Author | Year | Country | Challenge | Induced objective | Data origin | Dataset | Data language | Used system | Term. Sys. | In use | Source code | Ref |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Afshar | 2019 | USA | No | Information extraction | Clinical Data Warehouse Data | Own | English | New (+ existing) | UMLS (CPT, HCPCS, ICD-10, ICD10CM / ICD9CM, LOINC, MeSH, SNOMED-CT, RxNorm) | Not listed | No, only links to cTAKES source code | [29] |
Alnazzawi | 2016 | UK | No | Information enrichment | PhenoCHF corpus 1 | Existing | English | Existing | UMLS | Not listed | Not applicable | [30] |
Atutxa | 2018 | Spain | No | Information enrichment | EHR documents | Own | Spanish | New | ICD (SNOMED-CT for normalization) | Not yet, aim to embed it in human-supervised loop | Not listed | [31] |
Barrett | 2013 | USA | No | Information extraction | Palliative care consult letters | Own | English | New | SNOMED CT | Not listed | No, but planned | [32] |
Becker | 2016 | Germany | No | Information extraction | ShARe/CLEF corpus (2013) 2 | Existing | German | Existing | SNOMED CT (English), UMLS (German) | Not yet, still under development | Not applicable | [33] |
Becker | 2019 | Germany | No | Information extraction | Clinical notes of patients with known colorectal cancer | Own | German | New (+ existing) | UMLS | Yes, led to improved quality of care for colorectal patients | Not listed | [34] |
Bejan | 2015 | USA | No | Information extraction | Discharge summaries and i2b2/VA challenge dataset (2010) 3 | Own + Existing | English | Existing | UMLS | No | Not applicable | [35] |
Castro | 2010 | Spain | No | Information extraction | Clinical notes with ‘most relevant information’ | Own | Spanish | Existing | SNOMED CT | Not listed | Not applicable | [36] |
Catling | 2018 | UK | No | Software development and evaluation | MIMIC-III dataset 4 | Existing | English | New | ICD-9-CM | Not listed | Not listed | [37] |
Chapman | 2004 | USA | No | Information extraction | Emergency department reports | Own | English | Existing | UMLS | Not listed | Not applicable | [38] |
Chen | 2016 | USA | No | Information enrichment | Discharge summaries and progress notes | Own | English | New (+ existing) | UMLS | Not listed | Not listed | [39] |
Chiaramello | 2016 | Italy | No | Information extraction | Clinical notes (cardiology, diabetology, hepatology, nephrology, and oncology) | Own | Italian | Existing | UMLS | Not listed | Not applicable | [40] |
Chodey | 2016 | USA | SemEval (2014) | Information extraction | ICU Data: Discharge summaries, ECG, echo, and radiology | Existing | English | New (+ existing) | UMLS | Not listed | Not listed | [41] |
Chung | 2005 | USA | No | Information extraction | Echocardiogram reports | Own | English | New (+ existing) | UMLS | Not yet, it will be used to populate a registry | Not listed | [42] |
Combi | 2018 | Italy | No | Information extraction | VigiSegn (adverse drug reactions) reports | Own | Italian + English | New | MedDRA | Yes, implemented in VigiFarmaco | Pseudocode | [43] |
De Bruijn | 2011 | Canada | i2b2/VA (2010) | Information extraction | Hospital discharge summaries and progress reports | Existing | English | New (+ existing) | UMLS | Not listed | Not listed | [44] |
Deisseroth | 2019 | USA | No | Information extraction | Six sets of real patient data from four different medical centers. | Own | English | New | HPO | Not listed | Yes | [45] |
Demner-Fushman | 2017 | USA | No | Software development and evaluation | BioScope 5, NCBI disease corpus 6, i2b2/VA challenge corpus (2010) 3, ShARe corpus 7, LHC test collection (biological/clinical journal abstracts) | Existing | English | New (+ existing) | UMLS | Yes, used in other papers identified in literature search | Yes | [46] |
Divita | 2014 | USA | Parts: i2b2/VA (2010) | Software development and evaluation | Randomly selected clinical records from the most frequent document types | Own | English | New | UMLS (level 0 + 9) | Yes, used by VA Informatics and Computing Infrastructure | Yes | [47] |
Duarte | 2018 | Portugal | No | Information enrichment | Death certificates, clinical bulletins, and autopsy reports | Own | Portuguese | New | ICD-10 | Yes, used by Portugese Ministry of Health for near real-time death cause surveillance | Not listed | [48] |
Falis | 2019 | UK | No | Information extraction | MIMIC-III dataset 4 | Existing | English | New | ICD-9 | Not listed | Not listed | [49] |
Ferrão | 2013 | Portugal | No | Information enrichment | Inpatient adult episodes from the EHR | Own | Portuguese | New | ICD-9-CM | Not listed | Not listed | [50] |
Gerbier | 2011 | France | No | Information extraction | Computerized emergency department medical records | Own | French | New | ICD-10, CCAM, SNOMED CT, ATC, MeSH, ICPC-2, DCR | Not yet, will be integrated into a CDSS | Not listed | [51] |
Goicoechea Salazar | 2013 | Spain | No | Information enrichment | Diagnostic text from patient records | Own | Spanish | New | ICD-9-CM | Not listed | Not listed | [52] |
Hamid | 2013 | USA | No | Classification | Notes of Iraq and Afghanistan veterans from the VA national clinical database | Own | English | Existing | UMLS | Not listed | Not applicable | [53] |
Hassanzadeh | 2016 | Australia | No | Information extraction | ShARe/CLEF corpus (2013) 2 | Existing | English | Existing | UMLS, SNOMED CT | Not applicable | Not applicable | [54] |
Helwe | 2017 | Lebanon | No | Computer-assisted coding | MIMIC-III dataset | Existing | English | New | UMLS, ICD | Not listed | Not listed | [55] |
Hersh | 2001 | USA | No | Information enrichment | Radiology image reports | Own | English | Existing | UMLS | No, still in development/testing | Pseudocode | [56] |
Hoogendoorn | 2015 | Netherlands | No | Prediction | Consultation notes of patients in a primary care setting | Own | Dutch | New | SNOMED-CT, UMLS, ICPC | Not listed | Not listed | [57] |
Jindal | 2013 | USA | i2b2 (2012) | Information extraction | i2b2 challenge corpus (2012) 8 | Existing | English | New (+ existing) | UMLS, SNOMED CT, MeSH | Not listed | Not listed | [58] |
Kang | 2009 | Korea | No | Information extraction | Discharge summaries | Own | Korean | New | KOMET, UMLS | Not listed | Not listed | [59] |
Kersloot | 2019 | Netherlands | No | Information extraction | (Non-small cell) Lung cancer charts | Own | English | New (+ existing) | SNOMED CT | Not listed | Yes | [60] |
König | 2019 | Germany | No | Software development and evaluation | Discharge letters from BASE-II study | Own | German | New (+ existing) | Wingert-Nomenclature | No, still has to prove its value | Not listed | [61] |
Li | 2015 | USA | No | Information comparison | Clinical notes and discharge prescription lists | Own | English | New (+ existing) | UMLS, SNOMED CT, RxNorm | Not yet, plans to move to production | Pseudocode | [62] |
Li | 2019 | USA | No | Information extraction | EHR notes | Own | English | New (+ existing) | UMLS, SNOMED CT, MedDRA | Not listed | Not listed | [63] |
Lingren | 2016 | USA | No | Classification | Structured and unstructured data from two EHR databases | Own | English | New (+ existing) | UMLS, ICD-9, RxNorm | Not listed | Not listed | [12] |
Liu | 2019 | USA | No | Information extraction | Clinical notes from different institutions + PubMed Case report abstracts | Own + Existing | English | Existing | HPO | Not listed | Not applicable | [64] |
Lowe | 2009 | USA | No | Information extraction | Single-specimen pathology reports | Own | English | Existing | UMLS, SNOMED CT | Not listed | Not applicable | [65] |
Luo | 2014 | USA | No | Information extraction | Pathology reports | Own | English | New (+ existing) | UMLS, SNOMED CT | Yes, currently working on project in multiple hospitals | Not listed | [66] |
Meystre | 2006 | USA | No | Information enrichment | Clinical documents form adult inpatients in a cardiovascular unit | Own | English | New (+ existing) | UMLS (level 0), SNOMED CT | Not yet, testing in practice | Not listed | [67] |
Meystre | 2010 | USA | i2b2 (2009) | Information extraction | i2b2 challenge dataset (2009) 9 | Existing | English | New | UMLS | Not yet, possible integration in research infrastructure | Not listed | [68] |
Minard | 2011 | France | i2b2/VA (2010) | Information extraction | i2b2/VA challenge corpus (2010) 3 | Existing | English | New (+ existing) | UMLS | Not listed | Not listed | [69] |
Mishra | 2019 | USA | No | Information extraction | Clinical notes from NIH Clinical Center data warehouse | Own | English | Existing | UMLS, HPO | Not listed | Not applicable | [70] |
Nguyen | 2018 | Australia | No | Computer-assisted coding | Hospital progress notes | Own | English | New (+ existing) | SNOMED CT, ICD-10-AM | Not listed | Not listed | [71] |
Oellrich | 2015 | UK | No | Information extraction | PubMed abstracts, clinical trial information, i2b2/VA challenge corpus (2010) 3, SHARE/CLEF (2013) 2 | Existing | English | Existing | UMLS | Not listed | Not applicable | [72] |
Patrick | 2011 | Australia | i2b2/VA (2010) | Information extraction | i2b2/VA challenge corpus (2010) 3 | Existing | English | New | UMLS, SNOMED CT | Not listed | Not listed | [73] |
Pérez | 2018 | Spain | No | Text processing | Spontaneous DTs randomly selected entries | Own | Spanish | New | ICD | Not listed | Not listed | [74] |
Reátegui | 2018 | Canada | No | Information extraction | i2b2 challenge corpus (2008) 10 | Existing | English | New (+ existing) | UMLS, SNOMED CT, RxNorm | Not listed | Not listed | [75] |
Roberts | 2011 | USA | i2b2/VA (2010) | Information extraction | i2b2/VA challenge corpus (2010) 3 | Existing | English | New (+ existing) | UMLS, ICD-9 | Not listed | Not listed | [76] |
Rousseau | 2019 | USA | No | Information comparison | ED encounters for patients with headaches who received head CT | Own | English | Existing | UMLS: SNOMED CT, RadLex | Not listed | Not applicable | [77] |
Savova | 2010 | USA | i2b2 (2006, 2008) | Information extraction | Subset of clinical notes from the EMR | Own | English | New (+ existing) | UMLS, SNOMED CT, RxNorm | Yes, used in other papers identified in literature search | Yes | [78] |
Shivade | 2015 | USA | i2b2/UTHealth (2014) | Classification | i2b2 challenge corpus (2014) 11 | Existing | English | Existing | UMLS | Not listed | Not applicable | [11] |
Shoenbill | 2019 | USA | No | Information extraction | EHR notes from hypertension patients | Own | English | Existing | UMLS, SNOMED CT | Not listed | Not applicable | [79] |
Sohn | 2014 | USA | No | Information extraction | Clinical notes with medication mentions | Own | English | New | RxNorm | Not listed | Yes | [80] |
Solti | 2008 | USA | No | Information enrichment | Cardiology ambulatory progress notes | Own | English | Existing | UMLS | Not listed | Not applicable | [81] |
Soriano | 2019 | Spain | No | Information extraction | clinical emergency discharge reports | Own | Spanish | New | SNOMED CT | Not yet | Yes | [82] |
Soysal | 2018 | USA | Parts: i2b2 (2009 + 2010), ShARe/CLEF (2013), Sem-EVAL (2014) | Software development and evaluation | Discharge summaries from the i2b2/VA challenge corpus (2010) 3, outpatient clinic visit notes, mock clinical documents | Own + Existing | English | New | UMLS | Yes, used by various institutions and industrial entities | Yes | [83] |
Spasić | 2015 | UK | No | Information extraction | MRI reports of patients | Own | English | New (+ existing) | TRAK, UMLS, MEDCIN, RadLex | Not listed | Yes | [84] |
Strauss | 2013 | USA | No | Information extraction | Pathology reports of breast and prostate cancer patients | Own | English | New | SNOMED CT | Not listed | Yes | [85] |
Sung | 2018 | Taiwan | No | Information extraction | Cases of adult patients with AIS | Own | English | Existing | UMLS | Not listed | Not applicable | [86] |
Tchechmedjiev | 2018 | France | No | Information extraction | Quaero (French MEDLINE abstract titles + EMEA drug labels) + CépiDC (ICD-10 coding of death certificates) | Existing | French | New (+ existing) | UMLS terminologies (ICD-10) | Yes, available in SIFR BioPortal | Yes | [87] |
Ternois | 2018 | France | No | Classification | Endoscopy reports written between 2015 and 2016 | Own | French | New | CCAM | Not listed | Not listed | [88] |
Travers | 2004 | USA | No | Information extraction | Chief complaint text entries for all emergency department visits | Own | English | New | UMLS | Not listed | Not listed | [89] |
Tulkens | 2019 | Belgium | No | Information extraction | i2b2/VA challenge corpus (2010) 3 | Existing | English | New (+ existing) | UMLS | Not listed | Yes | [90] |
Usui | 2018 | Japan | No | Prediction | Electronic medication history data from pharmacy | Own | Japanese | New | ICD-10 | Not yet, expect to use it | Not listed | [91] |
Valtchinov | 2019 | USA | No | Classification | Radiology reports, emergency department notes + other clinical reports | Own | English | Existing | SNOMED CT, RadLex | Not listed | Not applicable | [92] |
Wadia | 2018 | USA | No | Classification | Chest CT reports | Own | English | Existing | SNOMED CT, UMLS | Not listed | Not applicable | [93] |
Walker | 2019 | USA | No | Information extraction | Treatment sites from EMR | Own | English | New | UMLS | Not listed | Not listed | [94] |
Xie | 2019 | China | No | Information extraction | MIMIC-III dataset 4 | Existing | English | New | ICD-9-CM, ICD-10 | Not listed | Not listed | [95] |
Xu | 2011 | USA | No | Classification | CRC patient cases from the Synthetic Derivative database | Own | English | Existing | UMLS | No, still under development | Not applicable | [96] |
Yadav | 2013 | USA | No | Prediction | Emergency department CT imaging reports | Own | English | Existing | UMLS | Not listed | Yes, command line command | [97] |
Yao | 2019 | USA | No | Prediction | i2b2 challenge corpus (2008) 10 | Existing | English | New (+ existing) | UMLS | Not listed | Part (Sorl) | [98] |
Zeng | 2018 | USA | No | Classification | Progress notes and breast cancer surgical pathology reports | Own | English | New (+ existing) | UMLS | Not listed | Not listed | [99] |
Zhang | 2013 | USA | No | Information extraction | i2b2/VA challenge corpus (2010) 3 and GENIA corpus (MEDLINE abstracts) | Existing | English | New | UMLS | Not listed | Not listed | [100] |
Zhou | 2006 | USA | No | Information extraction | Records of patients with breast complaints | Own | English | New | UMLS | No, still under development | Not listed | [101] |
Zhou | 2011 | USA | No | Software development and evaluation | COPD and CAD patients | Own | English | New | SNOMED CT, RxNorm, UMLS, PPL, MDD, HL7 value sets | Yes, described in other paper (103]) | Not listed | [102] |
Zhou | 2014 | USA | No | Information extraction | Admission notes and discharge summaries | Own | English | Existing | SNOMED CT, HL7 RoleCodes | Not listed | Not applicable | [103] |