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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