⚠️ 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 s init.
arc s register.
arc s addcan be used. This command combines init and register.
⚠️ A study identifier also defines the isa file name, so ensure to avoid special characters!
|Identifier (Mandatory)||A unique identifier, either a temporary identifier supplied by users or one generated by a repository or other database. For example, it could be an identifier complying with the LSID specification.||GelBasedProteomicsWT|
|Title||A concise phrase used to encapsulate the purpose and goal of the study.||Gel-based proteomics of wild type cells|
|Description||A textual description of the study, with components such as objective or goals.||Study to investigate the proteins of wild type yeast cells under standard growth conditions.|
|SubmissionDate:||The date on which the study is submitted to an archive.|
|PublicReleaseDate:||The date on which the study SHOULD be released publicly.|
If no study identifier is given, a study is created with the assay identifier as study identifier. Instead of using the editor, the following command can be used:
arc s add --identifier Test --title "Gel-based proteomics of wild type cells" --description " Study to investigate the proteins of wild type yeast cells under standard growth conditions."
arc s list.
arc s get. If no arguments are specified an editor will request a study identifier to print all registered information into the shell.
arc s edit.
arc s edit, but
arc s updatemust be used:
arc s update --identifier GelBasedProteomicsWT --submissiondate "13.04.2020"
arc s unregister.
arc s delete.
arc s removecan be used.
arc s unregister -s <study identifier>
arc s delete -s <study identifier>
arc s remove -s <study identifier>
arc s person register.
|StudyIdentifier (Mandatory)||Identifier of the study the person is associated with||GelBasedProteomicsWT|
|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 email@example.com|
|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|
|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||dentifies 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:|
arc s person register -s GelBasedProteomicsWT -l Doe -f John -m P --email firstname.lastname@example.org --phone "+49(0)631 205 3045" --address "Paul-Ehrlich-Straße 23, 67663 Kaiserslautern" --affiliation "Department of M21 Measurements, Technische Universität Kaiserslautern, Germany" --roles "supervisor"
arc s person list.
arc s person get. If no arguments are specified an editor will request a study identifier, a first and last name (mandatory) and optionally mid name initials to print all registered information into the shell.
arc s person edit.
arc s person edit, but
arc s person updatemust be used:
arc s person update -s GelBasedProteomicsWT -l Kunze -f Heinz-Rudolf --email email@example.com --address "Herzstraße 5, 12345 Musterstadt"
arc s person unregister. An editor will request the study identifier, first and last name (mandatory) and optionally mid name initials to unregister the person from the study in isa.investigation.xlsx.
arc s person unregister -s GelBasedProteomicsWT -l Doe -f John -m P
arc s publication register.
|StudyIdentifier (Mandatory)||Identifier of the study the publication is associated with||GelBasedProteomicsWT|
|DOI (Mandatory)||A Digital Object Identifier (DOI) for that publication (where available).||2021_ARC05_S01_01tmp|
|PubMedID||The PubMed IDs of the described publication(s) associated with this investigation.|
|AuthorList||The list of authors associated with that publication.||Lara Fox; Peter Croft|
|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.|
|StatusTermSourceREF||Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to match one the Term Source Name declared in the in the Ontology Source Reference section.|
arc s publication register -s GelBasedProteomicsWT -d 2021_ARC05_S01_01tmp --authorlist "John P Doe; Eva Muller" --title "abc"
arc s publication list.
arc s publication get. If no arguments are specified an editor will request the study identifier and doi to print all registered information into the shell.
arc s publication edit.
arc s publication edit, but
arc s publication updatemust be used:
arc s publication update -s "GelBasedProteomicsWT" -d 2021_ARC05_Pub01tmp --title "The peroxisomal Flux-Compensator-Cycle is heavily dependent on P09 accumulation under redox stress.".
arc s publication unregister. An editor will request the study identifier and DOI to unregister the publication from the study in the isa.investigation file.
arc s publication unregister -s GelBasedProteomicsWT -d 2021_ARC05_Pub01tmp
arc s design register.
arc s design register -s "GelBasedProteomicsWT" -d "YourDesignType"