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 <ddlig...@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 <ddlig...@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
>
