BioC data structures and encoder/decoder for Python
Project description
bioc - BioC data structures and encoder/decoder for Python
BioC XML / JSON 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/bionlplab/bioc
Getting started
Installing bioc
$ pip install bioc
XML
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:
from bioc import biocxml
with biocxml.iterwrite(filename) as writer:
writer.write_collection_info(collection)
for document in collection.documents:
writer.write_document(document)
Decoding the BioC XML file:
import bioc
# Deserialize ``s`` to a BioC collection object.
collection = bioc.loads(s)
# Deserialize ``fp`` to a BioC collection object.
with open(filename, 'r') as fp:
collection = bioc.load(fp)
Incrementally decoding the BioC XML file:
from bioc import biocxml
# read from a file
with biocxml.iterparse(filename) as reader:
collection_info = reader.get_collection_info()
for document in reader:
# process document
...
# read from a ByteIO
with biocxml.iterparse(open(filename, 'rb')) as reader:
collection_info = reader.get_collection_info()
for document in reader:
# process document
...
get_collection_info
can be called after the with
statement.
Together with Python coroutines, this can be used to generate BioC XML in an asynchronous, non-blocking fashion.
from bioc import biocxml
with biocxml.iterparse(source) as reader, biocxml.iterwrite(dest) as writer:
collection_info = reader.get_collection_info()
writer.write_collection_info(collection_info)
for document in reader:
# modify the document
...
writer.write_document(document)
Json
Encoding the BioC collection object collection
:
import bioc
# Serialize ``collection`` to a BioC Json formatted ``str``.
bioc.dumps(collection, BioCFileType.BIOC_JSON, indent=2)
# Serialize ``collection`` as a BioC Json formatted stream to ``fp``.
with open(filename, 'w') as fp
bioc.dump(collection, BioCFileType.BIOC_JSON, fp, indent=2)
Compact encoding:
import bioc
bioc.dumps(collection, BioCFileType.BIOC_JSON)
Decoding the BioC Json file:
import bioc
# Deserialize ``s`` to a BioC collection object.
collection = bioc.loads(s, BioCFileType.BIOC_JSON)
# Deserialize ``fp`` to a BioC collection object.
with open(filename, 'r') as fp:
collection = bioc.load(fp, BioCFileType.BIOC_JSON)
Json Lines
Incrementally encoding the BioC structure:
from bioc import BioCJsonIterWriter
with open(filename, 'w', encoding='utf8') as fp:
writer = BioCJsonIterWriter(fp, level=bioc.PASSAGE)
for doc in collection.documents:
for passage in doc.passages:
writer.write(passage)
or
from bioc import toJSON
import jsonlines
with jsonlines.open(filename, 'w') as writer:
for doc in collection.documents:
for passage in doc.passages:
writer.write(toJSON(passage))
Incrementally decoding the BioC Json lines file:
from bioc import BioCJsonIterReader
with open(filename, 'r', encoding='utf8') as fp:
reader = BioCJsonIterReader(fp, level=bioc.PASSAGE)
for passage in reader:
# process passage
...
or
from bioc import fromJSON
import jsonlines
with jsonlines.open(filename) as reader:
for obj in reader:
passage = fromJSON(obj, level=bioc.PASSAGE)
...
Developer guide
Testing the code
$ pytest cov=bioc tests
Publish BioC to PyPI and TestPyPI
First, you need a PyPI user account. You can create an account using the form on the PyPI/TestPyPI website.
Now you’ll create a PyPI/TestPyPI API token so you will be able to securely upload your project.
Go to https://pypi.org/manage/account/#api-tokens and create a new API token; don’t limit its scope to a particular project, since you are creating a new project.
$ python -m build
Using local package with pip
$ pip install --force-reinstall dist/PACKAGE.whl
Using TestPyPI with pip
$ twine upload --repository testpypi dist/*
$ pip install --index-url https://test.pypi.org/simple/ bioc
Developers
- Yifan Peng (yip4002@med.cornell.edu)
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.
Reference
If you use bioc in your research, please cite the following paper:
- Comeau DC, Doğan RI, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia V, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013;2013:bat064. doi: 10.1093/database/bat064. Print 2013. PMID: 24048470; PMCID: PMC3889917
- Peng Y, Tudor CO, Torii M , Wu CH, Vijay-Shanker K. iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. Database (Oxford). 2014;2014. doi: 10.1093/database/bau038. Print 2014. PMID: 24850848; PMCID: PMC4028706.
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