HED schema development guide¶
HED annotations consist of comma-separated terms drawn from a hierarchically structured vocabulary called a HED schema. The HED standard schema contains basic terms that are common across most human neuroimaging, behavioral, and physiological experiments. The HED ecosystem also supports (HED library schemas) to expand the HED vocabulary in a scalable manner to support specialized data.
Although you can create a private HED vocabulary for your
This guide describes how to begin developing your own schema.
This section describes how you can contribute to existing HED vocabularies or creating an entirely new one.
Setting up for schema development¶
Although schema developers work with HED schema in
.mediawiki format for ease in editing,
HED tools generally use XML versions of the HED schema.
Standard development process for XML schema.
Create or modify a
.mediawikifile containing the schema.
.mediawikifile using the HED online tools.
.xmlusing the HED online tools.
View in the expandable schema viewer to verify.
Design principles for schema¶
All HED schema (both the standard and library schemas) must conform to certain design principles in addition to properly validating.
Rules for HED schema design.
[Unique] Every term must be unique within the schema and must conform to the rules for HED schema terms.
[Meaningful] Schema terms should be readily understood by most users. The terms should not be ambiguous and should be meaningful in themselves without reference to their position in the schema hierarchy.
[Organized] If possible, a schema sub-tree should have no more than 7 direct subordinate sub-trees.
[Orthogonal] Terms that are used independently of one another should be in different sub-trees (orthogonality).
[Sub-classed]Every term in the hierarchy satistifies the is-a relationship with its parent. In other words if B has A as a parent in the schema hierarchy, then B is an example of A. Searching for A will also return B (search generality).
As in Python programming, we anticipate that many HED schema libraries may be defined and used, in addition to the base HED schema. Libraries allow individual research or clinical communities to annotate details of events in experiments designed to answer questions of interest to particular to those communities.
Since it would be impossible to avoid naming conflicts across schema libraries that may be built in parallel by different user communities, HED supports schema library namespaces. Users will be able to add library tags qualified with namespace designators. All HED schemas, including library schemas, adhere to semantic versioning.
Defining a schema¶
A HED library schema is defined in the same way as the base HED schema except that it has an
additional attribute name-value pair,
library="xxx" in the schema header. We will use as an
illustration a library schema for driving. Syntax details for a library schema are similar to
those for the base HED schema.
(See the HED schema format specification
for more details).
Example: Driving library schema (MEDIAWIKI template).
HED library="driving" version="1.0.0" !# start schema [... contents of the HED driving schema ...] !# end schema [... required sections specifying schema attribute definitions ...] !# end hed
The required sections specifying the schema attributes are unit-class-specification, unit-modifier-specification, value-class-specification, schema-attribute-specification, and property-specification.
Example: Driving library schema (XML template).
<?xml version="1.0" ?> <HED library="driving" version="1.0.0"> [... contents of the HED_DRIVE schema ... ] </HED>
The schema XML file should be saved as
HED_driving_1.0.0.xml to facilitate
specification in tools.
As part of the HED annotation process, users must associate a standard HED schema with their datasets. Users may also include tags from an arbitrary number of additional library schemas. For each library schema used to annotate a data recording, the user must associate a local name with the appropriate library schema name and version. Each library must be associated with a distinct local name within a recording annotations. The local names should be strictly alphabetic with no blanks or punctuation.
The user must pass information about the library schema and their associated local names to processing functions. HED uses a standard method of identifying namespace elements by prefixing HED library schema tags with the associated local names. Tags from different library schemas can be intermixed with those of the base schema. Since the node names within a library must be unique, annotators can use short form as well as fully expanded tag paths for library schema tags as well as those from the base-schema.
A colon (
:) is used to separate the qualifying local name from the remainder of the tag.
Notice that Action also appears in the standard HED schema. Identical terms may be used
in a library schema and the standard HED schema. Use of the same term implies a similar
purpose. Library schema developers should try not to reuse terms in the standard schema
unless the intention is to convey a close or identical relationship.
Attributes and classes¶
In addition to the specification of tags in the main part of a schema, a HED schema has sections that specify unit classes, unit modifiers, value classes, schema attributes, and properties. The rules for the handling of these sections for a library schema are as follows:
The required sections of a library schema are: the schema-specification, the unit-class-specification, the unit-modifier-specification, the value-class-specification section, the schema-attribute-specification section, and the property-specification. The library schema must include all required schema sections even if the content of these sections is empty.
Relation to base schema¶
Any schema attribute, unit class, unit modifier, value class, or property used in the library schema must be specified in the appropriate section of the library schema regardless of whether these appear in base schema. Validators check the library schema strictly on the basis of its own specification without reference to another schema.
HED only supports the schema properties listed in Table B.2: boolProperty,
unitClassProperty, unitModifierProperty, unitProperty, and valueClassProperty.
If the library schema uses one of these in the library schema specification, then its specification must appear in the property-specification section of the library schema.
The library schema may define unit classes and units as desired or include unit classes or units from the base schema. Similarly, library schema may define unit modifiers or reuse unit modifiers from the base schema. HED validation and basic analysis tools validate these based strictly on the schema specification and do not use any outside information for these.
The standard value classes (dateTimeClass, nameClass, numericClass, posixPath, textClass) if used, should have the same meaning as in the base schema. The hard-coded behavior associated with the starred ([*]) value classes will be the same. Library schema may define additional value classes and specify their allowed characters, but no additional hard-coded behavior will be available in the standard toolset. This does not preclude special-purpose tools from incorporating their own behavior.
The standard schema attributes (allowedCharacter, defaultUnits, extensionAllowed, recommended, relatedTag, requireChild, required, SIUnit, SIUnitModifier, SIUnitSymbolModifier, suggestedTag, tagGroup, takesValue, topLevelTagGroup, unique, unitClass, unitPrefix, unitSymbol, valueClass) should have the same meaning as in the base schema. The hard-coded behavior associated with the schema attributes will be the same. Library schema may define additional schema attributes. They will be checked for syntax, but no additional hard-coded behavior will be available in the standard toolset. This does not preclude special-purpose tools from incorporating their own behavior.
Regardless of whether a specification is in the standard schema or a library schema, HED tools can perform basic syntax checking.
Basic syntax checking for library schema.
All attributes used in the schema proper must be defined in the schema attribute section of the schema.
Undefined attributes cause an error in schema validation.
Similar rules apply to unit classes, unit modifiers, value classes, and properties.
Actual handling of the semantics by HED tools only occurs for entities appearing in the base schema.
Procedure for updating a schema.¶
As modifications to the HED schema are proposed, they are added to the PROPOSED.md file for the respective schema. As changes are accepted, they are incorporated into the prerelease version of the schema and added as part of the prerelease CHANGES.md. These files are located in the prerelease subdirectory for the respective schema. Examples of these files for the standard schema can be found in the standard schema prerelease directory. Expandable html view of the prerelease HED schema
Upon final review, the new HED schema is released, the XML file is copied to the hedxml directory, the mediawiki file is copied to the [**hed]
HED schema details¶
HED schema is the structured vocabulary from which HED annotations base on. HED annotations consist of comma-separated path strings, selected from the schema. In the newest versions of HED, all individual nodes in the vocabulary are unique, so users can annotate by simply giving the last node in the path string rather than the entire path string: Red instead of Attribute/Sensory/Sensory-property/Visual/Color/CSS-color/Red-color/Red.
This repository contains the HED schema specification, where discussions on schema terms and syntax are held via Github issue mechanism and where HED-supporting tools can find machine-readable format of the schema. The HED schema is available in MediaWiki and XML.
The MediaWiki markdown format, stored in
allows vocabulary developers to view and edit the vocabulary tree using a
human-readable markdown language available in Wikis and on GitHub repositories.
In addition, an expandable non-editable
HTML viewer is available
to help users explore the vocabulary.
All analysis and validation tools operate on an XML translation of the vocabulary
markdown document, stored in
The documentation on this page refers specifically to the HED vocabulary and supporting tools. Additional documentation is available on:
All of the HED software is open-source and organized into various repositories on the HED standards organization website: