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 Research Object Crate for ERGA Protein-coding gene annotation workflow LiveRO ResearchObject RoCrate Dataset ▼ comment approve/disapprove edit as derived nanopublication

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"# ERGA Protein-coding gene annotation workflow. Adapted from the work of Sagane Joye: https://github.com/sdind/genome_annotation_workflow ## Prerequisites The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: [https://github.com/nextflow-io/nextflow/issues/1659](https://github.com/nextflow-io/nextflow/issues/1659). `conda v 23.7.3` `singularity v 3.7.3` `snakemake v 7.32.3` You will also need to acquire a licence key for Genemark and place this in your home directory with name `~/.gm_key` The key file can be obtained from the following location, where the licence should be read and agreed to: http://topaz.gatech.edu/GeneMark/license_download.cgi ## Workflow The pipeline is based on braker3 and was tested on the following dataset from Drosophila melanogaster: [https://doi.org/10.5281/zenodo.8013373](https://doi.org/10.5281/zenodo.8013373) ### Input data - Reference genome in fasta format - RNAseq data in paired-end zipped fastq format - uniprot fasta sequences in zipped fasta format ### Pipeline steps - **Repeat Model and Mask** Run RepeatModeler using the genome as input, filter any repeats also annotated as protein sequences in the uniprot database and use this filtered libray to mask the genome with RepeatMasker - **Map RNAseq data** Trim any remaining adapter sequences and map the trimmed reads to the input genome - **Run gene prediction software** Use the mapped RNAseq reads and the uniprot sequences to create hints for gene prediction using Braker3 on the masked genome - **Evaluate annotation** Run BUSCO to evaluate the completeness of the annotation produced ### Output data - FastQC reports for input RNAseq data before and after adapter trimming - RepeatMasker report containing quantity of masked sequence and distribution among TE families - Protein-coding gene annotation file in gff3 format - BUSCO summary of annotated sequences ## Setup Your data should be placed in the `data` folder, with the reference genome in the folder `data/ref` and the transcript data in the foler `data/rnaseq`. The config file requires the following to be given: ``` asm: 'absolute path to reference fasta' snakemake_dir_path: 'path to snakemake working directory' name: 'name for project, e.g. mHomSap1' RNA_dir: 'absolute path to rnaseq directory' busco_phylum: 'busco database to use for evaluation e.g. mammalia_odb10' ``` "

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https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://schema.org/contentSize

contentSize

(this is a literal)

"76"

(xsd:integer) .

https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/21e37e3d-1372-4acd-9ce7-b1a005e9a41a/download/"

.

https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://schema.org/dateCreated

dateCreated

(this is a literal)

"2023-09-13 18:24:52.292399+00:00"

.

https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://schema.org/dateModified

dateModified

(this is a literal)

"2023-09-13 18:24:56.003168+00:00"

.

https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://schema.org/name

name

(this is a literal)

"protexcluder.yaml"

.

https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

"2023-09-13 18:24:52.292399+00:00"

.

https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...3d-1372-4acd-9ce7-b1a005e9a41a

21e37e3d-1372-4acd-9ce7-b1a005e9a41a

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://schema.org/author

author

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://schema.org/contentSize

contentSize

(this is a literal)

"91586491"

(xsd:integer) .

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/2dd40f39-d265-4afe-ab50-5238e7bd6b16/download/"

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://schema.org/dateCreated

dateCreated

(this is a literal)

"2023-09-13 18:24:52.663696+00:00"

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://schema.org/dateModified

dateModified

(this is a literal)

"2023-09-13 18:24:57.288292+00:00"

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://schema.org/name

name

(this is a literal)

"uniprot_sprot.fasta.gz"

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

"2023-09-13 18:24:52.663696+00:00"

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...39-d265-4afe-ab50-5238e7bd6b16

2dd40f39-d265-4afe-ab50-5238e7bd6b16

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://schema.org/author

author

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://schema.org/contentSize

contentSize

(this is a literal)

"7902"

(xsd:integer) .

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/52497c90-bae5-4fbd-aca5-b5175ff7a4fa/download/"

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://schema.org/dateCreated

dateCreated

(this is a literal)

"2023-09-13 18:24:52.665086+00:00"

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://schema.org/dateModified

dateModified

(this is a literal)

"2023-09-13 18:25:00.419280+00:00"

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://schema.org/name

name

(this is a literal)

"1_MaskRepeat.smk"

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

"2023-09-13 18:24:52.665086+00:00"

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...90-bae5-4fbd-aca5-b5175ff7a4fa

52497c90-bae5-4fbd-aca5-b5175ff7a4fa

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://schema.org/author

author

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://schema.org/contentSize

contentSize

(this is a literal)

"85"

(xsd:integer) .

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/5e018f3a-bc34-48db-b72e-f85214a13a9d/download/"

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://schema.org/dateCreated

dateCreated

(this is a literal)

"2023-09-13 18:24:52.294349+00:00"

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://schema.org/dateModified

dateModified

(this is a literal)

"2023-09-13 18:24:56.445276+00:00"

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://schema.org/name

name

(this is a literal)

"tePSI.yaml"

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

"2023-09-13 18:24:52.294349+00:00"

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...3a-bc34-48db-b72e-f85214a13a9d

5e018f3a-bc34-48db-b72e-f85214a13a9d

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://schema.org/author

author

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://schema.org/contentSize

contentSize

(this is a literal)

"86"

(xsd:integer) .

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/6420e76a-1e0e-42a0-9b9e-e355de2a88a5/download/"

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://schema.org/dateCreated

dateCreated

(this is a literal)

"2023-09-13 18:24:52.295311+00:00"

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://schema.org/dateModified

dateModified

(this is a literal)

"2023-09-13 18:24:56.846580+00:00"

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://schema.org/name

name

(this is a literal)

"trimm.yaml"

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

"2023-09-13 18:24:52.295311+00:00"

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...6a-1e0e-42a0-9b9e-e355de2a88a5

6420e76a-1e0e-42a0-9b9e-e355de2a88a5

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://schema.org/author

author

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://schema.org/contentSize

contentSize

(this is a literal)

"70"

(xsd:integer) .

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/64cb8be0-e907-41a0-8f6b-dbf642fe4372/download/"

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://schema.org/dateCreated

dateCreated

(this is a literal)

"2023-09-13 18:24:52.288353+00:00"

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://schema.org/dateModified

dateModified

(this is a literal)

"2023-09-13 18:24:54.812023+00:00"

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://schema.org/name

name

(this is a literal)

"blast.yaml"

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

"2023-09-13 18:24:52.288353+00:00"

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...e0-e907-41a0-8f6b-dbf642fe4372

64cb8be0-e907-41a0-8f6b-dbf642fe4372

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

https://w3id.org/ro-id/7019724...0c-925c-4b44-9b87-fc35c96eed2f

69f9d60c-925c-4b44-9b87-fc35c96eed2f

http://schema.org/author

author

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...0c-925c-4b44-9b87-fc35c96eed2f

69f9d60c-925c-4b44-9b87-fc35c96eed2f

http://schema.org/contentSize

contentSize

(this is a literal)

"0"

(xsd:integer) .

https://w3id.org/ro-id/7019724...0c-925c-4b44-9b87-fc35c96eed2f

69f9d60c-925c-4b44-9b87-fc35c96eed2f

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/69f9d60c-925c-4b44-9b87-fc35c96eed2f/download/"

.

https://w3id.org/ro-id/7019724...0c-925c-4b44-9b87-fc35c96eed2f

69f9d60c-925c-4b44-9b87-fc35c96eed2f

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...0c-925c-4b44-9b87-fc35c96eed2f

69f9d60c-925c-4b44-9b87-fc35c96eed2f

http://schema.org/dateCreated

dateCreated

(this is a literal)

"2023-09-13 18:24:52.287342+00:00"

.

https://w3id.org/ro-id/7019724...0c-925c-4b44-9b87-fc35c96eed2f

69f9d60c-925c-4b44-9b87-fc35c96eed2f

http://schema.org/dateModified

dateModified

(this is a literal)

"2023-09-13 18:24:54.625563+00:00"

.

https://w3id.org/ro-id/7019724...0c-925c-4b44-9b87-fc35c96eed2f

69f9d60c-925c-4b44-9b87-fc35c96eed2f

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...0c-925c-4b44-9b87-fc35c96eed2f

69f9d60c-925c-4b44-9b87-fc35c96eed2f

http://schema.org/name

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http://schema.org/sdDatePublished

sdDatePublished

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http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

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69f9d60c-925c-4b44-9b87-fc35c96eed2f

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

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http://schema.org/author

author

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http://schema.org/contentSize

contentSize

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http://schema.org/contentUrl

contentUrl

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http://schema.org/creator

creator

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http://schema.org/dateCreated

dateCreated

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https://w3id.org/ro-id/7019724...30-3b55-44e0-8c8d-8762952df493

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http://schema.org/dateModified

dateModified

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https://w3id.org/ro-id/7019724...30-3b55-44e0-8c8d-8762952df493

6aadc530-3b55-44e0-8c8d-8762952df493

http://schema.org/license

license

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http://schema.org/name

name

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http://schema.org/sdDatePublished

sdDatePublished

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http://www.w3.org/1999/02/22-rdf-syntax-ns#type

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http://purl.org/wf4ever/wf4ever#Resource

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http://www.w3.org/1999/02/22-rdf-syntax-ns#type

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http://schema.org/MediaObject

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http://schema.org/author

author

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http://schema.org/contentSize

contentSize

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http://schema.org/contentUrl

contentUrl

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"https://api.rohub.org/api/resources/70cec592-1fbe-4b53-a8ef-8dd3522246d6/download/"

.

https://w3id.org/ro-id/7019724...92-1fbe-4b53-a8ef-8dd3522246d6

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http://schema.org/creator

creator

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http://schema.org/dateCreated

dateCreated

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.

https://w3id.org/ro-id/7019724...92-1fbe-4b53-a8ef-8dd3522246d6

70cec592-1fbe-4b53-a8ef-8dd3522246d6

http://schema.org/dateModified

dateModified

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https://w3id.org/ro-id/7019724...92-1fbe-4b53-a8ef-8dd3522246d6

70cec592-1fbe-4b53-a8ef-8dd3522246d6

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

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70cec592-1fbe-4b53-a8ef-8dd3522246d6

http://schema.org/name

name

(this is a literal)

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.

https://w3id.org/ro-id/7019724...92-1fbe-4b53-a8ef-8dd3522246d6

70cec592-1fbe-4b53-a8ef-8dd3522246d6

http://schema.org/sdDatePublished

sdDatePublished

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https://w3id.org/ro-id/7019724...92-1fbe-4b53-a8ef-8dd3522246d6

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http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

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70cec592-1fbe-4b53-a8ef-8dd3522246d6

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

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7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://schema.org/author

author

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0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://schema.org/contentSize

contentSize

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(xsd:integer) .

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://schema.org/contentUrl

contentUrl

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"https://api.rohub.org/api/resources/7d430516-d8cb-4bc0-a4d9-e103a63e3478/download/"

.

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://schema.org/dateCreated

dateCreated

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.

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://schema.org/dateModified

dateModified

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.

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://schema.org/name

name

(this is a literal)

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.

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

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.

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...16-d8cb-4bc0-a4d9-e103a63e3478

7d430516-d8cb-4bc0-a4d9-e103a63e3478

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

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89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://schema.org/author

author

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0000-0003-2388-0744

.

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http://schema.org/contentSize

contentSize

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(xsd:integer) .

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89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/89e1f03d-e2e9-46f1-8386-8cdeff35386c/download/"

.

https://w3id.org/ro-id/7019724...3d-e2e9-46f1-8386-8cdeff35386c

89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...3d-e2e9-46f1-8386-8cdeff35386c

89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://schema.org/dateCreated

dateCreated

(this is a literal)

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.

https://w3id.org/ro-id/7019724...3d-e2e9-46f1-8386-8cdeff35386c

89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://schema.org/dateModified

dateModified

(this is a literal)

"2023-09-13 18:24:53.979999+00:00"

.

https://w3id.org/ro-id/7019724...3d-e2e9-46f1-8386-8cdeff35386c

89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://schema.org/encodingFormat

encodingFormat

(this is a literal)

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.

https://w3id.org/ro-id/7019724...3d-e2e9-46f1-8386-8cdeff35386c

89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...3d-e2e9-46f1-8386-8cdeff35386c

89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://schema.org/name

name

(this is a literal)

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.

https://w3id.org/ro-id/7019724...3d-e2e9-46f1-8386-8cdeff35386c

89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

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.

https://w3id.org/ro-id/7019724...3d-e2e9-46f1-8386-8cdeff35386c

89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...3d-e2e9-46f1-8386-8cdeff35386c

89e1f03d-e2e9-46f1-8386-8cdeff35386c

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

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b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://schema.org/author

author

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0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://schema.org/contentSize

contentSize

(this is a literal)

"2012"

(xsd:integer) .

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1/download/"

.

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://schema.org/dateCreated

dateCreated

(this is a literal)

"2023-09-13 18:24:52.666452+00:00"

.

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://schema.org/dateModified

dateModified

(this is a literal)

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.

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://schema.org/name

name

(this is a literal)

"3_braker.smk"

.

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

"2023-09-13 18:24:52.666452+00:00"

.

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...bb-5ce6-4ad9-8dcb-27a0325baeb1

b2864dbb-5ce6-4ad9-8dcb-27a0325baeb1

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://schema.org/author

author

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://schema.org/contentSize

contentSize

(this is a literal)

"327"

(xsd:integer) .

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://schema.org/contentUrl

contentUrl

(this is a literal)

"https://api.rohub.org/api/resources/d6d97bc9-1631-4347-920b-dec30f6aebea/download/"

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://schema.org/creator

creator

https://orcid.org/0000-0003-2388-0744

0000-0003-2388-0744

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://schema.org/dateCreated

dateCreated

(this is a literal)

"2023-09-13 18:24:52.285895+00:00"

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://schema.org/dateModified

dateModified

(this is a literal)

"2023-09-13 18:24:54.412314+00:00"

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://schema.org/license

license

https://choosealicense.com/no-permission/

no-permission

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://schema.org/name

name

(this is a literal)

"config.yaml"

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://schema.org/sdDatePublished

sdDatePublished

(this is a literal)

"2023-09-13 18:24:52.285895+00:00"

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/wf4ever/wf4ever#Resource

Resource

.

https://w3id.org/ro-id/7019724...c9-1631-4347-920b-dec30f6aebea

d6d97bc9-1631-4347-920b-dec30f6aebea

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/MediaObject

MediaObject

.

https://w3id.org/ro-id/7019724...cac85df/ro-crate-metadata.json

ro-crate-metadata.json

http://purl.org/dc/terms/conformsTo

conformsTo

https://w3id.org/ro/crate/1.1

1.1

.

https://w3id.org/ro-id/7019724...cac85df/ro-crate-metadata.json

ro-crate-metadata.json

http://schema.org/about

about

https://w3id.org/ro-id/7019724e-b5a0-4f7e-a7d6-a1baacac85df/

7019724e-b5a0-4f7e-a7d6-a1baacac85df

.

https://w3id.org/ro-id/7019724...cac85df/ro-crate-metadata.json

ro-crate-metadata.json

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/CreativeWork

CreativeWork

.

https://workflowhub.eu/people/554

people/554

http://schema.org/name

name

(this is a literal)

"Sagane Joye-Dind"

.

https://workflowhub.eu/people/554

people/554

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/Person

Person

.

https://workflowhub.eu/projects/191

projects/191

http://schema.org/name

name

(this is a literal)

"ERGA Annotation"

.

https://workflowhub.eu/projects/191

projects/191

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/Organization

Organization

.

https://workflowhub.eu/projects/191

projects/191

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://schema.org/Project

Project

.

This is the identifier for the assertion of this nanopublication. https://w3id.org/np/RAuZdwi5v3.../assertion The assertion above http://www.w3.org/ns/prov#wasDerivedFrom

wasDerivedFrom

https://api.rohub.org/api/ros/...ownload/ro-crate-metadata.json

ro-crate-metadata.json

.

This is the identifier for this whole nanopublication. https://w3id.org/np/RAuZdwi5v3... This nanopublication http://www.w3.org/2000/01/rdf-schema#label has the label (this is a literal)

"Research Object Crate for ERGA Protein-coding gene annotation workflow"

.

This is the identifier for this whole nanopublication. https://w3id.org/np/RAuZdwi5v3... This nanopublication date and time when the nanopublication was created http://purl.org/dc/terms/created was created on (this is a literal)

"2025-11-11T16:06:28.382+01:00"

(xsd:dateTime) .

This is the identifier for this whole nanopublication. https://w3id.org/np/RAuZdwi5v3... This nanopublication the nanopublication consists of an introduction of the given resource http://purl.org/nanopub/x/introduces introduces https://w3id.org/ro-id/7019724e-b5a0-4f7e-a7d6-a1baacac85df/

7019724e-b5a0-4f7e-a7d6-a1baacac85df

.

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAuZdwi5v3.../sig

sig

http://purl.org/nanopub/x/hasSignatureTarget has as target This is the identifier for this whole nanopublication. https://w3id.org/np/RAuZdwi5v3... this nanopublication .

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAuZdwi5v3.../sig

sig

http://purl.org/nanopub/x/hasAlgorithm has the algorithm (this is a literal)

"RSA"

.

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAuZdwi5v3.../sig

sig

http://purl.org/nanopub/x/hasPublicKey has the public key (this is a literal)

"MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA4pPaESKwmC6l37P86K6TNLq6yeQtc7m9CvcqauLs/1FC0viHvQnFBgxj0a+loPDv/Egwe6OqFpa0iW9Ypnyz9YPoh+pxbRXonbuMOb+8Ry9hXZ+TEKfWjhjVDGEaClwfRwglh2HI/xfV4CD9AgvDOEoZQiyta8a90PYwJ3G6e70oCHTn61+OWTkI9KRYHOYgg3btdy2Z7q/30PTFawb2ZT5aIfIJYobUYv2a7yhtcqWCHZeKv0bxGnRjTFNx1rscBMlLJSzvRtpQc1cCRVEPFZHo1adaXCI9tGvn4cxeNQ96y8dxkN1XhpaJairde+23MDzf42Oe97KG2HYzKiyVnQIDAQAB"

.

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAuZdwi5v3.../sig

sig

http://purl.org/nanopub/x/hasSignature has the signature (this is a literal)

"XaOMVbys4bSXed9t1NnW/3sNMTmSLOrSVEWnD8787WIpMB2mNwhumGbd1Zmp6USYCEMc3t22P3tMS25dtVO9/GM9KZJ5VT0PF7fg+b9o/fQaJyJVRytnoS4rzs2+D60QevqFtLF0XDQdKFW4PhFVuRoKIPL+eqmBvtZ+8Yrhwdb81KV2oWREkT7uydxEddU0jpaty01iUR680KlCcsIA5aiHJCifyOE2P5W4cGfiRFXclYylO0V+9LfRfUduS4cJyfu2zWQPcxx8VXlyOHXNs+rzCEaEGFm9EqgHLakyhxP/TEbBAMFFK+3uhR9a4VxR4PZsKQPMv0ejTJTtb6AoTA=="

.

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAuZdwi5v3.../sig

sig

http://purl.org/nanopub/x/signedBy is signed by https://w3id.org/kpxl/gen/terms/RoCrateBot

RO-Crate Bot

.

This is the identifier for this whole nanopublication. https://w3id.org/np/RAuZdwi5v3...

this nanopublication

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

http://purl.org/nanopub/x/RoCrateNanopub

RoCrateNanopub

.

RO-Crate Bot, 11 Nov 2025, 15:06:28 UTC

References