Health variables

Hospital Universitario 12 de Octubre + Hospital Clínic de Barcelona efforts

The ISARIC-WHO Case Report Forms (CRFs) are used to collect data on individuals presenting with suspected or confirmed COVID-19 diagnosis. This resource has made available a collection of standardised clinical data to support patient care and COVID-19 research worldwide.

Hospital Universitario 12 de Octubre efforts have made possible the collection of observational variables associated to COVID-19 cases from Electronical Health Records using a flexible methodology based on Detailed Clinical Models (see the full article).

Spanish clinical data diagram
This figure associates observational variables between the ISARIC COVID-19 Core Case Record Form (February 2, 2021) (resource) and the Dual Model of Observations from Hospital Universitario 12 de Octubre data models.

Clinical variables - ISARIC based model

COVID-19 ranks as the single largest health incident worldwide in decades. In such a scenario, electronic health records (EHRs) should provide a timely response to healthcare needs and to data uses that go beyond direct medical care and are known as secondary uses, which includes biomedical research. However, it is usual for each data analysis initiative to define its own information model in line with its requirements. These specifications share clinical concepts, but differ in format and recording criteria, something that creates data entry redundancy in multiple electronic data capture systems (EDCs) with the consequent investment of effort and time by the organization.

This study was undertaken at the Hospital Universitario 12 de Octubre, a 1,300-bed tertiary hospital situated in Madrid Region (Spain). It sought to design and implement a flexible methodology based on detailed clinical models (DCM), which would enable EHRs generated in a tertiary hospital to be effectively reused without loss of meaning and within a short time.

As part of the first stage of the methodology of this study a specification of an initial and expandable set of relevant concepts for COVID-19 was identified, modeled and formalized using ISO-13606 standard and SNOMED CT and LOINC terminologies. - text: The standard catalog of observable entities in COVID-19 is the specification and standardization of a set of 22 clinical observable entities and 36 laboratory-related observable entities of interest in COVID-19. These concepts, in consonance with the ISO 13606 standard and semantically linked to standard terminologies, are implemented in the multiple Hospital healthcare information systems, allowing homogenous data entry via clinical record forms or, transparently, through integration with laboratory equipment. Data are stored in each system’s database, following a dual key-value structure: standard concept of the observable entities and finding reported. This allows the reuse of data, while maintaining their original meaning unaltered.

The standard catalog and additional results of this study are the deliverables defined in the different stages of the methodology of the scientific publication cited below. Its implementation into the Hospital 12 de Octubre began on March 15, 2020 and the first EHR-derived extract was generated and validated on April 20, 2020.

Pedrera Jiménez, Miguel et al. Obtaining EHR-derived datasets for COVID-19 research within a short time: a flexible methodology based on Detailed Clinical Models. Journal of biomedical informatics, 103697. Feb 3 2021. DOI: 10.1016/j.jbi.2021.103697

+/- Component Description Context Standard Code
Cluster Observaciones epidemiológicas en relación con COVID-19 artefacto de registro SNOMED CT 63261000122108
Element Contacto con enfermo de infección respiratoria aguda observable SNOMED CT 63031000122109
Value hallazgo SNOMED CT 63101000122104
Value No hallazgo SNOMED CT 63171000122108
Value Desconocido - Null flavors UNK
Element Entorno contacto enfermo infección respiratoria aguda observable SNOMED CT 63041000122101
Value Hogar entorno SNOMED CT 63181000122106
Value Trabajo entorno SNOMED CT 63191000122109
Value Centro sanitario entorno SNOMED CT 63201000122107
Value Otro - Null flavors OTH
Value Desconocido - Null flavors UNK
Element Contacto con caso COVID-19 observable SNOMED CT 63051000122104
Value hallazgo SNOMED CT 63211000122105
Value No hallazgo SNOMED CT 63221000122104
Value Desconocido - Null flavors UNK
Element País contacto con caso COVID-19 observable SNOMED CT 63061000122102
Value Texto libre países ISO -
Element CCAA contacto con caso COVID-19 observable SNOMED CT 63061000122102
Value Diccionario de CCAAs comunidades autónomas ISO -
Element Entorno contacto con caso COVID-19 observable SNOMED CT 63081000122105
Value Hogar entorno SNOMED CT 63231000122101
Value Trabajo entorno SNOMED CT 63241000122109
Value Centro sanitario entorno SNOMED CT 63251000122106
Value Otro - Null flavors OTH
Value Desconocido - Null flavors UNK
Element Fecha del último contacto con caso COVID-19 observable SNOMED CT 63091000122108
Value dd/mm/aaaa - DATE -
Cluster Observaciones sobre síntomas en relación con COVID-19 artefacto de registro SNOMED CT 63271000122103
Element Síntomas y signos observados: artefacto de registro SNOMED CT 63671000122101
Value Disnea hallazgo SNOMED CT 267036007
Value Broncoespasmo hallazgo SNOMED CT 4386001
Value Expectoración hallazgo SNOMED CT 248596009
Value Vómitos hallazgo SNOMED CT 422400008
Value Diarrea hallazgo SNOMED CT 62315008
Value Fiebre hallazgo SNOMED CT 386661006
Value Tos hallazgo SNOMED CT 49727002
Value Mialgias hallazgo SNOMED CT 68962001
Value Disgeusia hallazgo SNOMED CT 247318005
Value Anosmia hallazgo SNOMED CT 44169009
Value Odinofagia hallazgo SNOMED CT 30233002
Value Rinorrea trastorno SNOMED CT 64531003
Value Dolor torácico hallazgo SNOMED CT 29857009
Value Alteracion del nivel de conciencia hallazgo SNOMED CT 3006004
Value Convulsiones hallazgo SNOMED CT 91175000
Value Malestar general hallazgo SNOMED CT 367391008
Value Congestion conjuntival hallazgo SNOMED CT 193894004
Value Neumonía hallazgo SNOMED CT 233604007
Value Dolor de garganta hallazgo SNOMED CT 162397003
Value Escalofríos hallazgo SNOMED CT 43724002
Value Síndrome de distrés respiratorio agudo hallazgo SNOMED CT 67782005
Value Fallo renal agudo hallazgo SNOMED CT 14669001
Cluster Observaciones clínicas en relación con COVID-19 artefacto de registro SNOMED CT 63281000122100
Element Peso observable SNOMED CT 27113001
Element Talla observable SNOMED CT 50373000
Element IMC observable SNOMED CT 60621009
Element Frecuencia respiratoria observable SNOMED CT 86290005
Element Frecuencia Cardíaca observable SNOMED CT 364075005
Element Tensión sistólica observable SNOMED CT 271649006
Element Tensión diastólica observable SNOMED CT 271650006
Element Tensión arterial media observable SNOMED CT 6797001
Element Temperatura observable SNOMED CT 386725007
Element Saturación O2 observable SNOMED CT 103228002
Element Flujo de oxígeno con gafas nasales observable SNOMED CT 63321000122109
Element Concentración de oxígeno con mascarilla observable SNOMED CT 63331000122107
Element Tipo de Soporte Respiratorio observable SNOMED CT 63341000122104
Value Gafas nasales hallazgo SNOMED CT 261974006
Value Mascarilla hallazgo SNOMED CT 336602003
Value Oxígeno ambiente sin soporte respiratorio hallazgo SNOMED CT 722742002
Value Mascarilla Reservorio hallazgo SNOMED CT 720742008
Value CPAP hallazgo SNOMED CT 47545007
Value Ventilación mecánica no invasiva hallazgo SNOMED CT 428311008
Value Alto flujo con gafas nasales régimen/tratamiento SNOMED CT 63351000122102
Element Deposiciones observable SNOMED CT 162098000
Element Vómitos observable SNOMED CT 63361000122100
Element Micciones observable SNOMED CT 364198000
Element Tabaquismo observable SNOMED CT 266918002
Value No fumador hallazgo SNOMED CT 8392000
Value Ex fumador hallazgo SNOMED CT 8517006
Value Fumador hallazgo SNOMED CT 77176002
Element Año de inicio del hábito tabáquico observable SNOMED CT 63371000122105
Element Cantidad cigarros al día observable SNOMED CT 230056004
Element Indice tabáquico acumulado observable SNOMED CT 63381000122108
Element Año de abandono del hábito tabáquico observable SNOMED CT 160625004
Element Candidato a valoración por uci observable SNOMED CT 63391000122106
Element Candidato a Ventilación Mecánica observable SNOMED CT 63401000122108
Element Resultado Rx COVID-19 observable SNOMED CT 63401000122108
Value Infiltrado parcheado hallazgo SNOMED CT 63521000122101
Value Opacidades en vidrio delustrado hallazgo SNOMED CT 63531000122103
Value Neumonía intersticial hallazgo SNOMED CT 63541000122106
Value Ninguna hallazgo SNOMED CT 63551000122108
Value Otros - Null flavors OTH
Element Resultado TAC COVID-19 observable SNOMED CT 63421000122100
Value Afectación de un lóbulo hallazgo SNOMED CT 63561000122105
Value Afectación de más de un lóbulo hallazgo SNOMED CT 63571000122100
Value Afectación difusa hallazgo SNOMED CT 63581000122102
Value Normal hallazgo SNOMED CT 63591000122104
Element Riesgo respiratorio observable SNOMED CT 704296008
Element Puntaje NEWS observable SNOMED CT 63431000122102
Element Resultado de Escala DOSOFA observable SNOMED CT 63441000122105
Element Resultado de Escala qSOFA observable SNOMED CT 63451000122107
Element Resultado de Escala Glasgow observable SNOMED CT 248241002
Element Evolución COVID-19 observable SNOMED CT 63461000122109
Value Vivo recuperado hallazgo SNOMED CT 63471000122104
Value Muerte por COVID-19 hallazgo SNOMED CT 63481000122101
Value Muerte por otra causa hallazgo SNOMED CT 63491000122103
Value Muerte por causa desconocida hallazgo SNOMED CT 63501000122109
Value Todavía en seguimiento hallazgo SNOMED CT 63511000122107
Value Desconocido - Null flavors UNK
Element Fecha de defunción observable SNOMED CT 399753006
Value dd/mm/aaaa - DATE -
Cluster Observaciones de laboratorio en relación con COVID-19 artefacto de registro SNOMED CT 63291000122102
Element Resultado PCR COVID-19 determinación LOINC 94315-9
Value Positivo hallazgo SNOMED CT 10828004
Value Negativo hallazgo SNOMED CT 260385009
Value Equívoco hallazgo SNOMED CT 42425007
Element Resultado Antígenos COVID-19 determinación LOINC 94558-4
Value Positivo hallazgo SNOMED CT 10828004
Value Negativo hallazgo SNOMED CT 260385009
Value Equívoco hallazgo SNOMED CT 42425007
Element Fecha prueba COVID-19 hallazgo SNOMED CT 63301000122101
Element Fecha resultado COVID-19 hallazgo SNOMED CT 63311000122103
Element Hemoglobina determinación LOINC 718-7
Element Leucocitos determinación LOINC 6690-2
Element Linfocitos determinación LOINC 731-0
Element Plaquetas determinación LOINC 777-3
Element Neutrófilos determinación LOINC 751-8
Element Eosinófilos determinación LOINC 711-2
Element Basófilos determinación LOINC 704-7
Element Hematocrito determinación LOINC 4544-3
Element Albúmina determinación LOINC 1751-7
Element ALT (GPT) determinación LOINC 1742-6
Element AST (GOT) determinación LOINC 1920-8
Element Bilirrubina determinación LOINC 1975-2
Element Creatinina determinación LOINC 2160-0
Element LDH determinación LOINC 2532-0
Element Ferritina determinación LOINC 2276-4
Element CK determinación LOINC 2157-6
Element Troponina T hs determinación LOINC 6598-7
Element ESR determinación LOINC 30341-2
Element TTPA determinación LOINC 3173-2
Element Urea determinación LOINC 3091-6
Element Lactato determinación LOINC 2524-7
Element Procalcitonina determinación LOINC 33959-8
Element Tiempo de Protrombina determinación LOINC 5964-2
Element INR determinación LOINC 6301-6
Element Sodio determinación LOINC 2951-2
Element Potasio determinación LOINC 2823-3
Element Dímeros D determinación LOINC 48067-3
Element Triglicéridos determinación LOINC 2571-8
Element Proteína C Reactiva determinación LOINC 1988-5
Element Interleuquina 6 determinación LOINC 26881-3
Element Fibrinógeno (Derivado) determinación LOINC 3255-7
Element SaO2 determinación LOINC 2708-6
Element pAO2 Arterial determinación LOINC 293472
Element pCO2 Arterial determinación LOINC 2019-8
Element pCO2 Capilar determinación LOINC 2020-6
Element pCO2 Venoso determinación LOINC 2021-4
Element pO2 Arterial determinación LOINC 19255-9
Element pO2 Capilar determinación LOINC 19256-7
Element pO2 Venoso determinación LOINC 19258-3
Element FIO2 determinación LOINC 24336-0
Element pO2/FiO2 determinación LOINC 50984-4

Chronic diseases variables - cohorts based

In the framework of the COVICAT study, the authors defined the chronic disease categories using the available information from COVICAT survey. The table contains self‐reported variables about chronic diseases within the COVICAT cross‐sectional survey that was answered by the participants between May 28th and July 31st 2020. Chronic diseases were defined as any long‐term condition lasting 6 or more months, being considered the variables H13_A2 to H13_A17. Those referring to asthma, chronic bronchitis and COPD, allergies and related treatments are considered in the variables H02 to H08.

This information has been extracted from a document prepared by Magda Bosch de Basea & Judith Garcia‐Aymerich in December, 2020.

The project aims to evaluate the evolution of incidences of infection by the coronavirus SARS-CoV-2 in the Catalan population during 12 months through a prospective epidemiological study of populational cohorts established before the pandemic. The study is being carried out with 24,000 people who volunteered and who are already members of different populational cohorts in a collaboration between the GCAT Genomes for Life Project of the Germans Trias i Pujol Research Institute (IGTP) and two research groups from ISGlobal, a centre supported by the "la Caixa" Foundation, and the Hospital Clínic, Barcelona.

Variable code Disease Possible values
H13_A2 chronic bronchitis, COPD, emphysema Yes/No
H13_A3 other respiratory diseases Yes/No
H13_A4 hypertension Yes/No
H13_A5 heart disease Yes/No
H13_A6 diabetes Yes/No
H13_A7 digestive diseases Yes/No
H13_A8 gynecological diseases Yes/No
H13_A9 joint problems, rheumatism Yes/No
H13_A10 cancer Yes/No
H13_A11 anxiety / depression Yes/No
H13_A16 other mental illnesses Yes/No
H13_A12 HIV and other immunodeficiency problems Yes/No
H13_A13 chronic liver disease Yes/No
H13_A14 chronic kidney disease Yes/No
H13_A15 autoimmune disease Yes/No
H13_A17 none of the above Yes/No
H02 Asthma ever Yes/No
H03 Doctor Diagnosis of asthma Yes/No
H04 Asthma attack last 12 months Yes/No
H05 Current asthma medication Yes/No
H06 Chronic bronchitis, COPD or emphysema Yes/No
H07 Nasal allergy (e.g. rhinitis) Yes/No
H08 Sometimes eczema or other skin allergy Yes/No
H13_other other Free text

COVID-19 ISCIII's funded projects variables

The table below shows health variables reported by projects funded by the ISCIII funds Fondo COVID19. This information will be updated regularly as projects report new variables.

Group Variable Number of projects % on projects
Comorbilidades previas
Asma 7 33.00%
Cáncer 15 71.00%
Diabetes 17 81.00%
Dislipidemia 6 29.00%
EPOC 11 52.00%
Enfermedad cardiovascular 6 29.00%
Enfermedad cerebrovascular 7 33.00%
Enfermedad hepática 10 48.00%
Enfermedad neurológica 5 24.00%
Enfermedad renal crónica 11 52.00%
Enfermedad respiratoria 7 33.00%
HTA 14 67.00%
Obesidad 10 48.00%
14 67.00%
Fecha de fallecimiento
13 62.00%
Fecha de ingreso en UCI
9 43.00%
Fecha ingreso en el hospital
12 57.00%
Fecha inicio de síntomas
10 48.00%
Medicación previa
AINES 6 29.00%
ARA II 6 29.00%
Antibióticos 2 10.00%
Estatinas 6 29.00%
IECAs 7 33.00%
ECMO 5 24.00%
Ventilación mecánica invasiva 9 43.00%
Ventilación mecánica no invasiva 9 43.00%
Altura 6 29.00%
Edad 21 100.00%
Hábito alcohólico 6 29.00%
Hábito tabáquico 14 67.00%
Peso 7 33.00%
Sexo 21 100.00%
Síntomas previos al ingreso
Ageusia 8 38.00%
Anosmia 9 43.00%
Cefalea 11 52.00%
Diarrea 11 52.00%
Disnea 10 48.00%
Fiebre 13 62.00%
Mialgias 10 48.00%
Tos 13 62.00%
Tratamiento durante hospitalización
Antibióticos 9 43.00%
Antivirales 9 43.00%
Corticoides 4 19.00%
Hidroxicloroquina 7 33.00%
Oxigeno alto flujo 9 43.00%
Oxígeno convencional 8 38.00%

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