Figure 1
The methodology diagram (own adaptation according to Wohlin (2014)).
Table 1
Semantic annotation tools and their compliance with the criteria.
| TOOL | USE OF ONTOLOGY | AUTOMATION | INPUT | OUTPUT | MATURITY AND APPLICATIONS | LICENSING AND ACCESSIBILITY | EVALUATION UNDERTAKEN |
|---|---|---|---|---|---|---|---|
| ABNER (Settles, 2005) | ○ | ● | ● | ● | ● | ● | ● |
| BeCAS (Nunes et al., 2013) | ◐ | ● | ● | ● | ◐ | ● | ○ |
| Bio-YODIE (Gorrell et al., 2018) | ◐ | ● | ● | ◐ | ● | ● | ● |
| TAKES (Savova et al., 2010) | ● | ● | ● | ○ | ◐ | ● | ● |
| Cerno (Kiyavitskaya et al., 2009) | ◐ | ◐ | ● | ● | ○ | ○ | ● |
| ChemSpot (Rocktäschel et al., 2012) | ◐ | ● | ● | ○ | ◐ | ◐ | ● |
| ConceptMapper (Tanenblatt et al., 2010) | ● | ● | ○ | ● | ● | ● | ● |
| CONANN (Reeve and Han, 2007) | ◐ | ● | ● | ◐ | ○ | ○ | ● |
| ContracT (Soavi et al, 2020) | ◐ | ◐ | ● | ○ | ○ | ○ | ◐ |
| EDGAR (Rindflesch et al., 1999) | ◐ | ● | ● | ● | ◐ | ○ | ○ |
| GENIES (Friedman et al., 2001) | ◐ | ◐ | ● | ◐ | ◐ | ○ | ◐ |
| Huang et al. (Huang et al., 2006) | ◐ | ● | ● | ● | ◐ | ○ | ● |
| KIM (Popov et al., 2003) | ● | ● | ● | ● | ◐ | ○ | ◐ |
| Marvin (Milosevic, 2016) | ● | ● | ● | ● | ◐ | ● | ○ |
| MedCAT (Kraljevic et al., 2021) | ● | ● | ● | ○ | ● | ● | ● |
| MetaMap (Aronson, 2001) | ◐ | ● | ● | ○ | ● | ○ | ● |
| NBCO Annotator (Jonquet et al., 2009) | ◐ | ● | ○ | ● | ◐ | ● | ○ |
| Neural Concept Recognizer (Arbabi et al., 2019) | ● | ● | ● | ◐ | ● | ● | ● |
| NOBLE Coder (Tseytlin et al., 2016) | ● | ● | ○ | ◐ | ◐ | ● | ● |
| OnTeA (Laclavık et al., 2006) | ◐ | ● | ● | ○ | ◐ | ○ | ● |
| OntoBlog (Shakya et al., 2007) | ◐ | ◐ | ● | ○ | ◐ | ○ | ◐ |
| OPTIMA (Vlachidis and Tudhope, 2016) | ◐ | ● | ● | ● | ◐ | ○ | ● |
| OSCAR4 (Jessop et al., 2011) | ● | ● | ○ | ◐ | ● | ◐ | ● |
| PASTA (Gaizauskas et al., 2003) | ◐ | ● | ● | ◐ | ◐ | ● | ○ |
| PANKOW (Cimiano et al., 2004) | ● | ● | ● | ● | ○ | ○ | ◐ |
| RysannMD (Cuzzola et al., 2017) | ◐ | ● | ● | ◐ | ◐ | ○ | ● |
| SemTag (Dill et al., 2003) | ◐ | ● | ○ | ● | ◐ | ○ | ● |
| SiGEG (Haghgoo et al., 2022) | ● | ● | ● | ● | ◐ | ◐ | ● |
| SnoMedTagger (Hina et al., 2013) | ◐ | ◐ | ● | ◐ | ◐ | ○ | ● |
| TaggerOne (Leaman and Lu, 2016) | ● | ● | ● | ○ | ◐ | ● | ● |
| Textpresso (Müller et al., 2004) | ◐ | ● | ● | ● | ● | ● | ◐ |
| Verdant (McKain et al., 2017) | ○ | ● | ○ | ○ | ● | ● | ◐ |
| Whatizit (Rebholz-Schuhmann et al., 2008) | ◐ | ● | ● | ○ | ◐ | ◐ | ○ |
| XONTO (Oro and Ruffolo, 2008) | ◐ | ◐ | ● | ◐ | ○ | ○ | ○ |
Figure 2
ConceptMapper (Tanenblatt et al., 2010) successfully identified the name but unsuccessfully identified the role, which is also highlighted in blue.
Figure 3
MedCAT (Kraljevic et al., 2021) successfully identified the data.
Table 2
Semantic annotation tools and their methodologies.