Command line tool the takes one or a list of Pubmed IDs or DOIs, searches Pubmed for corresponding author affiliations and outputs the information to file
| -h, --help | Show help text |
| -i PUBMEDID, --pubmedid PUBMEDID | |
| Search for author affiliations for single Pubmed ID | |
| -d doi, --doi doi | |
| Search for author affiliations for a single DOI | |
| -f file, --infile file | |
| File with a list of Pubmed IDs and DOIs (they can be mixed). One entry per line. | |
| -x format, --format format | |
| Output format. Choices=['json' (default),'text']. 'text' option produces tab separated table, denormalised in the sense that the pubmed ID/DOI is repeated on multiple rows if there are multiple authors with related affiliations. | |
Pubmed input and JSON output:
python pubmedAuthorAffiliation.py -i 27863242
Output:
{'articleTitle': 'Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes.', 'journalTitle': 'Cell', 'authorList': [{'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Shao', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'S'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Murray', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'J'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Brown', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'A'}, {'firstName': 'n/a', 'institute': 'University of California', 'lastName': 'Taunton', 'affiliation': 'Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.', 'country': 'USA', 'initials': 'J'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Ramakrishnan', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: ramak@mrc-lmb.cam.ac.uk.', 'country': 'UK', 'initials': 'V'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Hegde', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: rhegde@mrc-lmb.cam.ac.uk.', 'country': 'UK', 'initials': 'RS'}], 'pubmedId': '27863242', 'error': False}
{'articleTitle': 'Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes.', 'journalTitle': 'Cell', 'authorList': [{'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Shao', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'S'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Murray', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'J'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Brown', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK.', 'country': 'UK', 'initials': 'A'}, {'firstName': 'n/a', 'institute': 'University of California', 'lastName': 'Taunton', 'affiliation': 'Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.', 'country': 'USA', 'initials': 'J'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Ramakrishnan', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: ramak@mrc-lmb.cam.ac.uk.', 'country': 'UK', 'initials': 'V'}, {'firstName': 'n/a', 'institute': 'MRC-LMB', 'lastName': 'Hegde', 'affiliation': 'MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: rhegde@mrc-lmb.cam.ac.uk.', 'country': 'UK', 'initials': 'RS'}], 'pubmedId': '27863242', 'error': False}
DOI input and text output:
python pubmedAuthorAffiliation.py -d 10.1016/j.molcel.2016.11.013 -x text
Output:
27867008 Molecular cell Molecular Structures of Transcribing RNA Polymerase I. n/a L Tafur European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Germany European Molecular Biology Laboratory (EMBL) 27867008 Molecular cell Molecular Structures of Transcribing RNA Polymerase I. n/a Y Sadian European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Germany European Molecular Biology Laboratory (EMBL) 27867008 Molecular cell Molecular Structures of Transcribing RNA Polymerase I. n/a NA Hoffmann European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Germany European Molecular Biology Laboratory (EMBL) 27867008 Molecular cell Molecular Structures of Transcribing RNA Polymerase I. n/a AJ Jakobi European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany. Germany European Molecular Biology Laboratory (EMBL) 27867008 Molecular cell Molecular Structures of Transcribing RNA Polymerase I. n/a R Wetzel European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Germany European Molecular Biology Laboratory (EMBL) 27867008 Molecular cell Molecular Structures of Transcribing RNA Polymerase I. n/a WJH Hagen European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Germany European Molecular Biology Laboratory (EMBL) 27867008 Molecular cell Molecular Structures of Transcribing RNA Polymerase I. n/a C Sachse European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Germany European Molecular Biology Laboratory (EMBL) 27867008 Molecular cell Molecular Structures of Transcribing RNA Polymerase I. n/a CW Müller European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Electronic address: cmueller@embl.de. Germany European Molecular Biology Laboratory (EMBL)
Input file with mixed DOI and Pubmed. Text output written to a file:
python pubmedAuthorAffiliation.py -f emdb-2010.txt -x text > /tmp/out.txt
In this case unrecognized lines are ignored, e.g.:
WARNING:root:processList: id not recognized: id
This will go through lists of selected Pubmed and DOI known to work:
python test_pubmedAuthorAffiliation.py