BEHAVIOR PIPELINE LIBRARY
- Smoking Status Detection
DISEASE_SYMPTOM PIPELINE LIBRARY
GENERAL PIPELINE LIBRARY

BEHAVIOR PIPELINE LIBRARY

• Smoking Status Detection (Smoking_status)

This is dictionary and rule based pipeline to extract smoking status from notes. It will recognize all smoking mentions and then category them into ‘NonSmoker’, ‘PastSmoker’ or ‘Smoker’;

Smoking-comp — Smoking-status Pipeline Components

Smoking-out — Smoking-status Pipeline Components

DISEASE_SYMPTOM PIPELINE LIBRARY

• Bleeding Mentions (Bleeding_extraction)

This pipeline will extract bleeding related concept and then map them to the UMLS CUI;

bleed-comp — Bleeding_extraction Pipeline Components

• Colorectal Cancer Concept Extraction (Colorectal_cancer)

This pipeline will extract colorectal cancer mentions and then map them to the UMLS CUI;

colorectal-comp — SColorectal_cancer Pipeline Components

• Cancer Pathology Pipeline (PathoPipelineFinalML)

TThis pipeline will extract Site, Procedure, Histology etc. entities and relations among them from pathology notes.

ppfml-comp — PathoPipelineFinalML Pipeline Output

GENERAL PIPELINE LIBRARY

• General Clinical Concept Extraction (Clamp-ner)

This is the CLAMP’s default named entity recognition pipeline. It will recognize ‘problem’, ‘treatment’ and ‘test’ from clinical notes and negation information of each concept. Users can add the UMLS encoder component to the end of this pipeline to get the UMLS CUI concept id (UMLS account is required for this component).

Clamp-ner-comp — SClamp-ner Pipeline Components

Clamp-ner-out — SClamp-ner Pipeline Components

• General Clinical Concept and Attribute Extractione (Clamp-ner-attribute)

This is the default named entity recognition and relation extraction pipeline. The primary entities include ‘problem’, ‘treatment’ and ‘test’. For each entity, the pipeline will recognize its attribute as well.
• Problem with: subject, condition, negation, severity, location, uncertainty;
• Lab test with: test value;
• Medicine with: dose, form, route, frequency, duration, necessity;

Ner-att-comp — Clamp-ner-attribute Pipeline Components

Ner-att-out — Clamp-ner-attribute Pipeline Components

• De-identification Pipeline (Deid_pipeline)

This is the de-identification pipeline. It will recognize all PHI information and then replace them with placeholder strings that are defined by the users. It contains 3 sub pipelines which are Disease-attribute, Lab-attribute and Medication-attribute.