal 1 of the NIDCR Strategic Plan 2014-2019: “Support the best science to improve dental, oral, and craniofacial health”; specifically, Objective 1-1 (“Enable basic research to advance knowledge of dental, oral, and craniofacial health”) and Objective 1-2 (“Promote development and use of comprehensive, interoperable databases and informatics resources to advance prevention, diagnosis, and treatment of dental, oral, and craniofacial diseases”).

This initiative is also well aligned with NIH’s growing emphasis on data science and computational biology.

Selected References

Hochheiser H, Aronow B, Artinger K, Beaty T, Brinkley J, Chai Y, Clouthier D, Cunningham M, Dixon M, Donahue L, Fraser S, Hallgrimsson B, Iwata J, Klein O, Marazita M, Murray J, Murray S, Pardo-Manuel de Villena F, Postlethwait J, Potter S, Shapiro L, Spritz R, Visel A, Weinberg S, and Trainor P. The FaceBase Consortium: A comprehensive program to facilitate craniofacial research. Developmental Biology, 355: 175-182 (2011) http://ncbi.nlm.nih.gov/pmc/articles/PMC3440302/

Brinkley JF, Fisher S, Harris MP, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Maas RL, Marazita ML, Selleri L, Spritz RA, van Bakel H, Visel A, Williams TJ, Wysocka J; FaceBase Consortium, Chai Y. The FaceBase Consortium: a comprehensive resource for craniofacial researchers. Development, 143:2677-88 (2016). http://ncbi.nlm.nih.gov/pmc/articles/PMC4958338/

Samuels B. FaceBase: an online resource for craniofacial research. The Node (2016) http://thenode.biologists.com/facebase-online-resource-craniofacial-research/resources/

Last Reviewed on
February 2018