At NCBI BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.
This repository can be used to convert the original bioproject.xml file (2.1 Gb) available here:
https://ftp.ncbi.nlm.nih.gov/bioproject/bioproject.xml
into a more accessible ans smaller in size .json file. Python code used for the conversion is available.
We parsed in R by library(rjson) the .json file and created a tab separated table with some useful fields like ID, Name, Description.
R code to output a tab separated table from json input is available in R/main.R.
Output table is test/demo.tsv
Before using the repository, you need to install the following dependency:
pip install xmltodict
pip install pytest
Then you can check that the repository is correctly installed, by running:
pytest unit_test.py
If everything works properly, you can convert an xml file into a json file, by giving the input filename and the output filename. You can try it with the demo file that we have provided in the folder test, as follows:
python converter.py test/demo.xml test/demo.json
Check the "test" folder; a .json file should be there.