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From "Steven Bethard (JIRA)" <>
Subject [jira] [Commented] (CTAKES-57) Type System updates for 3.x-incubating
Date Fri, 15 Feb 2013 00:13:12 GMT


Steven Bethard commented on CTAKES-57:

So I finally got back around to this. Yes, TimeMention is okay as a band-aid for now. It has
the features I need, even if it's semantically wrong to have a getTime method for things of
type DATE, DURATION, SET, etc. 

I've also plugged away at the rest of SHARPKnowtatorXMLReader. And thank you guys for your
work on it!

Here are the remaining roadblocks:

* ElementRelation vs. BinaryTextRelation. All of the manual annotations describe spans of
text, so they're read in as XXXMention or XXXModifier types. Correspondingly, whenever the
annotations describe a relation between an XXXMention and an XXXModifier, this is read in
as a BinaryTextRelation so that we can set arguments appropriately. However, several of the
features on XXXMention types have *ElementRelation* values. For example, DiseaseDisorderMention:alleviatingFactor
is an ElementRelation, DiseaseDisorderMention:associatedSignSymptom is a ManifestationOf,
DiseaseDisorderMention:bodyLocation is a LocationOf, etc. I think these should be BinaryTextRelations,
since their arguments are Mentions/Modifiers, not Elements.

* Most of the MedicationEventMention features (medicationStatusChange, medicationDosage, medicationDuration,
etc.) take Attribute values, not Mention values (e.g. medicationStatusChange takes a MedicationStatusChange
value, but should take a MedicationStatusChangeModifier value).

* MedicationEventMention doesn't have any feature where I can put an associated MedicationAllergyModifier,
or an associated start date.

* There's no DateMention (or DateModifier?) for start dates. There's a DateAnnotation, but
it doesn't have the necessary "month" and "day" attributes.

* ProcedureMention doesn't have anywhere I can put an associated ProcedureDeviceModifier

> Type System updates for 3.x-incubating
> --------------------------------------
>                 Key: CTAKES-57
>                 URL:
>             Project: cTAKES
>          Issue Type: Improvement
>    Affects Versions: 2.6-incubating
>            Reporter: James Joseph Masanz
>            Assignee: James Joseph Masanz
>             Fix For: 3.1-incubating
> Opening 2 issues regarding the type system. This one is for changes that will require
refactoring and may affect current users.

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