ID

40116

Beschrijving

SBP is the national coordination platform for human and non-human biobanks. The dataset covers the different biobanking processes from sampling to retrieval and propose a common language to describe preanalytical attributes of samples. It also includes some health related data required for initial searches of suitable samples. Finally, it covers fields related to quality of biobanking processes. It contains variables related to general information on the bacterial sample, its history, growth conditions, storage information and other characteristics, such as strain resistances. More information can be found at https://swissbiobanking.ch

Link

https://swissbiobanking.ch

Trefwoorden

Versies (1)
  1. 12-03-20 12-03-20 -
Houder van rechten

Swiss Biobanking Platform (SBP)

Geüploaded op

12 maart 2020

DOI

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Licentie

Creative Commons BY-NC 4.0
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Swiss Biobanking Platform (SBP)

Engels

SBP Data Dictionary — Bacteria / Version 1.0

1 Formulieren  
General Information
Beschrijving

General Information

Alias
UMLS CUI-1
C1508263
Dataset applicable for bacterial microorganisms --> variable is per default "Bacteria"
Beschrijving

species_type

Datatype

text

Alias
UMLS CUI [1,1]
C1705920
UMLS CUI [1,2]
C0332307
Species name according NCBI taxonomy
Beschrijving

https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi

Datatype

text

Alias
UMLS CUI [1,1]
C1705920
UMLS CUI [1,2]
C0027365
Taxonomy ID according NCBI taxonomy browser
Beschrijving

Taxonomy ID according NCBI taxonomy browser https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi

Datatype

text

Alias
UMLS CUI [1,1]
C1705920
UMLS CUI [1,2]
C0600091
Name of the microorganism given by the laboratory
Beschrijving

strain_name

Datatype

text

Alias
UMLS CUI [1,1]
C0445623
UMLS CUI [1,2]
C0027365
UMLS CUI [1,3]
C0022877
Laboratory identifier ( e.g. BS, ZH)
Beschrijving

laboratory_ID

Datatype

text

Alias
UMLS CUI [1]
C2986056
Unique internal laboratory identifier for specimen (e.g. BS3545)
Beschrijving

specimen_lab_ID

Datatype

text

Alias
UMLS CUI [1,1]
C0205102
UMLS CUI [1,2]
C0022877
UMLS CUI [1,3]
C1299222
Unique external identifier for specimen
Beschrijving

A unique number generated automatically (tool / database not yet in place), laboratory independent and centralized. Back link to laboratory or host not possible.

Datatype

text

Alias
UMLS CUI [1,1]
C0439788
UMLS CUI [1,2]
C1299222
Risk group of strain
Beschrijving

Risk group might change, the level should be based on the last BAG list: https://www.bafu.admin.ch/bafu/de/home/themen/biotechnologie/publikationen-studien/publikationen/einstufung-von-organismen.html

Datatype

text

Alias
UMLS CUI [1,1]
C0035647
UMLS CUI [1,2]
C2946261
UMLS CUI [1,3]
C0445623
History
Beschrijving

History

Alias
UMLS CUI-1
C0019664
Institution/Laboratory name where microorganism is originated / was isolated.
Beschrijving

depositor_institution

Datatype

text

Alias
UMLS CUI [1,1]
C0022877
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0445623
Forename and surname of person determined by the institution
Beschrijving

depositor_name

Datatype

text

Alias
UMLS CUI [1,1]
C0022877
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0445623
UMLS CUI [1,4]
C1522390
Is the date of isolation known?
Beschrijving

isolation_date

Datatype

text

Alias
UMLS CUI [1,1]
C0022877
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0445623
UMLS CUI [1,4]
C2584899
If "Yes" selected, please specify:
Beschrijving

isolation_date_specify

Datatype

date

Alias
UMLS CUI [1,1]
C0022877
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0445623
UMLS CUI [1,4]
C2584899
Country of isolation
Beschrijving

ISO-standard (3166 alpha2), two-letter code for the country

Datatype

text

Alias
UMLS CUI [1,1]
C0454664
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0445623
ZIP code of isolation region
Beschrijving

isolation_region

Datatype

text

Alias
UMLS CUI [1,1]
C1549687
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0445623
Isolation source general
Beschrijving

isolation_source

Datatype

text

Alias
UMLS CUI [1,1]
C0445623
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0449416
Detailed isolation source as per laboratory nomenclature.
Beschrijving

Reference to SNOWMED CT based lists. http://browser.ihtsdotools.org/?

Datatype

text

Alias
UMLS CUI [1,1]
C0445623
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0449416
UMLS CUI [1,4]
C1522508
If "Other" selected : Presicion of isolation source
Beschrijving

Reference to SNOWMED CT based lists. http://browser.ihtsdotools.org/?

Datatype

text

Alias
UMLS CUI [1,1]
C0445623
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0449416
UMLS CUI [1,4]
C1522508
UMLS CUI [1,5]
C0205394
Important information on the source of the specimen - if any
Beschrijving

isolation_source_info

Datatype

text

Alias
UMLS CUI [1,1]
C0445623
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C0449416
UMLS CUI [1,4]
C1533716
UMLS CUI [1,5]
C3898777
Host species (human, animals, other) according NCBI taxonomy browser
Beschrijving

https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi

Datatype

text

Alias
UMLS CUI [1,1]
C0445623
UMLS CUI [1,2]
C0205409
UMLS CUI [1,3]
C2936412
Age of host at sampling
Beschrijving

host_age_at_collection

Datatype

text

Alias
UMLS CUI [1,1]
C0001779
UMLS CUI [1,2]
C1167395
UMLS CUI [1,3]
C0870078
If "Known" selected, please specify
Beschrijving

host_age_at_collection_specify

Datatype

integer

Alias
UMLS CUI [1,1]
C0001779
UMLS CUI [1,2]
C1167395
UMLS CUI [1,3]
C0870078
Unit for host age
Beschrijving

host_age_unit

Datatype

text

Alias
UMLS CUI [1,1]
C0001779
UMLS CUI [1,2]
C1167395
UMLS CUI [1,3]
C0870078
Sex of host
Beschrijving

Seperate fields for neuter status

Datatype

text

Alias
UMLS CUI [1,1]
C0079399
UMLS CUI [1,2]
C1167395
Precision if specimen was collected from an actual infected site or as part of a screening process (without evidence of infection)
Beschrijving

clinical_significance

Datatype

text

Alias
UMLS CUI [1,1]
C0200345
UMLS CUI [1,2]
C3714514
UMLS CUI [1,3]
C0332197
UMLS CUI [2,1]
C0200345
UMLS CUI [2,2]
C0439663
UMLS CUI [2,3]
C1515974
If "clinical sign of infection" selected: Infectious disease caused to the host by the microorganism
Beschrijving

disease

Datatype

text

Alias
UMLS CUI [1,1]
C3714514
UMLS CUI [1,2]
C1314792
UMLS CUI [1,3]
C0205409
UMLS CUI [1,4]
C0445623
Important information on the disease - if any
Beschrijving

disease_detailed

Datatype

text

Alias
UMLS CUI [1,1]
C1533716
UMLS CUI [1,2]
C3898777
UMLS CUI [1,3]
C0012634
If host is a human being and research is performed with coded health related data, the patient consent is required and research project requires EC approval
Beschrijving

Not applicable for anonymized data

Datatype

text

Alias
UMLS CUI [1,1]
C0086418
UMLS CUI [1,2]
C1167395
UMLS CUI [1,3]
C0021430
If host is an animal (host_species (17)): Neuter status of animal
Beschrijving

Not applicable for anonymized data

Datatype

text

Alias
UMLS CUI [1,1]
C0003062
UMLS CUI [1,2]
C1167395
Growth Conditions
Beschrijving

Growth Conditions

Alias
UMLS CUI-1
C0018270
UMLS CUI-2
C0348080
Suggested culture medium/media to regrow strain: 409594004 Buffered charcoal yeast extract agar (substance)
Beschrijving

Multiple selection possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C1443930
Suggested culture medium/media to regrow strain: 409593005 |Chocolate agar (substance)
Beschrijving

Multiple selection possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C1443929
Suggested culture medium/media to regrow strain: 409551009 |Eosin-methylene blue agar (substance)
Beschrijving

Multiple selection possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C1443891
Suggested culture medium/media to regrow strain: 446049000 |Heart infusion agar (substance)
Beschrijving

Multiple selection possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C2960801
Suggested culture medium/media to regrow strain: 409550005 |MacConkey agar (substance)
Beschrijving

Multiple selection possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C1443890
Suggested culture medium/media to regrow strain: 409591007 |Sheep blood agar (substance)
Beschrijving

Multiple selection possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C1443927
Suggested culture medium/media to regrow strain: 409592000 |Thayer-Martin agar (substance)
Beschrijving

Multiple selection possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C1443928
Suggested culture medium/media to regrow strain: 446475008 |Trypticase soy agar (substance)
Beschrijving

Multiple selection possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C2960802
Suggested culture medium/media to regrow strain: 74964007 |Other (qualifier value)
Beschrijving

Multiple selection possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C0205394
If "Other" selected: Presicion of culture medium
Beschrijving

Multiple selection possible

Datatype

text

Alias
UMLS CUI [1,1]
C0439536
UMLS CUI [1,2]
C0596932
UMLS CUI [1,3]
C0332307
UMLS CUI [1,4]
C0205394
Optimal growth temperature in [Cel]
Beschrijving

Multiple selection possible

Datatype

float

Alias
UMLS CUI [1,1]
C0596932
UMLS CUI [1,2]
C2698651
UMLS CUI [1,3]
C0018270
UMLS CUI [1,4]
C0039476
Growing environment of organism
Beschrijving

Multiple selection possible

Datatype

text

Alias
UMLS CUI [1,1]
C0018270
UMLS CUI [1,2]
C0014406
UMLS CUI [1,3]
C0029235
UMLS CUI [2,1]
C0030054
UMLS CUI [2,2]
C1704410
Characteristics - Strain resistance of antimicrobials
Beschrijving

Characteristics - Strain resistance of antimicrobials

Alias
UMLS CUI-1
C0860039
Antibiotics resistance of species known
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C0003232
UMLS CUI [1,2]
C1522618
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387266001 |Amikacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0002499
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372687004 |Amoxicillin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0002645
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 708558004 |Amoxicillin and clavulanate (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0054066
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387170002 |Ampicillin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0002680
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387531004 |Azithromycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0052796
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387386004 |Aztreonam (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0004521
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387091007 |Cefradine (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007738
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372651006 |Cefadroxil (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007538
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 373485007 |Cefalotin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007735
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372801003 |Cefamandole (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007541
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 87303007 |Cefapirin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007737
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387470007 |Cefazolin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007546
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 108677001 |Cefdinir (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0060405
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 96048006 |Cefepime (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0055003
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387536009 |Cefixime (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0060400
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 58343005 |Cefonicid (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007551
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372743004 |Cefoperazone (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007552
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372704003 |Cefotaxime (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007554
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387534007 |Cefpodoxime (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0055011
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387538005 |Cefprozil (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0053882
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387091007 |Cefradine (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007738
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387200005 |Ceftazidime (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007559
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387535008 |Ceftibuten (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0055014
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372670001 |Ceftriaxone (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007561
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372833007 |Cefuroxime (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0007562
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387549004 |Cinoxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0008806
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372840008 |Ciprofloxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0008809
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387487009 |Clarithromycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0055856
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372786004 |Clindamycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0008947
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387412007 |Colistin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0009316
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 406439009 |Daptomycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0057144
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 96035007 |Dirithromycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0058445
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372478003 |Doxycycline (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0013090
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387550004 |Enoxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0014310
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 396346003 |Ertapenem (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C1120106
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372694001 |Erythromycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0014806
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 96085003 |Fleroxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0085161
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387544009 |Flucloxacillin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0016267
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372534005 |Fosfomycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0016610
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387530003 |Fusidic acid (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0016875
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 116349004 |Gatifloxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0753645
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387321007 |Gentamicin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C3854019
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 386892006 |Grepafloxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0287721
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 46558003 |Imipenem (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0020933
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 713477009 |Josamycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0022419
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387396008 |Kanamycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0022487
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387552007 |Levofloxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0282386
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387056004 |Linezolid (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0663241
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387553002 |Lomefloxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0065162
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 96061006 |Loracarbef (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0065295
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387540000 |Meropenem (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0066005
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372602008 |Metronidazole (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0025872
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372653009 |Minocycline (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0026187
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 412439003 |Moxifloxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0536495
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387261006 |Nalidixic acid (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0027353
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 373528008 |Neomycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0027353
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387110005 |Netilmicin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0027780
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 373543005 |Nitrofurantoin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0028156
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387271008 |Norfloxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0028365
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387551000 |Ofloxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0028902
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 323389000 |Benzylpenicillin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0030827
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 703743007 |Piperacillin and tazobactam (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0250480
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387159009 |Rifampicin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0035608
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 96037004 |Roxithromycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0035891
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387554008 |Sparfloxacin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0052585
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387223008 |Streptomycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0038425
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 387529008 |Teicoplanin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0145106
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372809001 |Tetracycline (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0039644
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 418313005 |Tigecycline (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C1260298
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 373548001 |Tobramycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0040341
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 703745000 |Sulfamethoxazole and trimethoprim (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0041044
UMLS CUI [1,3]
C0004611
Antibiotics resistance of species against 372735009 |Vancomycin (substance)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0042313
UMLS CUI [1,3]
C0004611
Other antibiotics resistance of species
Beschrijving

74964007 |Other (qualifier value)

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0042313
UMLS CUI [1,3]
C0004611
If "Other" selected: Presicion of antimicrobial and ATC Code (if available)
Beschrijving

strain_resistance_antimicrobials

Datatype

boolean

Alias
UMLS CUI [1,1]
C4281815
UMLS CUI [1,2]
C0205394
UMLS CUI [1,3]
C0004611
Characteristics
Beschrijving

Characteristics

Alias
UMLS CUI-1
C1521970
Antibiotic class of above selected antibiotics (multiple classes possible)
Beschrijving

strain_resistance_class

Datatype

text

Alias
UMLS CUI [1,1]
C0456387
UMLS CUI [1,2]
C0003232
If "Known" selected, please specify the antibiotic class - multiple selection possible:
Beschrijving

Following antibiotic classes can be selected: 14443002 = Aminoglycoside -class of antibiotic- (substance) 703745000 = Sulfamethoxazole and trimethoprim (substance) 708558004 = Amoxicillin and clavulanate (substance) 703743007 = Piperacillin and tazobactam (substance) 396345004 = Carbapenem (substance) 372889003 = First generation cephalosporin (substance) 372814002 = Second generation cephalosporin (substance) 372859005 = Third generation cephalosporin (substance) 395959007 = Fourth generation cephalosporin (substance) 372534005 = Fosfomycin (substance) 414355008 = Glycopeptide antibiotic (substance) 373234002 = Lincomycin and derivatives (substance) 406440006 = Cyclic lipopeptide antibiotic (substance) 372480009 = Macrolide (class of antibiotic, substance) (substance) 409132008 = Monobactam (substance) 360201004 = Nitrofuran derivative (substance) 373235001 = Nitroimidazole (substance) 372649007 = Oxazolidinone -class of antibiotic- (substance) 373270004 = Penicillin -class of antibiotic- (substance) 372598006 = Penicillinase sensitive penicillins (substance) 373277001 = Penicillinase-resistant penicillin (substance) 373224006 = Polymyxins (substance) 372722000 = Quinolone -class of antibiotic- (substance) 406756000 = Rifamycins (substance) 387530003 = Fusidic acid (substance) 373206009 = Tetracycline (class of antibiotic, substance) (substance) 74964007 = Other (qualifier value)

Datatype

text

Alias
UMLS CUI [1,1]
C0456387
UMLS CUI [1,2]
C0003232
MIC for each antibiotic selected above
Beschrijving

MIC = Minimum inhibitory concentration

Datatype

text

Alias
UMLS CUI [1,1]
C0427978
UMLS CUI [1,2]
C0003232
If "Known" selected, please specify the MIC for each antibiotic selected above
Beschrijving

MIC = Minimum inhibitory concentration

Datatype

float

Maateenheden
  • ug/mL
Alias
UMLS CUI [1,1]
C0003232
UMLS CUI [1,2]
C0427978
ug/mL
Zone diameters for each antibiotic selected above
Beschrijving

strain_resistance_ZD

Datatype

text

Alias
UMLS CUI [1,1]
C0003232
UMLS CUI [1,2]
C4687934
If "Known" selected, please specify the zone diameter
Beschrijving

strain_resistance_ZD

Datatype

float

Maateenheden
  • mL
Alias
UMLS CUI [1,1]
C0003232
UMLS CUI [1,2]
C4687934
mL
SIR interpretation for each antibiotic selected above
Beschrijving

(interpretation/calculation of strain_resistance_MIC and/or strain_resistance_zone_diameter)

Datatype

text

Alias
UMLS CUI [1,1]
C0003232
UMLS CUI [1,2]
C4687934
UMLS CUI [1,3]
C0459471
Guideline and version used for interpretation for each antibiotic selected above
Beschrijving

used_resistance_guidelines

Datatype

text

Alias
UMLS CUI [1,1]
C0003232
UMLS CUI [1,2]
C4687934
UMLS CUI [1,3]
C0459471
UMLS CUI [1,4]
C0162791
If "EUCAST" selected, please specify:
Beschrijving

EUCAST version number (one decimal)

Datatype

float

Alias
UMLS CUI [1,1]
C0003232
UMLS CUI [1,2]
C4687934
UMLS CUI [1,3]
C0459471
UMLS CUI [1,4]
C0162791
If CLSI selected, please specify:
Beschrijving

MM/YYYY

Datatype

datetime

Alias
UMLS CUI [1,1]
C0003232
UMLS CUI [1,2]
C4687934
UMLS CUI [1,3]
C0459471
UMLS CUI [1,4]
C0162791
If "Other" selected: Precision which guideline and version
Beschrijving

used_resistance_guidelines_specify

Datatype

text

Alias
UMLS CUI [1,1]
C0003232
UMLS CUI [1,2]
C4687934
UMLS CUI [1,3]
C0459471
UMLS CUI [1,4]
C0162791
Antimicrobial resistance mechanism
Beschrijving

resistance_phenotype

Datatype

text

Alias
UMLS CUI [1,1]
C1456627
UMLS CUI [1,2]
C0441712
Antimicrobial resistance mechanism: Inactivation of drug by enzymes
Beschrijving

Multiple selections possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C1456627
UMLS CUI [1,2]
C0441712
UMLS CUI [2,1]
C0013227
UMLS CUI [2,2]
C0544461
UMLS CUI [2,3]
C0014442
Antimicrobial resistance mechanism: Alteration of membrane permeability
Beschrijving

Multiple selections possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C1456627
UMLS CUI [1,2]
C0441712
UMLS CUI [2,1]
C0007605
UMLS CUI [2,2]
C1515926
Antimicrobial resistance mechanism: Efflux pumps
Beschrijving

Multiple selections possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C1456627
UMLS CUI [1,2]
C0441712
UMLS CUI [1,3]
C3824504
Antimicrobial resistance mechanism: Alteration of intracellular target site
Beschrijving

Multiple selections possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C1456627
UMLS CUI [1,2]
C0441712
UMLS CUI [2,1]
C1515926
UMLS CUI [2,2]
C0682581
UMLS CUI [2,3]
C1521840
UMLS CUI [2,4]
C0205145
Antimicrobial resistance mechanism: Alteration of intracellular target enzyme
Beschrijving

Multiple selections possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C1456627
UMLS CUI [1,2]
C0441712
UMLS CUI [2,1]
C1515926
UMLS CUI [2,2]
C0682581
UMLS CUI [2,3]
C1521840
UMLS CUI [2,4]
C0014442
Antimicrobial resistance mechanism: Overproduction of target enzyme
Beschrijving

Multiple selections possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C1456627
UMLS CUI [1,2]
C0441712
UMLS CUI [2,1]
C3843660
UMLS CUI [2,2]
C1521840
UMLS CUI [2,3]
C0014442
Antimicrobial resistance mechanism: Auxotrophs that bypass blocked step
Beschrijving

Multiple selections possible Absence of autolytic enzymes

Datatype

boolean

Alias
UMLS CUI [1,1]
C1456627
UMLS CUI [1,2]
C0441712
UMLS CUI [2]
C3846158
Antimicrobial resistance mechanism: Absence of autolytic enzymes
Beschrijving

Multiple selections possible

Datatype

boolean

Alias
UMLS CUI [1,1]
C1456627
UMLS CUI [1,2]
C0441712
UMLS CUI [2,1]
C0004372
UMLS CUI [2,2]
C0014442
UMLS CUI [2,3]
C0332197
Genotypes associated with resistance according to the Comprehensive Antibiotic Resistance Database (CARD)
Beschrijving

Comprehensive Antibiotic Resistance Database (CARD): https://card.mcmaster.ca/model/list

Datatype

text

Alias
UMLS CUI [1,1]
C0017431
UMLS CUI [1,2]
C0332281
UMLS CUI [1,3]
C0949669
If "Known" selected, please specify:
Beschrijving

Comprehensive Antibiotic Resistance Database (CARD): https://card.mcmaster.ca/model/list

Datatype

text

Alias
UMLS CUI [1,1]
C0017431
UMLS CUI [1,2]
C0332281
UMLS CUI [1,3]
C0949669
Information on how resistance was tested
Beschrijving

Automated antimicrobial susceptibility testing system: e.g. Vitek, Walk-Away, Sensititre ARIS, Avantage Test, Micronaunt, Phonenix, etc. Mechanism-specific test: e.g. beta-lactamase detection test and chromogenic cephalosporin test Genotypic methods: e.g. PCR and DNA hybridization methods"

Datatype

text

Alias
UMLS CUI [1]
C3160797
Known virulence factors according to the VFDB reference database nomenclature (""VF_Name"" (column A) from VFs description file)
Beschrijving

VFDB reference database nomenclature (""VF_Name"" (column A) from VFs description file): http://www.mgc.ac.cn/VFs/download.htm

Datatype

text

Alias
UMLS CUI [1,1]
C0521009
UMLS CUI [1,2]
C1136170
If "Known" selected, please specify
Beschrijving

VFDB reference database nomenclature (""VF_Name"" (column A) from VFs description file): http://www.mgc.ac.cn/VFs/download.htm

Datatype

text

Alias
UMLS CUI [1,1]
C0521009
UMLS CUI [1,2]
C1136170
"Y" = Serotyping performed
Beschrijving

serotyping_performed

Datatype

text

Alias
UMLS CUI [1,1]
C0201217
UMLS CUI [1,2]
C1882330
If "Y" above (serotyping_performed (40)): Presicion of serogroup (free text)
Beschrijving

serotyping_serogroup

Datatype

text

Alias
UMLS CUI [1]
C0201217
Genetic data
Beschrijving

Genetic data

Alias
UMLS CUI-1
C0314603
UMLS CUI-2
C1511726
Any particular important genetic mutation, confirmed with sequencing. List and description of the mutation and/or deletion
Beschrijving

mutations

Datatype

text

Alias
UMLS CUI [1,1]
C3898777
UMLS CUI [1,2]
C0026882
Whole genome sequence available
Beschrijving

WGS_availability

Datatype

text

Alias
UMLS CUI [1]
C4483680
GenBank: NIH genetic sequence database, an annotated collection of all publicly available DNA sequences:
Beschrijving

https://www.ncbi.nlm.nih.gov/genbank/

Datatype

text

Alias
UMLS CUI [1,1]
C0027468
UMLS CUI [1,2]
C0950132
If "Known" selected, please specify:
Beschrijving

GenBank: NIH genetic sequence database, an annotated collection of all publicly available DNA sequences: https://www.ncbi.nlm.nih.gov/genbank/

Datatype

text

Alias
UMLS CUI [1,1]
C0027468
UMLS CUI [1,2]
C0950132
Additional genotypic information - if any
Beschrijving

other_genotype_information

Datatype

text

Alias
UMLS CUI [1,1]
C1524062
UMLS CUI [1,2]
C0017431
UMLS CUI [1,3]
C1533716
Storage
Beschrijving

Storage

Alias
UMLS CUI-1
C1698986
Storage type for long term preservation
Beschrijving

storage_format

Datatype

text

Alias
UMLS CUI [1,1]
C1698986
UMLS CUI [1,2]
C0332307
UMLS CUI [1,3]
C0443252
UMLS CUI [1,4]
C0033085
If "Other" selected: Presicion of storage type for long term preservation
Beschrijving

storage_format_other

Datatype

text

Alias
UMLS CUI [1,1]
C1698986
UMLS CUI [1,2]
C0332307
UMLS CUI [1,3]
C0443252
UMLS CUI [1,4]
C0033085
UMLS CUI [1,5]
C0205394
Storage temperature for long term preservation
Beschrijving

storage_temperature

Datatype

text

Alias
UMLS CUI [1,1]
C1698986
UMLS CUI [1,2]
C0039476
UMLS CUI [1,3]
C0443252
UMLS CUI [1,4]
C0033085
Type of samples available (in addition of the strain)
Beschrijving

derivative_type

Datatype

text

Alias
UMLS CUI [1,1]
C2347029
UMLS CUI [1,2]
C0470187
If "Other" selected: Precision of derivative type
Beschrijving

derivative_type_specify

Datatype

text

Alias
UMLS CUI [1,1]
C2347029
UMLS CUI [1,2]
C0470187
UMLS CUI [1,3]
C0205394
Actual sample status
Beschrijving

E.g. "2" = defrosted twice

Datatype

text

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0449438
If "Known" selected, please specify:
Beschrijving

E.g. "2" = defrosted twice

Datatype

integer

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0449438
References
Beschrijving

References

Alias
UMLS CUI-1
C1514811
PubMed unique identifier for publications related to the microorganism - if any
Beschrijving

PMID

Datatype

integer

Alias
UMLS CUI [1,1]
C1138432
UMLS CUI [1,2]
C2349022
UMLS CUI [1,3]
C2585021
UMLS CUI [1,4]
C0445623
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Similar models

SBP Data Dictionary — Bacteria / Version 1.0

1 Formulieren
Name
Type
Description | Question | Decode (Coded Value)
Datatype
Alias
Item Group
General Information
C1508263 (UMLS CUI-1)
species_type
Item
Dataset applicable for bacterial microorganisms --> variable is per default "Bacteria"
text
C1705920 (UMLS CUI [1,1])
C0332307 (UMLS CUI [1,2])
species_name
Item
Species name according NCBI taxonomy
text
C1705920 (UMLS CUI [1,1])
C0027365 (UMLS CUI [1,2])
species_ID
Item
Taxonomy ID according NCBI taxonomy browser
text
C1705920 (UMLS CUI [1,1])
C0600091 (UMLS CUI [1,2])
strain_name
Item
Name of the microorganism given by the laboratory
text
C0445623 (UMLS CUI [1,1])
C0027365 (UMLS CUI [1,2])
C0022877 (UMLS CUI [1,3])
laboratory_ID
Item
Laboratory identifier ( e.g. BS, ZH)
text
C2986056 (UMLS CUI [1])
specimen_lab_ID
Item
Unique internal laboratory identifier for specimen (e.g. BS3545)
text
C0205102 (UMLS CUI [1,1])
C0022877 (UMLS CUI [1,2])
C1299222 (UMLS CUI [1,3])
specimen_external_ID
Item
Unique external identifier for specimen
text
C0439788 (UMLS CUI [1,1])
C1299222 (UMLS CUI [1,2])
biosafety_level
Item
Risk group of strain
text
C0035647 (UMLS CUI [1,1])
C2946261 (UMLS CUI [1,2])
C0445623 (UMLS CUI [1,3])
Item Group
History
C0019664 (UMLS CUI-1)
depositor_institution
Item
Institution/Laboratory name where microorganism is originated / was isolated.
text
C0022877 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0445623 (UMLS CUI [1,3])
depositor_name
Item
Forename and surname of person determined by the institution
text
C0022877 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0445623 (UMLS CUI [1,3])
C1522390 (UMLS CUI [1,4])
isolation_date
Item
Is the date of isolation known?
text
C0022877 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0445623 (UMLS CUI [1,3])
C2584899 (UMLS CUI [1,4])
isolation_date_specify
Item
If "Yes" selected, please specify:
date
C0022877 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0445623 (UMLS CUI [1,3])
C2584899 (UMLS CUI [1,4])
isolation_country
Item
Country of isolation
text
C0454664 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0445623 (UMLS CUI [1,3])
isolation_region
Item
ZIP code of isolation region
text
C1549687 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0445623 (UMLS CUI [1,3])
isolation_source
Item
Isolation source general
text
C0445623 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,3])
isolation_source_det
Item
Detailed isolation source as per laboratory nomenclature.
text
C0445623 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,3])
C1522508 (UMLS CUI [1,4])
isolation_source_det_specify
Item
If "Other" selected : Presicion of isolation source
text
C0445623 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,3])
C1522508 (UMLS CUI [1,4])
C0205394 (UMLS CUI [1,5])
isolation_source_info
Item
Important information on the source of the specimen - if any
text
C0445623 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,3])
C1533716 (UMLS CUI [1,4])
C3898777 (UMLS CUI [1,5])
host_species
Item
Host species (human, animals, other) according NCBI taxonomy browser
text
C0445623 (UMLS CUI [1,1])
C0205409 (UMLS CUI [1,2])
C2936412 (UMLS CUI [1,3])
Item
Age of host at sampling
text
C0001779 (UMLS CUI [1,1])
C1167395 (UMLS CUI [1,2])
C0870078 (UMLS CUI [1,3])
freeze_thaw_cycle
Code List
Age of host at sampling
CL Item
Known (Known)
CL Item
Unknown (UNK)
CL Item
No answer (NA)
host_age_at_collection_specify
Item
If "Known" selected, please specify
integer
C0001779 (UMLS CUI [1,1])
C1167395 (UMLS CUI [1,2])
C0870078 (UMLS CUI [1,3])
host_age_unit
Item
Unit for host age
text
C0001779 (UMLS CUI [1,1])
C1167395 (UMLS CUI [1,2])
C0870078 (UMLS CUI [1,3])
host_sex
Item
Sex of host
text
C0079399 (UMLS CUI [1,1])
C1167395 (UMLS CUI [1,2])
clinical_significance
Item
Precision if specimen was collected from an actual infected site or as part of a screening process (without evidence of infection)
text
C0200345 (UMLS CUI [1,1])
C3714514 (UMLS CUI [1,2])
C0332197 (UMLS CUI [1,3])
C0200345 (UMLS CUI [2,1])
C0439663 (UMLS CUI [2,2])
C1515974 (UMLS CUI [2,3])
disease
Item
If "clinical sign of infection" selected: Infectious disease caused to the host by the microorganism
text
C3714514 (UMLS CUI [1,1])
C1314792 (UMLS CUI [1,2])
C0205409 (UMLS CUI [1,3])
C0445623 (UMLS CUI [1,4])
disease_detailed
Item
Important information on the disease - if any
text
C1533716 (UMLS CUI [1,1])
C3898777 (UMLS CUI [1,2])
C0012634 (UMLS CUI [1,3])
consent
Item
If host is a human being and research is performed with coded health related data, the patient consent is required and research project requires EC approval
text
C0086418 (UMLS CUI [1,1])
C1167395 (UMLS CUI [1,2])
C0021430 (UMLS CUI [1,3])
animal_neuter_status
Item
If host is an animal (host_species (17)): Neuter status of animal
text
C0003062 (UMLS CUI [1,1])
C1167395 (UMLS CUI [1,2])
Item Group
Growth Conditions
C0018270 (UMLS CUI-1)
C0348080 (UMLS CUI-2)
culture_medium_rcmd
Item
Suggested culture medium/media to regrow strain: 409594004 Buffered charcoal yeast extract agar (substance)
boolean
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C1443930 (UMLS CUI [1,4])
culture_medium_rcmd
Item
Suggested culture medium/media to regrow strain: 409593005 |Chocolate agar (substance)
boolean
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C1443929 (UMLS CUI [1,4])
culture_medium_rcmd
Item
Suggested culture medium/media to regrow strain: 409551009 |Eosin-methylene blue agar (substance)
boolean
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C1443891 (UMLS CUI [1,4])
culture_medium_rcmd
Item
Suggested culture medium/media to regrow strain: 446049000 |Heart infusion agar (substance)
boolean
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C2960801 (UMLS CUI [1,4])
culture_medium_rcmd
Item
Suggested culture medium/media to regrow strain: 409550005 |MacConkey agar (substance)
boolean
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C1443890 (UMLS CUI [1,4])
culture_medium_rcmd
Item
Suggested culture medium/media to regrow strain: 409591007 |Sheep blood agar (substance)
boolean
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C1443927 (UMLS CUI [1,4])
culture_medium_rcmd
Item
Suggested culture medium/media to regrow strain: 409592000 |Thayer-Martin agar (substance)
boolean
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C1443928 (UMLS CUI [1,4])
culture_medium_rcmd
Item
Suggested culture medium/media to regrow strain: 446475008 |Trypticase soy agar (substance)
boolean
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C2960802 (UMLS CUI [1,4])
culture_medium_rcmd
Item
Suggested culture medium/media to regrow strain: 74964007 |Other (qualifier value)
boolean
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C0205394 (UMLS CUI [1,4])
culture_medium_rcmd_specify
Item
If "Other" selected: Presicion of culture medium
text
C0439536 (UMLS CUI [1,1])
C0596932 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C0205394 (UMLS CUI [1,4])
temp_conditions_rcmd
Item
Optimal growth temperature in [Cel]
float
C0596932 (UMLS CUI [1,1])
C2698651 (UMLS CUI [1,2])
C0018270 (UMLS CUI [1,3])
C0039476 (UMLS CUI [1,4])
oxygen_tolerance
Item
Growing environment of organism
text
C0018270 (UMLS CUI [1,1])
C0014406 (UMLS CUI [1,2])
C0029235 (UMLS CUI [1,3])
C0030054 (UMLS CUI [2,1])
C1704410 (UMLS CUI [2,2])
Item Group
Characteristics - Strain resistance of antimicrobials
C0860039 (UMLS CUI-1)
strain_resistance_antimicrobials
Item
Antibiotics resistance of species known
boolean
C0003232 (UMLS CUI [1,1])
C1522618 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387266001 |Amikacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0002499 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372687004 |Amoxicillin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0002645 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 708558004 |Amoxicillin and clavulanate (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0054066 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387170002 |Ampicillin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0002680 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387531004 |Azithromycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0052796 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387386004 |Aztreonam (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0004521 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387091007 |Cefradine (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007738 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372651006 |Cefadroxil (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007538 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 373485007 |Cefalotin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007735 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372801003 |Cefamandole (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007541 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 87303007 |Cefapirin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007737 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387470007 |Cefazolin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007546 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 108677001 |Cefdinir (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0060405 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 96048006 |Cefepime (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0055003 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387536009 |Cefixime (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0060400 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 58343005 |Cefonicid (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007551 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372743004 |Cefoperazone (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007552 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372704003 |Cefotaxime (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007554 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387534007 |Cefpodoxime (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0055011 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387538005 |Cefprozil (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0053882 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387091007 |Cefradine (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007738 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387200005 |Ceftazidime (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007559 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387535008 |Ceftibuten (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0055014 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372670001 |Ceftriaxone (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007561 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372833007 |Cefuroxime (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0007562 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387549004 |Cinoxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0008806 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372840008 |Ciprofloxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0008809 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387487009 |Clarithromycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0055856 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372786004 |Clindamycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0008947 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387412007 |Colistin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0009316 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 406439009 |Daptomycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0057144 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 96035007 |Dirithromycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0058445 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372478003 |Doxycycline (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0013090 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387550004 |Enoxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0014310 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 396346003 |Ertapenem (substance)
boolean
C4281815 (UMLS CUI [1,1])
C1120106 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372694001 |Erythromycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0014806 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 96085003 |Fleroxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0085161 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387544009 |Flucloxacillin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0016267 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372534005 |Fosfomycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0016610 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387530003 |Fusidic acid (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0016875 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 116349004 |Gatifloxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0753645 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387321007 |Gentamicin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C3854019 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 386892006 |Grepafloxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0287721 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 46558003 |Imipenem (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0020933 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 713477009 |Josamycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0022419 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387396008 |Kanamycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0022487 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387552007 |Levofloxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0282386 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387056004 |Linezolid (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0663241 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387553002 |Lomefloxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0065162 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 96061006 |Loracarbef (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0065295 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387540000 |Meropenem (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0066005 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372602008 |Metronidazole (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0025872 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372653009 |Minocycline (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0026187 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 412439003 |Moxifloxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0536495 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387261006 |Nalidixic acid (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0027353 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 373528008 |Neomycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0027353 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387110005 |Netilmicin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0027780 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 373543005 |Nitrofurantoin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0028156 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387271008 |Norfloxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0028365 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387551000 |Ofloxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0028902 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 323389000 |Benzylpenicillin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0030827 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 703743007 |Piperacillin and tazobactam (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0250480 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387159009 |Rifampicin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0035608 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 96037004 |Roxithromycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0035891 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387554008 |Sparfloxacin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0052585 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387223008 |Streptomycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0038425 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 387529008 |Teicoplanin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0145106 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372809001 |Tetracycline (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0039644 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 418313005 |Tigecycline (substance)
boolean
C4281815 (UMLS CUI [1,1])
C1260298 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 373548001 |Tobramycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0040341 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 703745000 |Sulfamethoxazole and trimethoprim (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0041044 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Antibiotics resistance of species against 372735009 |Vancomycin (substance)
boolean
C4281815 (UMLS CUI [1,1])
C0042313 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
Other antibiotics resistance of species
boolean
C4281815 (UMLS CUI [1,1])
C0042313 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
strain_resistance_antimicrobials
Item
If "Other" selected: Presicion of antimicrobial and ATC Code (if available)
boolean
C4281815 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
C0004611 (UMLS CUI [1,3])
Item Group
Characteristics
C1521970 (UMLS CUI-1)
strain_resistance_class
Item
Antibiotic class of above selected antibiotics (multiple classes possible)
text
C0456387 (UMLS CUI [1,1])
C0003232 (UMLS CUI [1,2])
strain_resistance_class
Item
If "Known" selected, please specify the antibiotic class - multiple selection possible:
text
C0456387 (UMLS CUI [1,1])
C0003232 (UMLS CUI [1,2])
strain_resistance_MIC
Item
MIC for each antibiotic selected above
text
C0427978 (UMLS CUI [1,1])
C0003232 (UMLS CUI [1,2])
strain_resistance_MIC
Item
If "Known" selected, please specify the MIC for each antibiotic selected above
float
C0003232 (UMLS CUI [1,1])
C0427978 (UMLS CUI [1,2])
strain_resistance_ZD
Item
Zone diameters for each antibiotic selected above
text
C0003232 (UMLS CUI [1,1])
C4687934 (UMLS CUI [1,2])
strain_resistance_ZD
Item
If "Known" selected, please specify the zone diameter
float
C0003232 (UMLS CUI [1,1])
C4687934 (UMLS CUI [1,2])
strain_resistance_SIR
Item
SIR interpretation for each antibiotic selected above
text
C0003232 (UMLS CUI [1,1])
C4687934 (UMLS CUI [1,2])
C0459471 (UMLS CUI [1,3])
used_resistance_guidelines
Item
Guideline and version used for interpretation for each antibiotic selected above
text
C0003232 (UMLS CUI [1,1])
C4687934 (UMLS CUI [1,2])
C0459471 (UMLS CUI [1,3])
C0162791 (UMLS CUI [1,4])
used_resistance_guidelines_specify
Item
If "EUCAST" selected, please specify:
float
C0003232 (UMLS CUI [1,1])
C4687934 (UMLS CUI [1,2])
C0459471 (UMLS CUI [1,3])
C0162791 (UMLS CUI [1,4])
used_resistance_guidelines_specify
Item
If CLSI selected, please specify:
datetime
C0003232 (UMLS CUI [1,1])
C4687934 (UMLS CUI [1,2])
C0459471 (UMLS CUI [1,3])
C0162791 (UMLS CUI [1,4])
used_resistance_guidelines_specify
Item
If "Other" selected: Precision which guideline and version
text
C0003232 (UMLS CUI [1,1])
C4687934 (UMLS CUI [1,2])
C0459471 (UMLS CUI [1,3])
C0162791 (UMLS CUI [1,4])
resistance_phenotype
Item
Antimicrobial resistance mechanism
text
C1456627 (UMLS CUI [1,1])
C0441712 (UMLS CUI [1,2])
resistance_phenotype
Item
Antimicrobial resistance mechanism: Inactivation of drug by enzymes
boolean
C1456627 (UMLS CUI [1,1])
C0441712 (UMLS CUI [1,2])
C0013227 (UMLS CUI [2,1])
C0544461 (UMLS CUI [2,2])
C0014442 (UMLS CUI [2,3])
resistance_phenotype
Item
Antimicrobial resistance mechanism: Alteration of membrane permeability
boolean
C1456627 (UMLS CUI [1,1])
C0441712 (UMLS CUI [1,2])
C0007605 (UMLS CUI [2,1])
C1515926 (UMLS CUI [2,2])
resistance_phenotype
Item
Antimicrobial resistance mechanism: Efflux pumps
boolean
C1456627 (UMLS CUI [1,1])
C0441712 (UMLS CUI [1,2])
C3824504 (UMLS CUI [1,3])
resistance_phenotype
Item
Antimicrobial resistance mechanism: Alteration of intracellular target site
boolean
C1456627 (UMLS CUI [1,1])
C0441712 (UMLS CUI [1,2])
C1515926 (UMLS CUI [2,1])
C0682581 (UMLS CUI [2,2])
C1521840 (UMLS CUI [2,3])
C0205145 (UMLS CUI [2,4])
resistance_phenotype
Item
Antimicrobial resistance mechanism: Alteration of intracellular target enzyme
boolean
C1456627 (UMLS CUI [1,1])
C0441712 (UMLS CUI [1,2])
C1515926 (UMLS CUI [2,1])
C0682581 (UMLS CUI [2,2])
C1521840 (UMLS CUI [2,3])
C0014442 (UMLS CUI [2,4])
resistance_phenotype
Item
Antimicrobial resistance mechanism: Overproduction of target enzyme
boolean
C1456627 (UMLS CUI [1,1])
C0441712 (UMLS CUI [1,2])
C3843660 (UMLS CUI [2,1])
C1521840 (UMLS CUI [2,2])
C0014442 (UMLS CUI [2,3])
resistance_phenotype
Item
Antimicrobial resistance mechanism: Auxotrophs that bypass blocked step
boolean
C1456627 (UMLS CUI [1,1])
C0441712 (UMLS CUI [1,2])
C3846158 (UMLS CUI [2])
resistance_phenotype
Item
Antimicrobial resistance mechanism: Absence of autolytic enzymes
boolean
C1456627 (UMLS CUI [1,1])
C0441712 (UMLS CUI [1,2])
C0004372 (UMLS CUI [2,1])
C0014442 (UMLS CUI [2,2])
C0332197 (UMLS CUI [2,3])
resistance_genotype
Item
Genotypes associated with resistance according to the Comprehensive Antibiotic Resistance Database (CARD)
text
C0017431 (UMLS CUI [1,1])
C0332281 (UMLS CUI [1,2])
C0949669 (UMLS CUI [1,3])
resistance_genotype_specify
Item
If "Known" selected, please specify:
text
C0017431 (UMLS CUI [1,1])
C0332281 (UMLS CUI [1,2])
C0949669 (UMLS CUI [1,3])
method_resistance
Item
Information on how resistance was tested
text
C3160797 (UMLS CUI [1])
validated_virulence_factors
Item
Known virulence factors according to the VFDB reference database nomenclature (""VF_Name"" (column A) from VFs description file)
text
C0521009 (UMLS CUI [1,1])
C1136170 (UMLS CUI [1,2])
validated_virulence_factors_specify
Item
If "Known" selected, please specify
text
C0521009 (UMLS CUI [1,1])
C1136170 (UMLS CUI [1,2])
serotyping_performed
Item
"Y" = Serotyping performed
text
C0201217 (UMLS CUI [1,1])
C1882330 (UMLS CUI [1,2])
serotyping_serogroup
Item
If "Y" above (serotyping_performed (40)): Presicion of serogroup (free text)
text
C0201217 (UMLS CUI [1])
Item Group
Genetic data
C0314603 (UMLS CUI-1)
C1511726 (UMLS CUI-2)
mutations
Item
Any particular important genetic mutation, confirmed with sequencing. List and description of the mutation and/or deletion
text
C3898777 (UMLS CUI [1,1])
C0026882 (UMLS CUI [1,2])
WGS_availability
Item
Whole genome sequence available
text
C4483680 (UMLS CUI [1])
genbank_accession_nb
Item
GenBank: NIH genetic sequence database, an annotated collection of all publicly available DNA sequences:
text
C0027468 (UMLS CUI [1,1])
C0950132 (UMLS CUI [1,2])
genbank_accession_nb
Item
If "Known" selected, please specify:
text
C0027468 (UMLS CUI [1,1])
C0950132 (UMLS CUI [1,2])
other_genotype_information
Item
Additional genotypic information - if any
text
C1524062 (UMLS CUI [1,1])
C0017431 (UMLS CUI [1,2])
C1533716 (UMLS CUI [1,3])
Item Group
Storage
C1698986 (UMLS CUI-1)
storage_format
Item
Storage type for long term preservation
text
C1698986 (UMLS CUI [1,1])
C0332307 (UMLS CUI [1,2])
C0443252 (UMLS CUI [1,3])
C0033085 (UMLS CUI [1,4])
storage_format_other
Item
If "Other" selected: Presicion of storage type for long term preservation
text
C1698986 (UMLS CUI [1,1])
C0332307 (UMLS CUI [1,2])
C0443252 (UMLS CUI [1,3])
C0033085 (UMLS CUI [1,4])
C0205394 (UMLS CUI [1,5])
storage_temperature
Item
Storage temperature for long term preservation
text
C1698986 (UMLS CUI [1,1])
C0039476 (UMLS CUI [1,2])
C0443252 (UMLS CUI [1,3])
C0033085 (UMLS CUI [1,4])
derivative_type
Item
Type of samples available (in addition of the strain)
text
C2347029 (UMLS CUI [1,1])
C0470187 (UMLS CUI [1,2])
derivative_type_specify
Item
If "Other" selected: Precision of derivative type
text
C2347029 (UMLS CUI [1,1])
C0470187 (UMLS CUI [1,2])
C0205394 (UMLS CUI [1,3])
freeze_thaw_cycle
Item
Actual sample status
text
C2347026 (UMLS CUI [1,1])
C0449438 (UMLS CUI [1,2])
freeze_thaw_cycle_specify
Item
If "Known" selected, please specify:
integer
C2347026 (UMLS CUI [1,1])
C0449438 (UMLS CUI [1,2])
Item Group
References
C1514811 (UMLS CUI-1)
PMID
Item
PubMed unique identifier for publications related to the microorganism - if any
integer
C1138432 (UMLS CUI [1,1])
C2349022 (UMLS CUI [1,2])
C2585021 (UMLS CUI [1,3])
C0445623 (UMLS CUI [1,4])
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