Mailing-List: contact dev-help@ctakes.apache.org; run by ezmlm
Precedence: bulk
Reply-To: dev@ctakes.apache.org
Received-SPF: pass (athena.apache.org: domain of
 Sean.Finan@childrens.harvard.edu designates 134.174.13.91 as permitted
 sender)
From: "Finan, Sean" <Sean.Finan@childrens.harvard.edu>
To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Subject: RE: getSeverity etc. for relation extractor
Thread-Topic: getSeverity etc. for relation extractor
Thread-Index: 
 AQHPQ5yFRGhO22qeZEqlvkUIX/SIKZros0YAgABmgoD//9oUYIABFA7ggACOBQCAAAQMgIABbw2A///FdMCAAHbZAP//wwpw
Date: Fri, 21 Mar 2014 20:58:58 +0000
Message-ID: <393252F14C42F946952F1ED75D316CAD390328CB@CHEXMBX4A.CHBOSTON.ORG>
References: 
 <CAFqV=FDHF4FimUVc_fLNtd3usDCUC2zeJLyNT9JwMt=fUCbTDQ@mail.gmail.com>
 <924DE05C19409B438EB81DE683A942D9106AD237@CHEXMBX1A.CHBOSTON.ORG>
 <CAFqV=FDTr_26kiHD=BO2oaEwumGaEmftkz6XN83PCxskQdwVmw@mail.gmail.com>
 <924DE05C19409B438EB81DE683A942D9106AEA7F@CHEXMBX1A.CHBOSTON.ORG>
 <6e55ab$8il34q@ironport10.mayo.edu>
 <924DE05C19409B438EB81DE683A942D9106B2003@CHEXMBX1A.CHBOSTON.ORG>
 <6e55ab$8iojj7@ironport10.mayo.edu>
 <393252F14C42F946952F1ED75D316CAD39032873@CHEXMBX4A.CHBOSTON.ORG>
 <6e55ab$8ipru7@ironport10.mayo.edu>
In-Reply-To: <6e55ab$8ipru7@ironport10.mayo.edu>
Accept-Language: en-US
Content-Language: en-US
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable
MIME-Version: 1.0

Hi James,

It is starting to resemble a row of falling dominoes ...

I ran with an incubator version of the "location of" extractor and it did s=
eem to find multiple locations for a single d/d.  Functionality may have ch=
anged since then.

Thanks for all of your attention to this topic.

Sean

-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@mayo.edu]=20
Sent: Friday, March 21, 2014 4:34 PM
To: 'dev@ctakes.apache.org'
Subject: RE: getSeverity etc. for relation extractor

Running from trunk, I don't get any relations for "Rash on arm and leg" :(

If I change the text to "pain in arm and leg" I get one LocationOfTextRelat=
ion annotation with arg1=3DSignSymptomMention (pain) and arg2=3DAnatomicalS=
iteMention (arm)

Does the relation extractor support creating a 2nd relation involving pain =
- the one between pain and leg (is this just an unfortunate choice of examp=
le) or does the relation extractor need enhancement before it would create =
mutiple location_of for a single SignSymptomMention or DiseaseDisorderMenti=
on

BTW, I will have to debug the setting of bodyLocation in the code because e=
ven for "pain in arm", when running from trunk, the LocationOfTextRelation =
annotation is being created, but the bodyLocation within the SignSymptomMen=
tion is not being set because the code in TemplateFillerAnnotator expects a=
rg1 and arg2 to be swapped from what they currently are. I'll take a look a=
t what it was in cTAKES 3.1 and find out if this is a bug in TemplateFiller=
Annotator or something else.

-- James

-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Friday, March 21, 2014 12:30 PM
To: dev@ctakes.apache.org
Subject: RE: getSeverity etc. for relation extractor

> until we have a definite, well-defined need (from a user).

"Rash on arm and leg"

>  I don't follow what you mean by your item B) below

[Rash].getLocationRelation() > [Rash : Arm]
[Rash].getLocation() > [Arm]


-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
Sent: Friday, March 21, 2014 12:58 PM
To: 'dev@ctakes.apache.org'
Subject: RE: getSeverity etc. for relation extractor

Yes, if there is more than one severity or location relation for a given id=
entified annotation, currently the template filler does just take the last =
severity and or last location.

I suggest not changing the type system to allow a list (FSArray), or at lea=
st holding off until we have a definite, well-defined need (from a user).=20

I think instead, ideally, we would make the template filler smarter at pick=
ing which severity / which location  when there is more than one for the gi=
ven identified annotation. Therefore I'd rather not make it a list now, whe=
n in the long run I think it should be a single value. And in the meantime =
if someone has a need, they can look through the relations.

Pei, I don't follow what you mean by your item B) below

-- James

-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: Thursday, March 20, 2014 2:03 PM
To: dev@ctakes.apache.org
Subject: RE: getSeverity etc. for relation extractor

Awesome!
Thanks James...

On Sean's point about many-to-one relationships.  I think the current type =
system only supports 1 degree_of and severity_of for each IdentifiedAnnotat=
ion? =20
Does the TemplateFiller component currently just take the last one in the l=
ist currently?
Should we modify the type system to support this in the future- something l=
ike the below?
A) Support many-to-one
B) Separate out getting the relations and getting the actual identified ann=
otations.

One suggestion would be:
IdentifiedAnnotation.getBodyLocations(): FSArray<IdentifiedAnnotation>
IdentifiedAnnotation.getBodyLocationRelations(): FSArray<LocationOfTextRela=
tion>
IdentifiedAnnotation.getSeverity(): FSArray<Modifier>
IdentifiedAnnotation.getSeverityRelations(): FSArray<DegreeOfTextRelation>

What do others think?
--Pei

> -----Original Message-----
> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> Sent: Thursday, March 20, 2014 2:50 PM
> To: 'dev@ctakes.apache.org'
> Subject: RE: getSeverity etc. for relation extractor
>=20
> I saw the jira was assigned to me and had a few minutes so I=20
> implemented a fix and committed.
> It was more than just the one line.
> The name of the index in which the binary text relations has changed=20
> (now separate indexes instead of one for all binary text relations) so=20
> I had to change which index was searched.
>=20
> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Thursday, March 20, 2014 9:28 AM
> To: dev@ctakes.apache.org
> Subject: RE: getSeverity etc. for relation extractor
>=20
> Thanks for confirm James.  It seem like a bug...
> Chase,
> if you confirm if adding ddm.setSeverity(degreeOfTextRelation);  works=20
> for you, I can commit the changes in trunk.
>=20
> Which also brings up some interesting points:
> 1) Should we populate IdentifiedAnnotation.severity() and
> bodylocationof() Directly in RelationExtractorAnnotator instead of the te=
mplate filler?
> It would seem more intuitive and faster than iterating through the=20
> relations afterwards again.
> 2)Chase brought up a good point, should we add some of the commonly=20
> used components to the defaultpipeline?  (DrugNER, RelationExtractor,=20
> TemplateFiller)?  Seems easier to get onboard I think.
>=20
> --Pei
>=20
>=20
> > -----Original Message-----
> > From: Chen, Pei
> > Sent: Wednesday, March 19, 2014 5:58 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: getSeverity etc. for relation extractor
> >
> > Chase,
> > I am not sure why or the reasoning behind this, but it might explain=20
> > why Severity is null for your DiseaseDisorderMention example:
> > Line 319 in TemplateFillerAnnotator.java:
> >
> > If I'm reading this logic correctly, it will only populate severity for
> > SignSymptomMention....   Can't think of why not to populate it if it ex=
ists in
> > the BinaryTextRelations-
> > have you tried adding: ddm.setSeverity(degreeOfTextRelation);
> > instead of logging the error ???
> >
> > 	    			if (eventMention instanceof
> > DiseaseDisorderMention) {
> > 	    				DiseaseDisorderMention ddm =3D
> > (DiseaseDisorderMention) eventMention;
> > 	    				logger.error("Need to implement attr
> for " + relation + " for
> > DiseaseDisorderMention");
> > 	    			} else if (eventMention instanceof
> > SignSymptomMention) {
> > 	    				SignSymptomMention ssm =3D
> > (SignSymptomMention) eventMention;
> >
> > 	ssm.setSeverity(degreeOfTextRelation);
> >
> > Would you mind opening a Jira attach a patch/test if it works for you?
> > -Pei
> >
> > > -----Original Message-----
> > > From: Chase Master [mailto:chasemaster9@gmail.com]
> > > Sent: Wednesday, March 19, 2014 4:09 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: getSeverity etc. for relation extractor
> > >
> > > Thanks,
> > > I tried using the AggregateTemplateFiller.xml from the=20
> > > template-filler module, and I specified the relation extractor=20
> > > pipeline that I was using before from the relation-extractor=20
> > > project (there is also a different one in the template-filler=20
> > > project called "RelationExtractorAggregateWithoutOrangeBook").
> > > However, I don't see a difference, the severity is still null.
> > >
> > > Just wondering - is there some reason that the TemplateFiller is=20
> > > not included by default?  It seems confusing that there are=20
> > > getters for properties that aren't set in general ...even when one=20
> > > runs the default clinical pipeline instead of the=20
> > > RelationExtractorAggregate, these getters are there, but there are no=
 relations.
> > >
> > >
> > > Thanks
> > > Chase
> > >
> > >
> > > On Wed, Mar 19, 2014 at 1:04 PM, Chen, Pei
> > > <Pei.Chen@childrens.harvard.edu>wrote:
> > >
> > > > If I remember correctly, I think those attributes were set in=20
> > > > IdentifiedAnnotation via:
> > > > ctakes-template-filler/desc/analysis_engine/TemplateFillerAnnotator=
.
> > > > xm
> > > > l
> > > > One can look at the logic in:
> > > > org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator [1]
> > > >
> > > > Have you tried added that to the pipeline?
> > > >
> > > > [1]
> > > > http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-template-fil
> > > > le
> > > > r/
> > > > sr
> > > > c/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerA
> > > > nn
> > > > ot
> > > > at
> > > > or.java
> > > >
> > > > --Pei
> > > >
> > > > > -----Original Message-----
> > > > > From: Chase Master [mailto:chasemaster9@gmail.com]
> > > > > Sent: Wednesday, March 19, 2014 1:56 PM
> > > > > To: dev@ctakes.apache.org
> > > > > Subject: getSeverity etc. for relation extractor
> > > > >
> > > > > Hi,
> > > > >
> > > > > I am trying to output the relations associated with
> > > > DiseaseDisorderMentions
> > > > > and other types.  But I want to start by iterating over=20
> > > > > DiseaseDisorderMention, not BinaryTextRelations since I want=20
> > > > > to be sure
> > > > to
> > > > > find them all, even if they have no associated relation.
> > > > >
> > > > > I always get null when using any of the getters like=20
> > > > > "getSeverity()".  I
> > > > am
> > > > > using the example text "He had a slight fracture in the=20
> > > > > proximal right
> > > > fibula".
> > > > > When I iterate over BinaryTextRelations, I see the following=20
> > > > > valid
> > > > values:
> > > > > BinaryTextRelation slightFracture =3D iterator.next();
> > > > > slightFracture.getArg1().getArgument().getCoveredText() is
> "fracture"
> > > > > slightFracture.getArg2().getArgument().getCoveredText() is "sligh=
t".
> > > > > However, for the "fracture" DiseaseDisorderMention,
> > > > > getSeverity() is
> > > > null.
> > > > >  If it wasn't, I would then grab
> > > > > disease.getSeverity().getArg1().getArgument().getCoveredText()
> > > > > ,
> > > > > or for Arg2.
> > > > >
> > > > > Thanks,
> > > > > Chase
> > > >