Getting started with rocrateR

library(rocrateR)

Introduction

Reproducible research requires more than sharing files. We also need structured metadata describing:

What is an RO-Crate?

An RO-Crate is:

The metadata describes all files and their relationships using a graph model.

RO-Crate Structure

Example:

my_crate/
├── ro-crate-metadata.json
├── data/
│   └── results.csv
└── analysis.R

1. Functions Overview

Function Purpose
rocrate() Create an empty or initialized RO-Crate
entity() Define a new entity (Person, Dataset, etc.)
add_entity() / add_entities() Add entities to a crate. Note that add_entities() is now deprecated and add_entity() is preferred.
get_entity() Retrieve entities by @id or @type
remove_entity() / remove_entities() Remove one or more entities. Note that remove_entities() is now deprecated and remove_entity() is preferred.
load_rocrate() Higher level function that loads an RO-Crate from metadata file, crate directory or BagIt archive
write_rocrate() Save RO-Crate to disk
bag_rocrate() / is_rocrate_bag() / unbag_rocrate() Bagging and unbagging RO-Crates
validate_rocrate() Validate RO-Crate and generate report

2. First RO-Crate

The following command creates an RO-Crate Metadata descriptor (ro-crate-metadata.json). This should be stored inside the root (./) of your RO-Crate.

# library(rocrateR)
my_first_ro_crate <- rocrateR::rocrate()

This object is a list with the basic components of an RO-Crate. It can be visualised in the console as follows:

my_first_ro_crate
#> {
#>   "@context": "https://w3id.org/ro/crate/1.2/context",
#>   "@graph": [
#>     {
#>       "@id": "ro-crate-metadata.json",
#>       "@type": "CreativeWork",
#>       "about": {
#>         "@id": "./"
#>       },
#>       "conformsTo": {
#>         "@id": "https://w3id.org/ro/crate/1.2"
#>       }
#>     },
#>     {
#>       "@id": "./",
#>       "@type": "Dataset",
#>       "name": "",
#>       "description": "",
#>       "datePublished": "2026-04-07",
#>       "license": {
#>         "@id": "http://spdx.org/licenses/CC-BY-4.0"
#>       }
#>     }
#>   ]
#> }

This object can be saved to disk using the following command:

my_first_ro_crate |>
  rocrateR::write_rocrate("/path/to/ro-crate/ro-crate-metadata.json")

For example, using a temporary directory:

tmp <- file.path(tempdir(), "ro-crate-metadata.json")
my_first_ro_crate |>
  rocrateR::write_rocrate(tmp)

# load lines / flat file
readLines(tmp)
#>  [1] "{"                                                         
#>  [2] "  \"@context\": \"https://w3id.org/ro/crate/1.2/context\","
#>  [3] "  \"@graph\": ["                                           
#>  [4] "    {"                                                     
#>  [5] "      \"@id\": \"ro-crate-metadata.json\","                
#>  [6] "      \"@type\": \"CreativeWork\","                        
#>  [7] "      \"about\": {"                                        
#>  [8] "        \"@id\": \"./\""                                   
#>  [9] "      },"                                                  
#> [10] "      \"conformsTo\": {"                                   
#> [11] "        \"@id\": \"https://w3id.org/ro/crate/1.2\""        
#> [12] "      }"                                                   
#> [13] "    },"                                                    
#> [14] "    {"                                                     
#> [15] "      \"@id\": \"./\","                                    
#> [16] "      \"@type\": \"Dataset\","                             
#> [17] "      \"name\": \"\","                                     
#> [18] "      \"description\": \"\","                              
#> [19] "      \"datePublished\": \"2026-04-07\","                  
#> [20] "      \"license\": {"                                      
#> [21] "        \"@id\": \"http://spdx.org/licenses/CC-BY-4.0\""   
#> [22] "      }"                                                   
#> [23] "    }"                                                     
#> [24] "  ]"                                                       
#> [25] "}"

# delete temporary file
unlink(tmp)

3. Including additional entities

In the previous section we created a very basic RO-Crate with the rocrateR::rocrate() function; however, you are likely to include additional entities in your RO-Crate. Entities must contain at least two components @id and @type (see https://w3id.org/ro/crate/1.2/ for details).

For example, a contextual entity can be defined as follows:

# create entity for an organisation
organisation_uol <- rocrateR::entity(
  id = "https://ror.org/04xs57h96",
  type = "Organization",
  name = "University of Liverpool",
  url = "http://www.liv.ac.uk"
)

# create an entity for a person
person_rvd <- rocrateR::entity(
  id = "https://orcid.org/0000-0001-5036-8661",
  type = "Person",
  name = "Roberto Villegas-Diaz"
)

These entities can be attached to an RO-Crate using the rocrateR::add_entity() function:

my_second_ro_crate <- rocrateR::rocrate() |>
  rocrateR::add_entity(person_rvd) |>
  rocrateR::add_entity_value(
    id = "./", 
    key = "author", 
    value = list(`@id` = person_rvd$`@id`)
  ) |>
  rocrateR::add_entity(organisation_uol) |>
  rocrateR::add_entity_value(
    id = "https://orcid.org/0000-0001-5036-8661",
    key = "affiliation",
    value = list(`@id` = organisation_uol$`@id`)
  )

Alternatively, the same result can be achieved with the following code:

my_second_ro_crate <- rocrateR::rocrate(person_rvd, organisation_uol) |>
  rocrateR::add_entity_value(id = "./", key = "author", value = list(`@id` = person_rvd$`@id`))
my_second_ro_crate
#> {
#>   "@context": "https://w3id.org/ro/crate/1.2/context",
#>   "@graph": [
#>     {
#>       "@id": "ro-crate-metadata.json",
#>       "@type": "CreativeWork",
#>       "about": {
#>         "@id": "./"
#>       },
#>       "conformsTo": {
#>         "@id": "https://w3id.org/ro/crate/1.2"
#>       }
#>     },
#>     {
#>       "@id": "./",
#>       "@type": "Dataset",
#>       "name": "",
#>       "description": "",
#>       "datePublished": "2026-04-07",
#>       "license": {
#>         "@id": "http://spdx.org/licenses/CC-BY-4.0"
#>       },
#>       "author": {
#>         "@id": "https://orcid.org/0000-0001-5036-8661"
#>       }
#>     },
#>     {
#>       "@id": "https://orcid.org/0000-0001-5036-8661",
#>       "@type": "Person",
#>       "name": "Roberto Villegas-Diaz",
#>       "affiliation": {
#>         "@id": "https://ror.org/04xs57h96"
#>       }
#>     },
#>     {
#>       "@id": "https://ror.org/04xs57h96",
#>       "@type": "Organization",
#>       "name": "University of Liverpool",
#>       "url": "http://www.liv.ac.uk"
#>     }
#>   ]
#> }

4. Wrangle RO-Crate

Previously, we covered how to include additional entities, other valid operations are to extract (rocrateR::get_entity()) and remove (rocrateR::remove_entities()).

4.1. Set up

# create basic RO-Crate
basic_ro_crate <- rocrateR::rocrate()

# create some entities for a project and datasets
dataset_entities <- seq_len(2) |>
  lapply(\(x) rocrateR::entity(x, type = "Dataset", name = paste0("Data ", x)))
project_entity <- rocrateR::entity(
  "#proj101", 
  type = "Project", 
  name = "Project 101",
  hasPart = dataset_entities |>
      lapply(\(x) list(`@id` = x[["@id"]]))
  )

# add project and entities to the RO-Crate
basic_ro_crate <- basic_ro_crate |>
  rocrateR::add_entity(project_entity) |>
  # note that here we are using `rocrateR::add_entities` and `rocrateR::add_entity`
  rocrateR::add_entities(dataset_entities)
#> Warning: `add_entities()` was deprecated in rocrateR 0.1.0.
#> ℹ Please use `add_entity()` instead.
#> This warning is displayed once per session.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.

basic_ro_crate
#> {
#>   "@context": "https://w3id.org/ro/crate/1.2/context",
#>   "@graph": [
#>     {
#>       "@id": "ro-crate-metadata.json",
#>       "@type": "CreativeWork",
#>       "about": {
#>         "@id": "./"
#>       },
#>       "conformsTo": {
#>         "@id": "https://w3id.org/ro/crate/1.2"
#>       }
#>     },
#>     {
#>       "@id": "./",
#>       "@type": "Dataset",
#>       "name": "",
#>       "description": "",
#>       "datePublished": "2026-04-07",
#>       "license": {
#>         "@id": "http://spdx.org/licenses/CC-BY-4.0"
#>       }
#>     },
#>     {
#>       "@id": "#proj101",
#>       "@type": "Project",
#>       "name": "Project 101",
#>       "hasPart": [
#>         {
#>           "@id": 1
#>         },
#>         {
#>           "@id": 2
#>         }
#>       ]
#>     },
#>     {
#>       "@id": 1,
#>       "@type": "Dataset",
#>       "name": "Data 1"
#>     },
#>     {
#>       "@id": 2,
#>       "@type": "Dataset",
#>       "name": "Data 2"
#>     }
#>   ]
#> }

4.2. Extract entity

We can extract entities via the @id, @type or both:

4.2.1. Extract using @id

basic_ro_crate_project <- basic_ro_crate |>
  rocrateR::get_entity(id = "#proj101")

basic_ro_crate_project
#> [[1]]
#> <RO-Crate entity>
#>  @id = '#proj101'
#>  @type = 'Project'

4.2.2. Extract using @type

basic_ro_crate_datasets <- basic_ro_crate |>
  rocrateR::get_entity(type = "Dataset")

basic_ro_crate_datasets
#> [[1]]
#> <RO-Crate entity>
#>  @id = './'
#>  @type = 'Dataset'
#> 
#> [[2]]
#> <RO-Crate entity>
#>  @id = '1'
#>  @type = 'Dataset'
#> 
#> [[3]]
#> <RO-Crate entity>
#>  @id = '2'
#>  @type = 'Dataset'

4.2.3. Extract using @id and @type

basic_ro_crate_dataset_root <- basic_ro_crate |>
  rocrateR::get_entity(id = "./", type = "Dataset")

basic_ro_crate_dataset_root
#> [[1]]
#> <RO-Crate entity>
#>  @id = './'
#>  @type = 'Dataset'

4.3. Remove entity

Similarly, we can remove entities from an RO-Crate:

4.3.1. Remove using scalar @id

basic_ro_crate_alt <- basic_ro_crate |>
  rocrateR::remove_entity("#proj101")

4.3.2. Remove using entity object

basic_ro_crate_alt <- basic_ro_crate |>
  rocrateR::remove_entity(project_entity)

4.3.3. Remove multiple entities

basic_ro_crate_alt <- basic_ro_crate |>
  rocrateR::remove_entity(dataset_entities)

5. Create an RO-Crate Bag

Here we will explore the BagIt file packaging format, which is the recommended to use for bagging RO-Crates. BagIt is described in RFC 8493:

[BagIt is] … a set of hierarchical file layout conventions for storage and transfer of arbitrary digital content. A “bag” has just enough structure to enclose descriptive metadata “tags” and a file “payload” but does not require knowledge of the payload’s internal semantics. This BagIt format is suitable for reliable storage and transfer.

In this package, the function rocrateR::bag_rocrate will take either a path pointing to the root of an RO-Crate (must have at least an RO-Crate metadata descriptor file, ro-crate-metadata.json) or an RO-Crate object created with rocrateR::rocrate (and alternatives), as shown in step 1.

For more details, run the following command:

?rocrateR::bag_rocrate

5.1. rocrateR::bag_rocrate()

Here we will create an RO-Crate bag inside temporary directory:

# create basic RO-Crate
basic_ro_crate <- rocrateR::rocrate()

# create temporary directory
tmp_dir <- file.path(tempdir(), paste0("rocrate-", digest::digest(basename(tempfile()))))
dir.create(tmp_dir, showWarnings = FALSE, recursive = TRUE)

# then, we can create the RO-Crate bag
path_to_rocrate_bag <- basic_ro_crate |>
  rocrateR::bag_rocrate(path = tmp_dir)
#> RO-Crate successfully 'bagged'!
#> For details, see: /var/folders/59/4_l6kbyj2qsczmk2b52qg_f40000gn/T//RtmpTaDplX/rocrate-6593bf82ca985edcc85ffd6681839645/rocrate-bc41824bf4a6278f5d75cdebcd956e33.zip

5.2. rocrateR::is_rocrate_bag()

We can use the function rocrateR::is_rocrate_bag() to verify that a given path points to a ZIP file or a directory with a valid RO-Crate bag. The expected files are

path_to_rocrate_bag |>
  rocrateR::is_rocrate_bag()
#> [1] TRUE

And then, the RO-Crate can be displayed

path_to_rocrate_bag |>
  rocrateR::load_rocrate()
#> {
#>   "@context": "https://w3id.org/ro/crate/1.2/context",
#>   "@graph": [
#>     {
#>       "@id": "ro-crate-metadata.json",
#>       "@type": "CreativeWork",
#>       "about": {
#>         "@id": "./"
#>       },
#>       "conformsTo": {
#>         "@id": "https://w3id.org/ro/crate/1.2"
#>       }
#>     },
#>     {
#>       "@id": "./",
#>       "@type": "Dataset",
#>       "name": "",
#>       "description": "",
#>       "datePublished": "2026-04-07",
#>       "license": {
#>         "@id": "http://spdx.org/licenses/CC-BY-4.0"
#>       }
#>     }
#>   ]
#> }

5.3. rocrateR::unbag_rocrate()

We can explore the contents of the RO-Crate bag with the following commands:

# extract files in temporary directory
path_to_rocrate_bag_contents <- path_to_rocrate_bag |>
  rocrateR::unbag_rocrate(output = file.path(tmp_dir, "ROC"))
#> RO-Crate bag successfully extracted! For details, see:
#> Root directory: /private/var/folders/59/4_l6kbyj2qsczmk2b52qg_f40000gn/T/RtmpTaDplX/rocrate-6593bf82ca985edcc85ffd6681839645/ROC

# create tree with the files
fs::dir_tree(path_to_rocrate_bag_contents)
#> /private/var/folders/59/4_l6kbyj2qsczmk2b52qg_f40000gn/T/RtmpTaDplX/rocrate-6593bf82ca985edcc85ffd6681839645/ROC
#> ├── bag-info.txt
#> ├── bagit.txt
#> ├── data
#> │   └── ro-crate-metadata.json
#> ├── manifest-sha512.txt
#> └── tagmanifest-sha512.txt
# delete temporary directory
unlink(tmp_dir, recursive = TRUE, force = TRUE)

6. Validation

Advanced validation using the Python rocrate-validator is optional and requires {reticulate}.

Appendix

A1. Advanced Validation (experimental)

As you develop your RO-Crates, you might want to validate them. There are few validators online (some of which can be found at https://www.researchobject.org/ro-crate/tools), here we will explore the Python package rocrate-validator. For installation details, please visit https://github.com/crs4/rocrate-validator.

⚠ The validation workflow depends on Python’s rocrate-validator. Ensure you have a working Python installation and {reticulate} configured correctly (reticulate::py_config()). On Windows, you may need to restart R after installation.

A1.1. Install {reticulate}

pak::pkg_install("reticulate")

A1.2. Install rocrate-validator

reticulate::py_install("roc-validator", env = "rocrateR")

A1.3. Create example RO-Crate and validate it

basic_ro_crate <- rocrateR::rocrate()

# store crate inside temporary directory
tmp <- file.path(tempdir(), "ro-crate-metadata.json")
basic_ro_crate |>
  rocrateR::write_rocrate(tmp)
# wrap crate into zip file (expected by validator)
tmp_zip <- paste(tmp, ".zip")
zip(tmp_zip, tmp)

# validate (note the name of the module: rocrate_validator)
reticulate::use_virtualenv("rocrateR")
rocrate_validator <- reticulate::import("rocrate_validator")
status <- rocrate_validator$utils$validate_rocrate_uri(tmp_zip)

if (status) {
  message("RO-Crate is valid!")
} else {
  message("RO-Crate is invalid!")
}

# delete temporary files
unlink(tmp)
unlink(tmp_zip)