Abad, This was pointed out to you - a large portion (3-11) of these attributes have not been implemented. If you have a solution for one or all of them, we would welcome your contribution to cTAKES. Regards, -- Guergana Savova, PhD, FACMI Associate Professor PI Natural Language Processing Lab Computational Health Informatics Program (CHIP) Boston Children's Hospital and Harvard Medical School 401 Park, 5th floor East, 5523.3 Boston, MA 02215 Tel: (617) 919-2972 Fax: (617) 730-0817 [email protected]<mailto:[email protected]> Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova http://ctakes.apache.org<http://ctakes.apache.org/> http://thyme.healthnlp.org<http://thyme.healthnlp.org/> http://cancer.healthnlp.org<http://cancer.healthnlp.org/> http://share.healthnlp.org<http://share.healthnlp.org/> http://center.healthnlp.org<http://center.healthnlp.org/> T<https://twitter.com/bentleyu>witter<https://twitter.com/bostonchildrens> | LinkedIn<https://www.linkedin.com/company/bostonchildrenshospital/> | Facebook<https://www.facebook.com/BostonChildrensHospital> | Instagram<https://www.instagram.com/bostonchildrens/> [http://web2.tch.harvard.edu/homepagestories/Images/SigBlock.jpg]
From: [email protected] [mailto:[email protected]] Sent: Monday, March 9, 2020 1:01 AM To: [email protected] Subject: RE: Values missing for few attributes and how to populate demographic details [EXTERNAL] * External Email - Caution * Hi Team, A gentle reminder on this. Since this is a critical data for our profile it would be of a great help if you could confirm whether these data are available in cTAKES , This is a decision making factor for us now. So kindly advice. Thanks & Regards [cid:D3145E69-CD94-48C1-877F-5134EEAFB598] Abad Ayyub Vnet: 406170 | Cell : +91-9447379028 From: Ayyub, Abad (Cognizant) Sent: Wednesday, February 26, 2020 12:28 PM To: [email protected]<mailto:[email protected]> Subject: RE: Values missing for few attributes and how to populate demographic details Hi Team, A gentle reminder on this. Any advice will be of great help for us. Thanks & Regards [cid:D3145E69-CD94-48C1-877F-5134EEAFB598] Abad Ayyub Vnet: 406170 | Cell : +91-9447379028 From: Ayyub, Abad (Cognizant) Sent: Friday, February 21, 2020 5:50 PM To: [email protected]<mailto:[email protected]> Subject: Values missing for few attributes and how to populate demographic details Hello Team, We are working on extracting the clinical data from medical documents and some of the attributes that I list below are critical for our profile. Could you pls. advise on how can we get a valid values for the below attributes which is coming under every Event/EntityMention SlNO AttributeName Remarks 1 conditional Always got this as FALSE 2 originalText Always got this as NULL 3 event Always got this as NULL 4 alleviatingFactor Always got this as NULL 5 associatedSignSymptom Always got this as NULL 6 course Always got this as NULL 7 duration Always got this as NULL 8 endTime Always got this as NULL 9 exacerbatingFactor Always got this as NULL 10 startTime Always got this as NULL 11 relativeTemporalContext Always got this as NULL Also we need to identify how can we extract below details regarding Patient from the document * Demographic details - Patient Age, weight, BMI, BP, race, gender as present in the medical records * Patient history - Patient's past medical history and social history will be displayed. Social history includes smoking, alcohol and drug and other details * Family history - Patient's family history will also be displayed in this section Kindly advise whether we need to add any new AE's to our existing piper file so that cTAKES will provide us the requested O/P as mentioned above. PFB the contents of AE's configured in our piper file. // Load a simple token processing pipeline from another pipeline file load DefaultTokenizerPipeline.piper add ContextDependentTokenizerAnnotator addDescription POSTagger // Add Chunkers load ChunkerSubPipe.piper // Commands and parameters to create a default chunker processing sub-pipeline. This is not a full pipeline. // Default fast dictionary //lookup add DefaultJCasTermAnnotator load AttributeCleartkSubPipe.piper # Parameters for AssertionAnalysisEngine and ConceptConverterAnalysisEngine set assertionModelResource=file: org/apache/ctakes/assertion/models/i2b2.model set scopeModelResource=file: org/apache/ctakes/assertion/models/scope.model set cueModelResource=file: org/apache/ctakes/assertion/models/cue.model set enabledFeaturesResource=file: org/apache/ctakes/assertion/models/featureFile11b set posModelResource=file: org/apache/ctakes/assertion/models/pos.model package org.apache.ctakes.assertion.medfacts package org.apache.ctakes.assertion.attributes add ConceptConverterAnalysisEngine add GenericAttributeAnalysisEngine add SubjectAttributeAnalysisEngine // Creates modifier annotations needed to handle the drug mentions. add org.apache.ctakes.drugner.ae.DrugMentionAnnotator STATUS_BOUNDARY_ANN_TYPE="org.apache.ctakes.typesystem.type.textsem.MedicationMention" add org.apache.ctakes.constituency.parser.ae.ConstituencyParser // Modifiers. Use addLogged to log start and finish of processing. There aren't default models, so set specifically addLogged ModifierExtractorAnnotator classifierJarPath=/org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar // Degree of severity, etc. addLogged DegreeOfRelationExtractorAnnotator classifierJarPath=/org/apache/ctakes/relationextractor/models/degree_of/model.jar // Location. addLogged LocationOfRelationExtractorAnnotator classifierJarPath=/org/apache/ctakes/relationextractor/models/location_of/model.jar add org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator //Remaining statements not reflected in the XMI (Not checked). It is for relation extraction // 'Generic' Events. Use addDescription and let the EventAnnotator set itself up with defaults. //For getting the relation between the events addDescription EventAnnotator // Times. Use addLogged to log start and finish of processing. There aren't default models, so set specifically add BackwardsTimeAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/timeannotator/model.jar // DocTimeRel: the relation bin for Events to the Document Creation Time. // add DocTimeRelAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/doctimerel/model.jar // Event - Time binary relations. add EventTimeRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventtime/model.jar // Event - Event binary relations. add EventEventRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventevent/model.jar Thanks & Regards [cid:D3145E69-CD94-48C1-877F-5134EEAFB598] Abad Ayyub Vnet: 406170 | Cell : +91-9447379028 This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient(s), please reply to the sender and destroy all copies of the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email, and/or any action taken in reliance on the contents of this e-mail is strictly prohibited and may be unlawful. Where permitted by applicable law, this e-mail and other e-mail communications sent to and from Cognizant e-mail addresses may be monitored. This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient(s), please reply to the sender and destroy all copies of the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email, and/or any action taken in reliance on the contents of this e-mail is strictly prohibited and may be unlawful. Where permitted by applicable law, this e-mail and other e-mail communications sent to and from Cognizant e-mail addresses may be monitored.
