Metadata Reporting Standards
Documents Provided
The HuBMAP Metadata Reporting Standards include schemas for both descriptive and structural metadata. The descriptive metadata provides a standardized description of samples, experiments, and processing context. The structural metadata provides standardized file organization, including hierarchical file and directory specifications, file type and naming conventions.
While these standards vary slightly by experiment type, they are all delivered using the same set of files and file formats, detailed below.
metadata.jsonld (JSON-LD file)
Descriptive Metadata Schema as JSON
This JSON schema defines the structure and validation rules for metadata instances generated from a metadata template in the CEDAR framework. It is produced by the CEDAR Workbench and reflects the template's OpenView representation.
The schema follows JSON Schema conventions and includes a JSON-LD context so each field has semantic meaning. It defines the available properties, required fields, data types, and validation constraints used to check submitted metadata.
Each schema supports template metadata, field definitions, validation constraints, and the UI configuration used to render metadata entry forms.
deprecated.json (JSON file)
Deprecated Descriptive Schema Fields
This file tracks field names that have been retired across the schema history. When a field is removed from any schema version, it is added here so the list becomes an accumulating record of retired fields, not just the current version.
It helps consumers identify legacy fields that may still appear in older datasets even though they are no longer supported by the current schema.
metadata.yml (YAML file)
Descriptive Metadata Schema as YAML
This file provides a simplified YAML version of the descriptive metadata schema. It is intended to be easier for humans to read while still preserving a structured format that can be used computationally.
metadata.xlsx (Microsoft Excel file)
Descriptive Metadata Schema as Excel Spreadsheet Template
The Excel template is generated from a CEDAR metadata template and is designed for bulk submission workflows. It offers a table-based format for collecting multiple records and includes supporting sheets for permitted values and standardized term identifiers.
Those supporting sheets feed the dropdown choices in the data-entry sheet, which helps users select valid terms consistently, reduce manual entry errors, improve data quality, and make bulk submission easier.
The template is compatible with the Metadata Spreadsheet Validator, which can be used to verify records before submission.
metadata.tsv (tab-separated values file)
Descriptive Metadata Schema as Tab-Separated Values Template
The TSV template is also generated from a CEDAR metadata template and is intended for bulk submission in a lightweight, machine-readable format. It provides one row per record, with each column corresponding to a metadata field in the template.
Like the spreadsheet version, it is compatible with the Metadata Spreadsheet Validator for checking the correctness of bulk metadata records before submission.
directory.md (markdown file)
Markdown File Detailing Structural Metadata
This markdown file documents the structural metadata schema specification and is organized into three parts:
- File Organization Schema: a table of hierarchical file and directory specifications, including file type, naming conventions, and required status.
- Directory Tree: a more human-readable view of the directory structure.
- YAML: a YAML version of the file organization schema that can be used with the HuBMAP Ingest Validation Tools.
empty_tree.zip (ZIP archive)
ZIP Archive Containing Directory Structure
This archive contains the empty directory structure without any files. It preserves the metadata standards' hierarchical folder layout and, when unzipped, creates the dataset-specific directory tree on the destination system.
The archive can be used as a framework for structuring files so they conform to the dataset-specific file hierarchy standard.
