- From: Eric Prud'hommeaux <eric@w3.org>
- Date: Wed, 25 Feb 2009 10:42:04 -0500
- To: Holger Stenzhorn <holger.stenzhorn@deri.org>
- Cc: helen.chen@agfa.com, public-semweb-lifesci@w3.org
- Message-ID: <20090225154203.GC14185@w3.org>
* Holger Stenzhorn <holger.stenzhorn@deri.org> [2009-02-25 00:50-0300]
> 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
I think that's from a version back, so I'm guessing a bit at the error.
I pulled a couple silly classes out. try v430 (HEAD, as of now)
> 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.
--
-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 15:42:18 UTC