Skip to main content

BioC data structures and encoder/decoder for Python

Project description

BioC XML format can be used to share text documents and annotations.

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

Development of bioc happens on GitHub:

Getting started

Installing bioc

$ pip install --pre bioc

Encoding the BioC collection object `collection’:

import bioc
# Serialize ``collection`` to a BioC formatted ``str``.

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

Compact encoding:

import bioc
bioc.dumps(collection, pretty_print=False)

Decoding the BioC XML file:

import json
# Deserialize ``s`` to a BioC collection object.
collection = json.loads(s)
# Deserialize ``fp`` to a BioC collection object.
with open(filename, 'r') as fp:






The official BioC webpage is available with all up-to-date instructions, code, and corpora in the BioC format, and other research on, based on and related to BioC.


  • Comeau,D.C., Doğan,R.I., Ciccarese,P., Cohen,K.B., Krallinger,M., Leitner,F., Lu,Z., Peng,Y., Rinaldi,F., Torii,M., Valencia,V., Verspoor,K., Wiegers,T.C., Wu,C.H., Wilbur,W.J. (2013) BioC: A minimalist approach to interoperability for biomedical text processing. Database: The Journal of Biological Databases and Curation.
  • Peng,Y., Tudor,C., Torii,M., Wu,C.H., Vijay-Shanker,K. (2014) iSimp in BioC standard format: Enhancing the interoperability of a sentence simplification system. Database: The Journal of Biological Databases and Curation.
  • Marques,M., Rinaldi,F. (2012) PyBioC: a python implementation of the BioC core. In Proceedings of BioCreative IV workshop.

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for bioc, version 1.0.dev22
Filename, size File type Python version Upload date Hashes
Filename, size bioc-1.0.dev22-py2.7.egg (2.5 kB) File type Egg Python version 2.7 Upload date Hashes View hashes
Filename, size bioc-1.0.dev22.tar.gz (11.8 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page