Merge branch 'restructure' into 'main'

Restructure

See merge request !3

.gitattributes

@@ -346,3 +346,4 @@ _publications/Samuilov-2018-PSP/fpls-09-01830.pdf filter=lfs diff=lfs merge=lfs
 /_publications/Samuilov-2018-BOU/fpls-09-01709.pdf filter=lfs diff=lfs merge=lfs -text
 /_publications/Samuilov-2018-BOU/Data[[:space:]]Sheet[[:space:]]1.xlsx filter=lfs diff=lfs merge=lfs -text
 assays/CMML_17-0035_GCMS-MasshunterQuant/dataset/QuantReport_ISTD_ResultsSummary_B_06_00.xlsx filter=lfs diff=lfs merge=lfs -text
+assays/rnaseq-GEO-export-GSE112254/dataset/GSE112254_SupplementalDataset1.csv filter=lfs diff=lfs merge=lfs -text

README.md

@@ -10,6 +10,7 @@ This ARC contains data of the following publications
   - [Original publication](#original-publication-1)
   - [License (of publication)](#license-of-publication-1)
   - [Data availability](#data-availability-1)
+- [Overview Map](#overview-map)
 
 ## [Samuilov-2018-BOU](_publications/Samuilov-2018-BOU)
 
@@ -42,3 +43,57 @@ Copyright © 2018 Samuilov, Rademacher, Brilhaus, Flachbart, Arab, Kopriva, Webe
 ### Data availability
 
 The read data have been submitted to the NCBI GEO under accession number [GSE1122545](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE112254).
+
+## Overview Map
+
+<!--
+arc a list | grep "^--Assay" | uniq | sort | sed 's/--Assay: /assays\//g'
+arc s list | grep "^Study" | uniq | sort | sed 's/Study: /studies\//g'
+-->
+
+```mermaid
+graph TD
+
+a1[assays/CMML_16-0016_GCMS]
+a2[assays/CMML_16-0016_GCMS-MasshunterQuant]
+a3[assays/CMML_16-0016_HPLC]
+a4[assays/CMML_17-0035_GCMS]
+a5[assays/CMML_17-0035_GCMS-MasshunterQuant]
+
+a6[assays/rna-seq]
+a7[assays/rna-data-processing]
+
+a8[assays/rnaseq-GEO-export-GSE86380]
+a9[assays/rnaseq-GEO-export-GSE112254]
+
+s0[studies/arabidopsis-reference]
+s1[studies/bou_psp_DayNight]
+s2[studies/psp_DayNight_Cd]
+p2[_publications/Samuilov-2018-PSP]
+p1[_publications/Samuilov-2018-BOU]
+
+s0 --> a6 --> a7
+s1 --> a6
+s2 --> a6
+
+a7 --> a8 --> p1
+a7 --> a9 --> p2
+
+s1 --> a1 --> a2 --> p1
+s1 --> a3 --> p1
+s2 --> a4 --> a5 --> p2
+a2 --> p2
+
+%% Defining node styles
+  classDef study fill:#b4ce82, stroke:#333;
+  classDef assay fill:#ffc000;
+  classDef data fill:#c21f3a,color:white;
+  classDef publication fill:#2d3e50,color:white;
+
+%% Assigning styles to nodes
+    class s1,s2 study;
+    class a1,a2,a3,a4,a5,a6,a7,a8,a9 assay;
+    class d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,l4 D;
+    class p1,p2 publication;
+
+```