This repository contains tools and resources related to the corpus of the 2004 BioNLP / JNLPBA shared task.
This directory contains JNLPBA corpus data in standoff format and tools for recreating this data from the TAB-separated BIO format in which the corpus is distributed.
Contents:
- README.md: this file
- LICENSE: JNLBPA data license
- original-data/ JNLPBA data in BIO format and related resources
- standoff/ JNLBPA data in standoff format
- conversion/ resources for converting JNLPBA data into standoff format
Data sources:
The JNLPBA annotations are available via
http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/ERtask/report.html
The original packages were downloaded from
http://www.nactem.ac.uk/GENIA/current/Shared-tasks/JNLPBA/Train/Genia4ERtraining.tar.gz
http://www.nactem.ac.uk/GENIA/current/Shared-tasks/JNLPBA/Evaluation/Genia4ERtest.tar.gz
The text files in standoff/train and standoff/test were extracted from PubMed XML files, downloaded using the NCBI E-utilities (http://www.ncbi.nlm.nih.gov/books/NBK25499/) as in the following example
wget 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=308841&retmode=xml' -O 308841.xml
and title and abstract text content extracted as
python conversion/extractTIAB.py 308841.xml > 338841.txt
and converted into ASCII using unicode2ascii.py, distributed separately from https://github.com/spyysalo/unicode2ascii, as
python unicode2ascii.py 338841.txt > 338841-ASCII.txt
the texts were then semiautomatically processed to align with the tokens of the JNLPBA data. Three text files were additionally duplicated under different names (affixing "-2" to file base name) to account for duplicate IDs in JNLPBA data.
Note that as the JNLBPA data file names are not current PubMed IDs but rather older MedLine IDs, PubMed queries for the documents (as above) require mapping between these IDs. The file conversion/MUID-PMID-map.txt provides this mapping for the JNLPBA data IDs. This mapping was extracted from the following files distributed by NLM:
ftp://ftp.ncbi.nih.gov/pubmed/MuId-PmId-1.zip
ftp://ftp.ncbi.nih.gov/pubmed/MuId-PmId-2.zip
ftp://ftp.ncbi.nih.gov/pubmed/MuId-PmId-3.zip
ftp://ftp.ncbi.nih.gov/pubmed/MuId-PmId-4.zip
ftp://ftp.ncbi.nih.gov/pubmed/MuId-PmId-5.zip
ftp://ftp.ncbi.nih.gov/pubmed/MuId-PmId-6.zip
Conversion process
Given the packages Genia4ERtraining.tar.gz and Genia4ERtest.tar.gz and the text files (.txt) in standoff/train and standoff/test (see Data sources, above), the standoff annotations (.ann) can be created as follows (assuming bash shell):
tar xzf Genia4ERtraining.tar.gz
tar xzf Genia4ERtest.tar.gz
python conversion/jnlpbasplit.py -d standoff/train Genia4ERtask2.iob2
python conversion/jnlpbasplit.py -d standoff/test Genia4EReval2.iob2
for f in standoff/train/*.conll; do python conversion/jnlpba2standoff.py ${f%.conll}.txt $f > ${f%.conll}.ann; done
for f in standoff/test/*.conll; do python conversion/jnlpba2standoff.py ${f%.conll}.txt $f > ${f%.conll}.ann; done
(The last two steps takes some minutes to complete.)