--- a +++ b/docs/pipes/ner/index.md @@ -0,0 +1,56 @@ +# Named Entity Recognition Components + +We provide several Named Entity Recognition (NER) components. +Named Entity Recognition is the task of identifying short relevant spans of text, named entities, and classifying them into pre-defined categories. +In the case of clinical documents, these entities can be scores, disorders, behaviors, codes, dates, quantities, etc. + +## Span setters: where are stored extracted entities ? {: #edsnlp.pipes.base.SpanSetterArg } + +A component assigns entities to a document by adding them to the `doc.ents` or `doc.spans[group]` attributes. `doc.ents` only supports non overlapping +entities, therefore, if two entities overlap, the longest one will be kept. `doc.spans[group]` on the other hand, can contain overlapping entities. +To control where entities are added, you can use the `span_setter` argument in any of these component. + +::: edsnlp.pipes.base.SpanSetterArg + options: + heading_level: 2 + show_bases: false + show_source: false + only_class_level: true + +## Available components + +<!-- --8<-- [start:components] --> + +| Component | Description | +|-----------------------------------|---------------------------------------| +| `eds.covid` | A COVID mentions detector | +| `eds.charlson` | A Charlson score extractor | +| `eds.sofa` | A SOFA score extractor | +| `eds.elston_ellis` | An Elston & Ellis code extractor | +| `eds.emergency_priority` | A priority score extractor | +| `eds.emergency_ccmu` | A CCMU score extractor | +| `eds.emergency_gemsa` | A GEMSA score extractor | +| `eds.tnm` | A TNM score extractor | +| `eds.adicap` | A ADICAP codes extractor | +| `eds.drugs` | A drug mentions extractor | +| `eds.cim10` | A CIM10 terminology matcher | +| `eds.umls` | An UMLS terminology matcher | +| `eds.ckd` | CKD extractor | +| `eds.copd` | COPD extractor | +| `eds.cerebrovascular_accident` | Cerebrovascular accident extractor | +| `eds.congestive_heart_failure` | Congestive heart failure extractor | +| `eds.connective_tissue_disease` | Connective tissue disease extractor | +| `eds.dementia` | Dementia extractor | +| `eds.diabetes` | Diabetes extractor | +| `eds.hemiplegia` | Hemiplegia extractor | +| `eds.leukemia` | Leukemia extractor | +| `eds.liver_disease` | Liver disease extractor | +| `eds.lymphoma` | Lymphoma extractor | +| `eds.myocardial_infarction` | Myocardial infarction extractor | +| `eds.peptic_ulcer_disease` | Peptic ulcer disease extractor | +| `eds.peripheral_vascular_disease` | Peripheral vascular disease extractor | +| `eds.solid_tumor` | Solid tumor extractor | +| `eds.alcohol` | Alcohol consumption extractor | +| `eds.tobacco` | Tobacco consumption extractor | + +<!-- --8<-- [end:components] -->