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Going from pubmed esearch to protein fasta sequences: Biopython

After I run my esearch in pubmed I return a list of IDs for publications. I found the following info by running einfo on pubmed"

# {'Name': 'pubmed_protein_weighted', 'Menu': 'Protein (Weighted) Links', 'Description': 'Links to protein', 'DbTo': 'protein'}
# {'Name': 'pubmed_snp', 'Menu': 'SNP Links', 'Description': 'PubMed to SNP links', 'DbTo': 'snp'}
# {'Name': 'pubmed_protein_refseq', 'Menu': 'Protein (RefSeq) Links', 'Description': 'Link to Protein RefSeqs', 'DbTo': 'protein'}
# {'Name': 'pubmed_dbvar', 'Menu': 'dbVar', 'Description': 'Link from PubMed to dbVar', 'DbTo': 'dbva

My question is how do I use biopython entrez to link out to respective DBs? Like

 {'Name': 'pubmed_protein_weighted', 'Menu': 'Protein (Weighted) Links', 'Description': 'Links to protein', 'DbTo': 'protein'}?
protein fasta biopython entrez
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written by m.brathwaite 0

Can you provide an example of search terms? Looks like you are simply showing JOSN format link-out information above.

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written by GenoMax 16K 
handle = Entrez.esearch(db ="pubmed", retmax = 25, term="gefitinib")
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updated by Ram 4.5K • | written by m.brathwaite 0

Something like this:

$ esearch -db pubmed -query "gefitinib" | elink -target protein -name pubmed_protein_refseq | esummary | xtract -pattern DocumentSummary -element Caption,Title 
NP_001403494    endothelin-1 isoform 1 preproprotein [Homo sapiens]
NP_001403492    endothelin-1 isoform 1 preproprotein [Homo sapiens]
NP_001403493    endothelin-1 isoform 1 preproprotein [Homo sapiens]
NP_001402068    forkhead box protein O3 isoform 2 [Homo sapiens]
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written by GenoMax 16K

Makes sense! I totally forgot about the 'pipe' to with 'elink'. Much appreciated!

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written by m.brathwaite 0

This is good for working in UNIX, but I'm working on editing it for BioPython. Would you happen to have and example?

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written by m.brathwaite 0

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