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Table 1 The table gives an overview on the annotation solutions that have been used for the generation of the SSC-I and the SSC-II. For the generation of the SSC-I only the annotations from the 4 project partners (P01 – P04) have been integrated, whereas the SSC-II combines the annotations from the challenge participants (P06-P10, P13 and P15), not including P11, P12 and P14, since they have used the training data. Please refer to the proceedings of the first CALBC workshop for further details [8].

From: Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Solution

PPs | CPs

Use of Training Data

PRGE

CHED

DISO

SPE

Dictionary-based concept recognition

P01

[ / ]

UniProtKb

Jochem

UMLS

NCBI taxonomy

 

P02

[ / ]

Different resources incl. UniProtKb, EntrezGene

Jochem

UMLS

NCBI taxonomy

 

P04

[ / ]

UniProtKb, EntrezGene

Jochem

MeSH, MedDRA, NCI, SNOMED-CT UMLS

NCI, MeSH, SNOMED-CT

 

P06

[ / ]

    
 

P10

[ / ]

UniProtKb, EntrezGene

  

NCBI taxonomy

 

P13

[ / ]

    

Indexing of tokens and terms

P15

[ / ]

UMLS

UMLS

UMLS

UMLS

Both, trained & rule-based solutions

P03

[ / ]

UniProtKb, EntrezGene

Jochem

UMLS

NCBI taxonomy

Case-based reasoning

P09

[ / ]

  

UMLS

 

CRF based, trained NER solution

P07

[ / ]

    
 

P16

[ / ]

Genia

 

UMLS

 
 

P11

YES

[ / ]

[ / ]

[ / ]

[ / ]

 

P12

YES

[ / ]

[ / ]

[ / ]

[ / ]

 

P14

YES

[ / ]

[ / ]

[ / ]

[ / ]