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Class: SpecimenInfo

Information on specimen info

URI: portable_microhaplotype_object:SpecimenInfo

classDiagram class SpecimenInfo click SpecimenInfo href "../SpecimenInfo" SpecimenInfo : alternate_identifiers SpecimenInfo : collection_country SpecimenInfo : collection_date SpecimenInfo : collector SpecimenInfo : geo_admin1 SpecimenInfo : geo_admin2 SpecimenInfo : geo_admin3 SpecimenInfo : host_taxon_id SpecimenInfo : individual_id SpecimenInfo : lat_lon SpecimenInfo : parasite_density SpecimenInfo : plate_col SpecimenInfo : plate_name SpecimenInfo : plate_row SpecimenInfo : project_name SpecimenInfo : samp_collect_device SpecimenInfo : samp_store_loc SpecimenInfo : samp_taxon_id SpecimenInfo : sample_comments SpecimenInfo : specimen_id

Slots

Name Cardinality and Range Description Inheritance
specimen_id 1
String		 the name of the specimen of a individual direct
plate_name 0..1
String		 a name of plate the specimen was in direct
plate_row 0..1
String		 the row the specimen was in direct
plate_col 0..1
Integer		 the column the specimen was in direct
samp_taxon_id 1
Integer		 the NCBI taxonomy number of the organism of interest direct
individual_id 0..1
String		 an identifier for the individual a specimen was collected from direct
host_taxon_id 0..1
Integer		 optional the NCBI taxonomy number of the host of the organism direct
alternate_identifiers *
String		 a list of optional alternative names for the samples direct
parasite_density 0..1
Integer		 the parasite density in microliters direct
collection_date 1
String		 the date of the sample collection direct
collection_country 1
String		 the name of country collected in, would be the same as admin level 0 direct
geo_admin1 0..1
String		 geographical admin level 1, the secondary large demarcation of a nation (nati... direct
geo_admin2 0..1
String		 geographical admin level 2, the third large demarcation of a nation (nation =... direct
geo_admin3 0..1
String		 geographical admin level 3, the third large demarcation of a nation (nation =... direct
lat_lon 0..1
String		 the latitude and longitude of the collection site of the specimen direct
collector 1
String		 the name of the primary person managing the specimen direct
samp_store_loc 1
String		 the sample store site, address or facility name direct
samp_collect_device 1
String		 the way the sample was collected, e direct
project_name 1
String		 a name of the project under which the sample is organized direct
sample_comments 0..1
String		 any additional comments about the sample direct

Usages

used by used in type used
PortableMicrohaplotypeObject specimen_infos range SpecimenInfo

Identifier and Mapping Information

Schema Source

  • from schema: https://plasmogenepi.github.io/portable-microhaplotype-object

Mappings

Mapping Type Mapped Value
self portable_microhaplotype_object:SpecimenInfo
native portable_microhaplotype_object:SpecimenInfo

LinkML Source

Direct

name: SpecimenInfo
description: Information on specimen info
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slots:
- specimen_id
- plate_name
- plate_row
- plate_col
slot_usage:
  specimen_id:
    name: specimen_id
    identifier: true
    domain_of:
    - ExperimentInfo
    - SpecimenInfo
attributes:
  samp_taxon_id:
    name: samp_taxon_id
    description: the NCBI taxonomy number of the organism of interest
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: integer
    required: true
    pattern: ^[0-9]$
  individual_id:
    name: individual_id
    description: an identifier for the individual a specimen was collected from
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$
  host_taxon_id:
    name: host_taxon_id
    description: optional the NCBI taxonomy number of the host of the organism
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: integer
    required: false
    pattern: ^[0-9]$
  alternate_identifiers:
    name: alternate_identifiers
    description: a list of optional alternative names for the samples
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
    pattern: ^[A-z-._0-9 ]$
  parasite_density:
    name: parasite_density
    description: the parasite density in microliters
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: integer
    required: false
    pattern: r'^[-+]?\d*\.?\d+(?:[eE][-+]?\d+)?$'
  collection_date:
    name: collection_date
    description: the date of the sample collection
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: r"\d{4}-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12][0-9]|3[01]))?"
  collection_country:
    name: collection_country
    description: the name of country collected in, would be the same as admin level
      0
    examples:
    - value: Senegal
    - value: USA
    - value: Japan
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  geo_admin1:
    name: geo_admin1
    description: geographical admin level 1, the secondary large demarcation of a
      nation (nation = admin level 0)
    examples:
    - value: State/Province
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$
  geo_admin2:
    name: geo_admin2
    description: geographical admin level 2, the third large demarcation of a nation
      (nation = admin level 0)
    examples:
    - value: city
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$
  geo_admin3:
    name: geo_admin3
    description: geographical admin level 3, the third large demarcation of a nation
      (nation = admin level 0)
    examples:
    - value: district of a city
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$
  lat_lon:
    name: lat_lon
    description: the latitude and longitude of the collection site of the specimen
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: r'^[-+]?\d{1,2}(?:\.\d+)?,[-+]?\d{1,3}(?:\.\d+)?$'
  collector:
    name: collector
    description: the name of the primary person managing the specimen
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  samp_store_loc:
    name: samp_store_loc
    description: the sample store site, address or facility name
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  samp_collect_device:
    name: samp_collect_device
    description: the way the sample was collected, e.g. whole blood, dried blood spot,
      etc
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  project_name:
    name: project_name
    description: a name of the project under which the sample is organized
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  sample_comments:
    name: sample_comments
    description: any additional comments about the sample
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$

Induced

name: SpecimenInfo
description: Information on specimen info
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slot_usage:
  specimen_id:
    name: specimen_id
    identifier: true
    domain_of:
    - ExperimentInfo
    - SpecimenInfo
attributes:
  samp_taxon_id:
    name: samp_taxon_id
    description: the NCBI taxonomy number of the organism of interest
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: samp_taxon_id
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: integer
    required: true
    pattern: ^[0-9]$
  individual_id:
    name: individual_id
    description: an identifier for the individual a specimen was collected from
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: individual_id
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$
  host_taxon_id:
    name: host_taxon_id
    description: optional the NCBI taxonomy number of the host of the organism
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: host_taxon_id
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: integer
    required: false
    pattern: ^[0-9]$
  alternate_identifiers:
    name: alternate_identifiers
    description: a list of optional alternative names for the samples
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: alternate_identifiers
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
    pattern: ^[A-z-._0-9 ]$
  parasite_density:
    name: parasite_density
    description: the parasite density in microliters
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: parasite_density
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: integer
    required: false
    pattern: r'^[-+]?\d*\.?\d+(?:[eE][-+]?\d+)?$'
  collection_date:
    name: collection_date
    description: the date of the sample collection
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: collection_date
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: r"\d{4}-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12][0-9]|3[01]))?"
  collection_country:
    name: collection_country
    description: the name of country collected in, would be the same as admin level
      0
    examples:
    - value: Senegal
    - value: USA
    - value: Japan
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: collection_country
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  geo_admin1:
    name: geo_admin1
    description: geographical admin level 1, the secondary large demarcation of a
      nation (nation = admin level 0)
    examples:
    - value: State/Province
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: geo_admin1
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$
  geo_admin2:
    name: geo_admin2
    description: geographical admin level 2, the third large demarcation of a nation
      (nation = admin level 0)
    examples:
    - value: city
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: geo_admin2
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$
  geo_admin3:
    name: geo_admin3
    description: geographical admin level 3, the third large demarcation of a nation
      (nation = admin level 0)
    examples:
    - value: district of a city
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: geo_admin3
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$
  lat_lon:
    name: lat_lon
    description: the latitude and longitude of the collection site of the specimen
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: lat_lon
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: r'^[-+]?\d{1,2}(?:\.\d+)?,[-+]?\d{1,3}(?:\.\d+)?$'
  collector:
    name: collector
    description: the name of the primary person managing the specimen
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: collector
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  samp_store_loc:
    name: samp_store_loc
    description: the sample store site, address or facility name
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: samp_store_loc
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  samp_collect_device:
    name: samp_collect_device
    description: the way the sample was collected, e.g. whole blood, dried blood spot,
      etc
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: samp_collect_device
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  project_name:
    name: project_name
    description: a name of the project under which the sample is organized
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: project_name
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$
  sample_comments:
    name: sample_comments
    description: any additional comments about the sample
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: sample_comments
    owner: SpecimenInfo
    domain_of:
    - SpecimenInfo
    range: string
    required: false
    pattern: ^[A-z-._0-9 ]$
  specimen_id:
    name: specimen_id
    description: the name of the specimen of a individual
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    identifier: true
    alias: specimen_id
    owner: SpecimenInfo
    domain_of:
    - ExperimentInfo
    - SpecimenInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9]$
  plate_name:
    name: plate_name
    description: a name of plate the specimen was in
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: plate_name
    owner: SpecimenInfo
    domain_of:
    - ExperimentInfo
    - SpecimenInfo
    range: string
    pattern: ^[A-z-._0-9 ]$
  plate_row:
    name: plate_row
    description: the row the specimen was in
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: plate_row
    owner: SpecimenInfo
    domain_of:
    - ExperimentInfo
    - SpecimenInfo
    range: string
    pattern: ^[A-z]$
  plate_col:
    name: plate_col
    description: the column the specimen was in
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: plate_col
    owner: SpecimenInfo
    domain_of:
    - ExperimentInfo
    - SpecimenInfo
    range: integer
    pattern: ^[0-9]$