Does anyone know how I can easily download all of the pubmed article abstracts? I am working on a text mining project.
The closest one I can find can download one abstract at a time given an pmid, but that would be too slow for my purpose since I'd have to download them one at a time.
On
Searching for "0000/01/01"[PDAT] : "3000/12/31"[PDAT] should get you every article from the beginning of time.
Maybe the "sent to" function shown right-above the search results will let you download everything.
Alternatively, you can write a script and use the Entrez programming utility from the NCBI.
You can perform a search query using ESearch, which will return all PMID's. Then you can use EFetch to return all data. It is explained in this book/manual: http://www.ncbi.nlm.nih.gov/books/NBK25501/
Chapter 3 contains some example scripts which should get you started: http://www.ncbi.nlm.nih.gov/books/NBK25498/#chapter3
You will get xml files containing the abstract and all other data.
25 million XML files...
On
I am aware this has gone a bit stale, but they have a process for your exact same use case - large scale mining projects.
You can get the data via a free licensing agreement - more information here.
On
You can get ALL the data from NLM directly via FTP.
https://www.nlm.nih.gov/databases/download/terms_and_conditions_pubmed.html
Download and work away without worrying about e-utils.
On
I would use RESTful API provided by Europe PMC. They allow to download 25 articles per query in json or xml format. Example queries for articles about malaria would look like:
You can use different format of search query, it depends what you really want to retrieve.
As of 2021, you can access the corpus through simple API of Huggingface Datasets.
https://huggingface.co/datasets/pubmed