You are viewing a plain text version of this content. The canonical link for it is here.
Posted to dev@ctakes.apache.org by "Dligach, Dmitriy" <dd...@luc.edu> on 2019/10/24 20:27:42 UTC
duplicate types in ctakes types system?
Dear cTAKES developers,
Does anybody know why quite a few types are defined multiple times in TypeSystem.xml?
E.g. I see this at line 576:
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.LabReferenceRange</name>
<description>Holds a narrative (i.e. string) reference range</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
And then I see this at line 2165:
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.LabReferenceRange</name>
<description>Holds a narrative (i.e. string) reference range</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
Thank you in advance,
Dima
Re: duplicate types in ctakes types system? [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Dima,
At a guess this is a copy - paste artifact.
Have you tested the type system with copies removed? It seems like it should work as the types should be compiled into classes with only a single definition.
Sean
________________________________________
From: Dligach, Dmitriy <dd...@luc.edu>
Sent: Thursday, October 24, 2019 4:46 PM
To: cTAKES Developer list
Subject: Re: duplicate types in ctakes types system? [EXTERNAL]
Here’s the full list of the duplicate types:
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.LabReferenceRange</name>
<description>Holds a narrative (i.e. string) reference range</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.BodySide</name>
<description>Value set: unmarked (default), left, right, bilateral</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.LabValue</name>
<description>Quantitative results of a laboratory, with number and unit.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>number</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
<featureDescription>
<name>unit</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationForm</name>
<description>Form of this medication. Value set includes tablet, capsule, liquid, inhalant, gel, other, etc.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.Course</name>
<description>An indication of progress or decline of a condition. Value set: unmarked (default), changed, increased, decreased, improved, worsened, resolved</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange</name>
<description>Status refers to the whether the medication is currently being taken or not. Value set: start, stop, increase, decrease, no change.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description>Indicates the change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'.</description>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationFrequency</name>
<description>How often a medication should be used. e.g., BID or b.i.d. or "twice-a-day" would have a number=2 and unit=day.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>number</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
<featureDescription>
<name>unit</name>
<description>The periodic unit used, e.g day, month, hour, etc.</description>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag</name>
<description>An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.Severity</name>
<description>An explicitly-mentioned indication of the seriousness of a condition. Value Set: unmarked (default), severe, moderate, slight</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationStrength</name>
<description>Strength indicates the strength number and unit of the prescribed drug. E.g. "5 mg" in "one 5 mg tablet twice-a-day for 2 weeks"</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>number</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
<featureDescription>
<name>unit</name>
<description>the unit of measurement</description>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.ProcedureDevice</name>
<description>Corresponds to the UMLS Devices semantic group: medical device and research device.
Example: arterial line has a Medical Device semantic type. This is qualifying information on how a procedure was done.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationDuration</name>
<description>The amount of time after which a medication should stop being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2 weeks"</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationDosage</name>
<description>Dosage indicates how much of a prescribed drug should be taken. E.g. "one" in "one 5 mg tablet twice-a-day for 2 weeks"</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationRoute</name>
<description>Means by which the medication was taken or administered. Value set includes Topical, Enteral_Oral, Parenteral_Intravenous, Other, undetermined, etc.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.ProcedureMethod</name>
<description>The way or the equipment used to give or administration something (medication, test). This corresponds to the Procedures UMLS semantic group.
More qualifying information on how the procedure was done.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.BodyLaterality</name>
<description>The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.). This is finer-grained to allow combinations of values.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
Dima
> On Oct 24, 2019, at 15:27, Dligach, Dmitriy <dd...@luc.edu> wrote:
>
> Dear cTAKES developers,
>
> Does anybody know why quite a few types are defined multiple times in TypeSystem.xml?
>
> E.g. I see this at line 576:
>
> <typeDescription>
> <name>org.apache.ctakes.typesystem.type.refsem.LabReferenceRange</name>
> <description>Holds a narrative (i.e. string) reference range</description>
> <supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
> <features>
> <featureDescription>
> <name>value</name>
> <description/>
> <rangeTypeName>uima.cas.String</rangeTypeName>
> </featureDescription>
> </features>
> </typeDescription>
> <typeDescription>
>
> And then I see this at line 2165:
>
> <typeDescription>
> <name>org.apache.ctakes.typesystem.type.refsem.LabReferenceRange</name>
> <description>Holds a narrative (i.e. string) reference range</description>
> <supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
> <features>
> <featureDescription>
> <name>value</name>
> <description/>
> <rangeTypeName>uima.cas.String</rangeTypeName>
> </featureDescription>
> </features>
> </typeDescription>
> <typeDescription>
>
> Thank you in advance,
>
> Dima
>
Re: duplicate types in ctakes types system?
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Here’s the full list of the duplicate types:
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.LabReferenceRange</name>
<description>Holds a narrative (i.e. string) reference range</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.BodySide</name>
<description>Value set: unmarked (default), left, right, bilateral</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.LabValue</name>
<description>Quantitative results of a laboratory, with number and unit.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>number</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
<featureDescription>
<name>unit</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationForm</name>
<description>Form of this medication. Value set includes tablet, capsule, liquid, inhalant, gel, other, etc.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.Course</name>
<description>An indication of progress or decline of a condition. Value set: unmarked (default), changed, increased, decreased, improved, worsened, resolved</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange</name>
<description>Status refers to the whether the medication is currently being taken or not. Value set: start, stop, increase, decrease, no change.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description>Indicates the change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'.</description>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationFrequency</name>
<description>How often a medication should be used. e.g., BID or b.i.d. or "twice-a-day" would have a number=2 and unit=day.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>number</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
<featureDescription>
<name>unit</name>
<description>The periodic unit used, e.g day, month, hour, etc.</description>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag</name>
<description>An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.Severity</name>
<description>An explicitly-mentioned indication of the seriousness of a condition. Value Set: unmarked (default), severe, moderate, slight</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationStrength</name>
<description>Strength indicates the strength number and unit of the prescribed drug. E.g. "5 mg" in "one 5 mg tablet twice-a-day for 2 weeks"</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>number</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
<featureDescription>
<name>unit</name>
<description>the unit of measurement</description>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.ProcedureDevice</name>
<description>Corresponds to the UMLS Devices semantic group: medical device and research device.
Example: arterial line has a Medical Device semantic type. This is qualifying information on how a procedure was done.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationDuration</name>
<description>The amount of time after which a medication should stop being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2 weeks"</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationDosage</name>
<description>Dosage indicates how much of a prescribed drug should be taken. E.g. "one" in "one 5 mg tablet twice-a-day for 2 weeks"</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.MedicationRoute</name>
<description>Means by which the medication was taken or administered. Value set includes Topical, Enteral_Oral, Parenteral_Intravenous, Other, undetermined, etc.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.ProcedureMethod</name>
<description>The way or the equipment used to give or administration something (medication, test). This corresponds to the Procedures UMLS semantic group.
More qualifying information on how the procedure was done.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
<typeDescription>
<name>org.apache.ctakes.typesystem.type.refsem.BodyLaterality</name>
<description>The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.). This is finer-grained to allow combinations of values.</description>
<supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
<features>
<featureDescription>
<name>value</name>
<description/>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
Dima
> On Oct 24, 2019, at 15:27, Dligach, Dmitriy <dd...@luc.edu> wrote:
>
> Dear cTAKES developers,
>
> Does anybody know why quite a few types are defined multiple times in TypeSystem.xml?
>
> E.g. I see this at line 576:
>
> <typeDescription>
> <name>org.apache.ctakes.typesystem.type.refsem.LabReferenceRange</name>
> <description>Holds a narrative (i.e. string) reference range</description>
> <supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
> <features>
> <featureDescription>
> <name>value</name>
> <description/>
> <rangeTypeName>uima.cas.String</rangeTypeName>
> </featureDescription>
> </features>
> </typeDescription>
> <typeDescription>
>
> And then I see this at line 2165:
>
> <typeDescription>
> <name>org.apache.ctakes.typesystem.type.refsem.LabReferenceRange</name>
> <description>Holds a narrative (i.e. string) reference range</description>
> <supertypeName>org.apache.ctakes.typesystem.type.refsem.Attribute</supertypeName>
> <features>
> <featureDescription>
> <name>value</name>
> <description/>
> <rangeTypeName>uima.cas.String</rangeTypeName>
> </featureDescription>
> </features>
> </typeDescription>
> <typeDescription>
>
> Thank you in advance,
>
> Dima
>