Annie the annotator
Annotators for extracting epidemiologic information from text.
Annie provides the following classes for organizing annotations.
AnnoDoc - The document being annotated. The AnnoDoc links to the tiers of annotations applied to it.
AnnoTier - A group of AnnoSpans. Generally each annotator creates a new tier of annotations.
AnnoSpan - A span of text with an annotation applied to it.
The geoname annotator uses the geonames.org dataset to resolve mentions of geonames. A classifier is used to disambiguate geonames and rule out false positives.
To use the geoname annotator run the following command to import geonames.org data into an embedded sqlite3 database:
python -m annotator.sqlite_import_geonames
This annotator also requires installing the nltk name entitiy extractor.
Resolved Keyword Annotator
The resolved keyword annotator uses synonyms from the disease ontology to resolve mentions of diseases to doid uris.
To use the geoname annotator run the following command to import the disease ontology data into an embedded sqlite3 database:
python -m annotator.sqlite_import_disease_ontology
The count annotator identifies counts, and case counts in particular. The count's value is extracted and parsed. Attributes such as whether the count refers to cases or deaths, or whether the value is approximate are also extracted.
The jvm_nl_annotator relies on a server from this project to create annotations using Stanford's NLP library:
The AnnoTiers it creates include tokens, sentences, pos tags and named entities.
Copyright 2016 EcoHealth Alliance
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