[Biopython] author affiliations in Entrez / Medline

[Peter Cock]

See discussion on https://github.com/biopython/biopython/issues/4303
which has not reached a conclusion.

Peter

On Wed, Jan 3, 2024 at 8:59 PM Iddo Friedberg <idoerg at gmail.com> wrote:
>
> Hi,
>
> Does anyone know how to map author institutional affiliations in the Entrez module? Since one author can have several affiliations in a paper, the affiliations list can be longer than the author list, but there is no one-to-many mappings of the authors to the affiliations that I could see using Biopython?
>
> See snippet below. Outputs are in boldface.
>
> from Bio import Entrez, Medline
> Entrez.email="my_email at myplace.com"
> handle = Entrez.efetch(db="pubmed", id="37739408", rettype="medline", retmode="text")
> paper_list = list(Medline.parse(handle))
> len(paper_list[0]['AD']) # of affiliations
> 13
> len(paper_list[0]['FAU']) # of authors
> 8
>
> paper_list[0]['FAU']
> ['Mahlich, Yannick', 'Zhu, Chengsheng', 'Chung, Henri', 'Velaga, Pavan K', 'De Paolis Kaluza, M Clara', 'Radivojac, Predrag', 'Friedberg, Iddo', 'Bromberg, Yana']
> paper_list[0]['AD']
> ['Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA.', 'Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA.', 'Xbiome Inc., 1 Broadway, 14th fl, Cambridge, MA 02142, USA.', 'Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.', 'Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA.', 'Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA.', 'Khoury College of Computer Sciences, Northeastern University, 177 Huntington Avenue, Boston, MA 02115, USA.', 'Khoury College of Computer Sciences, Northeastern University, 177 Huntington Avenue, Boston, MA 02115, USA.', 'Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.', 'Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA.', 'Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA.', 'Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA.', 'Department of Computer Science, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA.']
>
>
> Thanks,
>
> Iddo
> --
> Iddo Friedberg
>
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