Samuels BD et al. (2020), FaceBase 3: analytical tools and FAIR resources...

XB-ART-57395

Development 2020 Sep 21;14718:. doi: 10.1242/dev.191213.

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

Samuels BD , Aho R , Brinkley JF , Bugacov A , Feingold E , Fisher S , Gonzalez-Reiche AS , Hacia JG , Hallgrimsson B , Hansen K , Harris MP , Ho TV , Holmes G , Hooper JE , Jabs EW , Jones KL , Kesselman C , Klein OD , Leslie EJ , Li H , Liao EC , Long H , Lu N , Maas RL , Marazita ML , Mohammed J , Prescott S , Schuler R , Selleri L , Spritz RA , Swigut T , van Bakel H , Visel A , Welsh I , Williams C , Williams TJ , Wysocka J , Yuan Y , Chai Y .

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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.

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Species referenced: Xenopus laevis
Genes referenced: elavl2 pdf

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	Fig. 1. Images and models of zebrafish craniofacial anatomy. (A) Confocal stack of the skull of a wild-type zebrafish at 11.83 mm standard length (41 days post fertilization); osteoblasts and chondrocytes are marked by expression of mCherry and eGFP, respectively. (B) 3D PDF model based on similar confocal data, showing the labeled buttons to hide or reveal individual elements. (C) High-resolution microCT of an adult zebrafish skull. (D) Orthotopic slices of the same data from the FaceBase online viewer. (E) 3-D model based on the microCT data. Different colors indicate distinct bones.
	Fig. 2. Interactive 3D model of an E18.5 typically developing mouse skull based on microCT data. Different colors indicate distinct bones. Blue dots indicate anatomical landmarks of the mandible; red dots indicate anatomical landmarks of the maxilla. Descriptions of landmarks are provided in the ‘Show landmarks’ menu of the FaceBase 3D mesh viewer. Inset shows digital dissection of the same model, performed using the ‘Rotate’ and ‘Clip plane’ functions. FaceBase Record ID 3V4A.
	Fig. 3. 3D morphometric library of craniofacial dysmorphic syndromes. (A) Sample size distribution for the database of 3D facial images of subjects with genetic syndromes. The images show average facial shapes for select syndromes with a heatmap vector distribution overlay to highlight the regions of greatest difference. Blue indicates an area is smaller in syndromic individuals than in unaffected unrelated individuals; red indicates an area is larger. (B) Age distributions for syndromic subjects and their relatives in the database.
	Fig. 4. Overview of the FaceBase platform and integrated services. The Hub's core data services drive the web-based data browser and search interface for accessing data (http://facebase.org/chaise/), visualization tools, analytical pipelines and the Resources Hub (https://www.facebase.org/resources/), which goes beyond the datasets accessible in the repository. Data submitters can use desktop utilities to upload data in bulk. Third-party identification providers including ORCID, Globus and Google are used to authenticate users. DOIs are minted for each dataset, facilitating accessibility and citation.
	Fig. 5. Dynamically updated mouse data summary. Dynamically rendered matrix of available mouse datasets by age and anatomical source, color coded by experiment type.

References [+] :

Attanasio, Fine tuning of craniofacial morphology by distant-acting enhancers. 2013, Pubmed