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](https://github.com/nfdi4plants/arcCommander).
Please note, this is work in progress and the ARC is example ARC is not completed yet.
Successively, it is planned to add and use more features.
## 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"
### Adding a contact person for the investigation - example
```bash
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.
```bash
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
```bash
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:
Term Source Name | EFO | SCORO
---|---|---
Term Source File | http://www.ebi.ac.uk/efo/efo.owl | http://purl.org/spar/scoro
Term Source Version | 3.49.0 | 1.9.1
Term Source Description | Experimental Factor Ontology | Scholarly Contributions and Roles Ontology
### Adding a second publication
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
```bash
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
```bash
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.
