Alexandria3k documentation
==========================

The *alexandria3k* package supplies a library and a command-line tool
providing efficient relational query access to diverse publication open
data sets.
The largest one is the entire `Crossref data
set <https://www.nature.com/articles/d41586-022-02926-y>`__ (157 GB
compressed, 1 TB uncompressed). This contains publication metadata from
about 134 million publications from all major international publishers
with full citation data for 60 million of them.
Alternatively, works can be selected from the
`PubMed <https://pubmed.ncbi.nlm.nih.gov/>`__
data set (43 GB compressed, 327 GB uncompressed),
which comprises more than 36 million citations
for biomedical literature from
`MEDLINE <https://www.nlm.nih.gov/medline/medline_overview.html>`__,
life science journals, and online books,
with rich domain-specific metadata,
such as `MeSH <https://www.nlm.nih.gov/mesh/meshhome.html>`__ indexing,
funding, genetic, and chemical details.
In addition,
the Crossref and PubMed data sets can be linked with the `ORCID summary
data
set <https://support.orcid.org/hc/en-us/articles/360006897394-How-do-I-get-the-public-data-file->`__
(25 GB compressed, 435 GB uuncompressed), containing about 78 million
author records,
the `US Patent and Trademark Office issued patents <https://bulkdata.uspto.gov>`__ 
(11 GB compressed, 115 GB uncompressed), containing about 5.4 million records from 2005 to present,
as well as data sets of funder bodies, journal names,
open access journals, and research organizations.


The *alexandria3k*
package installation contains all elements required to run it. It does
not require the installation, configuration, and maintenance of a third
party relational or graph database. It can therefore be used
out-of-the-box for performing reproducible publication research on the
desktop.

Publication
-----------

Details about the rationale, design, implementation, and use of this
software can be found in the following paper.

Diomidis Spinellis. Open reproducible scientometric research with Alexandria3k. *PLoS ONE* 18(11): e0294946. November 2023. `doi: 10.1371/journal.pone.0294946 <https://doi.org/10.1371/journal.pone.0294946>`__

Package name derivation
-----------------------

The *alexandria3k* package is named after the `Library of
Alexandria <https://en.wikipedia.org/wiki/Library_of_Alexandria>`__,
indicating how publication data can be processed in the third millenium
AD.

Contents
========

.. toctree::
   :maxdepth: 2

   installation
   downloading
   use
   cli-eg
   python-eg
   app-eg
   schema
   cli
   user-api
   plugin-api
   utility-api
   dev
   dev-plugin
   faq


Indices and tables
==================

* :ref:`genindex`
* :ref:`search`