This page contains descriptions of CFDE consortium standards, protocols, user guides, and other documents generated by the CFDE centers, partnerships, and Data Coordination Centers (DCCs).
These documents are intended to provide CFDE-partnered DCCs, other Common Fund (CF) programs, and the broader research community with documentation about digital object products developed by the CFDE. While many of these documents were created within the context of the CFDE, they may be useful and generalizable for other researchers who are interested in using or interoperating with CF datasets, or who are interested in improving the FAIRness of their own resources.
CFDE Data and Metadata Submission System
The CFDE Workbench Data Resource Portal allows users to download DCC datasets, files, and interoperability assets via the Data Matrix. Representatives from each DCC are encouraged to contribute assets from their CF programs by creating an account for submitting and approving uploads to the CFDE Workbench. Currently, the submission system accepts C2M2 metadata packages, entity matrix transpose (XMT) files, knowledge graph assertions, attribute tables, SmartAPI and OpenAPI specifications, extract-transform-load (ETL) scripts, entity pages, PWB metanodes, and chatbot specifications.
Learn more about submitting to the Data Resource Portal in the Contribution Guide.
C2M2
The Crosscut Metadata Model (C2M2) was designed to standardize metadata annotations across Common Fund DCCs by the original CFDE Coordination Center. C2M2 datapackage files are usually a zipfile containing a set of TSV files already standardized to a set of known ontologies, along with a single JSON schema.
Learn more about generating a C2M2 datapackage here.
RNA-seq Standard Pipeline
The CFDE RNA-seq Partnership aims to harmonize diverse RNA-seq datasets across the CFDE to improve their interoperability and reusability for the broader scientific research community. To this end, the partnership is developing common pipelines for both bulk and single cell RNA-seq data analysis, with the end goal of building a large, readily accessible, and harmonized resource of RNA-seq datasets and processing tools from various DCCs and CFDE projects.
More information about the standardized bulk and single cell RNA-seq pipelines will be available soon.
OpenAPI & SmartAPI
The OpenAPI specification allows for the standardization of application programming interfaces (APIs), and facilitates their interoperability.
The SmartAPI project builds on top of the OpenAPI specifications to maximize the findability, accessibility, interoperability, and reusability (FAIRness) of web-based tools, especially those within the biomedical sphere. Through richer metadata descriptions, SmartAPI enables users to search and use a connected network of tools.
Learn more about generating an OpenAPI or SmartAPI specification here.
Knowledge Graph Assertions
The CFDE Data Distillery Partnership aims to integrate data assertions across DCCs into a functional knowledge graph for knowledge query and discovery. The partnership has collected "distilled" data relationships from each DCC to be unified in a knowledge graph model with controlled ontology and vocabulary terms for exploring pre-defined, biologically relevant use cases.
Learn more about generating Data Distillery Knowledge Graph Assertions here.
FAIR Evaluations with FAIRshake
The FAIRshake toolkit enables manual and automated assessments of the findability, accessibility, interoperability, and reusability (FAIRness) of digital resources. FAIRshake provides community-driven metrics and rubrics for evaluation, and visualizes the results with a characteristic embeddable insignia. The primary goal of FAIRshake is to enable researchers and developers to objectively measure and improve the FAIRness of their tools.
Learn more about performing FAIR assessments with FAIRshake here.
Playbook Metanodes
The Playbook Workflow Builder (PWB) is a web-based knowledge resolution platform being developed by the CFDE Workflow Playbook Partnership and consisting of a growing network of datasets, semantically annotated API endpoints, and visualization tools from across the CFDE. Users can construct workflows from the individual building blocks, termed "metanodes", with little effort or technical expertise required.
Learn more about building PWB metanodes here.