Investigation

last updated at 2022-12-13

Addition of an isa.investigation.xlsx

⚠️ 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 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.

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

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

Field	Description	Input
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 YYYY-MM-DD	2022-12-13
PublicReleaseDate	The date on which the investigation was released publicly. Formatted as ISO8601 date YYYY-MM-DD	2022-12-13

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.

💡 You don't need to fill every row from the beginning, as ARCs are intended as an evolving object that shapes over time.

Registering persons to investigation

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

Field	Description	Input
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
Email	The email address of a person associated with the investigation.	jpdoe@mail.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
ORCID (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 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).

Listing and inspecting registered persons

Registered persons can be listed by arc i person list.
To get detailed information about a specific entry use 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.

Editing person information

A person can be edited using 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.
To circumvent editor pop ups, not arc i person edit, but arc i person update must be used:
arc i person update -l Kunze -f Heinz-Rudolf --email hrkunze@mail.com --address "Herzstraße 5, 12345 Musterstadt"

Removing a 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

Registering publications to investigation

Investigation publications may be a collection of all study publications or publications that emerge from study publications (reviews/integrating publications).
Investigation publications can be registered by arc i publication register.

Field	Description	Input
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

Listing and inspecting registered publications

Registered publications can be listed by arc i publication list.
To get detailed information about a specific entry use arc i publication get. If no arguments are specified an editor will request the doi to print all registered information into the shell.

Editing publication information

A publication can be edited using 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.
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".

Removing a 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

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