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Harmonize with Scaffold specs #42

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Feb 26, 2025
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Harmonize with Scaffold specs #42

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c7ccc42
#38: Add mandatory license property to investigation profile
kMutagene Feb 25, 2025
d620755
#38: Make datePublished mandatory
kMutagene Feb 25, 2025
2b7921f
#38: Make description mandatory
kMutagene Feb 25, 2025
6d7debb
#39: make object/result optional
kMutagene Feb 25, 2025
db1eb78
LabProcess: make `agent` optional #41
kMutagene Feb 25, 2025
bac8ecf
PropertyValue: make `value` optional #40
kMutagene Feb 25, 2025
bbf9a05
fix some typos
kMutagene Feb 25, 2025
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21 changes: 11 additions & 10 deletions profile/isa_ro_crate.md
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Expand Up @@ -5,11 +5,11 @@
* Authors
* Florian Wetzels - https://orcid.org/0000-0002-5526-7138
* Lukas Weil - https://orcid.org/0000-0003-1945-6342
* Kevin Schneider - https://orcid.org/0000-0002-2198-5262
* Sebastian Beier - https://orcid.org/0000-0002-2177-8781
* Stuart Owen - https://orcid.org/0000-0003-2130-0865
* Timo Muehlhaus - https://orcid.org/0000-0003-3925-6778


## Overview

A significant part of the previous work on this [RO-Crate](https://www.researchobject.org/ro-crate/) profile for [ISA](https://isa-tools.org/index.html) was produced as part of the [Annotated Research Context (ARC)](https://nfdi4plants.org/content/learn-more/annotated-research-context.html) project, through [arc-to-rocrate](https://github.com/nfdi4plants/arc-to-rocrate).
Expand All @@ -25,7 +25,7 @@ The ISA RO-Crate has led to a few changes to [Bioschemas](https://bioschemas.org
**LabProtocol** - Has been redefined as a child of [HowTo](https://schema.org/HowTo) to make it clearer that it is intended to specifically describe the planned instructions for a lab process.

**LabProcess** - A new type has been defined as a child of [Action](https://schema.org/Action), to specifically describe the details and outcomes of an executed LabProtocol.
Thereby seperating the "what was planned" and "what happened" between LabProtocol and LabProcess respectively.
Thereby separating the "what was planned" and "what happened" between LabProtocol and LabProcess respectively.
A working group is working on the new type and adaptations of existing types.

An important change to the [Bioschemas](https://bioschemas.org/) specification that is still pending is the following:
Expand Down Expand Up @@ -84,10 +84,11 @@ Is based upon [schema.org/Dataset](https://schema.org/Dataset) and maps to the [
|additionalType|MUST|Text or URL|‘Investigation’ or ontology term to identify it as an Investigation|
|identifier|MUST|Text or URL|Identifying descriptor of the investigation (e.g. repository name).|
|name|MUST|Text|A title of the investigation (e.g. a paper title).|
|description|MUST|Text|A description of the investigation (e.g. an abstract).|
|license|MUST|Text or URL|The license under which the RO-Crate may be used. When no license information is available on crate creation, use the default string `'ALL RIGHTS RESERVED BY THE AUTHORS'` |
|datePublished|MUST|DateTime|When the Investigation was published. If the Investigation is not (yet) published, use the date of the crate creation as default value.|
|creator|SHOULD|[schema.org/Person](https://schema.org/Person)|The creator(s)/authors(s)/owner(s)/PI(s) of the investigation.|
|dateCreated|SHOULD|DateTime|When the Investigation was created|
|datePublished|SHOULD|DateTime|When the Investigation was published|
|description|SHOULD|Text|A description of the investigation (e.g. an abstract).|
|hasPart|SHOULD|[schema.org/Dataset](https://schema.org/Dataset) (Study)|An Investigation object should contain other datasets representing the *studies* of the investigation. They must follow the Study profile.|
|citation|COULD|[schema.org/ScholarlyArticle](https://schema.org/ScholarlyArticle)|Publications corresponding with this investigation.|
|comment|COULD|[schema.org/Comment](https://schema.org/Comment)|Comment|
Expand All @@ -105,7 +106,7 @@ Is based upon [schema.org/Dataset](https://schema.org/Dataset) and maps to the [
|@type|MUST|Text|must be '[schema.org/Dataset](https://schema.org/Dataset)'|
|additionalType|MUST|Text or URL|‘Study’ or ontology term to identify it as a Study|
|identifier|MUST|Text or URL|Identifying descriptor of the study.|
|name|MUSR|Text|A title of the study.|
|name|MUST|Text|A title of the study.|
|about|SHOULD|[bioschemas.org/LabProcess](https://bioschemas.org/LabProcess)|The experimental processes performed in this study.|
|creator|SHOULD|[schema.org/Person](https://schema.org/Person)|The performer of the study.|
|dateCreated|SHOULD|DateTime|When the Study was created|
Expand All @@ -131,7 +132,7 @@ Is based upon [schema.org/Dataset](https://schema.org/Dataset) and maps to the [
|about|SHOULD|[bioschemas.org/LabProcess](https://bioschemas.org/LabProcess)|The experimental processes performed in this assay.|
|creator|SHOULD|[schema.org/Person](https://schema.org/Person)|The performer of the experiments.|
|hasPart|SHOULD|[File](https://schema.org/MediaObject)|The data files resulting from the process sequence|
|measurementMethod|SHOULD|URL or [schema.org/DefinedTerm](https://schema.org/DefinedTerm)|Describes the type measurement e.g Complexomics or transcriptomics as an ontology term|
|measurementMethod|SHOULD|URL or [schema.org/DefinedTerm](https://schema.org/DefinedTerm)|Describes the type measurement e.g Complexomics or Transcriptomics as an ontology term|
|measurementTechnique|SHOULD|URL or [schema.org/DefinedTerm](https://schema.org/DefinedTerm)|Describes the type of technology used to take the measurement, e.g mass spectrometry or deep sequencing|
|comment|COULD|[schema.org/Comment](https://schema.org/Comment)|Comment|
|url|COULD|URL|The filename or path of the metadata file describing the assay. Optional, since in some contexts like an ARC the filename is implicit.|
Expand All @@ -147,9 +148,9 @@ Has the new Bioschemas DRAFT [bioschemas.org/LabProcess](https://bioschemas.org/
|@type |MUST|Text|must be '[bioschemas.org/LabProcess](https://bioschemas.org/LabProcess)'|
|@id|MUST|Text or URL|Could identify the process using the isa metadata filename and the protocol reference or process name.|
|name|MUST|Text| -|
|agent|MUST|[schema.org/Person](https://schema.org/Person)|The performer|
|object|MUST|[bioschemas.org/Sample](https://bioschemas.org/Sample) or [File](https://schema.org/MediaObject)|The input|
|result|MUST|[bioschemas.org/Sample](https://bioschemas.org/Sample) or [File](https://schema.org/MediaObject)|The output|
|object|SHOULD|[bioschemas.org/Sample](https://bioschemas.org/Sample) or [File](https://schema.org/MediaObject)|The input|
|result|SHOULD|[bioschemas.org/Sample](https://bioschemas.org/Sample) or [File](https://schema.org/MediaObject)|The output|
|agent|SHOULD|[schema.org/Person](https://schema.org/Person)|The performer|
|executesLabProtocol|SHOULD|[bioschemas.org/LabProtocol](https://bioschemas.org/LabProtocol)|The protocol executed|
|parameterValue|SHOULD|[schema.org/PropertyValue](https://schema.org/PropertyValue)|A parameter value of the experimental process, usually a key-value pair using ontology terms|
|endTime|SHOULD|DateTime||
Expand Down Expand Up @@ -209,7 +210,7 @@ It is based on [schema.org/PropertyValue](https://schema.org/PropertyValue) and
|@id|MUST|Text or URL||
|@type |MUST|Text|must be '[schema.org/PropertyValue](https://schema.org/PropertyValue)'|
|name|MUST|Text|Key name|
|value|MUST|Text|Value text or number|
|value|SHOULD|Text|Value text or number|
|propertyID|SHOULD|URL|Key ontology reference|
|additionalType|COULD|Text|Can be used to describe if the value is a factor, characteristic or parameter.|
|unitCode|COULD|URL|Unit ontology reference|
Expand Down