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Project description

BioP JSON format can be used to share text documents and annotations.

biop exposes an API familiar to users of the standard library marshal and pickle modules.

Development of biop happens on GitHub:

Getting started

Installing biop (with conda)

$ git clone
$ cd pengyifan-biop
$ conda env create -f environment2.7.yml
$ source activate biop
$ python

Encoding the BioC collection object collection:

import bioj
# Serialize ``PDocument`` to a BioP formatted ``str``.

# Serialize ``PDocument`` as a BioP formatted stream to ``fp``.
with open(filename, 'w') as fp
    bioc.dump(document, fp)

Decoding the BioP JSON file:

import biop

# Deserialize ``fp`` to a BioP document object.
with open(filename, 'r') as fp:


To validate the dataset format, run

jsonschema -i tests/foo.json biop_schema.json


Please read CONTRIBUTING for details on our code of conduct, and the process for submitting pull requests to us.



see LICENSE.txt.


We are grateful to the folowing projects: BioC and Brat.

Project details

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