Exemplary scenario – Experimentalist user journey

Emma is a PhD student in the lab of Professor McGonagall. The group's research is focused on zebrafish proteome dynamics under changing environmental conditions. In Emma's first year she generated a knockout mutant that lacks in protein CV19. This already could demonstrate severe phenotypical responses under oxygen depleted conditions. Furthermore, she performed an proteomics experiment with a wild type and her mutant. She measured membrane protein samples from epithelial gill cells.

Professor McGonagall hands her an ARC named 'Response to chilling temperatures in Danio rerio' and instructs her to add her CV19 proteomics research to this ARC. After reading '1 – Before we start' she has set up all prerequisites and opened her shell accordingly. To check the state of the ARC structure, Emma enters arc a list to list the studies and assays included within the ARC:

• Investigation (Low-oxygen response in Danio rerio)
  • Study (Reproduction efficiency under low oxygen)
    • Assay (Reproduction efficiency under low oxygen)
  • Study (Structural protein involvement)
    • Assay (Phenotypical response of Keratin kd mutant)
    • Assay (Metabolic response of strucProt28 mutant)
  • Study (Gill degeneration effects)
    • Assay (Biomass and surface changes of gills under low oxygen)
    • Assay (Oxygen transport efficiency under low oxygen)

Adding a study to an existing study

After consultation with Prof. McGonagall, she decides to add her experiment to the 'gill study'. Since she needs to add a storage folder for her data, she aims to initialize a folder structure for her experiment. Furthermore, her work should be referenced in the isa.investigation (the ARC's central information registry). Both tasks can be realized by the usage of arc a add:

• Addition of an assay to an investigation with referencing an existing study: a) Enter arc a add b) Fill in the form. Avoid using special characters in identifiers. An assay identifier should be unique for each study. c) Save the document and close the editor.
• Emma decides to fill in the form as follows:

Field	Description	Input
StudyIdentifier	Name of the study in which the assay is situated	Gill degeneration effects
AssayIdentifier (Mandatory)	Name of the assay of interest	ProteomicsMemCV19
MeasurementType	A term to qualify the endpoint, or what is being measured (e.g. gene expression profiling or protein identification). 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.	Proteomics
MeasurementTypeTermAccessionNumber	The accession number from the Term Source associated with the selected term.
MeasurementTypeTermSourceREF	The Source REF has to match one of the Term Source Name declared in the Ontology Source Reference section.
TechnologyType	Term to identify the technology used to perform the measurement, e.g. DNA microarray, mass spectrometry. 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.	Mass spectrometry
TechnologyTypeTermAccessionNumber	The accession number from the Term Source associated with the selected term.
TechnologyTypeTermSourceREF	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.
TechnologyPlatform	Manufacturer and platform name, e.g. Bruker AVANCE	AB Sciex TT6600

• Note: If no appropriate study is present, a new study identifier can be given. A new study then is created with study identifier = assay identifier (without generating an isa.study.xlsx). It is not mandatory to group assays to studies.

Adding persons to investigation and study

All participants of the investigation can be registered in the investigation’s person directory. To group all researchers that are involved in a specialized field, they can be registered in a separate study contact directory. Emma registers herself to both by using:

• arc i person register for the investigation
• arc s person register for the study, where an additional study identifier must be defined

Field	Description	Input
StudyIdentifier (Mandatory)	Identifier of the study the person is associated with	Gill degeneration effects
LastName (Mandatory)	The last name of a person associated with the investigation.	Carlson
FirstName (Mandatory)	The first name of a person associated with the investigation.	Emma
MidInitials	The middle initials of a person associated with the investigation.
Email	The email address of a person associated with the investigation.	[email protected]
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, Germny
Affiliation	The organization affiliation for a person associated with the investigation.	Zoology, HTZ, Bielefeld, 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.	study design; sample preparation
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:

• She checks her entry in study and recognizes an error in her address. To correct or update her personal information, the uses arc s person edit. After entering her name, she is able to correct Germny to Germany.

Adding data to assay

By using the file explorer, Emma can now navigate to her freshly created folder within the ARC directory "\Low-oxygen response in Danio rerio\assays\ProteomicsMemCV19".

• ProteomicsMemCV19
  • dataset
  • protocol
  • assay.isa.xlsx (Swate)
  • readMe.md