pybibget • Dominik Schröder

Command line utility to automatically retrieve BibTeX citations from MathSciNet, arXiv, PubMed and doi.org (Github)

Installation

% pip install pybibget

Usage

Citation Keys

pybibget provides a command line interface to obtain BibTeX entries from citation keys of the form

Citation key	Format
MR0026286	MathSciNet (requires subscription)
1512.03385	arXiv identifier (new format)
hep-th/9711200	arXiv identifier (old format)
PMID:271968	PubMed
10.1109/CVPR.2016.90	DOI

pybibget key1 key2 ... prints the BibTeX entries stdout:

% pybibget MR0026286 10.1109/TIT.2006.885507 math/0211159 PMID:271968 10.1109/CVPR.2016.90 10.4310/ATMP.1998.v2.n2.a1

@article{MR0026286,
    AUTHOR = "Shannon, C. E.",
    TITLE = "A mathematical theory of communication",
    JOURNAL = "Bell System Tech. J.",
    FJOURNAL = "The Bell System Technical Journal",
    VOLUME = "27",
    YEAR = "1948",
    PAGES = "379--423, 623--656",
    ISSN = "0005-8580",
    MRCLASS = "60.0X",
    MRNUMBER = "26286",
    MRREVIEWER = "J. L. Doob",
    DOI = "10.1002/j.1538-7305.1948.tb01338.x",
    URL = "https://doi.org/10.1002/j.1538-7305.1948.tb01338.x"
}

@article{10.1109/TIT.2006.885507,
    AUTHOR = "Candes, Emmanuel J. and Tao, Terence",
    TITLE = "Near-optimal signal recovery from random projections: universal encoding strategies?",
    JOURNAL = "IEEE Trans. Inform. Theory",
    FJOURNAL = "Institute of Electrical and Electronics Engineers. Transactions on Information Theory",
    VOLUME = "52",
    YEAR = "2006",
    NUMBER = "12",
    PAGES = "5406--5425",
    ISSN = "0018-9448",
    MRCLASS = "94A12 (41A25 94A13)",
    MRNUMBER = "2300700",
    MRREVIEWER = "L. L. Campbell",
    DOI = "10.1109/TIT.2006.885507",
    URL = "https://doi.org/10.1109/TIT.2006.885507"
}

@unpublished{math/0211159,
    author = "Perelman, Grisha",
    title = "{The} entropy formula for the {Ricci} flow and its geometric applications",
    note = "Preprint",
    year = "2002",
    eprint = "math/0211159",
    archiveprefix = "arXiv"
}

@article{PMID:271968,
    author = "Sanger, F. and Nicklen, S. and Coulson, A. R.",
    doi = "10.1073/pnas.74.12.5463",
    url = "https://doi.org/10.1073/pnas.74.12.5463",
    year = "1977",
    publisher = "Proceedings of the National Academy of Sciences",
    volume = "74",
    number = "12",
    pages = "5463--5467",
    title = "{DNA} sequencing with chain-terminating inhibitors",
    journal = "Proceedings of the National Academy of Sciences",
    PMID = "271968"
}

@inproceedings{10.1109/CVPR.2016.90,
    author = "He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian",
    doi = "10.1109/cvpr.2016.90",
    url = "https://doi.org/10.1109/cvpr.2016.90",
    year = "2016",
    publisher = "{IEEE}",
    title = "{Deep} {Residual} {Learning} for {Image} {Recognition}",
    booktitle = "2016 {IEEE} Conference on Computer Vision and Pattern Recognition ({CVPR})"
}

@article{10.4310/ATMP.1998.v2.n2.a1,
    AUTHOR = "Maldacena, Juan",
    TITLE = "The large {$N$} limit of superconformal field theories and supergravity",
    JOURNAL = "Adv. Theor. Math. Phys.",
    FJOURNAL = "Advances in Theoretical and Mathematical Physics",
    VOLUME = "2",
    YEAR = "1998",
    NUMBER = "2",
    PAGES = "231--252",
    ISSN = "1095-0761",
    MRCLASS = "81T30 (81T60 83E30)",
    MRNUMBER = "1633016",
    MRREVIEWER = "Douglas J. Smith",
    DOI = "10.4310/ATMP.1998.v2.n2.a1",
    URL = "https://doi.org/10.4310/ATMP.1998.v2.n2.a1"
}

With the option -w filename the result can be appended to any given file directly:

% pybibget MR0026286 10.1109/TIT.2006.885507 math/0211159 PMID:271968 10.1109/CVPR.2016.90 10.4310/ATMP.1998.v2.n2.a1 -f bibliography.bib
Succesfully appended 6 BibTeX entries to bibliography.bib

TeX File Parsing

pybibparse automatically parses missing citations from the biber or bibtex log for a given TeX file

% pybibparse example

@article{math/0211159,
    author = "Perelman, Grisha",
    title = "{The} entropy formula for the {Ricci} flow and its geometric applications",
    journal = "preprint",
    year = "2002",
    eprint = "math/0211159",
    archiveprefix = "arXiv"
}

@article{PMID:271968,
    author = "Sanger, F. and Nicklen, S. and Coulson, A. R.",
    doi = "10.1073/pnas.74.12.5463",
    url = "https://doi.org/10.1073/pnas.74.12.5463",
    year = "1977",
    publisher = "Proceedings of the National Academy of Sciences",
    volume = "74",
    number = "12",
    pages = "5463--5467",
    title = "{DNA} sequencing with chain-terminating inhibitors",
    journal = "Proceedings of the National Academy of Sciences",
    PMID = "271968"
}

With the option -w [file_name] the obtained citations are automatically appended to the .bib file. [file_name] is optional if the .bib file has been specified in the TeX file.

% pybibparse example -w
Succesfully appended 2 BibTeX entries to bibliography.bib

Updating existing bibliographies

pybibupdate [file.bib] scans an existing .bib-file and searches for entries with updated information on Scopus. This functionality requires an API-key which can be obtained from https://dev.elsevier.com

Data Sources

MathSciNet

Directly accesses MathSciNet and uses the provided citation unmodified

DOI

First searches for the DOI on MathSciNet. If successful, uses the MathSciNet strategy, otherwise uses the citation from doi.org with the following modifications:

Author names and title are converted to TeX form (special characters like ö are converted to "{o})
Capital words in the title are surrounded by {...}to ensure capitalization
Publication month data is removed

PubMed

Searches for the DOI on PubMed, then uses the DOI strategy and appends pmid = [PMID] to the resulting citation.

arXiv

Uses DOI strategy if metadata contains doi. Otherwise creates an unpublished bib-entry with note = "Preprint" or note = [Journal Metadata] (if provided). In any-case appends eprint = [arXiv identifier] to the citation.