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Table 2 Widely used concept recognition systems

From: NOBLE – Flexible concept recognition for large-scale biomedical natural language processing

System

Approach

Availability

Interoperability

Terminologies

Terminology building tools

MetaMap (and MMTx) [911]

Noun-phrase, lexical variants

Open Source [12, 52]

Java API for MMTx

UMLS

MetamorphoSys, DataFileBuilder

MGrep [13] (and OBA) [53]

Single word variations,

Closed Source Binary Utility

Command line utility (MGrep) integrated with RESTful API in OBA

Custom dictionaries (MGrep) with UMLS and Bioportal in OBA

N/A

 

Radix-Tree search

Concept Mapper [19]

Word Lookup Table

Open Source [54]

UIMA plugin

XML file

N/A

cTAKES Dictionary Lookup Annotator [21]

Noun-phrase, dictionary lookup

Open Source [21]

Java API with full integration in UIMA

UMLS (RRF), Bar Separated Value (BSV) file

Example scripts available [55]

cTAKES Fast Dictionary Lookup Annotator [22]

Rare Word index

Open Source [22]

Java API with full integration in UIMA

UMLS (RRF), Bar Separated Value (BSV) file

Example scripts available [55]

Index Finder [14, 15]

Word Lookup Table

N/A

N/A

UMLS

N/A

Doublet [17, 18]

Bigram Lookup Table

Open Source [56]

Command line utility (Perl)

Custom dictionary format

N/A

MedLEE [16] concept recognition

Noun-phrase

Commercial

XML based input/output

UMLS

N/A

NOBLE Coder

Word Lookup Table

Open Source [57]

Java API, UIMA and GATE wrappers

UMLS (RRF), OWL, OBO, BioPortal

Terminology Loader UI