How to grow an ARC - an example

Andrea Schrader (github: @andreaschrader)

Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne

This work is supported by CEPLAS, funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) within Germany´s Excellence Strategy – EXC-2048/1 – project ID 390686111.

This example uses the command line.
It shows the process of growing an ARC to be used in demos and also while trying options and arguments of the ARC Commander.
Please note, this is work in progress and this "Grow-an-ARC" example ARC is not completed yet.
Successively, it is planned to add and use more features.

Information on the requirements for using the HUB and ARC Commander can be found in the manuals available in the DataPLANT Knowledge Base.

Used OS and ARC Commander version

Used for this example:

arc version: v0.5.0
macOS Ventura 13.5.1

Prepare the ARC

• Decide on and prepare:

"NAME" and/or "ARC_NAME" of the investigation
Here, used for both: Grow-an-ARC_Example

• create an empty project in the HUB (no README), name: "ARC_NAME"
• create an empty directory on the local device (Mac) with the same name, name: "ARC_NAME"
• go into this directory

Initiate the ARC locally

arc init

Create the investigation

arc i create -i ARC_NAME   

isa.investigation - general metadata

• More information can be added later.
• Decide and prepare:

"TITLE" of the investigation
"DESCRIPTION" of the investigation

arc investigation update --identifier "ARC_NAME" --title "TITEL" --description "DESCRIPTION"  

isa.investigation contact person(s) metadata

Adding a contact person for the investigation - example

arc i person register -l Schrader -f Andrea --email andrea.schrader@uni-koeln.de --address "50674 Cologne, Germany" --affiliation "Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne" --roles "contact person; data-curator; leads investigation; designs experiments; supervisor; performs experiments" --rolestermsourceref "SCORO; SCORO; SCORO; SCORO; SCORO; SCORO" --orcid "0000-0002-3879-7057"  

Adding a second contact person - with placeholders and example ontology entries

I am using here my ORCID iD as e.g. "0000-0000-0000-0000" will cause an error in the validation.
Of course, the ORCID iD of PERSON2 should be used here.

arc i person register -l LASTNAME_PERSON2 -f FIRSTNAME_PERSON2 -m MIDNAME_PERSON2 --email person2@uniX.de --address "XXXXX CITY, COUNTRY" --affiliation "AFFILIATION_PERSON2" --roles "principal investigator; leads investigation; designs experiments; supervisor" --rolestermsourceref "SCORO; SCORO; SCORO; SCORO" --orcid "0000-0002-3879-7057"  

isa.investigation publication(s) metadata

Adding a publication - Example with placeholders and example ontology entries

arc i publication register --doi "10.XXXX/pp.XXX.XXXXXX" -p "PUBMED_ID" --authorlist "Author1; Author2; Author3; Author4; Author5" --title "PUBLICATION_TITLE" --status "published" --statustermaccessionnumber "http://www.ebi.ac.uk/efo/EFO_0001796" --statustermsourceref "EFO"  

• switched manually statustermaccessionnumber and statustermsourceref in isa.investigation.xlsx which are interchanged due to a bug (already reported)
• added manually the ontology source reference information as no option is available for this yet:

Adding a second publication

Not done in this example.
(As above but ontology reference information do not need to be entered in duplicates.)

Connect the ARC with the HUB

Connect the local ARC with the HUB "project" and sync changes

• prepare a TOKENSTRING (personal access token (e.g. like here: https://github.com/nfdi4plants/arcCommander/discussions/157))
• replace TOKENSTRING,YourGitLabNAME and ARC_NAME below

arc sync -r https://oauth2:TOKENSTRING@git.nfdi4plants.org/YourGitLabNAME/ARC_NAME -m "Initiated an ARC, added investigation metadata added manually the ontology source reference information as no option is available for this so far."

Add a README, a LICENCE and a .gitignore file

Here: A template README has been added here as TEMPLATE_README.md.

When this is used, it needs to be named "README.md".

Here: A CC-BY 4.0 license has been added.
Here: An initial .gitignore file has been added with the entry ".DS_Store" for macOS.

Sync with the HUB

arc sync -m "Added a README template, .gitignore for macOS and a CC-BY 4.0 licence file."

Only for this Grow-an-ARC_Example - add the README.md which contains the procedure described here...

touch README.md

... and, of course, synchronize again with a message explaining what has been changed.

arc sync -m "Added the README for this Grow-an-ARC_Example ARC including the process of growing this ARC."