Schema information

Table of Contents

  1. Schema quick view
  2. International schema information
  3. Selection lists
    1. English
      1. is_plant_pathogen entry codes
      2. isolation_protocol entry codes
      3. isolation_soil_province entry codes
      4. isolation_source entry codes
      5. risk_group entry codes
  4. Language-independent schema details
  5. Language-specific schema details
    1. English
  6. Schema SAIDs

Name: CCASM Strain Collection
Description: Metadata associated with the bacterial strains deposited in the Canadian Collection of Agricultural Soil Microbes (CCASM)
Classification: RDF106
Author: George Colin diCenzo
Author Email: george.dicenzo@queensu.ca
ICT Group: BENEFIT
Schema package SAID: EFgo32vmhNVHNwEPnmN-cm54cMWBz8Yx30iuBqEQC–J

Download schema

Schema quick view

Attribute Label Description
CCASM_ID CCASM identifier The unique CCASM identifier of the strain
Queens_box_ID Queen’s freezer box ID The barcode on the freezer box of the replicate stored at Queen's University
Queens_box_name Queen’s freezer box name The common name of the freezer box of the replicate stored at Queen's University
Queens_well Queen’s freezer box well position The position within the freezer box of the replicate stored at Queen's University
Queens_barcode Queen’s freezer vial barcode The barcode on the freezer vial of the replicate stored at Queen's University
Manitoba_box_ID Manitoba freezer box ID The barcode on the freezer box of the replicate stored at the University of Manitoba
Manitoba_box_name Manitoba freezer box name The common name of the freezer box of the replicate stored at the University of Manitoba
Manitoba_well Manitoba freezer box well position The position within the freezer box of the replicate stored at the University of Manitoba
Manitoba_barcode Manitoba freezer vial barcode The barcode on the freezer vial of the replicate stored at the University of Manitoba
strain_name Strain name(s) Other strain name(s) of the isolate
binomial_classification Binomial classification The binomial classification (genus and species, if classified) of the isolate
taxonomic_lineage Full taxonomic lineage The full taxonomic lineage of the isolate
risk_group Risk group The risk group (1, 2, 3, 4) of the isolate, if known
is_plant_pathogen Is the strain a plant pathogen An indication of whether the strain is a known plant pathogen
colony_morphology Colony morphology Description of the colony morphology of the isolate
host_plant_species Associated plant species The plant species from which the microbe was isolated, or that was planted in the soil from which the microbe was isolated
isolation_source Isolation source The source (soil or plant tissue type) that the microbe was isolated from
isolation_year Isolation year The year that the microbe was isolated
isolation_protocol Isolation protocol The method used for isolating the microbe
isolation_growth_medium Isolation growth medium The name of the growth medium that was used to isolate the microbe
isolation_growth_temperature Isolation growth temperature The incubation temperature used when isolating the microbe
isolation_growth_medium_composition Isolation growth medium composition The full composition of the growth medium used to isolate the microbe
isolation_soil_ph Isolation soil pH The pH of the soil from which the microbe was isolated, if known and if relevant
isolation_soil_organic_matter Isolation soil organic matter (%) The organic matter content of the soil from which the microbe was isolated, if known and if relevant
isolation_soil_texture Isolation soil texture The texture of the soil from which the microbe was isolated, if known and if relevant
isolation_soil_province Isolation soil province The province from which the soil (or plant material) was isolated
longitude Longitute The longitude at which the soil or plant material was sampled
latitude Latitude The latitude at which the soil or plant material was sampled
genome_ncbi_association Genome NCBI accession NCBI accession code(s) for the genome assembly of the microbe, if available
genome_size Genome size The genome size of the microbe, if known
notes Notes Additional notes about the microbe
citation Citation Citation of the study reporting the microbe, if available

International schema information

Language Name Description
English CCASM Strain Collection Metadata associated with the bacterial strains deposited in the Canadian Collection of Agricultural Soil Microbes (CCASM)

Selection lists

English

is_plant_pathogen entry codes

Entry code Label
Yes Yes
No No
Unknown Unknown

isolation_protocol entry codes

Entry code Label
Soil dilution Soil dilution plating
Tissue dilution Tissue crushing and dilution plating
Nodule trapping Nodule trapping experiment
Other Other method as indicated in notes

isolation_soil_province entry codes

Entry code Label
AB Alberta
BC British Columbia
MB Manitoba
NB New Brunswick
NL Newfoundland and Labrador
NS Nova Scotia
ON Ontario
PE Prince Edward Island
QC Quebec
SK Saskatchewan
NT Northwest Territories
NU Nunavut
YT Yukon

isolation_source entry codes

Entry code Label
Soil Soil sample
Nodule Nodule tissue
Root Root tissue
Leaf Leaf tissue
Stem Stem tissue
Seed Seed tissue
Other Other source as indicated in notes

risk_group entry codes

Entry code Label
1 Risk Group 1
2 Risk Group 2
3 Risk Group 3
4 Risk Group 4
Unknown Unknown

Language-independent schema details

Attribute Sensitive Unit Type Character encoding Required entry Format rule
CCASM_ID false   Text   true ^.{0,50}$
Queens_box_ID false   Text   true ^.{0,50}$
Queens_box_name false   Text   true ^.{0,50}$
Queens_well false   Text   true ^.{0,50}$
Queens_barcode false   Text   true ^.{0,50}$
Manitoba_box_ID false   Text   true ^.{0,50}$
Manitoba_box_name false   Text   true ^.{0,50}$
Manitoba_well false   Text   true ^.{0,50}$
Manitoba_barcode false   Text   true ^.{0,50}$
strain_name false   Text   true ^.{0,4000}$
binomial_classification false   Text   true ^.{0,250}$
taxonomic_lineage false   Text   true ^.{0,4000}$
risk_group false   Numeric   true ^-?[0-9]+$
is_plant_pathogen false   Text   true ^.{0,50}$
colony_morphology false   Text   false ^.{0,4000}$
host_plant_species false   Text   true ^.{0,250}$
isolation_source false   Text   true ^.{0,250}$
isolation_year false   DateTime   true ^(\d{4})$
isolation_protocol false   Text   true ^.{0,250}$
isolation_growth_medium false   Text   true ^.{0,50}$
isolation_growth_temperature false   Numeric   true ^[-+]?\d*\.?\d+$
isolation_growth_medium_composition false   Text   true ^.{0,4000}$
isolation_soil_ph false   Numeric   false ^[-+]?\d*\.?\d+$
isolation_soil_organic_matter false   Numeric   false ^[-+]?\d*\.?\d+$
isolation_soil_texture false   Text   false ^.{0,250}$
isolation_soil_province false   Text   false ^.{0,50}$
longitude true   Numeric   true ^[-+]?\d*\.?\d+$
latitude true   Numeric   true ^[-+]?\d*\.?\d+$
genome_ncbi_association false   Text   false ^.{0,800}$
genome_size false   Numeric   false ^-?[0-9]+$
notes true   Text   false ^.{0,4000}$
citation false   Text   false ^.{0,4000}$

Language-specific schema details

English

Attribute Label Description List
CCASM_ID CCASM identifier The unique CCASM identifier of the strain Not a list
Queens_box_ID Queen’s freezer box ID The barcode on the freezer box of the replicate stored at Queen's University Not a list
Queens_box_name Queen’s freezer box name The common name of the freezer box of the replicate stored at Queen's University Not a list
Queens_well Queen’s freezer box well position The position within the freezer box of the replicate stored at Queen's University Not a list
Queens_barcode Queen’s freezer vial barcode The barcode on the freezer vial of the replicate stored at Queen's University Not a list
Manitoba_box_ID Manitoba freezer box ID The barcode on the freezer box of the replicate stored at the University of Manitoba Not a list
Manitoba_box_name Manitoba freezer box name The common name of the freezer box of the replicate stored at the University of Manitoba Not a list
Manitoba_well Manitoba freezer box well position The position within the freezer box of the replicate stored at the University of Manitoba Not a list
Manitoba_barcode Manitoba freezer vial barcode The barcode on the freezer vial of the replicate stored at the University of Manitoba Not a list
strain_name Strain name(s) Other strain name(s) of the isolate Not a list
binomial_classification Binomial classification The binomial classification (genus and species, if classified) of the isolate Not a list
taxonomic_lineage Full taxonomic lineage The full taxonomic lineage of the isolate Not a list
risk_group Risk group The risk group (1, 2, 3, 4) of the isolate, if known Risk Group 1, Risk Group 2, Risk Group 3, Risk Group 4, Unknown
is_plant_pathogen Is the strain a plant pathogen An indication of whether the strain is a known plant pathogen Yes, No, Unknown
colony_morphology Colony morphology Description of the colony morphology of the isolate Not a list
host_plant_species Associated plant species The plant species from which the microbe was isolated, or that was planted in the soil from which the microbe was isolated Not a list
isolation_source Isolation source The source (soil or plant tissue type) that the microbe was isolated from Soil sample, Nodule tissue, Root tissue, Leaf tissue, Stem tissue, Seed tissue, Other source as indicated in notes
isolation_year Isolation year The year that the microbe was isolated Not a list
isolation_protocol Isolation protocol The method used for isolating the microbe Soil dilution plating, Tissue crushing and dilution plating, Nodule trapping experiment, Other method as indicated in notes
isolation_growth_medium Isolation growth medium The name of the growth medium that was used to isolate the microbe Not a list
isolation_growth_temperature Isolation growth temperature The incubation temperature used when isolating the microbe Not a list
isolation_growth_medium_composition Isolation growth medium composition The full composition of the growth medium used to isolate the microbe Not a list
isolation_soil_ph Isolation soil pH The pH of the soil from which the microbe was isolated, if known and if relevant Not a list
isolation_soil_organic_matter Isolation soil organic matter (%) The organic matter content of the soil from which the microbe was isolated, if known and if relevant Not a list
isolation_soil_texture Isolation soil texture The texture of the soil from which the microbe was isolated, if known and if relevant Not a list
isolation_soil_province Isolation soil province The province from which the soil (or plant material) was isolated Alberta, British Columbia, Manitoba, New Brunswick, Newfoundland and Labrador, Nova Scotia, Ontario, Prince Edward Island, Quebec, Saskatchewan, Northwest Territories, Nunavut, Yukon
longitude Longitute The longitude at which the soil or plant material was sampled Not a list
latitude Latitude The latitude at which the soil or plant material was sampled Not a list
genome_ncbi_association Genome NCBI accession NCBI accession code(s) for the genome assembly of the microbe, if available Not a list
genome_size Genome size The genome size of the microbe, if known Not a list
notes Notes Additional notes about the microbe Not a list
citation Citation Citation of the study reporting the microbe, if available Not a list

Schema SAIDs

Capture base: EMN_7K_d-L8N9I0TGBBCp0drL0UfGFacvmbDrKSs1QOP

Bundle: EOkhgGcMv_Y-mmnRZpHodr61YSa1Nd2IGsCNaWAglfor

Package: EFgo32vmhNVHNwEPnmN-cm54cMWBz8Yx30iuBqEQC–J

Layer SAID Type
conformance EKFSGHTqTOWnrxEwAQLY40vm3DD6gVFipl_L7KjOwK_w spec/overlays/conformance/1.1
entry (eng) EC2Gz8xhY9ZFW_Hg4iRTaOBj7SMDr8Q5SHly87E9ck6h spec/overlays/entry/1.1
entry_code EJ7k44YNb9K2M0T7ozjZ7mjmJVJUPIjyT30Kq92W3Ak5 spec/overlays/entry_code/1.1
format EEUmbMB3Wa5MTzpX2T8Xz2E-iAEBvcnJo0IIN2RfT5G9 spec/overlays/format/1.1
information (eng) ED5_5AEIcxHaKN0hth_8VoZpv9jIcMN6pLt6M-WSvI57 spec/overlays/information/1.1
label (eng) EJk9P5qrxQmz4vLFq0hheVPZbU_LQclG0xXtzIsfN6Zr spec/overlays/label/1.1
meta (eng) EDzQs8AVmGfofTIb6x3Qhnhw8JJAvJFgzeiacdKy8JPH spec/overlays/meta/1.1
ordering EDpJaB5M0XV8WLtXFmH205vEsV9pnVMuCWisZVasYZZ9 community/overlays/adc/ordering/1.1
unit_framing EN4kmBlvAvhJZ97I_8znC-siH9BMxei7luOtYnhQ-JRU community/overlays/adc/unit_framing/1.1
sensitive EPFYFAa0uEpniYkEdWMDcNEnTgat6dg-SGF-4qvCXXNL community/overlays/adc/sensitive/1.1

Date created: 2025-05-20 11:43:22