The following sections describes the variables used in the different metadata tables. All tables should be machine-readable. Having key variables consistently named across tables make it possible to automatically bring them together
Code
library(knitr)library(dplyr)library(kableExtra)# find files with codebooksdirinput <-file.path('..','templates','templates_for_experiments','Facility_YYYY_month','metadata_tables')files <-dir(dirinput,pattern ='*codebook*')# gather codebooksfor (i in1:length(files)){ table <-read.csv(file.path(dirinput,files[i]), header =TRUE, sep =",")#make it markdown markdown_table <- knitr::kable(table) %>%kable_styling(bootstrap_options =c("striped", "hover"))# print it cat("\n")cat("\n")cat(paste0("## ",files[i]))cat("\n")print(markdown_table) }
Mouse_list_Facility_YYYY_month_codebook.csv
Variable
Description
SubjectID
“Mice unique identifier”
Research_group_University
University affiliation of the group who collected the data (e.g., UZH; see glossary)
Research_group_Abbreviation
Abbreviation describing the group who collected the data (e.g., TIG; see glossary)
Year
“Year of collection YYYY”
Month
Month of collection (Jan, Feb, Mar, etc)
Date_of_acquisition
“DD/MM/YYYY”
Data_type
Abbreviation describing the type of data collected (e.g., SRµCT; see glossary)
Dataproject_ID
(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF
Facility_proposal_ID
(optional) Number of the proposal for facility usage e.g., the beamline numbers
Facility_institution
“Name or acronym of the institution hosting the main facility (it can be the same as University)”
Facility_country
Country where the facility is located
Facility_name
Name or acronym of the main facility (e.g., CLS, SPring-8,etc)
Facility_subunit
(optional) Additional facility information (e.g., beamline)
Scan_list_Facility_month_YYYY_codebook.csv
Variable
Description
SubjectID
“Mice unique identifier”
University
University affiliation of the group who collected the data (e.g., UZH; see glossary)
Research_group
Abbreviation describing the group who collected the data (e.g., TIG; see glossary)
Year
“Year of collection YYYY”
Month
Month of collection (Jan, Feb, Mar, etc)
Date_acquisition
“DD/MM/YYYY”
Data_type
Abbreviation describing the type of data collected (e.g., SRµCT; see glossary)
Dataproject_ID
(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF
Facility_proposal_ID
(optional) Number of the proposal for facility usage e.g., the beamline numbers
Facility_institution
“Name or acronym of the institution hosting the main facility (it can be the same as University)”
Facility_country
Country where the facility is located
Facility_name
Name or acronym of the main facility (e.g., CLS, SPring-8,etc)
Facility_sub
(optional) Additional facility information (e.g., beamline)