Investigation

Caution

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.

Each ARC includes an isa.investigation file that serves as central information registry. The ARC’s content as well as global and detailed metadata are listed here. Any study or assay addition performed throughout the ARC’s working life must be registered in the isa.investigation.xlsx.

arc i create (Create Investigation)

Section titled arc i create (Create Investigation)

Creating an investigation

arc i create

will 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.

Caution

Avoid using spaces in the identifier. Use underscores and capital letters instead.

Tip

Suggestion: Use your ARC name (without spaces) as your temporary identifier.

Identifier (Mandatory)

Section titled Identifier (Mandatory)

A identifier or an accession number provided by a repository.

Example: 2021_TestARC05

Title

Section titled Title

A concise name given to the investigation.

Example: Redox behaviour of yeast mutant M21

Description

Section titled Description

A textual description of the investigation.

Example

M21 lacks in protein P09 and is susceptible to H2O2 Treatment. The molecular and phenotypical responses are studied.

SubmissionDate

Section titled SubmissionDate

The date on which the investigation was reported to the repository. Formatted as ISO8601 date (‘YYYY-MM-DD’)

Example: 2022-12-13

PublicReleaseDate

Section titled PublicReleaseDate

The date on which the investigation was released publicly. Formatted as ISO8601 date (‘YYYY-MM-DD’)

Example: 2022-12-13

CLI Flags

Section titled CLI Flags

Instead of using the editor, the following command can be used.

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."

The isa.investigation.xlsx is added to root directory.

Tip

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 (Registering Persons)

Section titled arc i person register (Registering Persons)

Every person that is involved in the investigation can be registered with personal information using:

Registering a person

arc i person register

Tip

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)

Section titled LastName (Mandatory)

The last name of a person associated with the investigation.

Example: Doe

FirstName (Mandatory)

Section titled FirstName (Mandatory)

The first name of a person associated with the investigation.

Example: John

MidInitials

Section titled MidInitials

The middle initials of a person associated with the investigation.

Example: P

Email

Section titled Email

The email address of a person associated with the investigation.

Example: jpdoe@mail.com

Phone

Section titled Phone

The telephone number of a person associated with the investigation.

Example: +49(0)631 205 3045

Fax

Section titled Fax

The fax number of a person associated with the investigation.

Address

Section titled Address

The address of a person associated with the investigation.

Example: Paul Ehrlich Straße 23, 67663 Kaiserslautern, Germany

Affiliation

Section titled Affiliation

The organization affiliation for a person associated with the investigation.

Example

Department of M21 Measurements, Technische Universität Kaiserslautern, Germany

ORCID

Section titled ORCID

(not ISA-Tab format, will be added as a comment)

The ORCID iD of the person.

Example: XXXX-XXXX-XXXX-XXXX

Roles

Section titled 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.

Example: supervisor

RolesTermAccessionNumber

Section titled RolesTermAccessionNumber

The accession number from the Term Source associated with the selected term.

RolesTermSourceREF

Section titled 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://github.com/data2health/contributor-role-ontology

Example: CRO

CLI Flags

Section titled CLI Flags

Instead of using the editor, the following command can be used:

arc i person register -l Doe -f John -m P --email jpdoe@mail.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 (Inspect Persons)

Section titled arc i person list (Inspect Persons)

arc i person list

arc i person get (Inspect Person)

Section titled arc i person get (Inspect Person)

Get detailed information about a specific perosn.

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 (Edit Person)

Section titled arc i person edit (Edit Person)

arc i person edit

If no further arguments are specified an editor opens, that asks for the person that should be edited. If the person exists, another editor opens with information already known for the respective person. The required values can be edited.

arc i person update (Update Person)

Section titled arc i person update (Update Person)

To avoid editor pop ups, instead of arc i person edit use arc i person update.

arc i person update -l Kunze -f Heinz-Rudolf --email hrkunze@mail.com --address "Herzstraße 5, 12345 Musterstadt"

arc i person unregister (Remove Person)

Section titled arc i person unregister (Remove Person)

A person can be removed from an investigation using:

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.

Instead of using the editor, the following command can be used:

arc i person unregister -l Doe -f John -m P

arc i publication register (Register Publication)

Section titled arc i publication register (Register Publication)

arc i publication register

Investigation publications may be a collection of all study publications or publications that emerge from study publications (reviews/integrating publications).

DOI (Mandatory)

Section titled DOI (Mandatory)

A Digital Object Identifier (DOI) for that publication (where available).

Example: 2021_ARC05_Pub01tmp

PubMedID

Section titled PubMedID

The PubMed IDs of the described publication(s) associated with this investigation.

AuthorList

Section titled AuthorList

The list of authors associated with that publication.

Example: John P Doe; Eva Muller

Title

Section titled Title

The title of publication associated with the investigation.

Status

Section titled Status

A term describing the status of that publication (i.e. submitted, in preparation, published).

Example: in preparation

StatusTermAccessionNumber

Section titled StatusTermAccessionNumber

The accession number from the Term Source associated with the selected term.

Example: http://www.ebi.ac.uk/efo/EFO_0001795

StatusTermSourceREF

Section titled 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.

Example: EFO

arc i publication list (List Publications)

Section titled arc i publication list (List Publications)

Registered publications can be listed by:

arc i publication list

arc i publication get (Inspect Publication)

Section titled arc i publication get (Inspect Publication)

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 (Edit Publication)

Section titled arc i publication edit (Edit Publication)

arc i publication edit

If no further arguments are specified an editor opens, that asks for the publication doi that should be edited.

If the publication exists, another editor opens with information already known for the respective publication. The required values can be edited.

arc i publication update (Update Publication)

Section titled arc i publication update (Update Publication)

Instead of using the editor, the following command can be used. To circumvent editor pop ups, not arc i publication edit, but arc i publication update must be used:

arc i publication update -d 2021_ARC05_Pub01tmp --title "Review on yeast P09 protein and its involvement in redox susceptibility"

arc i publication unregister (Remove Publication)

Section titled arc i publication unregister (Remove Publication)

A publication can be removed from an investigation using:

arc i publication unregister

A editor will request the doi to unregister the publication from the isa.investigation.xlsx.

Instead of using the editor, the following command can be used:

arc i publication unregister -d 2021_ARC05_Pub01tmp