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BioC data structures and encoder/decoder for Python

Project description

`bioc` -- BioC data structures and encoder/decoder for Python
============================================

`BioC XML format <http://bioc.sourceforge.net/>`_ 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:
https://github.com/yfpeng/pengyifan-pybioc

Getting started
---------------

Installing ``bioc``

.. code:: bash

$ pip install --pre bioc

Encoding the BioC collection object ``collection``:

.. code:: python

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

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

Compact encoding:

.. code:: python

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

Incremental BioC serialisation:

.. code:: python

import bioc
with bioc.iterwrite(filename, collection) as writer:
for document in collection.documents:
writer.writedocument(document)

Decoding the BioC XML file:

.. code:: python

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:
bioc.load(fp)

Incrementally decoding the BioC XML file:

.. code:: python

import bioc
with bioc.iterparse(filename) as parser:
collection_info = parser.get_collection_info()
for document in parser:
# process document
...

`get_collection_info` can be called after the construction of the `iterparse` anytime.

Together with Python coroutines, this can be used to generate BioC XML in an asynchronous, non-blocking fashion.

.. code:: python

import bioc
with bioc.iterparse(filename) as parser:
with bioc.iterwrite(dst, parser.get_collection_info()) as writer:
for document in parser:
# modify the document
...
writer.writedocument(document)


Requirements
------------

- lxml (http://lxml.de)

Developers
----------

- Yifan Peng (yifan.peng@nih.gov)

Acknowledgment
--------------

- Hernani Marques (https://github.com/2mh/PyBioC)

Webpage
-------

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.

- http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/
- http://bioc.sourceforge.net/

Reference
---------

- 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.

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