pmcfigurebot

Query figures indexed by PubMed Central and collect metadata

PubMed Image Query

The GitHub Action is configured to run scripts/fetch_pmc.R on demand and monthly (by default) in order to query PMC for any new figures published since the last run. The script downloads .jpg files and prepares a .yml file with metadata for each figure and its parent paper.

Configure your query

Enter your query terms and an optional date information in query_config.yml

terms - Enter either a list of terms to be used in a default AND query, or a valid query string, e.g., (network OR PPI) AND cytoscape

last_run - (Optional) Date of the last run. Auto-filled by script. Uses prior month if blank; overriden by date_range. Format: %Y/%m/%d, e.g., 2022/10/29

date_range - (Optional) Either a list of two dates (%Y/%m/%d) or a valid date string, e.g,. 2022/10/01[PUBDATE]:2023/01/01[PUBDATE] Important: If used, this field will override the use of last_run

Use Cases

The collected data files can be used in a variety of ways, including to generate social media posts, newsletters, feeds, annual reports, etc. See examples in the scripts folder.

Limitations

• Only accesses the first page of results from PMC with a maximum of 100 figures.