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34 changes: 20 additions & 14 deletions docs/pages/resources/profiles.md
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Expand Up @@ -338,30 +338,36 @@ evolved from this profile to conform with RO-Crate 1.1's

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## ARC RO-Crate profile
## ARC RO-Crate profile collection

The [ARC RO-Crate profile](https://github.com/nfdi4plants/arc-ro-crate-profile) describes [Annotated Research Contexts](https://arc-rdm.org/) (ARC), developed by [DataPLANT](https://nfdi4plants.org/).
An ARC consists of [ISA](https://isa-specs.readthedocs.io/en/latest/isamodel.html) metadata describing the experimental setup and computational workflows given in CWL.
The current profile is a combination of the [ISA RO-Crate profile](https://github.com/nfdi4plants/isa-ro-crate-profile) and the [ARC CWL RO-Crate profile](https://github.com/nfdi4plants/arc-cwl-ro-crate-profile), see details below.
It requires the crate to follow the ISA Investigation profile on the top level.
The investigation object contains studies and assays from the ISA model, as well as computational workflows.
The core entity of both sub-profiles is the type `LabProcess` defined by [Bioschemas](https://bioschemas.org/), which is used to describe processes leading to data files in a parametrized way.
*This section is adapted from [ARC RO-Crate Profile Collection](https://nfdi4plants.github.io/arc-ro-crate-profile/profiles/) under the MIT license.*

How such an RO-Crate can be generated from an ARC is described in the [arc-to-rocrate](https://github.com/nfdi4plants/arc-to-rocrate) repository, which also contains scripts to perform the conversion.
The Annotated Research Context (ARC) RO-Crate Profile Collection is a set of profiles that focus on providing meaning and context to research data, aligning with the [ARC](https://arc-rdm.org/) framework developed by [DataPLANT](https://nfdi4plants.org/).

## ISA RO-Crate Profile
An ARC consists of [ISA](https://isa-specs.readthedocs.io/en/latest/isamodel.html) metadata describing an experimental setup, computational workflows, and executions of those workflows.

The [ISA RO-Crate profile](https://github.com/nfdi4plants/arc-to-rocrate/blob/main/profiles/investigation.md) describes experimental data in plant sciences that is annotated by metadata following the [ISA model](https://isa-specs.readthedocs.io/en/latest/isamodel.html).
The collection contains five profiles: three "base" profiles, plus two further profiles that extend and combine them.

### Base profiles

The three "base" profiles focus on distinct aspects of research context, and can be useful beyond the ARC context:

* [Administrative Crate](https://nfdi4plants.github.io/arc-ro-crate-profile/profiles/administrative_crate/) for administrative information - creators, contributors, and rights holders
* [Datamap Crate](https://nfdi4plants.github.io/arc-ro-crate-profile/profiles/datamap_crate/) for structural and semantic details of data files and fragments of data files.
* [Process Core Crate](https://nfdi4plants.github.io/arc-ro-crate-profile/profiles/process_core_crate/) for capturing processes that generate and transform research entities.

### ISA RO-Crate Profile

The [ISA RO-Crate profile](https://nfdi4plants.github.io/arc-ro-crate-profile/profiles/isa_ro_crate/) describes experimental data in plant sciences that is annotated by metadata following the [ISA model](https://isa-specs.readthedocs.io/en/latest/isamodel.html).
Such datasets consist of three types of data entities: `Investigation`, `Study` and `Assay`.
The profile adds requirements of the crate such that the data folders match the Investigation, Study and Assay objects of the [ISA model](https://isa-specs.readthedocs.io/en/latest/isamodel.html).
The description of experimental processes that produce the data uses the [Bioschemas](https://bioschemas.org/) type `LabProcess` as its core entity.
It describes how data and samples are derived from each other in a graph model based on formalized parameters as key-value pairs.
Profiles for all included types can be found in the [full version](https://github.com/nfdi4plants/isa-ro-crate-profile).
The profile builds on Administrative Crate and Process Core Crate above.

## ARC CWL RO-Crate Profile
### ARC Workflow Run RO-Crate Profile

The [ARC CWL RO-Crate profile](https://github.com/nfdi4plants/arc-cwl-ro-crate-profile) extends the existing [Workflow Run Crate profile](https://w3id.org/ro/wfrun/workflow/) in an ARC-specific context.
It uses the same process graph types (`LabProtocol`,`LabProcess`) as the [ISA profile](#isa-ro-crate-profile) to further annotate parameters of workflows (equivalent to protocols in ISA) and runs (equivalent to processes in ISA).
The [ARC Workflow Run RO-Crate Profile](https://nfdi4plants.github.io/arc-ro-crate-profile/profiles/wr_ro_crate/) combines the existing [Workflow Run Crate profile](https://w3id.org/ro/wfrun/workflow/) and the ISA RO-Crate profile in an ARC-specific context.

## Electronic Lab Notebook (ELN)

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