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bionlplab / bioc

Data structures and code to read/write BioC XML and Json.
MIT License
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Cannot read ’annotation‘ in biocxml format #23

Open pyramid20002000 opened 1 year ago

pyramid20002000 commented 1 year ago

I’m writing a python script, to convert biocxml file into pubtator file. I did not find similar script, so all I can do is to write one on my own.

The bioc files are downloaded from : https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/BioRED.zip

I tried to read the "Test.BioC.XML" in two ways: 1: with open(fpath, 'r') as fp: collection = biocxml.load(fp) docs = collection.documents 2: with biocxml.iterparse(fpath) as reader: collection_info = reader.get_collection_info() for doc in reader:

It is strange to find that all annotations are missing, but relations are corrected parsed.

image

Any idea why this happens？

pyramid20002000 commented 1 year ago

image Above is the difference between the correct pubtator file and the one that I converted with bioc. I believe this is a bug in parsing the xml file somewhere.

pyramid20002000 commented 1 year ago

@ptlai Thanks to Dr. Lai's help.

In order to help more people, I will explain the problem and post the solution here : The problem is that each document object has empty annotation list. But relation annotation list is fine.

Actually the annotations are inside each passage node. They can be found by the following code.

from bioc import biocxml fpath = 'Test.BioC.XML' with open(fpath, 'r') as fp: collection = biocxml.load(fp) docs = collection.documents for doc in docs: for passage in doc.passages: for annotation in passage.annotations: print(annotation)