RE: Integrate cTakes with latest UMLS DB

Stuti Awasthi Thu, 31 Mar 2016 04:14:41 -0700

Hi All,

Sorry , I think I got confused with dictionary-gui and dictionary-tool projects. Jessica mentioned about dictionary tool and its README which I followed along with the previous mail threads to generate umls dictionary in file format. Im still to use this dictionary with cTakes so i might comeback with issues.

Also I would like to use dictionary-gui posted by Brandon. When I have checkout the code and imported in eclipse, its showing compilation error in classes due to which even I have created the jar of the project, it is not running. Any idea about the compilation errors or if there is a pre built binary which can be used (similar to dictionary tools jar) that would be great.

Thanks for your help and patience.

Regards

Stuti Awasthi

From: Stuti Awasthi
Sent: Thursday, March 31, 2016 11:58 AM
To: '[email protected]'
Subject: RE: Integrate cTakes with latest UMLS DB

Hi Brandon, Jessica

I lookedup at dictionary-gui utility. Here is what I did : Checkout the source code https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/ and imported in my eclipse IDE. Now I was not able to find any README with this project. Hence I checked the code and found that “CreaterGui.java” might be the mail class to launch the GUI. My queries are :

· Is there any README as Jessica mentioned or simply launching the CreaterGui.java class would be suffice.

· Is there any commands to execute tool on linux server (without gnome) . Something like command like options? Im asking this because Im working on linux machine where I have installed lated UMLS2015.

Few more questions:

· As Brandon mentioned : that I might need to create the tables that will have same information (based on rare /first word approach). Do we know how to create those tables ?? Any SQL statements or links will be useful.

· I found the following link in Ctakes3.1 documentation but looks like broken. Any clue on redirected path/links

Can I create full dictionary(not only the fast one) from dictionary tool.

Thanks &Regards

Stuti Awasthi

From: Stuti Awasthi
Sent: Tuesday, March 29, 2016 5:35 PM
To: '[email protected]'
Subject: RE: Integrate cTakes with latest UMLS DB

Thanks Brandon, then I will check dictionary-gui tool and try to use it and will get back with queries if any.

Regards

Stuti Awasthi

From: Geise, Brandon D. [mailto:[email protected]]
Sent: Tuesday, March 29, 2016 5:32 PM
To: Stuti Awasthi; '[email protected]'
Subject: RE: Integrate cTakes with latest UMLS DB

Hi Stuti,

Unless someone else has created another solution the current Dictionary Gui tool doesn’t have this support yet. It’s something that I plan to work on in the future for the GUI tool.

Thanks,

Brandon

Sent from Mail for Windows 10

From: Stuti Awasthi
Sent: Tuesday, March 29, 2016 7:59 AM
To: '[email protected]'
Subject: RE: Integrate cTakes with latest UMLS DB

Thanks Brandon, Jessica for response. I will look at dictionary tools as mentioned and will try to figure out how it can be used for my purpose. I will certainly get back on mailing list with more queries if any.

As of now with limited understanding, I understand that current UMLS2015 database will be converted to hsql format which I can use in the pipeline by changing configurations in required XMLs. One more query, cTakes also provides “DictionaryLookupAnnotatorDB” which is supposed to be used if we want to connect to required tables in umls database. Please correct my understanding but do we have similar tool/script to be execute on umls database to generate the required format table “umls2015ab” which can be directly included in dictionary lookup.

Thanks for the help!

Regards

Stuti Awasthi

From: Glover, Jessica [mailto:[email protected]]
Sent: Tuesday, March 29, 2016 5:17 PM
To: '[email protected]'
Subject: RE: Integrate cTakes with latest UMLS DB

Hi Stuti,

One thing to note about the dictionary tool is that it is still in sandbox mode, so there is no official documentation or step-by-step guide for it. However, it contains a readme, and it has been discussed on the mailing list, so you can search the archive for that “documentation.”

Searchable cTakes mailing list archive: http://ctakes.markmail.org/search/

Regards,

Jessica

From: Stuti Awasthi [mailto:[email protected]]
Sent: Tuesday, March 29, 2016 7:10 AM
To: '[email protected]'
Subject: RE: Integrate cTakes with latest UMLS DB

Hi All,

Any help will be good. Im still waiting for some response.

Thanks &Regards

Stuti Awasthi

From: Stuti Awasthi
Sent: Monday, March 28, 2016 2:46 PM
To: [email protected]
Subject: Integrate cTakes with latest UMLS DB

Hi All,

I have been exploring cTakes and wanted to use latest UMLS 2015ab with it. To achieve the same, I have installed UMLS in mysql database.

Database Name: umls

Numbers of Tables created : 53

Eg : mysql> show tables;

+--------------------------+

| Tables_in_umls |

+--------------------------+

| AMBIGLUI |

| AMBIGSUI |

| DELETEDCUI |

| DELETEDLUI |

| DELETEDSUI

……

| SRSTRE1 |

| SRSTRE2 |

Now im not able to find any step by step guide to integrate cTakes with umls database.

Here is what I have done :

1) Modified DictionaryLookupAnnotatorDB.xml with jdbc url of my database along with username and password.

Now I believe I also need to modify LookupDesc_DB.xml with some umls tablename which can get cui, tui and text info.

I need some help , which table should I be pointing to lookup ? Also after is there any other step or I should be good in executing clinical pipeline with umls database.

Also please point some steps guide/document of available for cTakes integration with UMLS.

Thanks &Regards

Stuti Awasthi

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RE: Integrate cTakes with latest UMLS DB

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