Search Engine Tools

NCBI Tools

ESearchQuery

 ESearchQuery (api_key=None, oa=False, db='pubmed')

Class to provide query interface for ESearch (i.e., query terms in elaborate ways, return a list of ids) Each instance of this class executes queries of a given type

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NCBI_Database_Type

 NCBI_Database_Type (value, names=None, module=None, qualname=None,
                     type=None, start=1, boundary=None)

Simple enumeration of the different NCBI databases supported by this tool

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EFetchQuery

 EFetchQuery (api_key=None, db='pubmed')

Class to provide query interface for EFetch (i.e., query based on a list of ids) Each instance of this class executes queries of a given type

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get_pdf_from_pubmed_doi

 get_pdf_from_pubmed_doi (doi, base_file_path)

Executes a query on the target database and returns a count of papers

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get_nxml_from_pubmed_doi

 get_nxml_from_pubmed_doi (doi, base_file_path)

Executes a query on the target database and returns a count of papers

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download_file

 download_file (url, local_filename)

Downloads a file from an URL to a local disk

EuroPMCQuery

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EuroPMCQuery

 EuroPMCQuery (oa=False, db='pubmed')

A class that executes search queries on the European PMC API

Open Alex

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read_references_from_openalex

 read_references_from_openalex (doi_or_oa_id)

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load_paper_from_openalex

 load_paper_from_openalex (doi_or_oa_id)

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read_authors_and_institutions_from_openalex

 read_authors_and_institutions_from_openalex (doi_list)

Full text downloads from multiple sources

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download_full_text_paper_for_doi

 download_full_text_paper_for_doi (doi, path, headless=True)

Attempts to download full text for a given DOI if the paper is listed as open access.