7. Library schema

The variety and complexity of events in electrophysiological experiments makes full documentation challenging. As more experiments move out of controlled laboratory environments and into less controlled virtual and real-world settings, the terminology required to adequately describe events has the potential to grow exponentially.

In addition, experiments in any given subfield can contribute to pressure to add overly-specific terms and jargon to the schema hierarchy—for example, adding musical terms to tag events in music-based experiments, video markup terms for experiments involving movie viewing, traffic terms for experiments involving virtual driving, and so forth.

Clinical fields using neuroimaging also have their own specific vocabularies for describing data features of clinical interest (e.g., seizure, sleep stage IV). Including these discipline-specific terms quickly makes the standard HED schema unwieldy and less usable by the broader user community.

Third generation HED instead introduces the concept of the HED library schema. To use a programming analogy, when programmers write a Python module, the resulting code does not become part of the Python language or core library. Instead, the module becomes part of a library used in conjunction with core modules of the programming language.

Similar to the design principles imposed on function names and subclass organization in software development, HED library schemas must conform to some basic rules:

Rules for HED library schema design.

  1. Library schema must be given a name containing only alphabetic chararacters. This name must appear in the schema header line in the required format.

  2. The library must use semantic versioning and follow the versioning update rules used by the HED standard schema.

  3. Every term must be unique within the library schema and must conform to the rules for HED schema terms.

  4. 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.

  5. If possible, no schema sub-tree should have more than 7 direct subordinate sub-trees.

  6. Terms that are used independently of one another should be in different sub-trees (orthogonality).

  7. The schema should include the schema attributes, unit classes, unit modifiers, value classes, and schema properties present in the standard HED schema.

As in Python programming, we anticipate that many HED schema libraries may be defined and used, in addition to the standard HED schema. Libraries allow individual research communities to annotate details of events in experiments designed to answer questions of interest to particular research or clinical 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.

In general, library schema developers should include the auxiliary schema classes from the standard HED schema: the schema attributes, unit classes, unit modifiers, value classes, and schema properties. The HED tools support these auxiliary classes but in general would not support special handling of added classes beyond basic verification.

If your schema requires schema classes that are not available in the standard HED schema and would like these classes to be supported, please make a request using the HED specification issues forum.

Please do not duplicate tags in the Property/Informational-property and Relation subtrees, as many of these tags have specialized uses and tool support. In particular, Definition, Def, Def-expand and Event-context should NEVER be duplicated in a library schema.

7.1. Defining a schema

A HED library schema is defined in the same way as the standard 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 standard HED schema. (See Appendix A: Schema format 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.

7.2. Schema namespaces

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 alphanumeric 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 standard 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 standard HED schema.

Example: Driving library schema example tags.

dp:Action/Drive/Change-lanes
dp:Drive/Change-lanes
dp:Change-lanes

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.

7.3. 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:

7.3.1. Required sections

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.

7.3.2. Relation to standard HED 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 the standard HEd schema. Validators check the library schema strictly on the basis of its own specification without reference to another schema.

7.3.3. Schema properties

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.

7.3.4. Unit classes

The library schema may define unit classes and units as desired or include unit classes or units from the standard HED schema. Similarly, library schema may define unit modifiers or reuse unit modifiers from the standard HED schema. HED validation and basic analysis tools validate these based strictly on the schema specification and do not use any outside information for these.

7.3.5. Value classes

The standard value classes (dateTimeClass[], nameClass, numericClass[], posixPath[], textClass[]) if used, should have the same meaning as in the standard HED 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.

7.3.6. Schema attributes

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 standard HED 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.

7.3.7. Syntax checking

Regardless of whether a specification is in the standard HED schema or not, HED tools can perform basic syntax checking.

Basic syntax checking for library schema.

  1. All attributes used in the schema proper must be defined in the schema attribute section of the schema.

  2. Undefined attributes cause an error in schema validation.

  3. Similar rules apply to unit classes, unit modifiers, value classes, and properties.

  4. Actual handling of the semantics by HED tools only occurs for entities appearing in the standard HED schema.

7.4. library schemas in BIDS

The most common use case (for 99.9% of the HED users) is to tag events using one of the standard HED schemas (preferably the latest one) available in the hedxml directory of the hed-specification repository of the hed-standard organization on GitHub. The standard schemas are available at: https://github.com/hed-standard/hed-specification/tree/master/hedxml.

This section explains the changes that are being proposed in BIDS to accommodate access to HED library schemas in addition to the standard HED schemas. This section will be updated as the proposals progress though the BIDS review process. The initial proposal only supports official standard schemas available at https://github.com/hed-standard/hed-specification/tree/master/hedxml and official library schemas available at https://github.com/hed-standard/hed-schema-library/tree/main/library_schemas.

Standard schemas are referenced by their version number (e.g., 8.0.0), while library schema are referenced by a combination of library name and version number (e.g., score_0.0.1).

The major change proposed to the BIDS specification is to allow the value associated with the "HEDVersion" key in the dataset_description.json file to be an array rather than a string expressing the HED version. This proposed change will allow users more flexibility in specifying the standard HED schema and will accommodate an arbitrary number of library schemas. The different cases are illustrated in the following examples.

The original BIDS specification just allows the standard HED schema, which is named using a version number.

Example: Using just the standard HED schema in BIDS.

{
    "Name": "A wonderful experiment",
    "BIDSVersion": "1.6.0",
    "HEDVersion":  "8.0.0"
}

The following example specifies that version 8.0.0 of the standard HED schema is to be used in addition to two library schemas: the score library version 0.0.1 and the testlib library version 1.0.2.

Example: Proposed specification of library schema in BIDS.

{
    "Name": "A wonderful experiment",
    "BIDSVersion": "1.6.0",
    "HEDVersion": ["8.0.0", "sc:score_0.0.1", "ts:testlib_1.0.2"]
}

Based on the above description tools will download:

  1. The standard HED schema:
    https://github.com/hed-standard/hed-specification/tree/master/hedxml/HED8.0.0.xml.

  2. The HED score library schema version 0.0.1:
    https://github.com/hed-standard/hed-schema-library/tree/main/library_schemas/score/hedxml/HED_score_0.0.1.xml.

  3. The HED testlib library schema version 1.0.2:
    https://github.com/hed-standard/hed-schema-library/tree/main/library_schemas/testlib/hedxml/HED_testlib_1.0.2.xml.

A schema browser is available for each library. For example the schema browser for the score library schema is available at https://www.hedtags.org/display_hed_score.html.

Given the HEDVersion specification from the previous example, annotators can use any combination of tags from the three indicated schemas. In this example the standard HED schema version appears without a prefix in the version specification, so tags from this schema may appear directly in the annotation.

The sc and ts are local names used to distinguish tags from the additional schema. Tags from the score library schema are of the form sc:XXX where XXX is a tag from the score schema. Similarly, tags from the testlib library schema are of the form ts:YYY where YYY is a tag from the testlib schema.

In the following sample annotation Data-feature is from the standard HED schema, while Photomyogenic-response and Wicket-spikes are from the score library.

Example: An annotation using tags from two schemas.

Data-feature, sc:Photomyogenic-response, sc:Wicket-spikes

The array specification of the schema versions can have at most one version appearing without a colon prefix.

For some applications, the annotator will only want to use a particular library schema. The following example specifies that only the score library will be used. No prefixes are required in this case.

Example: Use of only the score library schema for tagging.

{
    "Name": "A wonderful experiment",
    "BIDSVersion": "1.6.0",
    "HEDVersion": "score_0.0.1"
}