rociomer / data-sharing-perspective

Data and scripts to generate figures for the data sharing perspective.

data-sharing-perspective

Data and scripts to generate figures for the perspective "Data sharing in chemistry: lessons learned and a case for mandating structured reaction data" by R Mercado, SM Kearnes, and CW Coley.

Environment

You can use a conda environment to run the plotting scripts in this repo. To set up the environment, run:

conda create -n data-sharing-perspective seaborn -c anaconda
conda activate data-sharing-perspective`

Generating plots

To create the plot for figures 1 and 2 in the manuscript, run:

python plot-entries.py
python plot-contributors.py

The first script will plot data entries over time and the second script will plot contributors/sources over time, for the following databases:

• CSD
• PDB
• PubChem
• ChEMBL

Files will be created in plots/.

Illustrator files

Files used for making the figures shown in the paper are available in illustrator/. Made using Adobe Illustrator.

Raw data

The raw data for the above plots is available in data/. For individual sources, see below:

CSD

Structures available in the CSD (cumulative): Data collected from:

• CCDC documentation

PDB

Depositors for data in the PDB (cumulative): Entries available in the PDB (cumulative) Data collected from:

• PDB Annual Depositors

PubChem

Sources for data in PubChem (cumulative): Data entries in PubChem (cumulative): Data collected from:

• PubChem publications page where I got the data count for PubChem Compounds, BioAssays, and Substances:
  • 2005
  • 2006
  • 2007
  • 2007
  • 2008
  • 2009
  • 2012
  • 2013 & 2016
  • 2018
  • 2021
  • 2022*

* Accessed Dec 25, 2022.

ChEMBL

Sources (documents) for data in ChEMBL (cumulative): Compound entries in ChEMBL (cumulative): Data collected from:

• Breakdown of all data sources in the release notes

Links to icons used in paper figures

Flaticon images linked here (used freely with attribution): 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11