Re: Hello cTAKES Mailing List
Raymond, Probably a combination of UMLS *Consumer Health Vocabulary + Custom Dictionary (as Sean described) *may work for the use case*:* OAC CHV connects informal, common words and phrases about health to technical terms used by health care professionals. It includes jargon, slang, ambiguous, and misspelled words as used by consumers and health care professionals. Due to its nature, OAC CHV includes concepts that are not represented by other source vocabularies within the Metathesaurus. [1] http://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CHV/ On Sun, Feb 22, 2015 at 10:37 AM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Hi Raymond, If you use the dictionary-fast module there exists an entry feeling bad with cui 557911 and cui 231218. There is also feel bad and feeling bad emotionally You will find horrible present pain but no other entry with horrible. You will not find any terms with awful and probably many other desired words. If you are really interested in slang crappy, lousy, etc. then they are definitely not present. What you can do is create a second dictionary. There are example custom dictionaries in -dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/example/bsv/ You should look at custom_cui_bsv.bsv if you want to specify term unique id codes and term text alone. If you want to add tui/group codes then look at custom_cui_tui_bsv.bsv - you will probably want to model your dictionary after this so that you can tag your terms with tuis for symptoms. You will want to imitate sections from the corresponding .xml file in that directory. Make a copy of cTakesHsql.xml (two dirs up) and add lines: dictionary nameCustomCuiRareWord/name implementationNameorg.apache.ctakes.dictionary.lookup2.BsvRareWordDictionary/implementationName properties property key=bsvPath value=org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv/ /properties /dictionary And conceptFactory nameCustomCuiConcept/name implementationNameorg.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory/implementationName properties property key=bsvPath value=org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv/ /properties /conceptFactory And dictionaryConceptPair nameCustomPair/name dictionaryNameCustomCuiRareWord/dictionaryName conceptFactoryNameCustomCuiConcept/conceptFactoryName /dictionaryConceptPair Then make sure that you point to your custom cTakesHsql.xml in dictionary-fast/desc/analysis_engine/UmlsLookupAnnotator.xml (or Overlap depending upon your use): nameDictionaryDescriptorFile/name description/ fileResourceSpecifier fileUrlfile:org/apache/ctakes/dictionary/lookup/fast/cTakesHsqlYourCopy.xml/fileUrl /fileResourceSpecifier You can also skip the UMLS dictionary altogether and just use your custom dictionary. If you do give this a try then let me know how it goes. If you need additional assistance let me know and I will help the best I can. Sean -Original Message- From: Raymond Li [mailto:ray...@bu.edu] Sent: Saturday, February 21, 2015 1:26 PM To: dev@ctakes.apache.org Subject: Hello cTAKES Mailing List Hello, my name is is Raymond Li and I am currently working on a team project involving cTAKES. The goal of our project would be to use cTAKES to analyze posts on social media (such as tweets, forum posts, public available data) in order to catch in real-time any adverse effects of prescribed drugs and do a public service of protecting people from harmful drugs. Aside from this introduction, I do have only one question to ask to proceed with this project: Is cTAKES capable of understanding slang words as symptoms. An example is if I were to say I took Crestor and feeling bad is there a way for cTAKES to recognize that Crestor had a negative effect? My team has not been able to isolate 'bad' as a negative effect as it is not a defined medical symptom, but it would be nice to figure out if such a solution exists, or if we would need to develop our own solution and how we could go around doing it. My team and I would appreciate any comments or assistance regarding our project and this current issue. Thank you and have a nice day! -- Sincerely, Raymond Li
RE: Hello cTAKES Mailing List
The CHV is a good resource for some things, but before going through the motions of porting it to a ctakes format, take a look inside. -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Monday, February 23, 2015 1:52 PM To: dev@ctakes.apache.org Subject: Re: Hello cTAKES Mailing List Raymond, Probably a combination of UMLS *Consumer Health Vocabulary + Custom Dictionary (as Sean described) *may work for the use case*:* OAC CHV connects informal, common words and phrases about health to technical terms used by health care professionals. It includes jargon, slang, ambiguous, and misspelled words as used by consumers and health care professionals. Due to its nature, OAC CHV includes concepts that are not represented by other source vocabularies within the Metathesaurus. [1] https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nlm.nih.gov_research_umls_sourcereleasedocs_current_CHV_d=BQIBaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=1Bkpeno1tqLjX78o0wYm5DmJHCHlK7hrxpeEgPnGtRMs=-rEmTgTCe0mkSXT34XK56zkiuy_VxIfFvngGJzUwem8e= On Sun, Feb 22, 2015 at 10:37 AM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Hi Raymond, If you use the dictionary-fast module there exists an entry feeling bad with cui 557911 and cui 231218. There is also feel bad and feeling bad emotionally You will find horrible present pain but no other entry with horrible. You will not find any terms with awful and probably many other desired words. If you are really interested in slang crappy, lousy, etc. then they are definitely not present. What you can do is create a second dictionary. There are example custom dictionaries in -dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dicti onary/lookup/fast/example/bsv/ You should look at custom_cui_bsv.bsv if you want to specify term unique id codes and term text alone. If you want to add tui/group codes then look at custom_cui_tui_bsv.bsv - you will probably want to model your dictionary after this so that you can tag your terms with tuis for symptoms. You will want to imitate sections from the corresponding .xml file in that directory. Make a copy of cTakesHsql.xml (two dirs up) and add lines: dictionary nameCustomCuiRareWord/name implementationNameorg.apache.ctakes.dictionary.lookup2.BsvRareWordDictionary/implementationName properties property key=bsvPath value=org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv/ /properties /dictionary And conceptFactory nameCustomCuiConcept/name implementationNameorg.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory/implementationName properties property key=bsvPath value=org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv/ /properties /conceptFactory And dictionaryConceptPair nameCustomPair/name dictionaryNameCustomCuiRareWord/dictionaryName conceptFactoryNameCustomCuiConcept/conceptFactoryName /dictionaryConceptPair Then make sure that you point to your custom cTakesHsql.xml in dictionary-fast/desc/analysis_engine/UmlsLookupAnnotator.xml (or Overlap depending upon your use): nameDictionaryDescriptorFile/name description/ fileResourceSpecifier fileUrlfile:org/apache/ctakes/dictionary/lookup/fast/cTakesHsqlYourCopy.xml/fileUrl /fileResourceSpecifier You can also skip the UMLS dictionary altogether and just use your custom dictionary. If you do give this a try then let me know how it goes. If you need additional assistance let me know and I will help the best I can. Sean -Original Message- From: Raymond Li [mailto:ray...@bu.edu] Sent: Saturday, February 21, 2015 1:26 PM To: dev@ctakes.apache.org Subject: Hello cTAKES Mailing List Hello, my name is is Raymond Li and I am currently working on a team project involving cTAKES. The goal of our project would be to use cTAKES to analyze posts on social media (such as tweets, forum posts, public available data) in order to catch in real-time any adverse effects of prescribed drugs and do a public service of protecting people from harmful drugs. Aside from this introduction, I do have only one question to ask to proceed with this project: Is cTAKES capable of understanding slang words as symptoms. An example is if I were to say I took Crestor and feeling bad is there a way for cTAKES to recognize that Crestor had a negative effect? My team has not been able to isolate 'bad' as a negative effect as it is not a defined medical symptom, but it would be nice to figure out if such a solution exists, or if we would need to develop our own solution and how we could go around doing it. My team and I would appreciate any comments or assistance regarding
RE: Hello cTAKES Mailing List
Hi Raymond, If you use the dictionary-fast module there exists an entry feeling bad with cui 557911 and cui 231218. There is also feel bad and feeling bad emotionally You will find horrible present pain but no other entry with horrible. You will not find any terms with awful and probably many other desired words. If you are really interested in slang crappy, lousy, etc. then they are definitely not present. What you can do is create a second dictionary. There are example custom dictionaries in -dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/example/bsv/ You should look at custom_cui_bsv.bsv if you want to specify term unique id codes and term text alone. If you want to add tui/group codes then look at custom_cui_tui_bsv.bsv - you will probably want to model your dictionary after this so that you can tag your terms with tuis for symptoms. You will want to imitate sections from the corresponding .xml file in that directory. Make a copy of cTakesHsql.xml (two dirs up) and add lines: dictionary nameCustomCuiRareWord/name implementationNameorg.apache.ctakes.dictionary.lookup2.BsvRareWordDictionary/implementationName properties property key=bsvPath value=org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv/ /properties /dictionary And conceptFactory nameCustomCuiConcept/name implementationNameorg.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory/implementationName properties property key=bsvPath value=org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv/ /properties /conceptFactory And dictionaryConceptPair nameCustomPair/name dictionaryNameCustomCuiRareWord/dictionaryName conceptFactoryNameCustomCuiConcept/conceptFactoryName /dictionaryConceptPair Then make sure that you point to your custom cTakesHsql.xml in dictionary-fast/desc/analysis_engine/UmlsLookupAnnotator.xml (or Overlap depending upon your use): nameDictionaryDescriptorFile/name description/ fileResourceSpecifier fileUrlfile:org/apache/ctakes/dictionary/lookup/fast/cTakesHsqlYourCopy.xml/fileUrl /fileResourceSpecifier You can also skip the UMLS dictionary altogether and just use your custom dictionary. If you do give this a try then let me know how it goes. If you need additional assistance let me know and I will help the best I can. Sean -Original Message- From: Raymond Li [mailto:ray...@bu.edu] Sent: Saturday, February 21, 2015 1:26 PM To: dev@ctakes.apache.org Subject: Hello cTAKES Mailing List Hello, my name is is Raymond Li and I am currently working on a team project involving cTAKES. The goal of our project would be to use cTAKES to analyze posts on social media (such as tweets, forum posts, public available data) in order to catch in real-time any adverse effects of prescribed drugs and do a public service of protecting people from harmful drugs. Aside from this introduction, I do have only one question to ask to proceed with this project: Is cTAKES capable of understanding slang words as symptoms. An example is if I were to say I took Crestor and feeling bad is there a way for cTAKES to recognize that Crestor had a negative effect? My team has not been able to isolate 'bad' as a negative effect as it is not a defined medical symptom, but it would be nice to figure out if such a solution exists, or if we would need to develop our own solution and how we could go around doing it. My team and I would appreciate any comments or assistance regarding our project and this current issue. Thank you and have a nice day! -- Sincerely, Raymond Li
