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: