Wolfram Function Repository

Instant-use add-on functions for the Wolfram Language

Function Repository Resource:

 GetPubMedIdentifiers

Source Notebook

Find the PubMed entries corresponding to a given identifying NCBI succession for a biological sequence

Contributed by: John Cassel, Wolfram|Alpha Scientific Content

ResourceFunction["GetPubMedIdentifiers"][accession,type]

queries NCBI for PubMed identifiers corresponding to an accession of the given type, which can be "Nucleotide", "Protein" or a "BioSequenceType" entity.

ResourceFunction["GetPubMedIdentifiers"][accession]

queries NCBI for PubMed identifiers corresponding to the accession, guessing the appropriate query parameters from the content of the accession.

Details

This function calls the NCBI Entrez ELink service. The terms of service require that one insert a gap of at least a third of a second per call.
Lower case "protein" and "nucleotide" can be used for specifying those types.

Examples

Basic Examples (1) 

Obtain the PubMed identifiers corresponding to the reference SARS-CoV-2 leader protein:

Out[0]=

Scope (2) 

Obtain the PubMed entries for a particular SARS-CoV-1 DNA sequence:

In[1]:=
ResourceFunction["GetPubMedIdentifiers"]["MW885883.1", Entity["BioSequenceType", "DNA"]]
Out[1]=

Find the PubMed entries corresponding to the accession specified as a nucleotide:

In[2]:=
ResourceFunction["GetPubMedIdentifiers"]["MW885878.1", "Nucleotide"]
Out[2]=

Version History

  • 1.0.0 – 10 May 2021

Source Metadata

Related Resources

Author Notes

This function calls the NCBI Entrez ELink service. To honor the terms of service, insert a gap of at least a third of a second per call.

License Information