Publications Metadata Augmentation (PUMA) pipeline

PUMA is a python pipeline which aggregates third party metadata about journal articles to enable bibliometric research and easy exploration and searching of a collection of articles.

The technical documentation with screenshots is at: https://github.com/OllyButters/puma/wiki

A demo with some of the functionality is at: https://ollybutters.github.io/puma_web

Running the code

The wiki (https://github.com/OllyButters/puma/wiki) has the best instructions, but in overview:

Linux

• Assuming a linux environment with python 3 installed.

• Add all the required python libraries with the requirements.txt file in the source folder:

  pip3 install -r requirements.txt

• Edit the config.ini file in the config folder so it has your API keys etc.

• Run the pipeline from within the source folder with a command like:

  ./papers.py

or point to a specific config file with:

`./papers.py --config my_config.ini`

• Or you can run it from within an IDE.
• Once it has finished, have a look at the web pages in the html folder. Pay particular attention to the coverage_report.html file.

Windows

• Assuming a windows environment (I've only tried Windows 10) with python 3 installed (at least python 3.6 as utf-8 support is a little flakey before that).

• Add all the required python libraries with the requirements.txt file in the source folder by running a command like the following with the command prompt:

  py -3 -m pip install --user -r requirements.txt

• Edit the config.ini file in the config folder so it has your API keys etc.

• Run the pipeline with a command like:

  python papers.py

or point to a specific config file with:

`python papers.py --config my_config.ini`

• Or you can run it from within an IDE.
• Once it has finished, have a look at the web pages in the html folder. Pay particular attention to the coverage_report.html file.

Azure pipelines

The example instances of the output at https://ollybutters.github.io/puma_web are automatically built and deployed with the azure-pipelines.yml file in the root of the web repo at https://github.com/OllyButters/puma_web/.

PUMA project publications

• Butters et al., 2019. DOI: 10.12688/wellcomeopenres.14986.1
• Butters et al., 2021. DOI: 10.12688/f1000research.25484.2

Project Leads

• Dr Becca Wilson, University of Liverpool Co-I & project founder
• Dr Olly Butters, University of Liverpool Co-I

Contributors

• Hugh Garner, University of Newcastle
• Tom Burton, University of Bristol
• Amran Ismail, University of Bristol
• Sue Thompson, Newcastle University
• Katie Ward, University of Liverpool

Funding

Puma has been running for a couple of years and has been funded by a few different sources, of particular note are:

• Nuffield Foundation Summer Research placement
• D2K, University of Bristol
• CLOSER
• D2K, Newcastle University
• UKRI Innovation Fellowship with HDR UK
• NIHR ARC NWC