Merge pull request #201 from AlexTawse/repairing-csv-schema

Repairing CSV schema

Author: clairblacketer

OMOP_CDM_v5_3_1.csv

@@ -99,20 +99,20 @@
 "98","visit_occurrence_id","No","INTEGER","A foreign key to the Visit in the VISIT_OCCURRENCE table when the Note was taken.","note","cdm"
 "99","visit_detail_id","No","INTEGER","A foreign key to the Visit in the VISIT_DETAIL table when the Note was taken.","note","cdm"
 "100","note_source_value","No","VARCHAR(50)","The source value associated with the origin of the Note","note","cdm"
-"101","yes","integer","A UNIQUE IDENTIFIER FOR EACH TERM EXTRACTED FROM A NOTE.",NA,"note_nlp","cdm"
-"102","yes","integer","A FOREIGN KEY TO THE NOTE TABLE NOTE THE TERM WAS EXTRACTED FROM.",NA,"note_nlp","cdm"
-"103","no","integer","A FOREIGN KEY TO THE PREDEFINED CONCEPT IN THE STANDARDIZED VOCABULARIES REPRESENTING THE SECTION OF THE EXTRACTED TERM.",NA,"note_nlp","cdm"
-"104","no","varchar(250)","A SMALL WINDOW OF TEXT SURROUNDING THE TERM.",NA,"note_nlp","cdm"
-"105","no","varchar(50)","CHARACTER OFFSET OF THE EXTRACTED TERM IN THE INPUT NOTE.",NA,"note_nlp","cdm"
-"106","yes","varchar(250)","RAW TEXT EXTRACTED FROM THE NLP TOOL.",NA,"note_nlp","cdm"
-"107","no","integer","A FOREIGN KEY TO THE PREDEFINED CONCEPT IN THE STANDARDIZED VOCABULARIES REFLECTING THE NORMALIZED CONCEPT FOR THE EXTRACTED TERM. DOMAIN OF THE TERM IS REPRESENTED AS PART OF THE CONCEPT TABLE.",NA,"note_nlp","cdm"
-"108","no","integer","A FOREIGN KEY TO A CONCEPT THAT REFERS TO THE CODE IN THE SOURCE VOCABULARY USED BY THE NLP SYSTEM",NA,"note_nlp","cdm"
-"109","no","varchar(250)","NAME AND VERSION OF THE NLP SYSTEM THAT EXTRACTED THE TERM.USEFUL FOR DATA PROVENANCE.",NA,"note_nlp","cdm"
-"110","yes","date","THE DATE OF THE NOTE PROCESSING.USEFUL FOR DATA PROVENANCE.",NA,"note_nlp","cdm"
-"111","no","datetime","THE DATE AND TIME OF THE NOTE PROCESSING. USEFUL FOR DATA PROVENANCE.",NA,"note_nlp","cdm"
-"112","no","varchar(1)","A SUMMARY MODIFIER THAT SIGNIFIES PRESENCE OR ABSENCE OF THE TERM FOR A GIVEN PATIENT. USEFUL FOR QUICK QUERYING.",NA,"note_nlp","cdm"
-"113","no","varchar(50)","AN OPTIONAL TIME MODIFIER ASSOCIATED WITH THE EXTRACTED TERM. (FOR NOW “PAST” OR “PRESENT” ONLY). STANDARDIZE IT LATER.",NA,"note_nlp","cdm"
-"114","no","varchar(2000)","A COMPACT DESCRIPTION OF ALL THE MODIFIERS OF THE SPECIFIC TERM EXTRACTED BY THE NLP SYSTEM. (E.G. “SON HAS RASH” ? “NEGATED=NO,SUBJECT=FAMILY, CERTAINTY=UNDEF,CONDITIONAL=FALSE,GENERAL=FALSE”).",NA,"note_nlp","cdm"
+"101","note_nlp_id","Yes","INTEGER","A unique identifier for each term extracted from a Note.","note_nlp","cdm"
+"102","note_id","Yes","INTEGER","A foreign key to the note table note the term was extracted from.","note_nlp","cdm"
+"103","section_concept_id","No","INTEGER","A foreign key to the predefined concept in the standardized vocabularies representing the section of the extracted term.","note_nlp","cdm"
+"104","snippet","No","VARCHAR(250)","A small window of text surrounding the term.","note_nlp","cdm"
+"105","offset","No","VARCHAR(50)","Character offset of the extracted term in the input note.","note_nlp","cdm"
+"106","lexical_variant","Yes","VARCHAR(250)","Raw text extracted from the NLP tool.","note_nlp","cdm"
+"107","note_nlp_concept_id","No","INTEGER","A foreign key to the predefined concept in the standardized vocabularies reflecting the normalized concept for the extracted term. Domain of the term is represented as part of the concept table.","note_nlp","cdm"
+"108","note_nlp_source_concept_id","No","INTEGER","A foreign key to a concept that refers to the code in the source vocabulary used by the NLP system","note_nlp","cdm"
+"109","nlp_system","No","VARCHAR(250)","Name and version of the NLP system that extracted the term.useful for data provenance.","note_nlp","cdm"
+"110","nlp_date","Yes","DATE","The date of the note processing.useful for data provenance.","note_nlp","cdm"
+"111","nlp_datetime","No","DATETIME","The date and time of the note processing. Useful for data provenance.","note_nlp","cdm"
+"112","term_exists","No","VARCHAR(1)","A summary modifier that signifies presence or absence of the term for a given patient. Useful for quick querying.","note_nlp","cdm"
+"113","term_temporal","No","VARCHAR(50)","An optional time modifier associated with the extracted term. (For now “past” or “present” only). Standardize it later.","note_nlp","cdm"
+"114","term_modifiers","No","VARCHAR(2000)","A compact description of all the modifiers of the specific term extracted by the NLP system. (e.g. “son has rash” ? “negated=no,subject=family, certainty=undef,conditional=false,general=false”).","note_nlp","cdm"
 "115","observation_id","Yes","INTEGER","A unique identifier for each observation.","observation","cdm"
 "116","person_id","Yes","INTEGER","A foreign key identifier to the Person about whom the observation was recorded. The demographic details of that Person are stored in the PERSON table.","observation","cdm"
 "117","observation_concept_id","Yes","INTEGER","A foreign key to the standard observation concept identifier in the Standardized Vocabularies.","observation","cdm"