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Order data sources alphabetically
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dspinellis committed Jul 2, 2024
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39 changes: 19 additions & 20 deletions docs/downloading.rst
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Expand Up @@ -47,6 +47,25 @@ download the *summary file* of the ORCID Public Data File
works on the compressed file; there is no need to expand it (it expands
to about 0.5 TB).

PubMed data
~~~~~~~~~~~

You can populate a database with the data from the PubMed/MEDLINE database
from the National Library of Medicine (NLM).
The data are available from
`here <https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/>`__.
You can also download the data from the FTP server which is documented in
`this readme file <https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/README.txt>`__.
Publication data are overlapping with the Crossref dataset,
but the PubMed data contain additional information
such as MeSH terms and grants.
They also complement the Crossref data as for example some affiliations
are only available in the PubMed data.

The shell script ``examples/common/fetch-pubmed.sh`` or the
``$(PUBMED_DIR)`` dependency of the ``examples/common/Makefile``,
which uses it, can be used to download all PubMed data.

USPTO data
~~~~~~~~~~

Expand Down Expand Up @@ -88,26 +107,6 @@ The shell script ``examples/common/fetch-uspto.sh`` or the
``$(USPTO_DIR)`` dependency of the ``examples/common/Makefile``,
which uses it, can be used to download all USPTO data.

PubMed data
~~~~~~~~~~~

You can populate a database with the data from the PubMed/MEDLINE database
from the National Library of Medicine (NLM).
The data are available from
`here <https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/>`__.
You can also download the data from the FTP server which is documented in
`this readme file <https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/README.txt>`__.
Publication data are overlapping with the Crossref dataset,
but the PubMed data contain additional information
such as MeSH terms and grants.
They also complement the Crossref data as for example some affiliations
are only available in the PubMed data.

The shell script ``examples/common/fetch-pubmed.sh`` or the
``$(PUBMED_DIR)`` dependency of the ``examples/common/Makefile``,
which uses it, can be used to download all PubMed data.



Other data sources
~~~~~~~~~~~~~~~~~~
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