biblio-glutton

A framework dedicated to scientific bibliographic information. It includes:

• a bibliographical reference matching service: from an input such as a raw bibliographical reference and/or a combination of key metadata, the service will return the disambiguated bibliographical object with in particular its DOI and a set of metadata aggregated from Crossref and other sources,
• a fast metadata look-up service: from a "strong" identifier such as DOI, PMID, etc. the service will return a set of metadata aggregated from Crossref and other sources,
• various mapping between DOI, PMID, PMC, ISTEX ID and ark, integrated in the bibliographical service,
• Open Access resolver: Integration of Open Access links via the Unpaywall dataset from Impactstory,
• Gap and daily update for Crossref resources (via the Crossref REST API), so that your glutton data service stays always in sync with Crossref,
• MeSH classes mapping for PubMed articles.

biblio-glutton should be very handy if you need to run and scale a local full "Crossref" database and API, to aggregate Crossref, Pubmed and other common bibliographical records and to match a large amount of bibliographical records or raw bibliographical reference strings.

The framework is designed both for speed (with several thousands request per second for look-up) and matching accuracy. It can be scaled horizontally as needed and can provide high availability.

Benchmarking against the Crossref REST API is presented below.

In the Glutton family, the following complementary tools are available for taking advantage of Open Access resources:

• biblio-glutton-extension: A browser extension (Firefox & Chrome) for providing bibliographical services, like identifying dynamically Open Access resources on web pages and providing contextual citation services.

• biblio-glutton-harvester: A robust, fault tolerant, Python utility for harvesting efficiently (multi-threaded) a large Open Access collection of PDF (Unpaywall, PubMed Central), with the possibility to upload content on Amazon S3,

Current stable version of biblio-glutton is 0.3. Working version is 0.4-SNAPSHOT.

Documentation

The full documentation is available here, including an evaluation of the bibliographical reference matching and some expected runtime information.

How to cite

If you want to cite this work, please refer to the present GitHub project, together with the Software Heritage project-level permanent identifier and do please indicate any author name. For example, with BibTeX:

@misc{biblio-glutton,
    title = {biblio-glutton},
    url = {https://github.com/kermitt2/biblio-glutton},
    publisher = {GitHub},
    year = {2018--2024},
    archivePrefix = {swh},
    eprint = {1:dir:a5a4585625424d7c7428654dbe863837aeda8fa7}
}

Main authors and contact

• Patrice Lopez (@kermitt2, patrice.lopez@science-miner.com)

• Luca Foppiano (@lfoppiano)

License

Distributed under Apache 2.0 license.

If you contribute to this project, you agree to share your contribution following this license.