How to prepare for BNF
1. Open and edit the file in the application root.
Edit the following information according to your desktop configuration.
Normally, you don't need to change the database related configuration, unless you installed your own
Make sure the SPECIALIST lexical tool is installed.
If the lexical tool is not installed on your machine, you can download it form NLM:
After installing the lexical tool, set the "specialist_config" parameter in our software configuration file
(named in the software root folder).
Make sure this parameter is pointed to the configuration of installed lexical tool (a file named
Configuration example:
Please make sure each of the configurations is correct:
2. Select specific sentences from our database
(For details of how to connect to the database, see file “Guide to access to the database.docx”)
Example queries:
Use db_umls;
select * from clinical_trial_sentence_201006 left join clinical_trials_82976 on
clinical_trial_sentence_201006.url=clinical_trials_82976.url where clinical_trials_82976.conditions =
"lung cancer" order by rank desc limit 0, 3000 ;.,m
User can set two parameters in this query. See the red text in above example.
Condition: the name of the condition, such as: “lung cancer”, “diabetes”, “heart disease” etc.
Sentence number: the overall number of sentences retrieved (recommend default 3000, too
many sentences will excess the memory limit of JAVA heap space and cause an error.)
In the result list, select all rows. Press “shift” key and click the first and the last row.
Right click on the selected results, select “Export ResultSet”. Select “Export as Excel” file.
Wait for the exportation finish. Open the file and move to next step.
[This exported file contains trial information, and it’s requested by Meir.]
3. Prepare input sentences for the parsing program
Copy the “sentence” column from the database query results.
Paste the sentences into the “BNF_sentence_input.txt” file which Located in software directory.
Save the encoding of the file as UTF-8.
4. Run the application
Go to the software directory, and then double click on "run.bat". (JDK 1.6+ required).
A console window will show up.
Wait for the program finish its processing.
The output file in the software directory: BNF_annotated_output_[date].txt
Open this file using Excel. Save it as CSV or Excel file.
[The output file is requested by Meir.]