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Posted to dev@ctakes.apache.org by John Green <jo...@gmail.com> on 2014/07/25 19:05:21 UTC
Re: Fwd: UMLS integration with cTAKES 3.1
This sounds just like jira ctakes-306.
JG
—
On Fri, Jul 25, 2014 at 1:04 PM, John Green <he...@gmail.com>
wrote:
> —
> ---------- Forwarded message ----------
> From: "Natalia Connolly" <na...@gmail.com>
> Date: Fri, Jul 25, 2014 at 12:35 PM
> Subject: UMLS integration with cTAKES 3.1
> To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
>> Hello,
>> I am trying to supplement the basic cTAKES dictionary with the latest
>> UMLS release. Following the instructions here (
>> https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p258), I
>> built a mysql database and imported UMLS data into it as two tables,
>> umls_ms_2013 and umls_snomed_map. I then modified
>> DictionaryLookupAnnotatorDB.xml as follows:
>> <name>URL</name>
>> <value>
>> <string>jdbc:mysql://localhost:3306/umls</string>
>> </value>
>> and I also changed LookupDesc_Db.xml to reflect my two table names.
>> After I added DictionaryLookupAnnotatorDB.xml to my analysis engines in
>> runctakesCPE.sh, I got the following error:
>> org.apache.uima.analysis_engine.AnalysisEngineProcessException CausedBY:
>> org.apache.ctakes.dictionary.lookup.DictionaryException:
>> java.sql.SQLException: Table not found in statement [SELECT tui, text, cui
>> from UMLS_MS_2013 where fword =?]
>> This is strange because the table does exist and it's not empty:
>> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2;
>> +------+--------+----------+
>> | tui | text | cui |
>> +------+--------+----------+
>> | T121 | MSH | C0000005 |
>> | T121 | MSHFRE | C0000005 |
>> +------+--------+----------+
>> 2 rows in set (0.00 sec)
>> Can someone please help?
>> Thank you,
>> Natalia Connolly
Re: UMLS integration with cTAKES 3.1
Posted by Natalia Connolly <na...@gmail.com>.
Yes, I did. The same problem.
Natalia
On Fri, Jul 25, 2014 at 2:06 PM, Chen, Pei <Pe...@childrens.harvard.edu>
wrote:
> Did you also try lower case in the table name?
>
> Sent from my iPhone
>
> On Jul 25, 2014, at 2:02 PM, "Natalia Connolly" <
> natalia.v.connolly@gmail.com> wrote:
>
> Yes:
>
>
> mysql> use umls;
> Reading table information for completion of table and column names
> You can turn off this feature to get a quicker startup with -A
>
> Database changed
> mysql> show tables;
> +-----------------+
> | Tables_in_umls |
> +-----------------+
> | AMBIGLUI |
> | AMBIGSUI |
> | DELETEDCUI |
> | DELETEDLUI |
> …….
>
> | umls_ms_2013 |
> | umls_snomed_map |
> +-----------------+
> 49 rows in set (0.00 sec)
>
> Natalia
>
>
>
>
> On Fri, Jul 25, 2014 at 1:59 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu
> > wrote:
>
>> That is odd. Nothing seems out of the ordinary…
>>
>> And the database name is umls?
>>
>> jdbc:mysql://localhost:3306/*umls*
>>
>>
>>
>> *From:* Natalia Connolly [mailto:natalia.v.connolly@gmail.com]
>> *Sent:* Friday, July 25, 2014 1:54 PM
>> *To:* user@ctakes.apache.org
>>
>> *Subject:* Re: Fwd: UMLS integration with cTAKES 3.1
>>
>>
>>
>> Hi Pei,
>>
>>
>>
>> I can't see any issues with LookupDesc_Db, so I am attaching both it
>> and DictionaryLookupAnnotatorDB.xml. I only modified the
>> username/password in the second file to "myusername" and "mypassword" for
>> security purposes. They were correct before, I checked it many times.
>>
>>
>>
>> Thank you so much for your help,
>>
>>
>>
>> Natalia
>>
>>
>>
>>
>>
>> On Fri, Jul 25, 2014 at 1:34 PM, Chen, Pei <
>> Pei.Chen@childrens.harvard.edu> wrote:
>>
>> Natalia,
>> That is strange. It sounds like it isn't configured to use the right
>> resource.
>> Could you double check the mappings, in particular: in your
>> LookupDesc_Db.xml:
>> externalResourceKey="DbConnection" to ensure it's using the right
>> resource that was added in your DictionaryLookupAnnotatorDB.xml?
>> If it still doesn't work, would you mind attaching the xml config files?
>>
>> --Pei
>>
>> > -----Original Message-----
>> > From: John Green [mailto:john.travis.green@gmail.com]
>> > Sent: Friday, July 25, 2014 1:06 PM
>> > To: user@ctakes.apache.org; dev@ctakes.apache.org
>> > Subject: Re: Fwd: UMLS integration with cTAKES 3.1
>> >
>> > This sounds just like jira ctakes-306.
>> >
>> >
>> > JG
>> > —
>> >
>> > On Fri, Jul 25, 2014 at 1:04 PM, John Green <
>> hephaestus.studio@gmail.com>
>> > wrote:
>> >
>> > > —
>> > > ---------- Forwarded message ----------
>> > > From: "Natalia Connolly" <na...@gmail.com>
>> > > Date: Fri, Jul 25, 2014 at 12:35 PM
>> > > Subject: UMLS integration with cTAKES 3.1
>> > > To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
>> > >> Hello,
>> > >> I am trying to supplement the basic cTAKES dictionary with the
>> > >> latest UMLS release. Following the instructions here (
>> > >> https://cabig-
>> > kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25
>> > >> 8), I built a mysql database and imported UMLS data into it as two
>> tables,
>> > >> umls_ms_2013 and umls_snomed_map. I then modified
>> > >> DictionaryLookupAnnotatorDB.xml as follows:
>> > >> <name>URL</name>
>> > >> <value>
>> > >> <string>jdbc:mysql://localhost:3306/umls</string>
>> > >> </value>
>> > >> and I also changed LookupDesc_Db.xml to reflect my two table
>> names.
>> > >> After I added DictionaryLookupAnnotatorDB.xml to my analysis
>> > >> engines in runctakesCPE.sh, I got the following error:
>> > >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
>> > CausedBY:
>> > >> org.apache.ctakes.dictionary.lookup.DictionaryException:
>> > >> java.sql.SQLException: Table not found in statement [SELECT tui,
>> > >> text, cui from UMLS_MS_2013 where fword =?]
>> > >> This is strange because the table does exist and it's not empty:
>> > >> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2;
>> > >> +------+--------+----------+
>> > >> | tui | text | cui |
>> > >> +------+--------+----------+
>> > >> | T121 | MSH | C0000005 |
>> > >> | T121 | MSHFRE | C0000005 |
>> > >> +------+--------+----------+
>> > >> 2 rows in set (0.00 sec)
>> > >> Can someone please help?
>> > >> Thank you,
>> > >> Natalia Connolly
>>
>>
>>
>
>
Re: UMLS integration with cTAKES 3.1
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Did you also try lower case in the table name?
Sent from my iPhone
On Jul 25, 2014, at 2:02 PM, "Natalia Connolly" <na...@gmail.com>> wrote:
Yes:
mysql> use umls;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
mysql> show tables;
+-----------------+
| Tables_in_umls |
+-----------------+
| AMBIGLUI |
| AMBIGSUI |
| DELETEDCUI |
| DELETEDLUI |
…….
| umls_ms_2013 |
| umls_snomed_map |
+-----------------+
49 rows in set (0.00 sec)
Natalia
On Fri, Jul 25, 2014 at 1:59 PM, Chen, Pei <Pe...@childrens.harvard.edu>> wrote:
That is odd. Nothing seems out of the ordinary…
And the database name is umls?
jdbc:mysql://localhost:3306/umls
From: Natalia Connolly [mailto:natalia.v.connolly@gmail.com<ma...@gmail.com>]
Sent: Friday, July 25, 2014 1:54 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: Fwd: UMLS integration with cTAKES 3.1
Hi Pei,
I can't see any issues with LookupDesc_Db, so I am attaching both it and DictionaryLookupAnnotatorDB.xml. I only modified the username/password in the second file to "myusername" and "mypassword" for security purposes. They were correct before, I checked it many times.
Thank you so much for your help,
Natalia
On Fri, Jul 25, 2014 at 1:34 PM, Chen, Pei <Pe...@childrens.harvard.edu>> wrote:
Natalia,
That is strange. It sounds like it isn't configured to use the right resource.
Could you double check the mappings, in particular: in your LookupDesc_Db.xml:
externalResourceKey="DbConnection" to ensure it's using the right resource that was added in your DictionaryLookupAnnotatorDB.xml?
If it still doesn't work, would you mind attaching the xml config files?
--Pei
> -----Original Message-----
> From: John Green [mailto:john.travis.green@gmail.com<ma...@gmail.com>]
> Sent: Friday, July 25, 2014 1:06 PM
> To: user@ctakes.apache.org<ma...@ctakes.apache.org>; dev@ctakes.apache.org<ma...@ctakes.apache.org>
> Subject: Re: Fwd: UMLS integration with cTAKES 3.1
>
> This sounds just like jira ctakes-306.
>
>
> JG
> —
>
> On Fri, Jul 25, 2014 at 1:04 PM, John Green <he...@gmail.com>>
> wrote:
>
> > —
> > ---------- Forwarded message ----------
> > From: "Natalia Connolly" <na...@gmail.com>>
> > Date: Fri, Jul 25, 2014 at 12:35 PM
> > Subject: UMLS integration with cTAKES 3.1
> > To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
> >> Hello,
> >> I am trying to supplement the basic cTAKES dictionary with the
> >> latest UMLS release. Following the instructions here (
> >> https://cabig-
> kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25<http://kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25>
> >> 8), I built a mysql database and imported UMLS data into it as two tables,
> >> umls_ms_2013 and umls_snomed_map. I then modified
> >> DictionaryLookupAnnotatorDB.xml as follows:
> >> <name>URL</name>
> >> <value>
> >> <string>jdbc:mysql://localhost:3306/umls</string>
> >> </value>
> >> and I also changed LookupDesc_Db.xml to reflect my two table names.
> >> After I added DictionaryLookupAnnotatorDB.xml to my analysis
> >> engines in runctakesCPE.sh, I got the following error:
> >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
> CausedBY:
> >> org.apache.ctakes.dictionary.lookup.DictionaryException:
> >> java.sql.SQLException: Table not found in statement [SELECT tui,
> >> text, cui from UMLS_MS_2013 where fword =?]
> >> This is strange because the table does exist and it's not empty:
> >> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2;
> >> +------+--------+----------+
> >> | tui | text | cui |
> >> +------+--------+----------+
> >> | T121 | MSH | C0000005 |
> >> | T121 | MSHFRE | C0000005 |
> >> +------+--------+----------+
> >> 2 rows in set (0.00 sec)
> >> Can someone please help?
> >> Thank you,
> >> Natalia Connolly
Re: Fwd: UMLS integration with cTAKES 3.1
Posted by Natalia Connolly <na...@gmail.com>.
Yes:
mysql> use umls;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
mysql> show tables;
+-----------------+
| Tables_in_umls |
+-----------------+
| AMBIGLUI |
| AMBIGSUI |
| DELETEDCUI |
| DELETEDLUI |
…….
| umls_ms_2013 |
| umls_snomed_map |
+-----------------+
49 rows in set (0.00 sec)
Natalia
On Fri, Jul 25, 2014 at 1:59 PM, Chen, Pei <Pe...@childrens.harvard.edu>
wrote:
> That is odd. Nothing seems out of the ordinary…
>
> And the database name is umls?
>
> jdbc:mysql://localhost:3306/*umls*
>
>
>
> *From:* Natalia Connolly [mailto:natalia.v.connolly@gmail.com]
> *Sent:* Friday, July 25, 2014 1:54 PM
> *To:* user@ctakes.apache.org
>
> *Subject:* Re: Fwd: UMLS integration with cTAKES 3.1
>
>
>
> Hi Pei,
>
>
>
> I can't see any issues with LookupDesc_Db, so I am attaching both it
> and DictionaryLookupAnnotatorDB.xml. I only modified the
> username/password in the second file to "myusername" and "mypassword" for
> security purposes. They were correct before, I checked it many times.
>
>
>
> Thank you so much for your help,
>
>
>
> Natalia
>
>
>
>
>
> On Fri, Jul 25, 2014 at 1:34 PM, Chen, Pei <Pe...@childrens.harvard.edu>
> wrote:
>
> Natalia,
> That is strange. It sounds like it isn't configured to use the right
> resource.
> Could you double check the mappings, in particular: in your
> LookupDesc_Db.xml:
> externalResourceKey="DbConnection" to ensure it's using the right resource
> that was added in your DictionaryLookupAnnotatorDB.xml?
> If it still doesn't work, would you mind attaching the xml config files?
>
> --Pei
>
> > -----Original Message-----
> > From: John Green [mailto:john.travis.green@gmail.com]
> > Sent: Friday, July 25, 2014 1:06 PM
> > To: user@ctakes.apache.org; dev@ctakes.apache.org
> > Subject: Re: Fwd: UMLS integration with cTAKES 3.1
> >
> > This sounds just like jira ctakes-306.
> >
> >
> > JG
> > —
> >
> > On Fri, Jul 25, 2014 at 1:04 PM, John Green <hephaestus.studio@gmail.com
> >
> > wrote:
> >
> > > —
> > > ---------- Forwarded message ----------
> > > From: "Natalia Connolly" <na...@gmail.com>
> > > Date: Fri, Jul 25, 2014 at 12:35 PM
> > > Subject: UMLS integration with cTAKES 3.1
> > > To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
> > >> Hello,
> > >> I am trying to supplement the basic cTAKES dictionary with the
> > >> latest UMLS release. Following the instructions here (
> > >> https://cabig-
> > kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25
> > >> 8), I built a mysql database and imported UMLS data into it as two
> tables,
> > >> umls_ms_2013 and umls_snomed_map. I then modified
> > >> DictionaryLookupAnnotatorDB.xml as follows:
> > >> <name>URL</name>
> > >> <value>
> > >> <string>jdbc:mysql://localhost:3306/umls</string>
> > >> </value>
> > >> and I also changed LookupDesc_Db.xml to reflect my two table names.
> > >> After I added DictionaryLookupAnnotatorDB.xml to my analysis
> > >> engines in runctakesCPE.sh, I got the following error:
> > >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
> > CausedBY:
> > >> org.apache.ctakes.dictionary.lookup.DictionaryException:
> > >> java.sql.SQLException: Table not found in statement [SELECT tui,
> > >> text, cui from UMLS_MS_2013 where fword =?]
> > >> This is strange because the table does exist and it's not empty:
> > >> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2;
> > >> +------+--------+----------+
> > >> | tui | text | cui |
> > >> +------+--------+----------+
> > >> | T121 | MSH | C0000005 |
> > >> | T121 | MSHFRE | C0000005 |
> > >> +------+--------+----------+
> > >> 2 rows in set (0.00 sec)
> > >> Can someone please help?
> > >> Thank you,
> > >> Natalia Connolly
>
>
>
RE: Fwd: UMLS integration with cTAKES 3.1
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
That is odd. Nothing seems out of the ordinary…
And the database name is umls?
jdbc:mysql://localhost:3306/umls
From: Natalia Connolly [mailto:natalia.v.connolly@gmail.com]
Sent: Friday, July 25, 2014 1:54 PM
To: user@ctakes.apache.org
Subject: Re: Fwd: UMLS integration with cTAKES 3.1
Hi Pei,
I can't see any issues with LookupDesc_Db, so I am attaching both it and DictionaryLookupAnnotatorDB.xml. I only modified the username/password in the second file to "myusername" and "mypassword" for security purposes. They were correct before, I checked it many times.
Thank you so much for your help,
Natalia
On Fri, Jul 25, 2014 at 1:34 PM, Chen, Pei <Pe...@childrens.harvard.edu>> wrote:
Natalia,
That is strange. It sounds like it isn't configured to use the right resource.
Could you double check the mappings, in particular: in your LookupDesc_Db.xml:
externalResourceKey="DbConnection" to ensure it's using the right resource that was added in your DictionaryLookupAnnotatorDB.xml?
If it still doesn't work, would you mind attaching the xml config files?
--Pei
> -----Original Message-----
> From: John Green [mailto:john.travis.green@gmail.com<ma...@gmail.com>]
> Sent: Friday, July 25, 2014 1:06 PM
> To: user@ctakes.apache.org<ma...@ctakes.apache.org>; dev@ctakes.apache.org<ma...@ctakes.apache.org>
> Subject: Re: Fwd: UMLS integration with cTAKES 3.1
>
> This sounds just like jira ctakes-306.
>
>
> JG
> —
>
> On Fri, Jul 25, 2014 at 1:04 PM, John Green <he...@gmail.com>>
> wrote:
>
> > —
> > ---------- Forwarded message ----------
> > From: "Natalia Connolly" <na...@gmail.com>>
> > Date: Fri, Jul 25, 2014 at 12:35 PM
> > Subject: UMLS integration with cTAKES 3.1
> > To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
> >> Hello,
> >> I am trying to supplement the basic cTAKES dictionary with the
> >> latest UMLS release. Following the instructions here (
> >> https://cabig-
> kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25<http://kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25>
> >> 8), I built a mysql database and imported UMLS data into it as two tables,
> >> umls_ms_2013 and umls_snomed_map. I then modified
> >> DictionaryLookupAnnotatorDB.xml as follows:
> >> <name>URL</name>
> >> <value>
> >> <string>jdbc:mysql://localhost:3306/umls</string>
> >> </value>
> >> and I also changed LookupDesc_Db.xml to reflect my two table names.
> >> After I added DictionaryLookupAnnotatorDB.xml to my analysis
> >> engines in runctakesCPE.sh, I got the following error:
> >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
> CausedBY:
> >> org.apache.ctakes.dictionary.lookup.DictionaryException:
> >> java.sql.SQLException: Table not found in statement [SELECT tui,
> >> text, cui from UMLS_MS_2013 where fword =?]
> >> This is strange because the table does exist and it's not empty:
> >> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2;
> >> +------+--------+----------+
> >> | tui | text | cui |
> >> +------+--------+----------+
> >> | T121 | MSH | C0000005 |
> >> | T121 | MSHFRE | C0000005 |
> >> +------+--------+----------+
> >> 2 rows in set (0.00 sec)
> >> Can someone please help?
> >> Thank you,
> >> Natalia Connolly
Re: Fwd: UMLS integration with cTAKES 3.1
Posted by Natalia Connolly <na...@gmail.com>.
Hi Pei,
I can't see any issues with LookupDesc_Db, so I am attaching both it
and DictionaryLookupAnnotatorDB.xml. I only modified the
username/password in the second file to "myusername" and "mypassword" for
security purposes. They were correct before, I checked it many times.
Thank you so much for your help,
Natalia
On Fri, Jul 25, 2014 at 1:34 PM, Chen, Pei <Pe...@childrens.harvard.edu>
wrote:
> Natalia,
> That is strange. It sounds like it isn't configured to use the right
> resource.
> Could you double check the mappings, in particular: in your
> LookupDesc_Db.xml:
> externalResourceKey="DbConnection" to ensure it's using the right resource
> that was added in your DictionaryLookupAnnotatorDB.xml?
> If it still doesn't work, would you mind attaching the xml config files?
>
> --Pei
>
> > -----Original Message-----
> > From: John Green [mailto:john.travis.green@gmail.com]
> > Sent: Friday, July 25, 2014 1:06 PM
> > To: user@ctakes.apache.org; dev@ctakes.apache.org
> > Subject: Re: Fwd: UMLS integration with cTAKES 3.1
> >
> > This sounds just like jira ctakes-306.
> >
> >
> > JG
> > —
> >
> > On Fri, Jul 25, 2014 at 1:04 PM, John Green <hephaestus.studio@gmail.com
> >
> > wrote:
> >
> > > —
> > > ---------- Forwarded message ----------
> > > From: "Natalia Connolly" <na...@gmail.com>
> > > Date: Fri, Jul 25, 2014 at 12:35 PM
> > > Subject: UMLS integration with cTAKES 3.1
> > > To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
> > >> Hello,
> > >> I am trying to supplement the basic cTAKES dictionary with the
> > >> latest UMLS release. Following the instructions here (
> > >> https://cabig-
> > kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25
> > >> 8), I built a mysql database and imported UMLS data into it as two
> tables,
> > >> umls_ms_2013 and umls_snomed_map. I then modified
> > >> DictionaryLookupAnnotatorDB.xml as follows:
> > >> <name>URL</name>
> > >> <value>
> > >> <string>jdbc:mysql://localhost:3306/umls</string>
> > >> </value>
> > >> and I also changed LookupDesc_Db.xml to reflect my two table names.
> > >> After I added DictionaryLookupAnnotatorDB.xml to my analysis
> > >> engines in runctakesCPE.sh, I got the following error:
> > >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
> > CausedBY:
> > >> org.apache.ctakes.dictionary.lookup.DictionaryException:
> > >> java.sql.SQLException: Table not found in statement [SELECT tui,
> > >> text, cui from UMLS_MS_2013 where fword =?]
> > >> This is strange because the table does exist and it's not empty:
> > >> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2;
> > >> +------+--------+----------+
> > >> | tui | text | cui |
> > >> +------+--------+----------+
> > >> | T121 | MSH | C0000005 |
> > >> | T121 | MSHFRE | C0000005 |
> > >> +------+--------+----------+
> > >> 2 rows in set (0.00 sec)
> > >> Can someone please help?
> > >> Thank you,
> > >> Natalia Connolly
>
RE: Fwd: UMLS integration with cTAKES 3.1
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Natalia,
That is strange. It sounds like it isn't configured to use the right resource.
Could you double check the mappings, in particular: in your LookupDesc_Db.xml:
externalResourceKey="DbConnection" to ensure it's using the right resource that was added in your DictionaryLookupAnnotatorDB.xml?
If it still doesn't work, would you mind attaching the xml config files?
--Pei
> -----Original Message-----
> From: John Green [mailto:john.travis.green@gmail.com]
> Sent: Friday, July 25, 2014 1:06 PM
> To: user@ctakes.apache.org; dev@ctakes.apache.org
> Subject: Re: Fwd: UMLS integration with cTAKES 3.1
>
> This sounds just like jira ctakes-306.
>
>
> JG
> —
>
> On Fri, Jul 25, 2014 at 1:04 PM, John Green <he...@gmail.com>
> wrote:
>
> > —
> > ---------- Forwarded message ----------
> > From: "Natalia Connolly" <na...@gmail.com>
> > Date: Fri, Jul 25, 2014 at 12:35 PM
> > Subject: UMLS integration with cTAKES 3.1
> > To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
> >> Hello,
> >> I am trying to supplement the basic cTAKES dictionary with the
> >> latest UMLS release. Following the instructions here (
> >> https://cabig-
> kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25
> >> 8), I built a mysql database and imported UMLS data into it as two tables,
> >> umls_ms_2013 and umls_snomed_map. I then modified
> >> DictionaryLookupAnnotatorDB.xml as follows:
> >> <name>URL</name>
> >> <value>
> >> <string>jdbc:mysql://localhost:3306/umls</string>
> >> </value>
> >> and I also changed LookupDesc_Db.xml to reflect my two table names.
> >> After I added DictionaryLookupAnnotatorDB.xml to my analysis
> >> engines in runctakesCPE.sh, I got the following error:
> >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
> CausedBY:
> >> org.apache.ctakes.dictionary.lookup.DictionaryException:
> >> java.sql.SQLException: Table not found in statement [SELECT tui,
> >> text, cui from UMLS_MS_2013 where fword =?]
> >> This is strange because the table does exist and it's not empty:
> >> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2;
> >> +------+--------+----------+
> >> | tui | text | cui |
> >> +------+--------+----------+
> >> | T121 | MSH | C0000005 |
> >> | T121 | MSHFRE | C0000005 |
> >> +------+--------+----------+
> >> 2 rows in set (0.00 sec)
> >> Can someone please help?
> >> Thank you,
> >> Natalia Connolly
RE: Fwd: UMLS integration with cTAKES 3.1
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Natalia,
That is strange. It sounds like it isn't configured to use the right resource.
Could you double check the mappings, in particular: in your LookupDesc_Db.xml:
externalResourceKey="DbConnection" to ensure it's using the right resource that was added in your DictionaryLookupAnnotatorDB.xml?
If it still doesn't work, would you mind attaching the xml config files?
--Pei
> -----Original Message-----
> From: John Green [mailto:john.travis.green@gmail.com]
> Sent: Friday, July 25, 2014 1:06 PM
> To: user@ctakes.apache.org; dev@ctakes.apache.org
> Subject: Re: Fwd: UMLS integration with cTAKES 3.1
>
> This sounds just like jira ctakes-306.
>
>
> JG
> —
>
> On Fri, Jul 25, 2014 at 1:04 PM, John Green <he...@gmail.com>
> wrote:
>
> > —
> > ---------- Forwarded message ----------
> > From: "Natalia Connolly" <na...@gmail.com>
> > Date: Fri, Jul 25, 2014 at 12:35 PM
> > Subject: UMLS integration with cTAKES 3.1
> > To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
> >> Hello,
> >> I am trying to supplement the basic cTAKES dictionary with the
> >> latest UMLS release. Following the instructions here (
> >> https://cabig-
> kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p25
> >> 8), I built a mysql database and imported UMLS data into it as two tables,
> >> umls_ms_2013 and umls_snomed_map. I then modified
> >> DictionaryLookupAnnotatorDB.xml as follows:
> >> <name>URL</name>
> >> <value>
> >> <string>jdbc:mysql://localhost:3306/umls</string>
> >> </value>
> >> and I also changed LookupDesc_Db.xml to reflect my two table names.
> >> After I added DictionaryLookupAnnotatorDB.xml to my analysis
> >> engines in runctakesCPE.sh, I got the following error:
> >> org.apache.uima.analysis_engine.AnalysisEngineProcessException
> CausedBY:
> >> org.apache.ctakes.dictionary.lookup.DictionaryException:
> >> java.sql.SQLException: Table not found in statement [SELECT tui,
> >> text, cui from UMLS_MS_2013 where fword =?]
> >> This is strange because the table does exist and it's not empty:
> >> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2;
> >> +------+--------+----------+
> >> | tui | text | cui |
> >> +------+--------+----------+
> >> | T121 | MSH | C0000005 |
> >> | T121 | MSHFRE | C0000005 |
> >> +------+--------+----------+
> >> 2 rows in set (0.00 sec)
> >> Can someone please help?
> >> Thank you,
> >> Natalia Connolly