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]
|