Literature clients (indra.literature)

indra.literature.id_lookup(paper_id, idtype)[source]

Take an ID of type PMID, PMCID, or DOI and lookup the other IDs.

If the DOI is not found in Pubmed, try to obtain the DOI by doing a reverse-lookup of the DOI in CrossRef using article metadata.

Parameters:
  • paper_id (string) – ID of the article.
  • idtype ('pmid', 'pmcid', or 'doi) – Type of the ID.
Returns:

ids – A dictionary with the following keys: pmid, pmcid and doi.

Return type:

dict

Pubmed client (indra.literature.pubmed_client)

Search and get metadata for articles in Pubmed.

indra.literature.pubmed_client.expand_pagination(pages)[source]

Convert a page number to long form, e.g., from 456-7 to 456-457.

indra.literature.pubmed_client.get_abstract(pubmed_id, prepend_title=True)[source]

Get the abstract of an article in the Pubmed database.

indra.literature.pubmed_client.get_metadata_for_ids(pmid_list, get_issns_from_nlm=False)[source]

Get article metadata for up to 200 PMIDs from the Pubmed database.

Parameters:
  • pmid_list (list of PMIDs as strings) – Can contain 1-200 PMIDs.
  • get_issns_from_nlm (boolean) – Look up the full list of ISSN number for the journal associated with the article, which helps to match articles to CrossRef search results. Defaults to False, since it slows down performance.
Returns:

Contains the following fields: ‘doi’, ‘title’, ‘authors’, ‘journal_title’, ‘journal_abbrev’, ‘journal_nlm_id’, ‘issn_list’, ‘page’.

Return type:

dict

indra.literature.pubmed_client.get_title(pubmed_id)[source]

Get the title of an article in the Pubmed database.

Pubmed Central client (indra.literature.pmc_client)

indra.literature.pmc_client.filter_pmids(pmid_list, source_type)[source]

Filter a list of PMIDs for ones with full text from PMC.

Parameters:
  • pmid_list (list) – List of PMIDs to filter.
  • source_type (string) – One of ‘fulltext’, ‘oa_xml’, ‘oa_txt’, or ‘auth_xml’.
Returns:

Return type:

list of PMIDs available in the specified source/format type.

indra.literature.pmc_client.id_lookup(paper_id, idtype=None)[source]

This function takes a Pubmed ID, Pubmed Central ID, or DOI and use the Pubmed ID mapping service and looks up all other IDs from one of these. The IDs are returned in a dictionary.

CrossRef client (indra.literature.crossref_client)

indra.literature.crossref_client.doi_query(pmid, search_limit=10)[source]

Get the DOI for a PMID by matching CrossRef and Pubmed metadata.

Searches CrossRef using the article title and then accepts search hits only if they have a matching journal ISSN and page number with what is obtained from the Pubmed database.

Return a list of links to the full text of an article given its DOI. Each list entry is a dictionary with keys: - URL: the URL to the full text - content-type: e.g. text/xml or text/plain - content-version - intended-application: e.g. text-mining

Elsevier client (indra.literature.elsevier_client)

For information on the Elsevier API, see:
indra.literature.elsevier_client.download_article(doi)[source]

Download an article in XML format from Elsevier.

indra.literature.elsevier_client.get_abstract(doi)[source]

Get the abstract of an article from Elsevier.

indra.literature.elsevier_client.get_article(doi, output=u'txt')[source]

Get the full body of an article from Elsevier. There are two output modes: ‘txt’ strips all xml tags and joins the pieces of text in the main text, while ‘xml’ simply takes the tag containing the body of the article and returns it as is . In the latter case, downstream code needs to be able to interpret Elsever’s XML format.