Hi Taposh, Instructions on leaving lists can be found here: http://apache.org/foundation/mailinglists.html
Sean -----Original Message----- From: Taposh D. Roy [mailto:taposh.d....@kp.org] Sent: Monday, February 06, 2017 1:29 PM To: dev@ctakes.apache.org Subject: Re: jcas work with a list of schemas Please remove me from mailing list for now. I am not active and I don't see an unsubscribe link in the email chain. Regards, Taposh Taposh Roy, MBA (Finance), MS (Comp. E), MS (EE-Physics) | Innovation Team | Delivery System Analytics, Decision Support | Kaiser Permanente | 1800 Harrison, 7th Floor, #072R22, Oakland, CA, 94521| cell: 510-206-1633 | taposh.d....@kp.org On 2/6/17, 10:27 AM, "Alaa al Barari" <alaa.albar...@gmail.com> wrote: Caution: This email came from outside Kaiser Permanente. Do not open attachments or click on links if you do not recognize the sender. ______________________________________________________________________ I know alittle bit of java. I have like 14 different schemes. I was hoping for away to call only for a set (lets say 3) of schemas without ctakes get the data for the 14 then filter the wanted 3. This would be much faster. On Feb 6, 2017 8:21 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu> wrote: Hi Alaa, Are you a java developer or do you have a different background? If you are not a developer, could you please enumerate exactly what you need? Thanks -----Original Message----- From: Alaa al Barari [mailto:alaa.albar...@gmail.com] Sent: Monday, February 06, 2017 1:15 PM To: dev@ctakes.apache.org Subject: RE: jcas work with a list of schemas Thanks. I was hoping for away to fetch only whats needed for performance enhancement. On Feb 6, 2017 8:09 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu> wrote: > Yes. You do not need to use the code directly if it doesn't fit your > needs. You can look at the code within that class and within those > methods to do something similar. > > -----Original Message----- > From: Alaa al Barari [mailto:alaa.albar...@gmail.com] > Sent: Monday, February 06, 2017 1:07 PM > To: dev@ctakes.apache.org > Subject: RE: jcas work with a list of schemas > > Thanks sean but internally this fetch data for all schemas then filter > the needed schema right ? > > On Feb 6, 2017 7:57 PM, "Finan, Sean" > <sean.fi...@childrens.harvard.edu> > wrote: > > > Hi Alaa, > > > > Have a look at the OntologyConceptUtil class in ctakes-core. You > > can use the getCodes(..) method to obtain the codes for a scheme. > > > > For all codes of all annotations: > > Collection<String> allCodes = OntologyConceptUtil.getCodes( jcas, > > schemeName ); > > > > For all codes of all annotations in a window (paragraph, segment, > > sentence): > > Collection<String> windowCodes = OntologyConceptUtil.getCodes( jcas, > > windowAnnotation, schemeName ); > > > > For all codes in a single annotation: > > Collection<String> annotationCodes = OntologyConceptUtil.getCodes( > > annotation, schemeName ); > > > > For all codes in multiple annotations: > > Collection<String> annotationsCodes = OntologyConceptUtil.getCodes( > > annotations, schemeName ); > > > > If you want a map of scheme names and codes: > > Map<String,Collection<String>> getSchemeCodes( jcas ); > > Map<String,Collection<String>> getSchemeCodes( jcas, window ); ... > > getSchemeCodes( annotation ); ... getSchemeCodes( annotations ); > > > > > > If you have some other need, like getting all annotations with codes > > of a certain scheme, let me know. > > Sean > > > > > > > > -----Original Message----- > > From: Alaa al Barari [mailto:alaa.albar...@gmail.com] > > Sent: Monday, February 06, 2017 4:30 AM > > To: dev@ctakes.apache.org > > Subject: jcas work with a list of schemas > > > > Hi, > > > > I have my own dictionary and it has a lot of schemas which takes a > > lot of time. please see code below, how to make it work with > > specific list of schemas instead of all of them > > > > jcas = pipeline.newJCas(); > > jcas.setDocumentText(sentence.getCoveredText()); > > pipeline.process(jcas); > > String previousEntity = ""; > > for ( IdentifiedAnnotation entity : JCasUtil.select( jcas, > > IdentifiedAnnotation.class ) ) { > > > > final FSArray fsArray = entity.getOntologyConceptArr(); if ( fsArray > > == null ) { continue; } String entityString = > > entity.getCoveredText(); System.out.println( "Entity: " + > > entity.getCoveredText() > > + " === Polarity: " + entity.getPolarity() " === Subject: " + > > + entity.getSubject() " === History? " + (entity.getHistoryOf() == > > CONST.NE_HISTORY_OF_PRESENT)); > > > > final FeatureStructure[] featureStructures = fsArray.toArray(); > > final Collection<String> entityCodes = new ArrayList<>( > > featureStructures.length ); previousEntity = entityString; for ( > > FeatureStructure featureStructure : featureStructures ) { if ( > > featureStructure instanceof UmlsConcept ) { final UmlsConcept > > umlsConcept = (UmlsConcept)featureStructure; String entityCode = > > umlsConcept.getCode(); String entityScheme = > > umlsConcept.getCodingScheme(); String description = > > umlsConcept.getCodeDescription(); if (entityCode == null || > > entityScheme == null) { continue; } if > > (schemes.contains(entityScheme) > > || schemes.contains("all")) { System.out.println(entityScheme + "_" > > || + > > entityCode + "_" + description); } } } > > > > } > > } > > > > > > Regards. > > -- > > Eng Alaa Al-Barari > > phone 0599297470 > > > NOTICE TO RECIPIENT: If you are not the intended recipient of this e-mail, you are prohibited from sharing, copying, or otherwise using or disclosing its contents. 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