diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..a2f4f41e516066e7e4d67f924aab48b1aee5de20 --- /dev/null +++ b/README.md @@ -0,0 +1,120 @@ +# How to grow an ARC - an example + +[Andrea Schrader](https://orcid.org/0000-0002-3879-7057) (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](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" +- go into this directory + +### Initiate the ARC locally + +```bash +arc init +``` + +### Create the investigation + +```bash +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 + +```bash +arc investigation update --identifier "ARC_NAME" --title "TITEL" --description "DESCRIPTION" +``` + +## isa.investigation contact person(s) metadata + +### 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. + +```bash +touch README.md +``` \ No newline at end of file