W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > February 2009

Re: [COI] Re: COI protocol #8 demo progress

From: Holger Stenzhorn <holger.stenzhorn@deri.org>
Date: Wed, 25 Feb 2009 00:50:52 -0300
Message-ID: <49A4C01C.7080107@deri.org>
To: helen.chen@agfa.com
CC: eric@w3.org, public-semweb-lifesci@w3.org
Helen,

Have you tried installing the "Microsoft Visual C++ 2008 Redistributable 
Package (x86)" on your computer, as I mentioned to you in an earlier 
mail? (Thus we are not using the exact same environment... :-)) Well, 
that should make the SWtransformer.exe that I compiled with Visual 
Studio 2008 run on your machine as well.

Also it is not quite the case that I have the same compilation problems 
for Cygwin as I do. It is only true that I also cannot compile the 
latest SVN version - versions before worked (if I remember right). When 
you add the boost-include (included in Cygwin and as shown in the log 
[1] I sent you earlier) then the whole missing boost errors disappear. 
But still, with the latest SVN checkout I get the error in [1]

Cheers,
Holger

[1]
bash-3.2$ PWD=. INCLUDES="-Iwin 
-I/cygdrive/c/cygwin/usr/include/boost-1_33_1" make test
g++ -DYYTEXT_POINTER=1  -g -O0 -W -Wall -Wextra -Wnon-virtual-dtor -ansi 
-std=c++98 -Iwin -I/cygdrive/c/cygwin/usr/include/boost-1_33_1 -I. 
-I/usr/include/libxml2 -I./SPARQLfedParser -I./TurtleSParser
-pipe    -c -o RdfDB.o RdfDB.cpp
In file included from RdfDB.hpp:9,
                from RdfDB.cpp:5:
ResultSet.hpp:362: error: base `w3c_sw::ResultSet' with only non-default 
constructor in class without a constructor
make: *** [RdfDB.o] Error 1


helen.chen@agfa.com schrieb:
>
> Eric
>
> Thanks for continuing working on SWtranformer program.  It is indeed 
> an important piece of work.
>
> We have been trying to compile the program without much success.
>
> My colleague Jos De Roo is using Linux and your r398 compiles and 
> works on his machine, but not the latest version.
> Holger and I use cygwin, and we can not compile it at all, see some of 
> the compile log in the attached file.
> Holger also made a window exe file but I can not run on my computer, 
> although we are using the same Window XP system, may due to missing 
> some vc++ library.
>
> Will you please take a quick look at the log and see if you can give 
> us some advises?
>
> Thanks for your help.
>
>
> Helen
>
>
>
>
>
>
>
> *Eric Prud'hommeaux <eric@w3.org>*
> Sent by: public-semweb-lifesci-request@w3.org
>
> 02/21/2009 10:27 AM
>
> 	
> To
> 	public-semweb-lifesci@w3.org
> cc
> 	
> Subject
> 	[COI] Re: COI protocol #8 demo progress
>
>
>
> 	
>
>
>
>
>
>
> * Eric Prud'hommeaux <eric@w3.org> [2008-10-11 12:11-0400]
> > I've created an sdtm query                 — sdtm.rq
> > to query data mapped from hl7                 — hl7-sdtm.rq
> > which is mapped from the db                 — db-hl7.rq
> >
> > I poked around to look for things like the relationship between a
> > patient and a medication, but am not super confident that I've aligned
> > with existing structures (say, in XML).
> >
> > You can try this at home by downloading an executable for your
> > operating system from http://www.w3.org/2008/04/SPARQLfed/ and running
> >   cat sdtm.rq | \
> >   SWtransformer -q - hl7-sdtm.rq | \
> >   SWtransformer -q - db-hl7.rq -s http://hospital.example/DB/ | \
> >   mysql -u root DiabeticPatientsDataSet --table
> > where the db comes from 
> http://www.w3.org/2008/04/DiabeticPatientsDataSet/
>
> The latest from the const-happy branch (390) pushes filters down to SQL
> sdtm:  FILTER (?code = 6809 || ?code = 6810)
> becomes rim:  FILTER ( ?code = 6809  || ?code = 6810 )
> becomes sql:  WHERE (indicCode_gen0.ingredient = 6809 OR 
> indicCode_gen0.ingredient = 6810)
>
> This should build with [[
>  svn co 
> https://swobjects.svn.sourceforge.net/svnroot/swobjects/branches/const-happy 
> const-happy
>  cd const-happy
>  make bin/SWtransformer
> ]]
>
> and then you can test it à la:
> [[
> eric@mouni:/tmp/const-happy$ bin/SWtransformer -q 
> tests/healthCare/in-list/sdtm.rq tests/healthCare/in-list/hl7-sdtm.rq 
> | bin/SWtransformer -q - tests/healthCare/in-list/db-hl7.rq -s 
> http://hospital.example/DB/ | mysql -u root DiabeticPatientsDataSet
> patient                 dob                 sex                 takes 
>                 indicDate
> 1517441                 1964-09-01 00:00:00                 Female     
>             Glucophage TABS                 2007-07-23 00:00:00
> 1517441                 1964-09-01 00:00:00                 Female     
>             Glucophage TABS                 2007-07-23 00:00:00
> 1517000                 1958-01-01 00:00:00                 Male       
>           Metformin HCl 500 MG Tablet                 2007-06-29 00:00:00
> 1517000                 1958-01-01 00:00:00                 Male       
>           Metformin HCl 500 MG Tablet                 2007-06-29 00:00:00
> 1517403                 1981-05-11 00:00:00                 Male       
>           Metformin HCl 500 MG Tablet                 2008-01-03 00:00:00
> 1505583                 1950-02-25 00:00:00                 Female     
>             Metformin HCl 500 MG Tablet                 2008-01-14 
> 00:00:00
> 1234561                 1983-01-02 00:00:00                 Male       
>           GlipiZIDE-Metformin HCl 2.5-250 MG Tablet                 
> 2007-09-28 00:00:00
> 1234561                 1983-01-02 00:00:00                 Male       
>           GlipiZIDE-Metformin HCl 2.5-250 MG Tablet                 
> 2007-09-28 00:00:00
> 1234562                 1963-12-27 00:00:00                 Female     
>             GlipiZIDE-Metformin HCl 2.5-250 MG Tablet                 
> 2007-09-28 00:00:00
> 1234562                 1963-12-27 00:00:00                 Female     
>             GlipiZIDE-Metformin HCl 2.5-250 MG Tablet                 
> 2008-07-28 00:00:00
> 1234563                 1983-02-25 00:00:00                 Male       
>           GlipiZIDE-Metformin HCl 2.5-250 MG Tablet                 
> 2007-07-28 00:00:00
> 1517441                 1964-09-01 00:00:00                 Female     
>             Glucophage TABS                 2007-07-23 00:00:00
> 1517441                 1964-09-01 00:00:00                 Female     
>             Glucophage TABS                 2007-07-23 00:00:00
> 1516986                 1995-06-13 00:00:00                 Male       
>           Metformin HCl 1000 MG Tablet                 2007-12-04 00:00:00
> ]] — (sample run, using healthCare/in-list tests)
>
>
> > * Eric Prud'hommeaux <eric@w3.org> [2008-10-01 05:45-0400]
> > > I've extended these queries to include (contra)indications by 
> ingredient:
> > > [[
> > > PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
> > > PREFIX Person: <http://hospital.example/DB/Person#>
> > > PREFIX Sex_DE: <http://hospital.example/DB/Sex_DE#>
> > > PREFIX Item_Medication: <http://hospital.example/DB/Item_Medication#>
> > > PREFIX Medication: <http://hospital.example/DB/Medication#>
> > > PREFIX Medication_DE: <http://hospital.example/DB/Medication_DE#>
> > > PREFIX NDCcodes: <http://hospital.example/DB/NDCcodes#>
> > >
> > > SELECT ?person ?dob ?sex ?takes ?contraItem WHERE {
> > >   ?person     Person:MiddleName  ?middleName ;
> > >               Person:DateOfBirth ?dob ;
> > >               Person:SexDE       ?sexEntry   .
> > >   ?sexEntry   Sex_DE:EntryName   ?sex .
> > >
> > >   ?indicItem  Item_Medication:PatientID   ?person ;
> > >               Item_Medication:EntryName ?takes .
> > >   ?indicMed   Medication:ItemID   ?indicItem ;
> > >               Medication:MedDictDE ?indicDE .
> > >   ?indicDE    Medication_DE:NDC    ?indicNDC .
> > >   ?indicCode  NDCcodes:NDC         ?indicNDC ;
> > >               NDCcodes:ingredient  6809 .
> > >
> > >   OPTIONAL {
> > >     ?contraItem Item_Medication:PatientID   ?person .
> > >     ?contraMed  Medication:ItemID   ?contraItem ;
> > >                 Medication:MedDictDE ?contraDE .
> > >     ?contraDE   Medication_DE:NDC    ?contraNDC .
> > >     ?contraCode NDCcodes:NDC         ?contraNDC ;
> > >                 NDCcodes:ingredient  11289
> > >   }
> > >   FILTER (?dob < "1984-01-01T00:00:00"^^xsd:dateTime && 
> !BOUND(?contraItem))
> > > } LIMIT 30
> > > ]]
> > >
> > > yielding:
> > > [[
> > > 
> +---------+---------------------+--------+-------------------------------------------+
> > > | person  | dob                 | sex    | takes                   
>                   |
> > > 
> +---------+---------------------+--------+-------------------------------------------+
> > > | 1517441 | 1964-09-01 00:00:00 | Female | Glucophage TABS         
>                   |
> > > | 1517441 | 1964-09-01 00:00:00 | Female | Glucophage TABS         
>                   |
> > > | 1517000 | 1958-01-01 00:00:00 | Male   | Metformin HCl 500 MG 
> Tablet               |
> > > | 1517000 | 1958-01-01 00:00:00 | Male   | Metformin HCl 500 MG 
> Tablet               |
> > > | 1517403 | 1981-05-11 00:00:00 | Male   | Metformin HCl 500 MG 
> Tablet               |
> > > | 1505583 | 1950-02-25 00:00:00 | Female | Metformin HCl 500 MG 
> Tablet               |
> > > | 1234561 | 1983-01-02 00:00:00 | Male   | GlipiZIDE-Metformin HCl 
> 2.5-250 MG Tablet |
> > > | 1234561 | 1983-01-02 00:00:00 | Male   | GlipiZIDE-Metformin HCl 
> 2.5-250 MG Tablet |
> > > | 1234562 | 1963-12-27 00:00:00 | Female | GlipiZIDE-Metformin HCl 
> 2.5-250 MG Tablet |
> > > | 1234562 | 1963-12-27 00:00:00 | Female | GlipiZIDE-Metformin HCl 
> 2.5-250 MG Tablet |
> > > | 1517441 | 1964-09-01 00:00:00 | Female | Glucophage TABS         
>                   |
> > > | 1517441 | 1964-09-01 00:00:00 | Female | Glucophage TABS         
>                   |
> > > 
> +---------+---------------------+--------+-------------------------------------------+
> > > ]]
> > >
> > >
> > > The birthdate limitation is set for < 1984-01-01 in order to eliminate
> > > 
> +---------+---------------------+------+-------------------------------------------+
> > > | person  | dob                 | sex  | takes                     
>                 |
> > > 
> +---------+---------------------+------+-------------------------------------------+
> > > | 1234563 | 1983-02-25 00:00:00 | Male | GlipiZIDE-Metformin HCl 
> 2.5-250 MG Tablet |
> > > 
> +---------+---------------------+------+-------------------------------------------+
> > >
> > > The dupes appear to come from identical Medication.ItemID for probably
> > > different dates:
> > > [[
> > > mysql> select * from Medication where ItemID=10276300039;
> > > 
> +-------------+-------------+--------------------+-------------+------+--------+------------------------+--------------------+------------+----------------+-----------+
> > > | ID          | ItemID      | FormOfMedicationDE | FreqUnitsDE | 
> Dose | Refill | RoutOfAdministrationDE | QuantityToDispense | 
> DaysToTake | PrescribedByID | MedDictDE |
> > > 
> +-------------+-------------+--------------------+-------------+------+--------+------------------------+--------------------+------------+----------------+-----------+
> > > | 10276300041 | 10276300039 | 0                  |           2 |   
>  1 |      0 |                     15 |                  0 |          0 
> |        1524566 |     90346 |
> > > | 10307800003 | 10276300039 | 0                  |           2 |   
>  1 |      0 |                     15 |                  0 |          0 
> |        1524566 |     90346 |
> > > 
> +-------------+-------------+--------------------+-------------+------+--------+------------------------+--------------------+------------+----------------+-----------+
> > > ]]
> > > Fixing date ranges in the query will help this, I expect.
> > >
> > >
> > > * Eric Prud'hommeaux <eric@w3.org> [2008-10-01 01:32-0400]
> > > > Given some data that Helen added to db:
> > > >   <http://www.w3.org/2008/04/DiabeticPatientsDataSet/MockPerson.csv>
> > > >   
> <http://www.w3.org/2008/04/DiabeticPatientsDataSet/MockMedication.csv>
> > > >   
> <http://www.w3.org/2008/04/DiabeticPatientsDataSet/MockItem_Medication.csv>
> > > > and the latest version of SWObjects:
> > > >   <http://www.w3.org/2008/04/SPARQLfed/>
> > > > I tested the SPARQL-SQL mapping on a sample query
> > > >   tests/execute_HealthCare1 tests/query_stem:Person.rq -s 
> http://hospital.example/DB/
> > > >   <http://www.w3.org/2008/04/SPARQLfed/tests/query_stem:Person.rq>
> > > >
> > > > got an SQL query:
> > > > [[
> > > > SELECT person.id AS person, person.DateOfBirth AS dob, 
> sexEntry.EntryName AS sex, medication.id AS medication, 
> opt1.contraIndic AS contraIndic
> > > >        FROM Person AS person
> > > >             INNER JOIN Sex_DE AS sexEntry ON 
> sexEntry.id=person.SexDE
> > > >             INNER JOIN Item_Medication AS medication ON 
> medication.PatientID=person.id AND 
> medication.EntryName="GlipiZIDE-Metformin HCl 2.5-250 MG Tablet"
> > > >             LEFT OUTER JOIN (
> > > >     SELECT contraIndic.PatientID AS person, contraIndic.id AS 
> contraIndic
> > > >            FROM Item_Medication AS contraIndic
> > > >      WHERE contraIndic.EntryName="Warfarin Sodium 5 MG Tablet"
> > > >              ) AS opt1 ON opt1.person=person.id
> > > >  WHERE (person.DateOfBirth < "1980-01-01 00:00:00" AND 
> !(opt1.contraIndic IS NOT NULL))
> > > >  LIMIT 10
> > > > ]]
> > > >
> > > > executed it, and got:
> > > > 
> +---------+---------------------+--------+-------------+-------------+
> > > > | person  | dob                 | sex    | medication  | 
> contraIndic |
> > > > 
> +---------+---------------------+--------+-------------+-------------+
> > > > | 1234562 | 1963-12-27 00:00:00 | Female | 99999999003 |       
>  NULL |
> > > > | 1234562 | 1963-12-27 00:00:00 | Female | 99999999004 |       
>  NULL |
> > > > 
> +---------+---------------------+--------+-------------+-------------+
> > > >
> > > > I encourage folks to play more. Also, probably time to start 
> working on
> > > > the construct rules that allow the SPARQL query to work over HL7 
> data.
> > > >
> > > > Holger, could you build a DOS/WIN version of the code and 
> distribute it
> > > > or make it available to folks who want to help?
> > > > --
> > > > -eric
> > > >
> > > > office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
> > > > mobile: +1.617.599.3509
> > > >
> > > > (eric@w3.org)
> > > > Feel free to forward this message to any list for any purpose 
> other than
> > > > email address distribution.
> > >
> > >
> > >
> > > --
> > > -eric
> > >
> > > office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
> > > mobile: +1.617.599.3509
> > >
> > > (eric@w3.org)
> > > Feel free to forward this message to any list for any purpose 
> other than
> > > email address distribution.
> >
> >
> >
> > --
> > -eric
> >
> > office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
> > mobile: +1.617.599.3509
> >
> > (eric@w3.org)
> > Feel free to forward this message to any list for any purpose other than
> > email address distribution.
>
> > PREFIX sdtm: <http://www.sdtm.org/vocabulary#>
> > PREFIX spl: 
> <http://www.hl7.org/v3ballot/xml/infrastructure/vocabulary/vocabulary#>
> >
> > SELECT ?patient ?dob ?sex ?takes ?indicDate # ?indicEnd ?contra
> >  WHERE {
> >   ?patient a sdtm:Patient ;
> >           sdtm:middleName ?middleName ;
> >           sdtm:dateTimeOfBirth ?dob ;
> >           sdtm:sex ?sex .
> >
> >   [                   sdtm:subject ?patient ;
> >                    sdtm:standardizedMedicationName ?takes ;
> >
> >                    # nothing by ingredient in sdtm/caBIG/...
> >                    spl:activeIngredient [ spl:classCode 6809 ] ;
> >           sdtm:startDateTimeOfMedication ?indicDate
> >                    # ; sdtm:endDateTimeOfMedication ?indicEnd
> >   ] .
> > #  OPTIONAL {
> > #  [                   sdtm:subject ?patient ;
> > #                   sdtm:standardizedMedicationName ?contra ;
> > #                   spl:activeIngredient [ spl:classCode 11289 ]
> > #         sdtm:effectiveTime [
> > #         sdtm:startDateTimeOfMedication ?contraDate
> > #                   # ; sdtm:endDateTimeOfMedication   ?contraEnd
> > #  ] .
> > #  }
> > } LIMIT 30
> > PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
> > PREFIX hl7: 
> <http://www.hl7.org/v3ballot/xml/infrastructure/vocabulary/vocabulary#>
> > PREFIX spl: 
> <http://www.hl7.org/v3ballot/xml/infrastructure/vocabulary/vocabulary#>
> >
> > PREFIX sdtm: <http://www.sdtm.org/vocabulary#>
> > PREFIX bridg: <>
> > PREFIX caBIG: <>
> > PREFIX CDASH: <>
> > PREFIX MHONG: <>
> > PREFIX dam: <>
> >
> > CONSTRUCT {
> > ?patient
> >     a                                                               
>                         sdtm:Patient ;
> >     sdtm:middleName                                                 
>     ?middleName ;
> >     sdtm:dateTimeOfBirth                                    ?dob ;
> >     sdtm:sex ?sex .
> > [                 a                        sdtm:ConcomitantMedication ;
> >                  sdtm:subject   ?patient ;
> >                  sdtm:standardizedMedicationName                 
>  ?takes ;
> >
> >                  # nothing by ingredient in sdtm/caBIG/...
> >                  spl:activeIngredient [ spl:classCode ?ingred ] ;
> >                  sdtm:startDateTimeOfMedication ?start
> >                  # ; sdtm:endDateTimeOfMedication ?end
> >     ] .
> > } WHERE {
> > ?patient
> >     a                                                               
>                         hl7:Person ;
> >     hl7:entityName                                                   
>   ?middleName ;
> >     hl7:livingSubjectBirthTime                                    ?dob ;
> >     hl7:administrativeGenderCodePrintName ?sex ;
> >     hl7:substanceAdministration                                    [
> >                  a                        hl7:SubstanceAdministration ;
> >                   hl7:consumable [
> >                      hl7:displayName                  ?takes ;
> >                      spl:activeIngredient [
> >                                   spl:classCode ?ingred
> >                      ]
> >                  ] ;
> >                  hl7:effectiveTime [
> >                      hl7:start ?start
> >                      # hl7:end   ?end
> >                  ]
> >     ] .
> > }
>
> > PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
> > PREFIX Person: <http://hospital.example/DB/Person#>
> > PREFIX Sex_DE: <http://hospital.example/DB/Sex_DE#>
> > PREFIX Item_Medication: <http://hospital.example/DB/Item_Medication#>
> > PREFIX Medication: <http://hospital.example/DB/Medication#>
> > PREFIX Medication_DE: <http://hospital.example/DB/Medication_DE#>
> > PREFIX NDCcodes: <http://hospital.example/DB/NDCcodes#>
> >
> > PREFIX hl7: 
> <http://www.hl7.org/v3ballot/xml/infrastructure/vocabulary/vocabulary#>
> > PREFIX spl: 
> <http://www.hl7.org/v3ballot/xml/infrastructure/vocabulary/vocabulary#>
> >
> > CONSTRUCT {
> > ?person
> >     a                                                               
>                         hl7:Person ;
> >     hl7:entityName                                                   
>   ?middleName ;
> >     hl7:livingSubjectBirthTime                                    ?dob ;
> >     hl7:administrativeGenderCodePrintName ?sex ;
> >     hl7:substanceAdministration                                    [
> >                  a                        hl7:SubstanceAdministration ;
> >                   hl7:consumable [
> >                      hl7:displayName                  ?takes ;
> >                      spl:activeIngredient [
> >                                   spl:classCode ?ingred
> >                      ]
> >                  ] ;
> >                  hl7:effectiveTime [
> >                      hl7:start ?indicDate
> >                      # hl7:end   (?indicDate + ?indicDuration)
> >                  ]
> >     ] .
> > } WHERE {
> >   ?person     Person:MiddleName                                     
>   ?middleName ;
> >               Person:DateOfBirth                      ?dob ;
> >               Person:SexDE                                       
> ?sexEntry   .
> >
> >   OPTIONAL {
> >               ?sexEntry   Sex_DE:EntryName   ?sex .
> >   }
> >
> >   OPTIONAL {
> >   ?indicItem  Item_Medication:PatientID                      ?person ;
> >               Item_Medication:PerformedDTTM  ?indicDate ;
> >               Item_Medication:EntryName                      ?takes .
> >   ?indicMed   Medication:ItemID                                     
>   ?indicItem ;
> >               Medication:DaysToTake                     
>  ?indicDuration ;
> >               Medication:MedDictDE                      ?indicDE .
> >   ?indicDE    Medication_DE:NDC                                     
>   ?indicNDC .
> >   }
> >
> >   OPTIONAL {
> >   ?indicCode  NDCcodes:NDC         ?indicNDC ;
> >               NDCcodes:ingredient  ?ingred .
> >   }
> > } LIMIT 30
>
>
>
>
> -- 
> -eric
>
> office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
> mobile: +1.617.599.3509
>
> (eric@w3.org)
> Feel free to forward this message to any list for any purpose other than
> email address distribution.
>
> There are subtle nuances encoded in font variation and clever layout
> which can only be seen by printing this message on high-clay paper.
Received on Wednesday, 25 February 2009 03:51:31 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:54 GMT