bioc 1.0.dev29

BioC data structures and encoder/decoder for Python

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: https://github.com/yfpeng/bioc

Getting started

Installing bioc

$ pip install --pre bioc

Encoding the BioC collection object collection:

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:

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

Incremental BioC serialisation:

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

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:
    bioc.load(fp)

Incrementally decoding the BioC XML file:

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.

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 ([e-mail])

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.