⚠️ Make sure to close all isa.*.xlsx files before submitting a new command to the command line, as otherwise the information cannot be saved by the ARC Commander.
arc i createwill open an editor that asks for basic investigation information to create an ISA-TAB conform Excel file. If arguments are applied with the given command, no editor will open.
⚠️ Avoid using spaces in the identifier. Use underscores and capital letters instead.
💡 Suggestion: Use your ARC name (without spaces) as your temporary identifier.
|Identifier (Mandatory)||A identifier or an accession number provided by a repository.||2021_TestARC05|
|Title||A concise name given to the investigation.||Redox behaviour of yeast mutant M21|
|Description||A textual description of the investigation.||M21 lacks in protein P09 and is susceptible to H2O2 Treatment. The molecular and phenotypical responses are studied.|
|SubmissionDate||The date on which the investigation was reported to the repository. Formatted as ISO8601 date
|PublicReleaseDate||The date on which the investigation was released publicly. Formatted as ISO8601 date
arc investigation create --identifier "2021_TestARC05" --title "Redox behaviour of yeast mutant M21" --description "M21 lacks in protein P09 and is susceptible to H2O2 Treatment. The molecular and phenotypical responses are studied."
💡 You don't need to fill every row from the beginning, as ARCs are intended as an evolving object that shapes over time.
arc i person register.
💡 If an investigation covers several studies with various groups and persons, it may be beneficial to register corresponding contacts to the investigation and register all study-related persons in each study.
|LastName (Mandatory)||The last name of a person associated with the investigation.||Doe|
|FirstName (Mandatory)||The first name of a person associated with the investigation.||John|
|MidInitials||The middle initials of a person associated with the investigation.||P|
|The email address of a person associated with the firstname.lastname@example.org|
|Phone||The telephone number of a person associated with the investigation.||+49(0)631 205 3045|
|Fax||The fax number of a person associated with the investigation.|
|Address||The address of a person associated with the investigation.||Paul Ehrlich Straße 23, 67663 Kaiserslautern, Germany|
|Affiliation||The organization affiliation for a person associated with the investigation.||Department of M21 Measurements, Technische Universität Kaiserslautern, Germany|
(not ISA-Tab format, will be added as a comment)
|The ORCID iD of the person||XXXX-XXXX-XXXX-XXXX|
|Roles||Term to classify the role(s) performed by this person in the context of the investigation, which means that the roles reported here need not correspond to roles held withing their affiliated organization. Multiple annotations or values attached to one person can be provided by using a semicolon (“;”) Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor). The term can be free text or from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and Term Source REF fields below are required.||supervisor|
|RolesTermAccessionNumber||The accession number from the Term Source associated with the selected term.|
|RolesTermSourceREF||Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to match one of the Term Source Names declared in the Ontology Source Reference section. RolesTermSourceREF: e.g. https://sparontologies.github.io/scoro/current/scoro.html||SCORO|
Instead of using the editor, the following command can be used:
arc i person register -l Doe -f John -m P --email email@example.com --phone "+49(0)631 205 3045" --address "Paul-Ehrlich-Straße 23, 67663 Kaiserslautern" --affiliation "Department of M21 Measurements, Technische Universität Kaiserslautern, Germany" --roles "supervisor"
optional: You can add with
--orcid XXXX-XXXX-XXXX-XXXX the respective ORCID iD of the person to be registered as a comment (only possible via command line).
arc i person list.
arc i person get. If no arguments are specified, an editor will request first and last name (mandatory) and optionally mid name initials to print all registered information into the shell.
arc i person edit.
arc i person edit, but
arc i person updatemust be used:
arc i person update -l Kunze -f Heinz-Rudolf --email firstname.lastname@example.org --address "Herzstraße 5, 12345 Musterstadt"
arc i person unregister. An editor will request first and last name (mandatory) and optionally mid name initials to unregister the person from the isa.investigation.xlsx.
arc i person unregister -l Doe -f John -m P
arc i publication register.
|DOI (Mandatory)||A Digital Object Identifier (DOI) for that publication (where available).||2021_ARC05_Pub01tmp|
|PubMedID||The PubMed IDs of the described publication(s) associated with this investigation.|
|AuthorList||The list of authors associated with that publication.||John P Doe; Eva Muller|
|Title||The title of publication associated with the investigation.|
|Status||A term describing the status of that publication (i.e. submitted, in preparation, published).||in preparation|
|StatusTermAccessionNumber||The accession number from the Term Source associated with the selected term.||http://www.ebi.ac.uk/efo/EFO_0001795|
|StatusTermSourceREF||Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to match one of the Term Source Names declared in the Ontology Source Reference section. The Experimental Factor Ontology (EFO) is an example for describing the status.||EFO|
arc i publication list.
arc i publication get. If no arguments are specified an editor will request the doi to print all registered information into the shell.
arc i publication edit.
arc i publication update -d 2021_ARC05_Pub01tmp --title "Review on yeast P09 protein and its involvement in redox susceptibility".
arc i publication unregister. A editor will request the doi to unregister the publication from the isa.investigation.xlsx.
arc i publication unregister -d 2021_ARC05_Pub01tmp