A web-based publications reference database system.
All publication reference data is visible to all. No login is required for viewing.
Publication references can be added by fetching data from:
Publication references can be added manually.
A powerful subset selection expression evaluator, to produce a wide range of publication subsets from the data. New in version 6.0.
Curator accounts for adding and editing the publication entries can be created by the admin of the instance.
All curators can edit every publication reference. There is a log for each publication, so it is possible to see who did what when.
Publication references can be labeled. The labels can be used to indicate e.g. research group, facility or some other classification. A label can have a qualifier, e.g. to denote if the publication was due to facility service or to a collaboration.
A curator can use only the labels that she has been assigned by the admin.
There is a blacklist registry based on the PMID and/or DOI of publications. When a publication is blacklisted, it will not be fetched when using PMID, DOI or automatic scripts. This is to avoid adding publications that have already been determined to be irrelevant.
Researcher entity, which can be associated with a publication. This is done automatically if the PubMed or Crossref data specifies ORCID for a publication author. New in version 4.0.
Allow setting a flag 'Open Access' for a publication. New in version 4.0.
The publications data can be extracted in JSON, CSV, XLSX and TXT formats.
API to ask the server to fetch publications from PubMed or Crossref. See its README.
Since version 8.0, Python 3.9 or later is required.
Since version 8.0, the main file to be executed is called main.py rather
than app_publications.py. The Docker file has been changed accordingly.
Since version 6.4, the GitHub wiki has been discontinued. Installation information is available below, and other information is available in the web app interface.
Since version 6.3, the directory containing site-specific data
(e.g. settings.yaml, static directory for favicon and logo image files)
has been moved from Publications/publications/site to Publications/site.
The installation procedure has changed accordingly.
Since version 6.0, the Python module
CouchDB2 is used instead of
CouchDB. Upgrade your packages
according to the requirements.txt.
This system requires Python 3.6 or higher.
NOTE: tornado is difficult (even impossible?) to set up on Windows systems, so Linux is strongly recommended.
Ensure that you have Python 3.9 or higher.
Your Python environment must include the Publications directory in its path, e.g.:
$ cd wherever/Publications
$ export PYTHONPATH=$PWdInstall the required Python modules (see Publications/requirements.txt)
Ensure that you have the CouchDB server installed and running.
Create the database publications in the CouchDB server using its
own interface. Ensure that the database allows read/write access
for the CouchDB server account of your choice. Record the CouchDB
server account name and password for the settings.yaml file (see below).
Copy the directory Publications/site_template and all its contents to
Publications/site. The latter directory contains files that can or
should be modified for your site.
Edit your settings file Publications/site/settings.yaml.
In particular, set the CouchDB connection, site name, etc.
The Publications CouchDB database must be initialized using the CLI.
This also tests that the CouchDB variables in the settings.yaml
file are correct.
$ python cli.py initializeCreate an admin account using the CLI. This admin account is needed to create other accounts (admin or curator) in the web interface.
$ python cli.py adminSet up the tornado web server to start on boot, using the port
number you have defined in the settings.yaml file. You need to figure
this out yourself.
Set a proxy from your outward-facing web server (Apache, nginx, or whatever your site supports) for the tornado server. You need to figure this out yourself.
There is a command-line interface (CLI) for admin work on the machine the system is running on. See its help texts. The top-level help text is:
$ python cli.py --help
Usage: cli.py [OPTIONS] COMMAND [ARGS]...
Options:
-s, --settings TEXT Name of settings YAML file.
--log Enable logging output.
--help Show this message and exit.
Commands:
add-label Add a label to a set of publications.
admin Create a user account having the admin role.
counts Output counts of database entities.
curator Create a user account having the curator role.
dump Dump all data in the database to a .tar.gz dump file.
fetch Fetch publications given a file containing PMIDs...
find-pmid Find the PMID for the publications in the CSV file.
initialize Initialize the database, which must exist; load all...
password Set the password for the given account.
remove-label Remove a label from a set of publications.
select Select a subset of publications and output to a file.
show Display the JSON for the single item in the database.
undump Load a Publications database .tar.gz dump file.
update-crossref Use Crossref to update the publications in the CSV file.
update-pubmed Use PubMed to update the publications in the CSV file.
xrefs Output all xrefs as CSV data to the given file.SciLifeLab Infrastructure Units Publications which keeps track of the publications to which the infrastructure units of SciLifeLab have contributed. This was the need that the system was designed for.
Covid-19 Publications for publications with contributions from Swedish research.