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Table 1 Overview of the ontology matching systems that participated in OAEI biomedical tracks

From: Tackling the challenges of matching biomedical ontologies

System Size Lexicon Relations Repair Background knowledge OAEI Bio tracks
AgrMaker [19] + weights part of - Bio; Man; Med A
AML [11] +++ WN; weights all Logic Bio; Auto; M/E all
Anchor-Flood [40] + WN - - Man; Exp A
Aroma [41] +++ - - - - A, LB
ASMOV [42] + WN - - Bio; Man; Exp A
AUTOMSv2[43] ++ WN; weights - - Man; Exp LB-
BLOOMS [20] + WN part of - Bio; Man; Med A
COMMAND [44] + - - Logic - A
CroMatcher [45] + WN - - Man; Exp A
DKP-AOM [46] + WN - - Man; Exp A, LB-
DSSim [47] + WN - - Man; Exp A
FCA-Map [16] ++ UMLS - Logic Man; Exp all-
GMap [48] + external? - Logic Man; Exp A
GOMMA [49] +++ - - - Bio; Auto; Med A, LB
kosimap [50] + - - - - A
LogMap [13] +++ WN; UMLS - Logic Bio; Auto; M/E all
LP HOM [51] + - - -   A
Lyam++[52] ++ BabelNet - - Man; Exp all-
MapPSO [53] + - - - - A
OACAS [54] + - - - - A
PhenomeNET [21] ++ (AML) part of - Bio; Man; Med DP
SAMBO [22] + WN part of - Bio; Man; Exp A
ServOMap [55] +++ WN - Logic Man; Exp A, LB
TaxoMap [56] + - - - - A
TOAST [57] + - - - - A
WikiMatch [58] ++ Wikipedia - - Man; Exp A, LB-
YAM++[59] +++ WN - Rules Man; Exp A, LB
  1. Size details the systems’ capability of handling medium-sized (+), large (++) or very large (+++) ontologies; Lexicon lists their use of lexical tools such as WordNet (WN) or the UMLS SPECIALIST Lexicon (UMLS), as well as whether they use synonym weights; Relations lists the types of relations they contemplate in addition to subclass relations; Repair details whether they perform alignment repair based on logic or rules; Background Knowledge describes whether they use biomedical ontologies as background knowledge (Bio), whether the process of background knowledge selection is manual (Man) or automatic (Auto), and whether background knowledge is used as a mediator (Med) or for lexical expansion (Exp); OAEI Bio Tracks lists the tracks in which the system successfully competed in out of Anatomy (A), Large Biomedical Ontologies (LB), and Disease & Phenotype (DP), with - indicating that the system did not complete the largest LB tasks