Types#

Note

Even though the EntrezDatabaseType and CommandType types might appear as class objects in the documentation, you can simply provide the appropriate string to the function of your interest.

class Citation#

Dictionary with the citation input data having the following keys and values:

author#

Author name, e.g. ‘mann bj‘ or ‘palmenberg ac‘

first_page#

First page

journal#

Journal title, e.g. ‘science‘ or ‘proc natl acad sci u s a‘

key#

Identifier that will help you recognise the citation in the results, e.g. ‘Art1‘ or ‘Art2‘

volume#

Volume

year#

Year

class CommandType#

The command for the ELnk query, one of:

  • 'neighbor'

    return a set of UIDs in database linked to the input UIDs in database_from.

  • 'neighbor_score'

    return a set of UIDs within the same database as the input UIDs along with computed similarity scores.

  • 'neighbor_history'

    post the output UIDs to the Entrez History server and returns a query_key and WebEnv corresponding to the location of the output set.

  • 'acheck'

    list all links available for a set of UIDs.

  • 'ncheck'

    check for the existence of links within the same database for a set of UIDs. These links are equivalent to setting database and database_from to the same value.

  • 'lcheck'

    check for the existence of external links (LinkOuts) for a set of UIDs.

  • 'llinks'

    for each input UID, list the URLs and attributes for the LinkOut providers that are not libraries.

  • 'llinkslib'

    for each input UID, list the URLs and attributes for all LinkOut providers including libraries.

  • 'prlinks'

    list the primary LinkOut provider for each input UID, or links directly to the LinkOut provider’s web site for a single UID if return_mode is set to ref.

class EntrezDatabaseType#

The database to be used, one of:

  • 'bioproject' - BioProject

  • 'biosample' - BioSample

  • 'biosystems' - Biosystems

  • 'books' - Books

  • 'cdd' - Conserved Domains

  • 'gap' - dbGaP

  • 'dbvar' - dbVar

  • 'epigenomics' - Epigenomics

  • 'nucest' - EST

  • 'gene' - Gene

  • 'genome' - Genome

  • 'gds' - GEO Datasets

  • 'geoprofiles' - GEO Profiles

  • 'nucgss' - GSS

  • 'homologene' - HomoloGene

  • 'mesh' - MeSH

  • 'toolkit' - NCBI C++ Toolkit

  • 'ncbisearch' - NCBI Web Site

  • 'nlmcatalog' - NLM Catalog

  • 'nuccore' - Nucleotide

  • 'omia' - OMIA

  • 'popset' - PopSet

  • 'probe' - Probe

  • 'protein' - Protein

  • 'proteinclusters' - Protein Clusters

  • 'pcassay' - PubChem BioAssay

  • 'pccompound' - PubChem Compound

  • 'pcsubstance' - PubChem Substance

  • 'pubmed' - PubMed

  • 'pmc' - PubMed Central

  • 'snp' - SNP

  • 'sra' - SRA

  • 'structure' - Structure

  • 'taxonomy' - Taxonomy

  • 'unigene' - UniGene

  • 'unists' - UniSTS

References:

Sayers E. The E-utilities In-Depth: Parameters, Syntax and More. 2009 May 29 [Updated 2018 Oct 24]. In: Entrez Programming Utilities Help [Internet]. Bethesda (MD): NCBI (US); 2010-.