Table 1:
Biomedical Entity Linking Datasets
| Domain | Doc Type | Citation | Date | Entity(ies) | Ontology | Doc Count | Mentions | Unique Concepts |
|---|---|---|---|---|---|---|---|---|
| Scientific Literature | Biomedical Abstract | GENIA [43] | 2003 | Biomedical (broad) | MeSH | 2,000 | 93,293 | – |
| NCBI Disease [15] | 2014 | Disorder | MeSH | 793 | 6,892 | 790 | ||
| MedMentions [44] | 2019 | Biomedical (broad) | UMLS | 4,392 | 352,496 | 34,724 | ||
| MM-ST21pv [44] | 2019 | Biomedical (broad) | UMLS | 4,392 | 203,282 | 25,419 | ||
| PubMedDS [45] | 2021 | Biomedical (broad) | MeSH | 13,197,430 | 57,943,354 | 44,881 | ||
| RegEl [46] | 2022 | DNA Regulatory Elements | Various | 419 | 8,369 | 2,947 | ||
| Biomedical Article | BC5CDR [47] | 2016 | Chemical, Disorder | MeSH | 1,500 | 10,227 | – | |
| CRAFT [48] | 2016 | Biomedical (broad) | Many– | 97 | – | – | ||
| BioNLP-2019 [49] | 2019 | Bacteria Biotope | NCBI | 392 | 7,232 | 1,072 | ||
| PhaarmaCoNER [50] (ESP) | 2019 | Chemical, Drug | UMLS | 1,000 | 7,624 | – | ||
| BC7NLMCHEM [51] | 2021 | Chemical | MeSH | 150 | 38,342 | 2,064 | ||
| Multi Source | Quaero [52] (FRA) | 2014 | Biomedical (broad) | UMLS | 2,538 | 26,407 | 5,796 | |
| Mantra [53] | 2014 | Biomedical (broad) | UMLS | 1,450 | 5,530 | 3,780 | ||
| Figure Caption | BC6BioID [54] | 2017 | Gene,Chemical | ChEBI,UniProt | 17,883 | 133,003 | 7,652 | |
| Clinical | Clinical Note | ShARe/CLEF [14] | 2013 | Disorder | UMLS | 431 | 19,557 | 1,871 |
| CUILESS2016 [55] | 2018 | Disorder | UMLS | 431 | 5,397 | 1,738 | ||
| n2c2 2019 [56] (Luo, 2019) | 2019 | Problem, Test, Treatment | UMLS | 100 | 10,919 | 3,792 | ||
| MADE [57] | 2019 | ADE, Drug, Indication | MedDRA | 1,089 | 43,000 | – | ||
| Cantemist [58] (ESP) | 2020 | Oncology | ICD-O | 1,301 | 16,030 | 850 | ||
| BRONCO [59] (DE) | 2021 | Oncology | ICD-10, OPS, ATC | 200 | 11,124 | 4,027 | ||
| Social Media/Online Literature | Drug Label | TAC2017 [60] | 2017 | ADE | MedDRA | 200 | 26,488 | – |
| Tweets | Twitter ADR [61] | 2015 | ADE, Indication | UMLS | 1,784 | 1,693 | – | |
| SMM4H-17 [62] | 2017 | ADE | MedDRA | 25,678 | – | – | ||
| TwADR-L [63] | 2016 | ADE | SIDER? | 1,436 | – | 273 | ||
| Drug Forum | DailyStrength ADR [61] | 2015 | ADE, Indication | UMLS | 6,279 | 4,929 | – | |
| CADEC [64] | 2015 | ADE,Disorder,Drug | AMT,MedDRA,SNOMED | 1,253 | 9,111 | 3,591 | ||
| PsyTAR [65] | 2019 | ADE,Disorder | UMLS | 891 | 7,414 | 1,671 | ||
| COMETA [66] | 2020 | Biomedical (broad) | UMLS | – | 20,000 | 3,645 | ||
| Wikipedia | WikiMed [45] | 2021 | Biomedical (broad) | UMLS | 393,618 | 1,067,083 | 57,739 |
International Classification of Diseases for Oncology (ICD-O); Operationen und Prozedurenschlüssel (OPS); Anatomical Therapeutic Chemical Classification System (ATC);