Extract Publication Text from Full Text Articles - Githubissues

ndexbio / gsoc_llm

GSOC 2024 LLM Project

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Extract Publication Text from Full Text Articles #5

Open cannin opened 6 months ago

cannin commented 6 months ago

Try the tools below. Try BioPython first otherwise you'll need to extract text from the EBI or NCBI XML documents using XPath queries.

[ ] https://biopython-tutorial.readthedocs.io/en/latest/notebooks/09%20-%20Accessing%20NCBIs%20Entrez%20databases.html
[ ] https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6302245/fullTextXML (if no full text exists then a 404 error returns)
[ ] https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=PMC3661049&retmode=xml (if no full text exists only the abstract returns)

This API can be used to convert from Pubmed (PMID) to PMC IDs: https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/