From db44ef7fc90880cdff681b21b1d84ca01d48eeb4 Mon Sep 17 00:00:00 2001
From: Sheeba Samuel <sheeba.samuel@uni-jena.de>
Date: Sat, 13 Apr 2024 02:35:25 +0200
Subject: [PATCH] Update documentation.

---
 docs/content/index.md                    | 34 ++++++++++++++++++++++++
 docs/content/stylesheets/fairjupyter.css |  6 ++---
 mkdocs.yml                               |  3 +++
 3 files changed, 40 insertions(+), 3 deletions(-)

diff --git a/docs/content/index.md b/docs/content/index.md
index 56b591b..47b24be 100644
--- a/docs/content/index.md
+++ b/docs/content/index.md
@@ -1,2 +1,36 @@
 # FAIR Jupyter
 
+FAIR Jupyter is a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset.
+
+## Computational reproducibility of Jupyter notebooks from biomedical publications
+We present the dataset for the study of computational reproducibility of Jupyter notebooks from biomedical publications. Our focus lies in evaluating the extent of reproducibility of Jupyter notebooks derived from GitHub repositories linked to publications present in the biomedical literature repository, PubMed Central. We analyzed the reproducibility of Jupyter notebooks from GitHub repositories associated with publications indexed in the biomedical literature repository PubMed Central. The dataset includes the metadata information of the journals, publications, the Github repositories mentioned in the publications and the notebooks present in the Github repositories.
+
+## FAIR Jupyter Knowledge Graph
+FAIR Jupyter Knowledge Graph is based on the computational reproducibility dataset that we had previously shared in bulk. This dataset can now be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. We took this dataset, converted it into semantic triples and loaded these into a triple
+store to create a knowledge graph – FAIR Jupyter – that we made accessible via a webservice. This enables granular data exploration and
+analysis through queries that can be tailored to specific use cases.
+
+## Permanent URL
+[https://w3id.org/fairjupyter](https://w3id.org/fairjupyter)
+
+## Resources
+
+### SPARQL Endpoint
+
+### Original Dataset
+Data: Sheeba Samuel, & Daniel Mietchen. (2023). Dataset of a Study of Computational reproducibility of Jupyter notebooks from biomedical publications [Data set]. Zenodo. [https://doi.org/10.5281/zenodo.8226725](https://doi.org/10.5281/zenodo.8226725)
+
+Code: [https://github.com/fusion-jena/computational-reproducibility-pmc](https://github.com/fusion-jena/computational-reproducibility-pmc)
+
+### Documentation
+
+### FAIR Jupyter KG N-Triples Dump
+
+### FAIR Jupyter KG Schema
+
+### FAIR Jupyter KG Data Used (CSV)
+
+
+## Publication
+
+* Sheeba Samuel, Daniel Mietchen, Computational reproducibility of Jupyter notebooks from biomedical publications, GigaScience, Volume 13, 2024, giad113, [https://doi.org/10.1093/gigascience/giad113](https://doi.org/10.1093/gigascience/giad113)
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diff --git a/docs/content/stylesheets/fairjupyter.css b/docs/content/stylesheets/fairjupyter.css
index 362a542..bc80076 100644
--- a/docs/content/stylesheets/fairjupyter.css
+++ b/docs/content/stylesheets/fairjupyter.css
@@ -1,3 +1,3 @@
-:root>* {
-    --md-typeset-a-color: #1b80cf;
-}
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+:root {
+    --md-primary-fg-color:        #1b80cf;
+  }
diff --git a/mkdocs.yml b/mkdocs.yml
index c675851..3469f9e 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -6,5 +6,8 @@ nav:
   - Home: index.md
 theme:
   name: material
+  features:
+    - toc.follow
 extra_css:
   - stylesheets/fairjupyter.css
+