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

Repairing CSV schema
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clairblacketer 2018-07-24 12:06:36 -04:00 committed by GitHub
parent d1cb3c28e3 4be77a499b
commit 97764a6473
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1 changed files with 14 additions and 14 deletions
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OMOP_CDM_v5_3_1.csv
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@ -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"

1 field required type description table schema
99 98 visit_occurrence_id No INTEGER A foreign key to the Visit in the VISIT_OCCURRENCE table when the Note was taken. note cdm
100 99 visit_detail_id No INTEGER A foreign key to the Visit in the VISIT_DETAIL table when the Note was taken. note cdm
101 100 note_source_value No VARCHAR(50) The source value associated with the origin of the Note note cdm
102 101 yes note_nlp_id integer Yes A UNIQUE IDENTIFIER FOR EACH TERM EXTRACTED FROM A NOTE. INTEGER NA A unique identifier for each term extracted from a Note. note_nlp cdm
103 102 yes note_id integer Yes A FOREIGN KEY TO THE NOTE TABLE NOTE THE TERM WAS EXTRACTED FROM. INTEGER NA A foreign key to the note table note the term was extracted from. note_nlp cdm
104 103 no section_concept_id integer No A FOREIGN KEY TO THE PREDEFINED CONCEPT IN THE STANDARDIZED VOCABULARIES REPRESENTING THE SECTION OF THE EXTRACTED TERM. INTEGER NA A foreign key to the predefined concept in the standardized vocabularies representing the section of the extracted term. note_nlp cdm
105 104 no snippet varchar(250) No A SMALL WINDOW OF TEXT SURROUNDING THE TERM. VARCHAR(250) NA A small window of text surrounding the term. note_nlp cdm
106 105 no offset varchar(50) No CHARACTER OFFSET OF THE EXTRACTED TERM IN THE INPUT NOTE. VARCHAR(50) NA Character offset of the extracted term in the input note. note_nlp cdm
107 106 yes lexical_variant varchar(250) Yes RAW TEXT EXTRACTED FROM THE NLP TOOL. VARCHAR(250) NA Raw text extracted from the NLP tool. note_nlp cdm
108 107 no note_nlp_concept_id integer No 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. INTEGER NA 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
109 108 no note_nlp_source_concept_id integer No A FOREIGN KEY TO A CONCEPT THAT REFERS TO THE CODE IN THE SOURCE VOCABULARY USED BY THE NLP SYSTEM INTEGER NA A foreign key to a concept that refers to the code in the source vocabulary used by the NLP system note_nlp cdm
110 109 no nlp_system varchar(250) No NAME AND VERSION OF THE NLP SYSTEM THAT EXTRACTED THE TERM.USEFUL FOR DATA PROVENANCE. VARCHAR(250) NA Name and version of the NLP system that extracted the term.useful for data provenance. note_nlp cdm
111 110 yes nlp_date date Yes THE DATE OF THE NOTE PROCESSING.USEFUL FOR DATA PROVENANCE. DATE NA The date of the note processing.useful for data provenance. note_nlp cdm
112 111 no nlp_datetime datetime No THE DATE AND TIME OF THE NOTE PROCESSING. USEFUL FOR DATA PROVENANCE. DATETIME NA The date and time of the note processing. Useful for data provenance. note_nlp cdm
113 112 no term_exists varchar(1) No A SUMMARY MODIFIER THAT SIGNIFIES PRESENCE OR ABSENCE OF THE TERM FOR A GIVEN PATIENT. USEFUL FOR QUICK QUERYING. VARCHAR(1) NA A summary modifier that signifies presence or absence of the term for a given patient. Useful for quick querying. note_nlp cdm
114 113 no term_temporal varchar(50) No AN OPTIONAL TIME MODIFIER ASSOCIATED WITH THE EXTRACTED TERM. (FOR NOW PAST OR PRESENT ONLY). STANDARDIZE IT LATER. VARCHAR(50) NA An optional time modifier associated with the extracted term. (For now “past” or “present” only). Standardize it later. note_nlp cdm
115 114 no term_modifiers varchar(2000) No 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). VARCHAR(2000) NA 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
116 115 observation_id Yes INTEGER A unique identifier for each observation. observation cdm
117 116 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
118 117 observation_concept_id Yes INTEGER A foreign key to the standard observation concept identifier in the Standardized Vocabularies. observation cdm