Plot total number of bed files in GEO database.

All GEO bed files are related to GSM (samples) and samples are related to GSE (series).

All projects (series) are downloaded and served in PEPhub: https://pephub.databio.org/bedbase. So the easiest way to count total number of bed files in GEO is to count the number of samples under bedbase namespace. Important to note, that one sample can have multiple project, that's why we need to count distinct samples.

To do so we can use sql query:

select EXTRACT(YEAR FROM b.submission_date) AS year,
  count(distinct a.sample_name) from samples as a join projects as b on a.project_id = b.id
  where b.namespace='bedbase'
  group by EXTRACT(YEAR FROM b.submission_date)
  order by year;

It is a heavy query, that will take a while to run. (up to 3 minutes)

This will give you the number of samples per year. e.g.

year  count
2007  47
2008  197
2009  2260
2010  1608
2011  5800
2012  5796
2013  5154
2014  4145
2015  3800
2016  12242
2017  12238
2018  10876
2019  19227
2020  11886
2021  24966
2022  21280
2023  17458
2024  13348
2025  2602

After you have a csv with the number of samples per year, you can use it to plot the number of samples per year.

import pandas as pd
import matplotlib.pyplot as plt

data = pd.read_csv("geo2025_06.csv")

data["summary"] = data["count"].cumsum()
data["year_str"] = data["year"].astype(str)


fig, ax = plt.subplots()
plt.xticks(rotation=45)
ax.bar(data["year_str"], data["summary"], label=data["year_str"], color="green")

ax.set_xlabel("Year")
ax.set_ylabel("Number of files")
ax.set_title("Cumulative number of BED files")


fig.savefig("./bed_geo_2025_06_summary.svg")

Plot total number of bed files in GEO database.

The output plot: