biocreative-background-set-pipeline

Library to download PubMed abstracts with metadata. Originally created to obtain the DrugProt (BioCreative VII) background set.
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Requirements

• Python3
• biopython

Usage

It has 2 modes:

• get_pmids mode. This mode is intented to be used when we have a set of PubMed queries and we want to extract the PMIDs that match them. It returns a list (or several lists) of PMIDs.
• fetch mode. This mode receives a list of PMIDs and downloads the PubMed titles and abstracts together with their metadata. It returns a tab-separated file (or several ones) with PMID, title, abstract, PMC id, MeSH terms and language. It also stores the complete object downloaded from PubMed into a JSON file (or several files). The titles and abstracts have UFT-8 encoding, with NFKC Unicode normalization and all whitespaces are normalized (meaning, there are no tabs, new lines, etc).

To modify the execution mode, line 241 must be changed.

Usage in the get_pmids mode

1. Go to line 241 and write

    mode = 'get_pmids'

2. Execute python code

python get_background.py -i /path/ -o toy-data/queries-example --logfile ~/outfolder/log.log

Script Arguments

• -i: directory where the pubmed queries file is. It is also the directory where the output will be created
• -o: name of file with pubmed queries
• --logfile: path to logfile

Usage in the fetch mode

1. Go to line 241 and write

    mode = 'fetch'

2. Execute python code

python get_background.py --input toy-data/pmids-example --output ~/outfolder --logfile ~/outfolder/log.log

Script Arguments

• --input: text file with the list of PMIDs you want to download, one per line
• --output: folder where we will store the output
• --logfile: path to logfile

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