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- /webpage_contents/_quarto.yml
- /webpage_contents/content_glossary.md
- /webpage_contents/content_metadata_tables.md
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webpage_contents/_quarto.yml 0 → 100644
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project:
type: book
book:
title: Fluid Dynamics of the Central Nervous System
page-navigation: true
back-to-top-navigation: true
sidebar:
logo: images/Logo_fluidDynamicsCNS.png
chapters:
- index.qmd
- content_glossary.qmd
- content_metadata_tables.qmd
format:
html:
toc: true
number-sections: false
toc-depth: 4
webpage_contents/content_glossary.md 0 → 100644
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---
title: Glossary of abbreviations
toc-depth: 4
toc-expand: 4
---
## Global {.unnumbered}
These abbreviations are used in the project gran proposal and in the central index to find data from the different research groups. Local indices for the different data types will have additional type-specific set of abbreviations.
| | |
|:------|:---------------------------------------------|
| FDCNS | Fluid Dynamics of the Central Nervous System |
#### Research groups
| | |
|:----|:----------------------------|
| BMC | Biomaterials Science Center |
| TKI | Theodor Kocher Institute |
| TIG | The Interface Group |
#### Universities
| | |
|:------|:---------------------|
| UNIBA | University of Basel |
| UNIBE | University of Bern |
| UZH | University of Zurich |
#### Data types and techniques
| | |
|:-------|:-----------------------------------------------|
| CSU-W1 | Confocal microscopy |
| CFD | Computational Fluid Dynamics Modeling |
| 2P-IVM | Two-photon Microscopy |
| GRIN | Gradient-index lens |
| IVM | Intravital Fluorescence Microscopy |
| MRI | Magnetic Resonance Imaging |
| NIR | Near-infrared imaging |
| PC-MRI | Phase-contrast Magnetic Resonance Imaging |
| SRµCT | Synchrotron Radiation Computed Microtomography |
#### Data descriptors
::: {.callout-note collapse="true"}
The metadata table can have different resolutions:
For example
- **File_locations** tables may have one row per data package or bundles of datasets (e.g., multiple mice)
- **Mice_info** tables have one row per mice
- **Scan_list** can have one row per folder with scans or one row per reference image files
:::
| | |
|:-------|:-----------------------------------------------|
| Data file | Each of the individual files that makes a data set |
| Data set | A bundle of files for one mice. One mice can have several data sets (e.g., each is a collection synchrotron images under different conditions) |
| Data package | Collection of data sets collected in one facility for a specific time period (e.g., synchrotron images from Japan in 2023 ) |
| Metadata | Data describing data , necessary for reuse and interpretation of the data |
| Documentation | Metadata aimed primarily at being read by humans, e.g., README files, protocols, filenaming conventions, etc |
| Structured metadata | Metadata that can be read by humans and machine, e.g., sidecar files, tables|
| Tabular metadata | Tables with metadata (machine-readable) |
| JSON | JavaScript Object Notation: format of 'sidecar' metadata files which are stored next to the data files |
## Sinergia domain-specific {.unnumbered}
#### Pathologies
| | |
|:----------------------------|:--------------------|
| AD | Alzheimer's Disease |
| Cerebral amyloid angiopathy | CAA |
| MS | Multiple Sclerosis |
#### Mice
| | |
|:---------------|:-------------------------------------------------------|
| arcA𝛽 | genetically modified mouse strain, mouse model for Alzheimer's disease. |
| EAE | Experimental autoimmune encephalomyelitis. Mouse model for multiple sclerosis. Disease is induced via treatment |
#### Biology and physiology
| | |
|:------|:----------------------------------|
| BBB | Blood-brain-barrier |
| BCSFB | Blood-cerebrospinal Fluid Barrier |
| ChP | Choroid plexus |
| CNS | Central Nervous System |
| CSF | Cerebrospinal Fluid |
| EpC | Ependymal cilia |
| ISF | Interstitial Fluid |
| PVS | Perivascular spaces |
| SAS | Subarachnoide space |
### Misc abbreviations
| | |
|:-----|:---------------------------------------------------------------|
| URL | Uniform Resource Locato, is the address of a unique resource on the internet.|
| FOV | Field of View |
| JSON | JavaScript Object Notation: format of 'sidecar' metadata files |
| SOP | Standard Operating Procedure |
webpage_contents/content_metadata_tables.md 0 → 100644
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---
title: 'Metadata tables'
mermaid:
theme: forest
---
The following sections describes the **variables** used in the different metadata tables. All tables should be machine-readable. They should have one or more **key variables** which are **shared** across all tables so that we can linked them (or create a full joined table containing all information)
| | Metadata table | Content |
|-------------------|---------------------------|---------------------------|
| ![](images/clipboard-1705609629.png){width="51" height="38"} | Data Storage Information | Server(s) address and disks. One row per bundle of data packages / datasets stored in different disks (containing data from multiple mice) |
| ![](images/clipboard-1705609629.png){width="51" height="38"} | Mice Information | Mice features. One row per mouse. |
| ![](images/clipboard-18485090.png){width="47" height="63"} | Scan Information | List of folders/files available for each mice |
: Metadata table {.light}
- 🔑 **SubjectID** (mice ID) used as key variable to combine Mice Information and Scan Information
- 🔑 **Datapackage ID** is used as key variable to combine Data Storage table with the Mice or Scan Information
# Data Storage Table
::: panel-tabset
## Variable codebook
#### Data provenance
Describe origin of the data, where, when and by whom they were collected and whether the data package is complete.
| | |
|:-------------------------|:---------------------------------------------|
| 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 data curation |
| 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_1 | Name or acronym of the main facility (e.g., CLS, SPring-8,etc) |
| Facility_2 | (optional) Additional facility information (e.g., beamline) |
| Facility_Country | Country where the facility is located |
| Start_date_acquisition | DD/MM/YYYY |
| Contact_researcher | Main researcher responsible for data collection, ideally can be contacted if there are issues with the data package or dataset |
| Status | Indicate if 'complete' or 'in progress' |
| Status_comment | (optional) additional comments on the status of these data |
: {.striped .hover}
#### File descriptors
Describe more details of the files, like the type of images they contain and how much volume they take on disk
| | |
|:--------------------------|:--------------------------------------------|
| Files_type | (If applicable) more detailed description of the files depending on the data type. E.g., if data_type is synchrotron: projections, reconstructions or both. |
| Data_size | The total volume of the data stored |
| File_subjectIDs | List which samples (mice) were in this location be precise e.g., `CA001-CA030` should be used only if there are really 30 subjects with IDs 001 to 030 |
: {.striped .hover}
#### Storage locations
Show the paths to the data. The columns should provide enough information to find the data and access it (whenever the right permissions are in place). There can be several locations accessible offline or online.
##### Online locations
If available, indicate the address in the servers maintained by the research group who collected the data, e.g., if synchrotron data collected by TIG the server is expected to be maintained at the TIG facilities
::: {.callout-caution collapse="true"}
Make sure paths are machine-readable: avoid entries like "123.54.666.10\\data\\folder (additional info)", where the information in brackets has to be removed. Also, beware of any white spaces at the end of the path.
:::
| | |
|:--------------------------|:--------------------------------------------|
| Source_server_path | Full path to the data (provide the IP-internet protocol server address, e.g.,'\\\\123.45.679.01\\data\\synchrotron\\brains' and not the arbitrary letter used to map the network drive, like 'O:\\data\\synchrotron\\brains') |
| Source_server_type | Specify if the path refers to a: disk, tape, server, online repository |
| Source_server_access | Public or private, specify any special access rules |
: {.striped .hover}
<br>
##### Physical devices and copies
*Disk\_\<research_group\>*: indicates a copy of the content of the disk in the different research group facilities. Groups cn be TIG, BMC, TKI (see Glossary)
| | |
|:--------------------------|:--------------------------------------------|
| Disk\_\<research_group\>\_status | *Copied* if there is a copy at the facilities of this group |
| Disk\_\<research_group\>\_ID | Unique identifier of the harddisk, e.g., serial number and model |
| Disk\_\<research_group\>\_speed | Copy speed of this disk |
| Disk\_\<research_group\>\_time | Track how long did it take to copy the data |
: {.striped .hover}
## Table example
```{r readtbl}
#| code-fold: true
library(DT)
input_table = 'Data_locations.csv'
miss_values_spec = c("","NA")
tbl <- read.csv(input_table, na.strings = miss_values_spec)
datatable(
tbl,
filter = "top",
escape = FALSE,
rownames = FALSE,
width = "100%",
class = 'compact cell-border hover',
extensions = c('Buttons', 'Select','ColReorder', 'Scroller', 'KeyTable'),
selection = 'none',
options = list(
pageLength = 10,
dom = 'Bfrtip',
buttons = list(list(extend = "colvis", text = "select Columns"),'selectAll', 'selectNone', 'copy' ),
select = list(style = 'os', items = 'row'),
scrollX = TRUE,
scrollY = '600px',
paging = FALSE,
scrollCollapse = FALSE,
autoWidth = TRUE,
colReorder = TRUE,
columnDefs = list(
list(
keys = TRUE,
search = list(regex = TRUE),
targets=0
)
),
initComplete = JS(
"function(settings, json) {",
"$('td').css('font-size', 'smaller');",
"}"
)
)
)
```
:::
# Mice Information Table
::: panel-tabset
## Variable codebook
#### Common variables to all Sinergia datasets
#### Data type-specific variables
These are not documented here as they will vary with each data type (e.g., synchrotron, microscopy, etc.)
:::
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