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| Lemmas(P,D,Word,Lem)<-Docs(P,D,"raw_text"),lemma(D)->(Word,Lem). | ||
|
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nbs/banchmark/covid_data/rules_data/concept_tags_rules.csv
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| (?i)(?:hcov|covid(?:(?:-)?(?:\s)?19|10)?|2019-cov|cov2|ncov-19|covd 19|no-cov|sars cov|covid),COVID-19,lemma | ||
| (?i)(?:coivid|(?:novel )?corona(?:virus)?(?: (?:20)?19)?|sars(?:\s)?(?:-)?(?:\s)?cov(?:id)?(?:-)?(?:2|19)),COVID-19,lemma | ||
| (?i)(?:\+(?: ve)?|\(\+\)|positive|\bpos\b|active|confirmed),positive,lemma | ||
| (?i)(?:pneum(?:onia)?|pna|hypoxia|septic shoc|ards\(?(?:(?:[12])/2)\)?|(?:hypoxemic|acute|severe)? resp(?:iratory)? failure(?:\(?(?:[12]/2)\)?)?)",associated_diagnosis,lemma | ||
| (?i)(?:(?:diagnos(?:is|ed)|dx(?:\.)?)(?:of|with)?),diagnosis,lemma | ||
| (?i)(?:^screen),screening,lemma | ||
| (?i)(?:in contact with|any one|co-worker|at work|(?:the|a)(?:wo)?man|(?:another|a) (?:pt|patient|pt\.)),other_experiencer,lemma | ||
| (?i)(?:patient|pt(?:\.)?|vt|veteran),patient,lemma | ||
| (?i)(?:like_num (?:days|day|weeks|week|months|month) (?:ago|prior)),timesx,lemma | ||
| (?i)(?:(?:antibody|antibodies|ab) test),antibody test,lemma | ||
| (?i)(?:(?:coronavirus|hcovs?|ncovs?|covs?)(?:\s)?(?:-)?(?:\s)?(?: infection)?(?: strain)?(?:\s)?(?:229(?:e)?|oc(?:-)?(?:43)?|o43|0c43|43|nl(?:16(?:3|5))?|hku(?:t|-)?1|hkui|emc|63)),OTHER_CORONAVIRUS,lemma | ||
| (?i)(?:(?:229(?:e)?|oc(?:-)?(?:43)?|o43|0c43|43|nl(?:16(?:3|5))?|hku(?:t|-)?1|hkui|emc|63) (?:coronavirus|hcovs?|ncovs?|covs?)),OTHER_CORONAVIRUS,lemma | ||
| (?i)(?:non(?:\s)?(?:-)?(?:\s)?(?:novel|covid|ncovid|covid-19)(?: coronavirus)?|other coronavirus),OTHER_CORONAVIRUS,lemma | ||
| (?i)(?:wife|husband|spouse|family|member|girlfriend|boyfriend|mother|father|nephew|niece|grandparent|grandparents|granddaughter|relative|relatives|caregiver),family,pos | ||
| (?i)(?:grandchild|grandson|cousin|grandmother|grandfather|parent|son|daughter|mom|dad|brother|sister|aunt|uncle|child|children|sibling|siblings),family,pos | ||
| (?i)(?:someone|somebody|person|anyone|anybody|people|individual|individuals|teacher|anybody|employees|employer|customer|client|residents),other_experiencer,pos | ||
| (?i)(?:resident|pts|patients|coworker|coworkers|workers|colleague|captain|captains|pilot|pilots|sailor|sailors|meeting),other_experiencer,pos | ||
| (?i)(?:boyfriend|persons|person|church|convention|guest|party|attendee|conference|roommate|friend|friends|coach|player|neighbor|manager|boss),other_experiencer,pos | ||
| (?i)(?:cashier|landlord|worked|works|^mate|nobody|mates|housemate|housemates|hotel|soldier|airport|tsa|lady|ladies|lobby|staffer|staffers),other_experiencer,pos |
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| be | ||
| man | ||
| woman | ||
| have | ||
| do | ||
| emergency | ||
| epidemic | ||
| outbreak | ||
| crisis | ||
| breakout | ||
| pandemic | ||
| spread | ||
| confirm | ||
| person | ||
| patient | ||
| veteran | ||
| limit | ||
| reduce | ||
| factor | ||
| contact | ||
| case | ||
| lower | ||
| minimize | ||
| risk | ||
| chance | ||
| possibility | ||
| care | ||
| clean | ||
| desire | ||
| flight | ||
| trip | ||
| plan | ||
| reschedule | ||
| postpone | ||
| barrier |
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nbs/banchmark/covid_data/rules_data/positive_section_tags.csv
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| diagnoses | ||
| observation_and_plan | ||
| past_medical_history | ||
| problem_list |
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nbs/banchmark/covid_data/rules_data/postprocess_attributes_rules.csv
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| .*pending.*#negated#no_negated | ||
| .*(?:should|unless|either|if comes back|if returns|if s?he tests positive).*#positive#uncertain | ||
| .*precaution.*#positive#no_future | ||
| .*(?:re[ -]?test|second test|repeat).*#negated#no_negated | ||
| .*(?:sign|symptom|s/s).*#positive#uncertain |
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nbs/banchmark/covid_data/rules_data/postprocess_pattern_next_sentence_rules.csv
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| (?i)(?:^(?:positive|detected)|results?(?: be)? positive),positive |
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nbs/banchmark/covid_data/rules_data/postprocess_pattern_rules.csv
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| .*education.*#IGNORE | ||
| .* \?#IGNORE | ||
| (?=.*\b(?:deny|denies|denied)\b)(?=.*\b(?:contact|confirm)\b).*#IGNORE | ||
| (?=.*\b(?:setting of|s/o)\b)(?!.*\b(?:COVID-19 infection|COVID-19 ards)\b).*#no_positive | ||
| (?i)(.*benign.*)#uncertain | ||
| admitted to COVID-19 unit#positive |
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| (?i)(?:Lab results :),labs : | ||
| (?i)(?:Addendum :),addendum : | ||
| (?i)(?:(?:ALLERGIC REACTIONS|ALLERGIES) :),allergies : | ||
| (?i)(?:(?:CC|Chief Complaint) :),chief_complaint : | ||
| (?i)(?:COMMENTS :),comments : | ||
| (?i)(?:(?:(?:ADMISSION )?DIAGNOSES|Diagnosis|Primary Diagnosis|Primary|Secondary(?: (?:Diagnoses|Diagnosis))) :),diagnoses : | ||
| (?i)(?:(?:Brief Hospital Course|CONCISE SUMMARY OF HOSPITAL COURSE BY ISSUE/SYSTEM|HOSPITAL COURSE|SUMMARY OF HOSPITAL COURSE) :),hospital_course : | ||
| (?i)(?:(?:Imaging|MRI|INTERPRETATION|Radiology) :),imaging : | ||
| (?i)(?:(?:ADMISSION LABS|Discharge Labs|ECHO|Findings|INDICATION|Labs|Micro|Microbiology|Studies|Pertinent Results) :),labs_and_studies : | ||
| (?i)(?:(?:ACTIVE MEDICATIONS(?: LIST)|ADMISSION MEDICATIONS|CURRENT MEDICATIONS|DISCHARGE MEDICATIONS|HOME MEDICATIONS|MEDICATIONS) :),medications : | ||
| (?i)(?:(?:MEDICATIONS AT HOME|MEDICATIONS LIST|MEDICATIONS ON ADMISSION|MEDICATIONS ON DISCHARGE|MEDICATIONS ON TRANSFER|MEDICATIONS PRIOR TO ADMISSION) :),medications : | ||
| (?i)(?:Neuro :),neurological : | ||
| (?i)(?:(?:A/P|MEDICATIONS LIST|ASSESSMENT/PLAN|ASSESSMENT|Clinical Impression|DISCHARGE DIAGNOSES|DISCHARGE DIAGNOSIS) :),observation_and_plan : | ||
| (?i)(?:(?:Discharge Condition|Discharge Disposition|FINAL DIAGNOSES|FINAL DIAGNOSIS|IMPRESSION|Impression and Plan|Impression and Recommendation) :),observation_and_plan : | ||
| (?i)(?:(?:Facility|Service) :),other : | ||
| (?i)(?:(?:Current Medical Problems|History of Chronic Illness|MHx|PAST HISTORY|PAST MEDICAL Hx|PAST SURGICAL HISTORY|PMH|PMHx|PAST MEDICAL HISTORY|UNDERLYING MEDICAL CONDITION) :),past_medical_history : | ||
| (?i)(?:(?:Education|Patient Education|DISCHARGE INSTRUCTIONS/FOLLOWUP|DISCHARGE INSTRUCTIONS|Followup Instructions) :),patient_education : | ||
| (?i)(?:(?:PE|PHYSICAL EXAM|PHYSICAL EXAMINATION) :),physical_exam : | ||
| (?i)(?:(?:Active Problem List|Current Problems|Medical Problems|PROBLEM LIST) :),problem_list : | ||
| (?i)(?:REASON FOR THIS EXAMINATION :),reason_for_examination : | ||
| (?i)(?:(?:Electronic Signature|Signed electronically by) :),signature : | ||
| (?i)(?:(?:PMHSx|PSH|SH|Sexual History:|Social History) :),social_history : |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| Lab results:,labs | ||
| ADDENDUM:,addendum | ||
| Addendum:,addendum | ||
| ALLERGIC REACTIONS:,allergies | ||
| ALLERGIES:,allergies | ||
| CC:,chief_complaint | ||
| CHIEF COMPLAINT:,chief_complaint | ||
| Chief Complaint:,chief_complaint | ||
| COMMENTS:,comments | ||
| ADMISSION DIAGNOSES:,diagnoses | ||
| DIAGNOSES:,diagnoses | ||
| Diagnosis:,diagnoses | ||
| Primary Diagnosis:,diagnoses | ||
| Primary:,diagnoses | ||
| SECONDARY DIAGNOSES:,diagnoses | ||
| Secondary Diagnoses:,diagnoses | ||
| Secondary Diagnosis:,diagnoses | ||
| Secondary:,diagnoses | ||
| Family History:,family_history | ||
| Brief Hospital Course:,hospital_course | ||
| CONCISE SUMMARY OF HOSPITAL COURSE BY ISSUE/SYSTEM:,hospital_course | ||
| HOSPITAL COURSE:,hospital_course | ||
| SUMMARY OF HOSPITAL COURSE:,hospital_course | ||
| IMAGING:,imaging | ||
| INTERPRETATION:,imaging | ||
| Imaging:,imaging | ||
| MRI:,imaging | ||
| Radiology:,imaging | ||
| ADMISSION LABS:,labs_and_studies | ||
| Admission Labs:,labs_and_studies | ||
| Discharge Labs:,labs_and_studies | ||
| ECHO:,labs_and_studies | ||
| FINDINGS:,labs_and_studies | ||
| Findings:,labs_and_studies | ||
| INDICATION:,labs_and_studies | ||
| LABS:,labs_and_studies | ||
| Labs:,labs_and_studies | ||
| MICRO:,labs_and_studies | ||
| Micro:,labs_and_studies | ||
| Microbiology:,labs_and_studies | ||
| Pertinent Results:,labs_and_studies | ||
| STUDIES:,labs_and_studies | ||
| Studies:,labs_and_studies | ||
| ACTIVE MEDICATIONS LIST:,medications | ||
| ACTIVE MEDICATIONS:,medications | ||
| ADMISSION MEDICATIONS:,medications | ||
| CURRENT MEDICATIONS:,medications | ||
| DISCHARGE MEDICATIONS:,medications | ||
| Discharge Medications:,medications | ||
| HOME MEDICATIONS:,medications | ||
| MEDICATIONS AT HOME:,medications | ||
| MEDICATIONS LIST:,medications | ||
| MEDICATIONS ON ADMISSION:,medications | ||
| MEDICATIONS ON DISCHARGE:,medications | ||
| MEDICATIONS ON TRANSFER:,medications | ||
| MEDICATIONS PRIOR TO ADMISSION:,medications | ||
| MEDICATIONS:,medications | ||
| MEDICATIONS:,medications | ||
| Neuro:,neurological | ||
| A/P:,observation_and_plan | ||
| ASSESSMENT/PLAN:,observation_and_plan | ||
| ASSESSMENT:,observation_and_plan | ||
| Assessment/Plan:,observation_and_plan | ||
| Clinical Impression:,observation_and_plan | ||
| DISCHARGE DIAGNOSES:,observation_and_plan | ||
| DISCHARGE DIAGNOSIS:,observation_and_plan | ||
| Discharge Condition:,observation_and_plan | ||
| Discharge Diagnoses:,observation_and_plan | ||
| Discharge Diagnosis:,observation_and_plan | ||
| Discharge Disposition:,observation_and_plan | ||
| FINAL DIAGNOSES:,observation_and_plan | ||
| FINAL DIAGNOSIS:,observation_and_plan | ||
| IMPRESSION:,observation_and_plan | ||
| Impression and Plan:,observation_and_plan | ||
| Impression and Recommendation:,observation_and_plan | ||
| Facility:,other | ||
| Service:,other | ||
| Current Medical Problems:,past_medical_history | ||
| History of Chronic Illness:,past_medical_history | ||
| MHx:,past_medical_history | ||
| PAST HISTORY:,past_medical_history | ||
| PAST MEDICAL HISTORY:,past_medical_history | ||
| PAST MEDICAL Hx:,past_medical_history | ||
| PAST SURGICAL HISTORY:,past_medical_history | ||
| PMH:,past_medical_history | ||
| PMHx:,past_medical_history | ||
| Past Medical History:,past_medical_history | ||
| UNDERLYING MEDICAL CONDITION:,past_medical_history | ||
| Education:,patient_education | ||
| Patient Education:,patient_education | ||
| DISCHARGE INSTRUCTIONS/FOLLOWUP:,patient_instructions | ||
| DISCHARGE INSTRUCTIONS:,patient_instructions | ||
| Discharge Instructions:,patient_instructions | ||
| Followup Instructions:,patient_instructions | ||
| PE:,physical_exam | ||
| PHYSICAL EXAM:,physical_exam | ||
| PHYSICAL EXAMINATION:,physical_exam | ||
| Physical Exam:,physical_exam | ||
| Active Problem List:,problem_list | ||
| Current Problems:,problem_list | ||
| Medical Problems:,problem_list | ||
| PROBLEM LIST:,problem_list | ||
| Problem List:,problem_list | ||
| REASON FOR THIS EXAMINATION:,reason_for_examination | ||
| Electronic Signature:,signature | ||
| Signed electronically by:,signature | ||
| PMHSx:,social_history | ||
| PSH:,social_history | ||
| SH:,social_history | ||
| Sexual History:,social_history | ||
| Social History:,social_history |
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