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Mapping the ISA Process Model to RO-Crate/schema.org/bioschemas

Abstract/simplified version of the core ISA Process Model with its mapping to schema.org/bioschemas types (green types and properties are new proposals, blue types and properties exist in bioschemas, red properties are optional):

flowchart TD

dataset[<h2>Study/Assay=Dataset</h3>- <font color=green>process_sequence=processSequence</font><br>- hasPart<br>- ...]

Process[<h2>Process=<font color=green>LabProcess</font></h2>- name<br>- performer=agent<br>- date=endTime<br>- inputs=object<br>- outputs=result<br>- <font color=green>parameter_values=parameterValues</font><br>- <font color=green>executes_protocol=executesProtocol</font>]

Protocol[<h2>Protocol=<font color=blue>LabProtocol</font></h2>- name<br>- <font color=blue>protocol_type=purpose</font><br>- <font color=blue>components=labEquipment/reagent/software</font><br>- <font color=red>protocol_parameters=?</font><br>- version<br>- comment<br>- description<br>- url]

BioSample[<h2>Source/Sample/Material=<font color=blue>Sample</font></h2>- name<br>- characteristics=additionalProperty<br>- factors=additionalProperty<br>- <font color=red>derivesFrom=?</font>]

DataFile[<h2>Data=MediaObject</h2>- name<br>- <font color=red>type=?</font><br>- comment]

ont[<h2>OntologyAnnotation=DefinedTerm</h2>- annotationValue=name<br>termSource=inDefinedTermSet<br>- termAccession=termCode]

prop[<h2>ParameterValue=PropertyValue</h2>- category=propertyID/name<br>- unit=unitCode/unitText<br>- value=valueReference/value]

dataset --hasPart--> dataset
dataset --hasPart----> DataFile
dataset --process_sequence--> Process

Process --"output"---> DataFile
Process --"output"--> BioSample
Process --input--> BioSample
Process --executesProtocol--> Protocol
Process --parameterValues---> prop

BioSample --derivesFrom--> BioSample
BioSample --additionalProperty--> prop

Protocol --protocolType---> ont
Protocol --parameters---> ont

prop --category--> ont
prop --value--> ont
prop --unit--> ont
Loading

When only considering the core "functionality" of ISA, seven types need to be mapped: Study/Assay (merged since they both represent a process sequence with additional metadata), Process, Protocol, Source/Sample (merged since a source is a sample without factors), Data, OntologyAnnotation, and ParameterValue (representing all forms of values, e.g. FactorValue, MaterialAttributeValue, etc.).

Study/Assay should be a Dataset, as required by RO-Crate. Data should be a MediaObject/File, again as required by RO-Crate.

For Material, the type BioSample already exists in bioschemas. An OntologyAnnotation can be mapped to DefinedTerm and a ParameterValue to PropertyValue.

Apart from the process sequence, only minor changes are necessary for these types (more details later). Mapping the process sequence is the core problem, which we explain now.

Main types missing

In terms of ISA, the LabProtocol type is an incomplete mixture of two things at once:

  • Protocol (properties protocolPurpose, protocolAdvantage, protocolOutcome, etc.)
  • Process (sampleUsed, executionTime).

It can also interpreted as a ProcessSequence, considering the step property.

For a Process the following concepts are missing:

  • output/"sampleProduced"
  • parameters and their values
  • inputs and outputs might both either be physical entities (samples) or digital entities (data)
  • maybe executed protocol

For a Protocol the following concepts are missing:

  • parameters

Further minor problems when mapping these ISA types to a LabProtocol:

  • labEquipment/reagent/software are components in ISA, but components are CV key-value pairs (in particular in the ARC), which would make PropertyValue more suitable than DefinedTerm
  • protocolType does not exist in LabProtocol
  • nextProcess/previousProcess do not exist in LabProtocol

Parameter Values

ParameterValues in ISA are very generic key-value pairs. Thus, the PropertyValue type seems to fit well.

However, in schema.org, only the key (valueReference) can be an ontology annotation (DefinedTerm). In ISA, the value and the unit can also be ontology terms.

In a PropertyValue, the value can only be StructuredValue, not DefinedTerm. The unit only has a code and a text, not an ontology reference.

Our desired schema for PropertyValue would look like this:

{
    "valueReference" : {
        "anyOf" : [
            {"$ref": "DefinedTerm_schema.json#"},
            ...
        ]
    },
    "value": {
        "anyOf" : [
            { "$ref": "DefinedTerm_schema.json#"},
            { "type": "string"},
            { "type": "number"}
        ]
    },
    "unitReference": {
        "$ref": "DefinedTerm_schema.json#"
    }
}

Type Definitions

According to the problems decribed above, we propose the following new or adapted types: