FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community.

P W Harrison,J Fan,A L Archibald,L Clarke,D Richardson,P Flicek,C J Schmidt,D Zerbino,G Cochrane

doi:10.1111/age.12736

Abstract

SummaryThe Functional Annotation of ANimal Genomes (FAANG) project aims, through a coordinated international effort, to provide high quality functional annotation of animal genomes with an initial focus on farmed and companion animals. A key goal of the initiative is to ensure high quality and rich supporting metadata to describe the project's animals, specimens, cell cultures and experimental assays. By defining rich sample and experimental metadata standards and promoting best practices in data descriptions, deposition and openness, FAANG champions higher quality and reusability of published datasets. FAANG has established a Data Coordination Centre, which sits at the heart of the Metadata and Data Sharing Committee. It continues to evolve the metadata standards, support submissions and, crucially, create powerful and accessible tools to support deposition and validation of metadata. FAANG conforms to the findable, accessible, interoperable, and reusable (FAIR) data principles, with high quality, open access and functionally interlinked data. In addition to data generated by FAANG members and specific FAANG projects, existing datasets that meet the main—or more permissive legacy—standards are incorporated into a central, focused, functional data resource portal for the entire farmed and companion animal community. Through clear and effective metadata standards, validation and conversion software, combined with promotion of best practices in metadata implementation, FAANG aims to maximise effectiveness and inter‐comparability of assay data. This supports the community to create a rich genome‐to‐phenotype resource and promotes continuing improvements in animal data standards as a whole.

Highlights

The Functional Annotation of ANimal Genomes (FAANG) project is a global initiative aiming to accelerate research in genome biology by creating a rich genome-to-phenome resource with a particular focus on farmed and companion animals (Andersson et al 2015; Tuggle et al 2016)
The starting point for the standards developed by the working group were those developed as part of the EU-funded BLUEPRINT project, a component project of the International Human Epigenome Consortium, which focused on reference epigenomes from cell types and diseases of the haematopoietic system (Martens & Stunnenberg 2013; Fernandez et al 2016)
The web tabular representation is automatically generated from the underlying master JavaScript Object Notation (JSON) rule-set documents held in the GitHub repository, ensuring that both versions remain completely in sync

Summary

The Functional Annotation of ANimal Genomes (FAANG) project aims, through a coordinated international effort, to provide high quality functional annotation of animal genomes with an initial focus on farmed and companion animals. FAANG has established a Data Coordination Centre, which sits at the heart of the Metadata and Data Sharing Committee It continues to evolve the metadata standards, support submissions and, crucially, create powerful and accessible tools to support deposition and validation of metadata. Through clear and effective metadata standards, validation and conversion software, combined with promotion of best practices in metadata implementation, FAANG aims to maximise effectiveness and inter-comparability of assay data. This supports the community to create a rich genome-to-phenotype resource and promotes continuing improvements in animal data standards as a whole. FAIR principles, farmed animals, functional annotation, genome to phenome, livestock, metadata validation

Introduction

Conclusion