RE: getSeverity etc. for relation extractor
Hi James, I don't have an exact phrase to use. We used the location_of with a brain aneurysm project, but the corpus is elsewhere now. However, it would tag things such as [aneurysm] : [middle cerebral artery] and [aneurysm] : [cerebral artery] - which is different from arm/leg, but an example of 2 locations for one entity. From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Monday, March 24, 2014 11:05 AM To: 'dev@ctakes.apache.org' Subject: RE: getSeverity etc. for relation extractor I ran 3.1 against pain in arm and leg and I get just one location_of relation. And again no location_of relations for rash on arm and leg Sean, what was the exact phrase you used with the incubator version? (or was that a while ago and lost) -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Friday, March 21, 2014 3:59 PM To: dev@ctakes.apache.org Subject: RE: getSeverity etc. for relation extractor 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 seem to find multiple locations for a single d/d. Functionality may have changed since then. Thanks for all of your attention to this topic. Sean -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] 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 LocationOfTextRelation annotation with arg1=SignSymptomMention (pain) and arg2=AnatomicalSiteMention (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 example) or does the relation extractor need enhancement before it would create mutiple location_of for a single SignSymptomMention or DiseaseDisorderMention BTW, I will have to debug the setting of bodyLocation in the code because even for pain in arm, when running from trunk, the LocationOfTextRelation annotation is being created, but the bodyLocation within the SignSymptomMention is not being set because the code in TemplateFillerAnnotator expects arg1 and arg2 to be swapped from what they currently are. I'll take a look at what it was in cTAKES 3.1 and find out if this is a bug in TemplateFillerAnnotator or something else. -- James -Original Message- From: Finan, Sean [mailto:sean.fi...@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.ja...@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 identified 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 least holding off until we have a definite, well-defined need (from a user). I think instead, ideally, we would make the template filler smarter at picking which severity / which location when there is more than one for the given identified annotation. Therefore I'd rather not make it a list now, when 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.c...@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 IdentifiedAnnotation? Does the TemplateFiller component currently just take the last one in the list currently? Should we modify the type system to support this in the future- something like the below? A) Support many-to-one B) Separate out getting the relations and getting the actual identified annotations. One suggestion would be: IdentifiedAnnotation.getBodyLocations(): FSArrayIdentifiedAnnotation IdentifiedAnnotation.getBodyLocationRelations(): FSArrayLocationOfTextRelation IdentifiedAnnotation.getSeverity(): FSArrayModifier IdentifiedAnnotation.getSeverityRelations(): FSArrayDegreeOfTextRelation What do others think? --Pei -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
RE: getSeverity etc. for relation extractor
For the text aneurysm in the middle cerebral artery 3.1 creates 3 location of relations aneurysm : middle cerebral artery aneurysm : cerebral artery aneurysm : artery trunk also creates 3 location of relations aneurysm : middle cerebral artery aneurysm : cerebral artery aneurysm : artery bodyLocation is not set for the IdentifiedAnnotation for aneurysm in either case. I've created CTAKES-290 That jira issue will not address the fact the relation extractor does not create annotations for location of relations in Rash on arm and leg. I'll leave that determination to someone more familiar with the relation extractor -- James -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Monday, March 24, 2014 12:52 PM To: dev@ctakes.apache.org Subject: RE: getSeverity etc. for relation extractor Hi James, I don't have an exact phrase to use. We used the location_of with a brain aneurysm project, but the corpus is elsewhere now. However, it would tag things such as [aneurysm] : [middle cerebral artery] and [aneurysm] : [cerebral artery] - which is different from arm/leg, but an example of 2 locations for one entity. From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Monday, March 24, 2014 11:05 AM To: 'dev@ctakes.apache.org' Subject: RE: getSeverity etc. for relation extractor I ran 3.1 against pain in arm and leg and I get just one location_of relation. And again no location_of relations for rash on arm and leg Sean, what was the exact phrase you used with the incubator version? (or was that a while ago and lost) -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Friday, March 21, 2014 3:59 PM To: dev@ctakes.apache.org Subject: RE: getSeverity etc. for relation extractor 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 seem to find multiple locations for a single d/d. Functionality may have changed since then. Thanks for all of your attention to this topic. Sean -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] 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 LocationOfTextRelation annotation with arg1=SignSymptomMention (pain) and arg2=AnatomicalSiteMention (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 example) or does the relation extractor need enhancement before it would create mutiple location_of for a single SignSymptomMention or DiseaseDisorderMention BTW, I will have to debug the setting of bodyLocation in the code because even for pain in arm, when running from trunk, the LocationOfTextRelation annotation is being created, but the bodyLocation within the SignSymptomMention is not being set because the code in TemplateFillerAnnotator expects arg1 and arg2 to be swapped from what they currently are. I'll take a look at what it was in cTAKES 3.1 and find out if this is a bug in TemplateFillerAnnotator or something else. -- James -Original Message- From: Finan, Sean [mailto:sean.fi...@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.ja...@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 identified 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 least holding off until we have a definite, well-defined need (from a user). I think instead, ideally, we would make the template filler smarter at picking which severity / which location when there is more than one for the given identified annotation. Therefore I'd rather not make it a list now, when 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.c...@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
