Genomic Epidemiology Ontology
type: Ontology
version IRI: genepio.owl
imports: bfo.owl
imports: chebi import.owl
imports: deprecation import.owl
imports: doid import.owl
imports: envo import.owl
imports: foodon import.owl
imports: gaz insdc mapping.owl
imports: gazetteer import.owl
imports: general import.owl
imports: hardcoded.owl
imports: model import.owl
imports: ncbitaxon import.owl
imports: obi import.owl
imports: ontology-metadata.owl
imports: ro import.owl
imports: specification enum import.owl
imports: specification field import.owl
imports: specification import.owl
imports: specification mint import.owl
imports: temporary mint import.owl
imports: uberon import.owl
date: 2023-08-19
description: The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata.
license: http://creativecommons.org/licenses/by/3.0/
default-namespace: GENEPIO

metadata section
type: AnnotationProperty

term as in existing standard
type: AnnotationProperty

term source
type: AnnotationProperty

user interface label
type: AnnotationProperty
IAO_0000115: The user interface label is the label that should be placed on a datum when presented on a form or report
IAO_0000117: Damion Dooley

user interface definition
type: AnnotationProperty

user interface help
type: AnnotationProperty
IAO_0000115: A user interface help annotation is a textual phrase to display with an entity on a form or report that provides some detail about what the entity is or how it is being used.
IAO_0000117: Damion Dooley
deprecated: true

user interface hidden
type: AnnotationProperty
IAO_0000117: Damion Dooley
IAO_0000231: IAO_0000103
deprecated: true

user interface feature
type: AnnotationProperty
IAO_0000115: A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report
IAO_0000117: Damion Dooley

obsolete: user interface value specification
type: AnnotationProperty
IAO_0000115: This annotation can be used to select the value specification that a referenced entity or specification component has for data entry. Can be scalar value specification / categorical tree specification etc.
IAO_0000117: Damion Dooley
deprecated: true

user interface regular epression normalize
user interface label: UI regex normalize
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

user interface regular expression validate
user interface label: UI regex validate
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

user interface regular expression display format
user interface label: UI regex format
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

label
type: AnnotationProperty

see also
type: AnnotationProperty

part of
type: ObjectProperty

BFO_0000051
type: ObjectProperty
comment: Damion comments: In GenEpiO, If an entity has more than one value specification (in a conjunction), then it means the entitiy is a complex entity that can have a value for each specification. Minimum data requirements can be spelled out using some, min 1, max 10 etc. restrictions.

realized in
type: ObjectProperty

obsolete has string specification of
type: ObjectProperty
deprecated: true

after
type: ObjectProperty
inverse of: RO_0002083
type: TransitiveProperty
IAO_0000114: IAO_0000428
IAO_0000115: T1 after t2 iff:= t2 before_or_simulataneous_with t1 and not (t1 simultaeous_with t2)
IAO_0000117: Damion Dooley
comment: Damion Dooley's note: Intention is to have it be the inverse of "before". This allows axioms like "B after A" to be placed in class B, rather than having to phrase them as "A before B" in class A. I believe time dependency relations (conditions) don't imply existence by themselves. If B after A, and B exists, this doesn't necessarily mean that A exists, only that if A does exist, it must be before B. To add that extra existence implication probably requires the "causally downstream of" and "immediately causally downstream of" RO relations, in a closed system where B cannot exist any other way.

obsolete: has string value specification
type: ObjectProperty
sub property of: OBI_0001938
range: string value specification
deprecated: true

obsolete: has categorical specification of
type: ObjectProperty
deprecated: true

obsolete: has categorical value specification
type: ObjectProperty
sub property of: OBI_0001938
range: OBI_0001930
deprecated: true

IAO_0000039
type: ObjectProperty
user interface label: has unit

is about
type: ObjectProperty
domain: IAO_0000030

OBI_0001927
user interface label: specifies

inheres in
type: ObjectProperty

has participant
type: ObjectProperty

location of
type: ObjectProperty

located in
type: ObjectProperty

aligned with
type: ObjectProperty

RO_0002083
type: ObjectProperty
IAO_0000115: T1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)

has component
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty

adjacent to
type: ObjectProperty
type: SymmetricProperty

has input
type: ObjectProperty
sub property of: has participant

has output
type: ObjectProperty
sub property of: has participant

member of
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty

has member
type: ObjectProperty

exactMatch
type: ObjectProperty
IAO_0000114: IAO_0000122
IAO_0000115: link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.
IAO_0000119: skos:exactMatch

local names
type: ObjectProperty
IAO_0000115: An object relation between a LinkML SlotDefinition to a LocalName.

abstract
type: DatatypeProperty
sub property of: topDataProperty
range: boolean
IAO_0000115: An abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated.

comments
type: DatatypeProperty
sub property of: topDataProperty
IAO_0000115: Notes and comments about an element intended for external consumption.

created on
type: DatatypeProperty
sub property of: topDataProperty
range: Datatype
  union of: date
  union of: dateTime
  union of: dateTimeStamp
IAO_0000115: Date/time at which the element was created.

data collection state
type: DatatypeProperty
sub property of: topDataProperty
IAO_0000112: Not Applicable; Missing; Not Collected; Not Provided; Restricted Access
IAO_0000115: A value (string or URI) indicating the data collection state an instance of a slot has.

description
type: DatatypeProperty
sub property of: topDataProperty
IAO_0000115: A description of the element's purpose and use

exact mappings
type: DatatypeProperty
sub property of: topDataProperty
IAO_0000115: A list of terms from different schemas or terminology systems that have identical meaning.

from schema
type: DatatypeProperty
range: anyURI
IAO_0000115: Id of the schema that defined the element.

imported from
type: DatatypeProperty
sub property of: topDataProperty
range: string
IAO_0000115: The imports entry that this element was derived from. Empty means primary source

local_name_source
type: DatatypeProperty
sub property of: topDataProperty
domain: LocalName
range: NCName
IAO_0000115: The ncname of the source of the name.
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2021-04-26T22:15:07Z

local name value
type: DatatypeProperty
sub property of: topDataProperty
domain: LocalName
range: string
IAO_0000115: A name assigned to an element in a given ontology.

maximum value
type: DatatypeProperty
sub property of: topDataProperty
range: int
IAO_0000115: For slots with ranges of type number, the value must be equal to or lowe than this

minimum value
type: DatatypeProperty
sub property of: topDataProperty
range: int
IAO_0000115: For slots with ranges of type number, the value must be equal to or higher than this

multivalued
type: DatatypeProperty
sub property of: topDataProperty
range: boolean
IAO_0000115: true means that slot can have more than one value

name
type: DatatypeProperty
sub property of: topDataProperty
range: string
IAO_0000115: The unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class.

pattern
type: DatatypeProperty
sub property of: topDataProperty
range: string
IAO_0000115: The string value of the slot must conform to this regular expression

permissible values
type: DatatypeProperty
sub property of: topDataProperty
IAO_0000115: A list of possible values for a slot range.

recommended
type: DatatypeProperty
sub property of: topDataProperty
range: boolean
IAO_0000115: true if this slot is not required, but is recommended.

required
type: DatatypeProperty
sub property of: topDataProperty
range: boolean
IAO_0000115: true means that the slot must be present in the loaded definition.

see also
type: DatatypeProperty
sub property of: topDataProperty
range: anyURI
IAO_0000115: A reference.

status
type: DatatypeProperty
sub property of: topDataProperty
range: anyURI
IAO_0000112: IAO:0000122 ('ready for release')
IAO_0000115: status of the element.

type uri
type: DatatypeProperty
sub property of: topDataProperty
IAO_0000115: The uri that defines the possible values for the type definition
comment: URI is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps)

value description
type: DatatypeProperty
sub property of: topDataProperty
domain: Example
range: string
IAO_0000115: Description of what the value is doing.

values from
type: DatatypeProperty
sub property of: topDataProperty
range: anyURI
IAO_0000115: The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot

sequence accession
type: Class
subclass of: sequence identifier
IAO_0000115: A persistent, unique identifier of a molecular sequence database entry.
IAO_0000117: Damion Dooley
IAO_0000412: EDAM

database field name
type: Class
subclass of: IAO_0000577
IAO_0000115: The name of a field in a database.

APOLLO SV 00000153
type: Class
subclass of: Restriction
  on property: is about
  some values from: earth area boundary census
subclass of: Restriction
  on property: is about
  some values from: OBI_0000181
subclass of: Restriction
  on property: has component
  qualified cardinality: 1
  on class: Class
    intersection of: unsigned integer value specification
    intersection of: Restriction
      on property: OBI_0001927
      some values from: STATO_0000047
subclass of: Restriction
  on property: has component
  qualified cardinality: 1
  on class: Class
    intersection of: date value specification (ISO 8601)
    intersection of: Restriction
      on property: OBI_0001927
      some values from: APOLLO SV 00000240
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

ARO_3004366
type: Class
has alternative id: CLSI
has exact synonym: NCCLS
has exact synonym: National Committee on Clinical Laboratory Standards (NCCLS)
comment: On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI

ARO_3004430
subclass of: awaiting ontology review
user interface feature: depth:1

ARO_3004440
subclass of: ARO_3004299
user interface feature: order: ARO:3004303 # nonsensitive ARO:3004300 # intermediate ARO:3004302 # sensitive ARO:3004304 # sensitive - dose dependant ARO:3004301 # resistant

BFO_0000029
comment: Note that this can refer to a material entity like an organ or muscle, or an immaterial entity (a site or fiat boundary) like skin, stomach cavity or lung surface.

CHEBI_135278
subclass of: second line or reserve tuberculosis drug
IAO_0000118: Trd

deoxyribonucleic acid
type: Class
subclass of: CHEBI_33696

CHEBI_17076
subclass of: second line or reserve tuberculosis drug
subclass of: first line tuberculosis drug
IAO_0000118: STR
IAO_0000118: Sm
IAO_0000118: Stm

obsolete: antibiotic
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/CHEBI_33281
deprecated: true

CHEBI 2637
subclass of: second line or reserve tuberculosis drug
IAO_0000118: Am
IAO_0000118: Amk

CHEBI 2676
subclass of: second line or reserve tuberculosis drug
IAO_0000118: Amx

CHEBI_27565
subclass of: second line or reserve tuberculosis drug
IAO_0000118: PAS

CHEBI_28077
subclass of: first line tuberculosis drug
IAO_0000118: Rif

CHEBI_32066
subclass of: second line or reserve tuberculosis drug
IAO_0000118: Pto

CHEBI 3371
subclass of: second line or reserve tuberculosis drug
IAO_0000118: CAP
IAO_0000118: Cm

CHEBI 3732
subclass of: second line or reserve tuberculosis drug
IAO_0000118: Clr

CHEBI 3749
subclass of: second line or reserve tuberculosis drug
IAO_0000118: Cfz

CHEBI_40009
subclass of: second line or reserve tuberculosis drug
IAO_0000118: CYC
IAO_0000118: Cs

CHEBI_45285
subclass of: first line tuberculosis drug
user interface label: pyrazinamide
IAO_0000118: Pza

CHEBI 4877
subclass of: first line tuberculosis drug
IAO_0000118: E
IAO_0000118: ETB
IAO_0000118: Emb

CHEBI 4885
type: Class
subclass of: second line or reserve tuberculosis drug
subclass of: antimicrobial resistance test drug
IAO_0000118: ETH
IAO_0000118: Eto

CHEBI_59132
IAO_0000116: Currently "K antigen" is a CHEBI_73772 chemical entity rather than a role.
see also: K antigen

CHEBI 6030
subclass of: first line tuberculosis drug
IAO_0000118: Inh
IAO_0000118: isoniazid

CHEBI 6104
subclass of: second line or reserve tuberculosis drug
IAO_0000118: Kan

CHEBI_63598
subclass of: second line or reserve tuberculosis drug
IAO_0000118: Lfx

CHEBI_63607
type: Class
subclass of: second line or reserve tuberculosis drug
subclass of: antimicrobial resistance test drug
IAO_0000118: Lzd

CHEBI_63611
type: Class
subclass of: second line or reserve tuberculosis drug
subclass of: antimicrobial resistance test drug
IAO_0000118: MXF
IAO_0000118: Mfx

Axiom
annotated source: CHEBI_63611
annotated property: IAO_0000118
annotated target: Mfx
term source: https://www.ncbi.nlm.nih.gov/books/NBK247415/bin/part3-m17.pdf

CHEBI_72292
subclass of: second line or reserve tuberculosis drug
IAO_0000118: Bdq

CHEBI_73772
subclass of: Restriction
  on property: RO_0000087
  some values from: CHEBI_59132
IAO_0000116: Damion Dooley's note: 'K antigen' can't be a subclass of antigen as chemical entity is disjoint from role.
has db xref: Snomed: Concept 260824002

CHEBI 7731
type: Class
subclass of: second line or reserve tuberculosis drug
subclass of: antimicrobial resistance test drug
IAO_0000118: Ofx

CHMO_0002743
type: Class
user interface label: specimen extraction matrix
comment: "This observable is important where process of capturing sample can affect dna extraction."

ENVO_00000005
type: Class
subclass of: SIO_000415
subclass of: Restriction
  on property: located in
  some values from: NCIT C25464
user interface label: state / province / territory / region
user interface feature: lookup:http://purl.obolibrary.org/obo/GAZ_00000448

common vehicle transmission
type: Class
subclass of: indirect transmission
IAO_0000115: Transmission of a disease agent (infectious pathogen, toxic chemical, etc.) from a source that is common to those who acquire the disease. Common vehicles include air, water, food, injected substances. Legionellosis is an example of common vehicle spread in air that has passed through air conditioning equipment contaminated by the causal organism. HIV disease and hepatitis B and C can be spread among illicit drug users by the common vehicle of contaminated needles and syringes. Cholera and many other waterborne diseases are spread by the common vehicle of contaminated water.

experimental subject role
type: Class
subclass of: person role
IAO_0000115: A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken)

ExO_0000038
type: Class
subclass of: organism datum
subclass of: Restriction
user interface feature: depth:1
IAO_0000114: IAO_0000428
IAO_0000119: https://en.wikipedia.org/wiki/Medical_state
has exact synonym: condition
has exact synonym: medical condition
has exact synonym: medical state
comment: Damion Dooley note: GenEpiO includes various health status descriptors here; many are annotated as included in the American AHA HIPPA or United Kingdom NHS terminologies. The challenge is to map them or order them in such a way that merged data can be analyzed.

Condition
type: Axiom
annotated source: ExO_0000038
annotated property: subClassOf
annotated target: Restriction

Condition
type: Axiom
annotated source: ExO_0000038
annotated property: subClassOf
annotated target: Restriction

inhalation
type: Class
subclass of: common vehicle transmission
IAO_0000115: The process of drawing in by breathing.

FIX_0000278
type: Class
subclass of: environmental datum
IAO_0000115: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
IAO_0000119: MIxS

symptom onset date
type: Class
subclass of: symptom history item
IAO_0000114: IAO_0000428
IAO_0000115: A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness
IAO_0000117: Damion Dooley

foodon product type
type: Class
subclass of: FOODON_03400361
IAO_0000114: IAO_0000428
IAO_0000115: A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure.
IAO_0000117: Damion Dooley
IAO_0000412: foodon.owl

FOODON_00002381
type: Class
user interface feature: lookup

FOODON_03311737
type: Class
user interface feature: lookup

FOODON_03420116
type: Class
user interface feature: lookup

FOODON_03480020
type: Class
user interface label: food packing medium

GAZ_00000590
subclass of: NCIT C25464
user interface label: [Oceans and Seas]

GAZ_00003092
type: Class
subclass of: subnational region
IAO_0000114: IAO_0000122
IAO_0000115: Census Regions and Divisions are groupings of States that subdivide the United States.
IAO_0000117: Damion Dooley
IAO_0000119: United States Census Bureau

GAZ_00003093
type: Class
subclass of: GAZ_00003092
IAO_0000115: A census region in the United States of America
IAO_0000117: Damion Dooley

GAZ_00003094
type: Class
subclass of: GAZ_00003092
IAO_0000115: A census region in the United States of America
IAO_0000117: Damion Dooley

GAZ_00003095
type: Class
subclass of: GAZ_00003092
IAO_0000115: A census region in the United States of America
IAO_0000117: Damion Dooley

GAZ_00003096
type: Class
subclass of: GAZ_00003092
IAO_0000115: A census region in the United States of America
IAO_0000117: Damion Dooley

GAZ_00010090
type: Class
subclass of: NCIT C80234
user interface label: directly governed city (North Korea)

GSCID-BRC Project and Sample Application Standard
type: Class
subclass of: National Institute of Allergy and Infectious Disease standard
user interface label: GSCID-BRC standard
IAO_0000114: IAO_0000428
IAO_0000115: The GSCID-BRC Project and Sample Application Standard captures standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases.
IAO_0000116: The NIAID page for specifications has a broken link for Core Project. This is the existing page: https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project Link page is: https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards
IAO_0000117: Damion Dooley
IAO_0000600: This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists.

Minimum Information about any (x) Sequence (MIxS)
type: Class
subclass of: Genomic Standards Consortium (GSC) standard
user interface label: MIxS standard
IAO_0000114: IAO_0000122
IAO_0000115: MixS is a unified standard for describing sequence data provided by the Genomic Standards Consortium (GSC)
IAO_0000117: Damion Dooley

Minimum information about a marker gene sequence
type: Class
subclass of: Genomic Standards Consortium (GSC) standard
user interface label: MIMARKS standard
IAO_0000115: The "minimum information about a marker gene sequence" (MIMARKS) is a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences.
IAO_0000119: http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html

other (metadata value)
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000428
IAO_0000115: "other (metadata choice)" indicates that for the given categorical variable, a respondent has chosen an other or additional response not listed.
IAO_0000116: This class cannot be referred to directly as a subclass of more than one class without involving inference from the respective classes. Instances of it may exist as a kind of metadata. Usually a reference to a parent categorical class, but not a subordinate, carries the same information.
IAO_0000117: Damion Dooley

other relevance
type: Class
subclass of: project relevance

other specimen scope
type: Class
subclass of: OBI_0001884
user interface label: other
IAO_0000114: IAO_0000122
IAO_0000115: Other: specify the sample scope that was used.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

other material derived from specimen
type: Class
subclass of: OBI_0001882
user interface label: other material
IAO_0000114: IAO_0000122
IAO_0000115: Other: specify the material that was used.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

other capture type
type: Class
subclass of: OBI_0001899
IAO_0000114: IAO_0000122
IAO_0000115: "other capture type" is a free text description provided to indicate a target capture specification not covered by the other types.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

other project method
type: Class
subclass of: OBI_0001896
IAO_0000114: IAO_0000122
IAO_0000115: Specify the project method
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

obsolete: draft GenEpiO BioSample standard
type: Class
IAO_0000115: This is an organizational category for grouping parameters relevant to a biomedical sample.
IAO_0000117: Damion Dooley
IAO_0100001: draft sequence repository contextual data standard
deprecated: true

obsolete: NCBI antibiogram data item
type: Class
IAO_0000115: An NCBI antibiogram data item is an antimicrobial susceptibility and resistance datum related to drug resistant pathogens. This information is provided within an antibiogram table on BioSample records.
IAO_0000117: Damion Dooley
IAO_0000231: IAO_0000227
IAO_0100001: NCBI Antibiogram standard
deprecated: true

American HIPPA Protected Health Information (PHI) guidelines
type: Class
subclass of: public health data standard
user interface label: HIPPA PHI guideline
IAO_0000115: The American HIPPA Protected Health Information (PHI) guidelines cover information, including demographic information, which relates to: - the individual’s past, present, or future physical or mental health or condition, - the provision of health care to the individual, or - the past, present, or future payment for the provision of health care to the individual, and that identifies the individual or for which there is a reasonable basis to believe can be used to identify the individual. Protected health information includes many common identifiers (e.g., name, address, birth date, Social Security Number) when they can be associated with the health information listed above."
IAO_0000119: https://en.wikipedia.org/wiki/Health_Insurance_Portability_and_Accountability_Act

obsolete: subject species
type: Class
IAO_0000115: The natural (as opposed to laboratory) full scientific taxonomic name of a subject related to a given investigation, study and/or specimen.
IAO_0000117: Damion Dooley
IAO_0000231: IAO_0000227
IAO_0100001: subject organism (host) taxonomic species
deprecated: true

obsolete: intersex
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C45908
has db xref: NCBI BioSample: intersex
deprecated: true

obsolete: isolation date
type: Class
term as in existing standard: Isolation date
term source: inferred from BCCDC interviews
IAO_0000115: date the strain was isolated
IAO_0000117: Damion Dooley
IAO_0100001: culture isolation date
deprecated: true

culture isolation date
type: Class
subclass of: isolate history item
metadata section: Collection
term as in existing standard: Culture isolation date
term source: suggested in metadata feedback
IAO_0000112: year/month/day
IAO_0000115: A culture isolation date is a date-time entity marking the end of a process in which a sample is isolated as a single colony or non-mixture culture
IAO_0000117: Damion Dooley
IAO_0000119: GROUP: IRIDA Ontology (Morag)
in subset: GENEPIO

culture frozen date
type: Class
subclass of: isolate history item
metadata section: Collection
term as in existing standard: Frozen date
term source: NML Labware LIMS
IAO_0000112: year/month/day
IAO_0000115: A culture frozen date is a date-time entity marking the beginning of a process in which a sample culture is frozen for preservation.
IAO_0000117: Damion Dooley
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

isolate received date
type: Class
subclass of: isolate history item
metadata section: Collection
term as in existing standard: Received date
term source: NML Labware LIMS
IAO_0000112: year/month/day
IAO_0000115: date lab received isolate
IAO_0000119: NML LIMS
in subset: GENEPIO

isolate upload date
type: Class
subclass of: isolate history item
metadata section: Collection
term as in existing standard: Upload date
term source: NML Labware LIMS
IAO_0000112: month/day/year
IAO_0000115: date the isolate was entered into the database
IAO_0000119: NML LIMS
has db xref: PulseNet: UploadDate
in subset: GENEPIO

subject anatomical site
type: Class
subclass of: CHMO_0000993
subclass of: Restriction
  on property: part of
  some values from: subject organism
metadata section: Pathogen Isolate
term source: inferred from BCCDC interviews
IAO_0000112: gut, spine, tongue, lung
IAO_0000115: Name of body site where the specimen was obtained from, such as a specific organ or tissue.
IAO_0000116: Damion Dooley's note: Although term mentions "site" in label, this cannot be placed under "site" as it is intended to refer to organism material, and leads to unsatisfiable terms otherwise.
IAO_0000119: GROUP: MIxS
in subset: GENEPIO

subject health status at time of specimen collection
type: Class
subclass of: personal health datum
user interface feature: depth:1
user interface feature: order: NCIT:C115935 # healthy NCIT:C25610 # pathologic NCIT:C28554 # deceased
IAO_0000112: diseased
IAO_0000114: IAO_0000428
IAO_0000115: Health or disease status of a given subject at time of specimen collection.
IAO_0000116: Currently this does not differ from the 'subject health status (GSCID-BRC)' item. It may be revised to have more options in the future.
IAO_0000117: Damion Dooley

specimen source context
type: Class
subclass of: specimen datum
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: specimen source substance specification
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: Class
    intersection of: OBI_0001930
    intersection of: Restriction
      on property: OBI_0001927
      some values from: outbreak exposure event location
metadata section: Environmental Isolate
IAO_0000112: sediment, chicken feces, cheese
IAO_0000114: IAO_0000428
IAO_0000115: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.
IAO_0000117: Damion Dooley
IAO_0000119: NCBI Biosample

subject body product
type: Class
subclass of: CHMO_0000993
subclass of: Restriction
  on property: RO_0003001
  some values from: subject organism
metadata section: Pathogen Isolate
IAO_0000112: feces, cerebral spinal fluid (CSF)
IAO_0000114: IAO_0000428
IAO_0000115: Substance produced by the body, e.g. stool, mucus, where the specimen was obtained from.
IAO_0000117: Damion Dooley

collection depth datum
type: Class
subclass of: environmental datum
metadata section: Environmental Isolate
term as in existing standard: Geographic location depth
term source: GROUP: MIxS
IAO_0000112: value (5m)
IAO_0000115: Please refer to the definitions of depth in the environmental packages
IAO_0000119: GROUP: MIxS
in subset: GENEPIO

obsolete: specimen source environmental material
type: Class
IAO_0000115: The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_00010483
deprecated: true

subject sex specification
type: Class
subclass of: OBI_0001930
subclass of: Restriction
  on property: OBI_0001927
  some values from: PATO_0001894
IAO_0000114: IAO_0000428
IAO_0000115: A subject sex is the phenotypic sex of given subject (human or animal) related to a given investigation, study, and/or specimen.
IAO_0000117: Damion Dooley
comment: Gender is not used because it is a term referencing human social and cultural convention.

specimen collection site land use
type: Class
subclass of: environmental datum
metadata section: Environmental Isolate
term as in existing standard: Land use where sample was taken
term source: Environment Canada Metadata
IAO_0000112: descriptive; type of human use (park, farm, urban)
IAO_0000115: Human use of land involving the management and modification of natural environment or wilderness into built environment.
IAO_0000119: URI: http://en.wikipedia.org/wiki/Land_use
in subset: GENEPIO

fecal indicator bacteria count
type: Class
subclass of: STATO_0000047
subclass of: Restriction
  on property: IAO_0000039
  some values from: Class
    union of: UO_0000210
    union of: UO_0000212
subclass of: Restriction
  on property: is about
  some values from: fecal indicator
metadata section: Environmental Isolate
term as in existing standard: Fecal Indicator Bacteria Number
term source: Environment Canada Metadata
IAO_0000112: 12,456 cfu
IAO_0000115: Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens.
IAO_0000119: URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf
in subset: GENEPIO

conductivity measurement datum
type: Class
subclass of: environmental datum
metadata section: Environmental Isolate
term as in existing standard: Conductivity
term source: GROUP: MIxS
IAO_0000112: milliSiemens per centimeter
IAO_0000115: electrical conductivity of water
IAO_0000119: GROUP: MIxS enviro package
in subset: GENEPIO

dissolved oxygen concentration
type: Class
subclass of: environmental datum
metadata section: Environmental Isolate
term as in existing standard: Dissolved oxygen
term source: GROUP: MIxS
IAO_0000112: micromole per kilogram
IAO_0000115: concentration of dissolved oxygen
IAO_0000119: GROUP: MIxS enviro package
in subset: GENEPIO

the Global Microbial Identifier Minimum Data for Matching (MDM) Standard
type: Class
subclass of: NCIT C103180
user interface label: GMI MDM standard
IAO_0000114: IAO_0000428
IAO_0000115: The Global Microbial Identifier "Minimum data for Matching" (MDM) standard is a standard that defines essential contextual data fields to be included in genomic sequence repository records.
IAO_0000117: Damion Dooley

soluble inorganic material
type: Class
subclass of: test specification
metadata section: Environmental Isolate
term as in existing standard: Soluble inorganic material
term source: GROUP: MIxS
IAO_0000112: soluble organic material name;measurement value
IAO_0000115: concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
IAO_0000119: GROUP: MIxS enviro package
in subset: GENEPIO

soluble inorganic material concentration
type: Class
subclass of: environmental datum
metadata section: Environmental Isolate
term as in existing standard: Soluble inorganic material
term source: GROUP: MIxS
in subset: GENEPIO

nitrite concentration
type: Class
subclass of: environmental datum
metadata section: Environmental Isolate
term as in existing standard: Nitrite
term source: GROUP: MIxS
IAO_0000112: micromole per liter
IAO_0000115: concentration of nitrite
IAO_0000119: GROUP: MIxS enviro package
in subset: GENEPIO

nitrate concentration
type: Class
subclass of: environmental datum
metadata section: Environmental Isolate
term as in existing standard: Nitrate
term source: GROUP: MIxS
IAO_0000112: micromole per liter
IAO_0000115: concentration of nitrate
IAO_0000119: GROUP: MIxS enviro package
in subset: GENEPIO

total phosphorous concentration
type: Class
subclass of: environmental datum
metadata section: Environmental Isolate
term as in existing standard: Total phosphorous
term source: GROUP: MIxS
IAO_0000112: micromole per liter
IAO_0000115: total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus
IAO_0000119: GROUP: MIxS enviro package
in subset: GENEPIO

stream order categorical measurement datum
type: Class
subclass of: environmental datum
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: unsignedInt
    with restrictions:
      max inclusive: 12
metadata section: Environmental Isolate
term as in existing standard: Stream order
term source: Environment Canada Metadata
IAO_0000112: value, 1-12
IAO_0000115: Stream order is a measure of the relative size of streams (The smallest tributaries are referred to as first-order streams, while the largest river in the world, the Amazon, is a twelfth-order waterway).
IAO_0000119: GROUP: Environment Canada Metadata
in subset: GENEPIO

bacteria density
type: Class
subclass of: environmental datum
metadata section: Environmental Isolate
term as in existing standard: Density of bacteria in sample
term source: Environment Canada Metadata
IAO_0000112: OD reading or cfu's or cells per millilitre
IAO_0000115: number of bacteria in sample
IAO_0000119: GROUP: Environment Canada Metadata
in subset: GENEPIO

primary enzyme (LMAAI)
type: Class
subclass of: lab test datum
metadata section: Lab Analytic
term as in existing standard: Host Primary Enzyme
term source: PulseNet Data Capture
IAO_0000112: pick list (XbaI, BlnI)
IAO_0000115: Restriction enzyme for first characterization
IAO_0000119: GROUP: IRIDA Ontology (Emma)

PFGE test specification
type: Class
subclass of: test specification
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: PFGE primary test
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: PFGE secondary test
IAO_0000114: IAO_0000428
in subset: GENEPIO

PFGE primary test
type: Class
subclass of: PFGE test specification
metadata section: Lab Analytic
term as in existing standard: Host Primary PFGE Pattern
term source: NML LIMS
IAO_0000114: IAO_0000428
IAO_0000115: First PFGE pattern from given diagnostic restriction enzyme
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

secondary enzyme (LMACI)
type: Class
subclass of: lab test datum
metadata section: Lab Analytic
term as in existing standard: Host Secondary Enzyme
term source: PulseNet Data Capture
IAO_0000112: pick list (XbaI, BlnI)
IAO_0000115: Restriction enzyme for second characterization
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

PFGE secondary test
type: Class
subclass of: PFGE test specification
metadata section: Lab Analytic
term as in existing standard: Host Secondary PFGE Pattern
term source: NML LIMS
IAO_0000114: IAO_0000428
IAO_0000115: Second PFGE pattern from given diagnostic restriction enzyme
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

MLST clonal complex
type: Class
subclass of: test specification
metadata section: Lab Analytic
term as in existing standard: MLST Clonal Complex
term source: inferred from BCCDC interviews and Bionumerics
IAO_0000112: pick list?
IAO_0000115: Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). As such, clonal complexes represent sequence types that share a number of identical alleles e.g. 5/7
IAO_0000119: URI: http://en.wikipedia.org/wiki/Multilocus_sequence_typing ; http://eburst.mlst.net/3.asp
in subset: GENEPIO

MLST sequence typing
type: Class
subclass of: diagnostic test
metadata section: Lab Analytic
term as in existing standard: MLST Sequence Type
term source: inferred from BCCDC interviews and Bionumerics
IAO_0000112: pick list?
IAO_0000115: Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST).
IAO_0000119: Multilocus sequence typing
in subset: GENEPIO

core genome fingerprinting assay
type: Class
subclass of: OBI_0000070
IAO_0000114: IAO_0000428
IAO_0000115: The process of fingerprinting the core genome of a bacteria.
IAO_0000116: Add under upcomming OBI "DNA fingerprinting assay".
IAO_0000117: Damion Dooley
IAO_0000600: Some bacteria like E coli have a highly variable genome, and so to type them methods must focus on typing the core genome that is common to all strains.
in subset: GENEPIO

CGF type
type: Class
subclass of: test specification
metadata section: Lab Analytic
term as in existing standard: CGF type
term source: inferred from BCCDC interviews
IAO_0000112: pick list
IAO_0000114: IAO_0000428
IAO_0000115: output of CGF
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

16S rRNA sequencing
type: Class
subclass of: OBI_0001177
metadata section: Lab Analytic
term as in existing standard: 16S rRNA sequencing
term source: inferred from BCCDC interviews
IAO_0000115: 16S ribosomal RNA sequencing is a sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.
IAO_0000119: URI: http://www.illumina.com/applications/microbiology/microbial-sequencing-methods/16S-rrna-sequencing.html
in subset: GENEPIO

Stx toxin type datum
type: Class
subclass of: IAO_0000109
subclass of: Restriction
  on property: is about
  some values from: NCIT C1225
metadata section: Lab Analytic
term as in existing standard: Stx toxin type
term source: metadata feedback
IAO_0000112: Stx1 or Stx2
IAO_0000115: pathogenic shiga toxin produced by STEC E. coli
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

Stx toxin subtype datum
type: Class
subclass of: IAO_0000109
subclass of: Restriction
  on property: is about
  some values from: NCIT C1225
metadata section: Lab Analytic
term as in existing standard: Stx toxin subtype
term source: metadata feedback
IAO_0000112: stx1a, stx1c
IAO_0000115: shiga toxin variant
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

Stx1 Toxin PCR result
type: Class
subclass of: IAO_0000109
subclass of: Restriction
  on property: is about
  some values from: Shiga toxin 1
metadata section: Lab Analytic
term as in existing standard: Stx1 Toxin PCR result
term source: NML Labware LIMS
IAO_0000112: CT value?
IAO_0000115: qPCR result of Stx1 gene amplification
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

Stx1 cell culture level
type: Class
subclass of: IAO_0000109
subclass of: Restriction
  on property: is about
  some values from: Shiga toxin 1
metadata section: Lab Analytic
term as in existing standard: Stx1 Cell Culture
term source: NML Labware LIMS
IAO_0000115: level of Stx1 toxin derived tissue culture toxicity
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

Stx2 Toxin PCR result
type: Class
subclass of: IAO_0000109
subclass of: Restriction
  on property: is about
  some values from: Shiga toxin 2
metadata section: Lab Analytic
term as in existing standard: Stx2 Toxin PCR result
term source: NML Labware LIMS
IAO_0000112: CT value?
IAO_0000115: qPCR result of Stx2 gene amplification
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

Stx2 cell culture level
type: Class
subclass of: IAO_0000109
subclass of: Restriction
  on property: is about
  some values from: Shiga toxin 2
metadata section: Lab Analytic
term as in existing standard: Stx2 Cell Culture
term source: NML Labware LIMS
IAO_0000112: value?
IAO_0000115: level of Stx2 toxin derived tissue culture toxicity
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

AccuProbe culture identification assay
type: Class
subclass of: OBI_0000070
subclass of: Restriction
  on property: has output
  some values from: AccuProbe test result
IAO_0000114: IAO_0000122
IAO_0000115: An AccuProbe assay that uses a luminometer and DNA probe designed to identify a specific bacteria or fungus species within a culture.
IAO_0000117: Damion Dooley
IAO_0000600: Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (6). The ACCUPROBE method uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal RNA of the target organism. After the ribosomal RNA is released from the target organism, the labeled DNA probe combines with the target organism’s ribosomal RNA to form a stable DNA:RNA hybrid. The Selection Reagent allows for the differentiation of non-hybridized and hybridized probes.The light signal emitted by the DNA:RNA hybrids is measured by a GEN-PROBE luminometer. A positive result is a luminometer reading equal to or greater than the cut-off. A value below this cut-off is the negative result.
in subset: GENEPIO

AccuProbe Listeria monocytogenes culture identification reagent kit
type: Class
subclass of: OBI_0001879
IAO_0000114: IAO_0000122
IAO_0000115: An AccuProbe reagent kit for identifying Listeria monocytogenes.
IAO_0000117: Damion Dooley
IAO_0000119: URI: http://www.hologic.com/sites/default/files/package%20inserts/103051F-EN-RevC.pdf
in subset: GENEPIO

AccuProbe test result
type: Class
subclass of: IAO_0000109
subclass of: Restriction
  on property: output of
  some values from: AccuProbe culture identification assay
metadata section: Lab Analytic
term source: NML Labware LIMS
IAO_0000112: positive, negative, not done
IAO_0000115: A categorical diagnostic result of an AccuProbe test.
IAO_0000119: NML LIMS
in subset: GENEPIO

ribotyping
type: Class
subclass of: diagnostic test
IAO_0000115: Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated. By performing a Gel electrophoresis with the digested samples, the fragments can be visualised as lines on the gel, where larger fragments are close to the start of the gel, and smaller fragments further down. After blotting onto a matrix and probing, these lines form a unique pattern for each species and can be used to identify the origin of the DNA, almost like a barcode can identify a product.
IAO_0000119: Ribotyping
in subset: GENEPIO

riboprinting
type: Class
subclass of: diagnostic test
IAO_0000115: This method is based on restriction endonuclease digestion of bacterial chromosomal DNA, followed by Southern hybridization to probes for sequences in the regions of bacterial DNA coding for the 5S-16S-23S (the Escherichia coli rrnB rRNA operon) rRNA operon. The probes have been developed that are directed to highly conserved regions of the rRNA operon present in all eubacteria and can therefore be used for ribotyping most bacteria
IAO_0000119: PMC92620
in subset: GENEPIO

Qualicon (DuPont) RiboPrinter Microbial Characterization System
type: Class
subclass of: OBI_0000968
IAO_0000115: an automated system that takes a purified bacterial suspension, lyses the cells, extracts the DNA, restriction endonuclease digests the DNA, separates the digest on a gel, transfers the DNA bands to a membrane, probes the bands with non-radioisotope-labeled, 5S-16S-23S rRNA-specific probes (Southern hybridization), photographs the membrane, and finally compares the bar code-like pattern to databases in order to identify the genus and species.
IAO_0000119: PMC92620
in subset: GENEPIO

DuPont identification pattern library
type: Class
subclass of: IAO_0000100
IAO_0000115: a library of RiboPrinter recognised patterns
in subset: GENEPIO

RiboPrinter DUP Number
type: Class
subclass of: IAO_0000109
metadata section: Lab Analytic
term as in existing standard: Riboprinter DUP Number
term source: NML Labware LIMS
IAO_0000112: DUP-PST1-1211
IAO_0000115: DuPont identification number from the DuPont identification library
IAO_0000119: NML LIMS
in subset: GENEPIO

RiboPrinter DUP similarity
type: Class
subclass of: IAO_0000109
metadata section: Lab Analytic
term as in existing standard: Riboprinter DUP similarity
term source: NML Labware LIMS
IAO_0000112: The identification of an isolate was determined when the corresponding patterns matched one of the patterns of the DuPont Identification library of the RiboPrinter1 with a similarity of >0.85. The similarity threshold for an isolate joining a ribogroup is an adaptive value between 0.90 and 0.96, depending on the size of the ribogroup.
IAO_0000115: Similarity of pattern to one of the patterns of the DuPont Identification library of the RiboPrinter
IAO_0000119: http://www.tandfonline.com/doi/pdf/10.1080/09603120903254041
in subset: GENEPIO

sequencing run date
type: Class
subclass of: isolate history item
subclass of: laboratory sequencing datum
subclass of: Restriction
  on property: after
  some values from: culture isolation date
metadata section: Sequencing
term as in existing standard: Sequencing Run Date
term source: NML NGS Archive
IAO_0000112: yyyy/mm/dd
IAO_0000115: Date the sequencing run was performed
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

sequencing location
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Sequencing Location
term source: inferred from BCCDC interviews
IAO_0000115: location the sequencing run was performed
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

sequencing platform (brand)
type: Class
subclass of: IAO_0000027
metadata section: Sequencing
term as in existing standard: Platform
term source: https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._platform_descriptor_t/
IAO_0000112: Illumina (MiSeq, HiSeq), PacBio, Ion Torrent, (Roche 454), SOLiD ABI
IAO_0000114: IAO_0000428
IAO_0000115: A sequencing plaform (brand) is a name of a company that produces sequencer equipment.
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

sequencing workflow
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Workflow
term source: Derived from Sample Sheet
IAO_0000112: Resequencing, FastQ only
IAO_0000115: the workflow is the pre-defined sequence of steps to run the automated sequencing pipeline.
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

sequencing application
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Application
term source: Derived from Illumina Sample Sheet
IAO_0000112: amplicon sequencing, WGS
IAO_0000115: the sequencing application is the use or purpose of the sequencing
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

obsolete: sequencing assay
type: Class
term source: Derived from Illumina Sample Sheet
IAO_0000115: the sequencing conditions and the analyte being measured
IAO_0000119: GROUP: IRIDA Ontology (Emma)
IAO_0100001: OBI_0600047
deprecated: true

sequencing chemistry
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Chemistry
term source: Derived from Illumina Sample Sheet
IAO_0000112: amplicon, resequencing (WGS)
IAO_0000115: lab method to determine the order of nucleotides in a DNA molecule
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

read length
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Read Length
term source: Derived from Illumina Sample Sheet
IAO_0000112: 151, 251
IAO_0000115: number of base pairs per read
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

obsolete: GSCID-BRC data item
type: Class
IAO_0000115: A GSCID/BRC data item is a field in one of the GSCID/BRC Project and Sample Application Standard subsets.
IAO_0000117: Damion Dooley
IAO_0000231: IAO_0000103
deprecated: true

sequencing run multiplex identifiers
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Multiplex identifiers
term source: Derived from Illumina Sample Sheet
IAO_0000112: S017
IAO_0000115: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
IAO_0000119: GROUP: MIxS
in subset: GENEPIO

sequencing run sample identifier
type: Class
subclass of: IAO_0000577
metadata section: Sequencing
term as in existing standard: Sample Name
term source: Derived from Illumina Sample Sheet specification: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-sample-sheet-quick-ref-guide-15028392-j.pdf
IAO_0000112: 1,2,3, AX234, etc.
IAO_0000112: Control1, Tank1, Froglet1
IAO_0000115: A sequencing run sample identifier is an alphanumeric identifier for a sample. In bioinformatics processing this identifier is assigned to a sample in order to track it through the process of sequencing and analysis.
IAO_0000119: GROUP: IRIDA Ontology (Emma)
has db xref: Illumina SampleSheet: Sample_ID
has db xref: PulseNet: SubmittedNumber
has exact synonym: sample name
has exact synonym: sample title
in subset: GENEPIO

sequencing count of chemistry cycles
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Number of cycles
term source: Derived from Illumina Sample Sheet
IAO_0000112: 500
IAO_0000115: Number of sequencing chemistry cycles
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

sequencing kit
type: Class
subclass of: OBI_0000047
metadata section: Sequencing
term as in existing standard: Sequencing Kit
term source: Derived from Illumina Sample Sheet
IAO_0000112: MiSeq reagent kit
IAO_0000115: Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications.
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

sequencing kit version
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Sequencing Kit version
term source: Derived from Illumina Sample Sheet
IAO_0000112: v2, v3
IAO_0000115: A string datum which is the version/configuration of the reagent cartidge.
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

adapter sequence
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Adapters
term source: Derived from Illumina Sample Sheet
IAO_0000112: adapter A and B sequence
IAO_0000115: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
IAO_0000119: GROUP: MIxS
in subset: GENEPIO

read adapter trimming
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term as in existing standard: Adapter Trimming
term source: Derived from Illumina Sample Sheet
IAO_0000115: The removal of adapter sequences from demultiplexed data reads
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

library preparation kit
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
term source: inferred from BCCDC interviews
IAO_0000112: Illumina metagenomic protocol (part 15044223), with Nextera
IAO_0000115: Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids.
IAO_0000119: GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html

number of expected base pairs per genome
type: Class
subclass of: assembly quality control datum
metadata section: Sequencing
term as in existing standard: Number of base pairs
term source: inferred from BCCDC interviews
IAO_0000112: 300 000
IAO_0000115: The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period.
IAO_0000119: GROUP: MIxS
in subset: GENEPIO

number of reads passing filter
type: Class
subclass of: assembly quality control datum
metadata section: Run QC
term as in existing standard: Number of Reads Passing Filter
term source: Output from MiSeq
IAO_0000112: 0.92
IAO_0000115: Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities. Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6.
IAO_0000119: URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html
in subset: GENEPIO

sequencer flow cell cluster density
type: Class
subclass of: laboratory sequencing datum
metadata section: Run QC
term as in existing standard: Cluster density
term source: Output from MiSeq
IAO_0000112: 800 k/mm^2
IAO_0000115: Cluster Generation is a process by which libraries amplified into clonal clusters on a flow cell. The density of those clusters in the lane, is the cluster density.
IAO_0000119: URI: https://www.broadinstitute.org/files/shared/illuminavids/clusterGenSlides.pdf

phred quality score
type: Class
subclass of: assembly quality control datum
metadata section: Run QC
term as in existing standard: above 30 Qscore
term source: Output from MiSeq
IAO_0000112: >75%
IAO_0000115: percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly
IAO_0000119: URI: http://en.wikipedia.org/wiki/Phred_quality_score
in subset: GENEPIO

assembly method
type: Class
equivalent class: Class
  union of: de-novo assembly
  union of: mapping (reference based)
subclass of: sequencing assembly datum
metadata section: Assembly QC
term as in existing standard: Assembly
term source: Standard Term
IAO_0000112: the GROUP: MIxS term encompasses assembly method; estimated error rate; method of calculation
IAO_0000115: Assembly method refers to how the reads were assembled into contigs for which either a de novo or mapping (reference based) strategy is used.
IAO_0000119: GROUP: MIxS
in subset: GENEPIO

assembly status
type: Class
subclass of: assembly quality control datum
metadata section: Assembly QC
term as in existing standard: Assembly status
term source: from within "Finishing strategy" in GROUP: MIxS
IAO_0000112: standard draft or finished
IAO_0000114: IAO_0000428
IAO_0000115: "Attempting to convey the relative integrity and reliability of the data, six levels or terms have been proposed and applied to describe genome sequences." See subclass choices.
IAO_0000117: Damion Dooley
IAO_0000119: CITATION: Chain, P.S., Grafham, D.V., Fulton, R.S., Fitzgerald, M.G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D.C., Buhay, C., et al. (2009). Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237.
in subset: GENEPIO

read coverage
type: Class
subclass of: assembly quality control datum
metadata section: Assembly QC
term as in existing standard: Coverage
term source: from within "Finishing strategy" in GROUP: MIxS
IAO_0000112: 30
IAO_0000114: IAO_0000428
IAO_0000115: Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
IAO_0000119: URI: http://en.wikipedia.org/wiki/Shotgun_sequencing
in subset: GENEPIO
comment: Damion Dooley's note: Wikipedia defines calculation with: "the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G"

contig count
type: Class
subclass of: assembly quality control datum
subclass of: STATO_0000047
subclass of: Restriction
  on property: is about
  some values from: SO_0001462
metadata section: Assembly QC
term as in existing standard: Number of Contigs
IAO_0000112: 20
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000428
IAO_0000115: A contig count is the count of contigs that belong to a sequence assembly.
IAO_0000117: Damion Dooley
in subset: GENEPIO

assembly name (identifier)
type: Class
subclass of: sequencing assembly datum
subclass of: Restriction
  on property: is about
  some values from: SO_0000353
metadata section: Assembly QC
term as in existing standard: Assembly name
term source: Standard Term
IAO_0000112: name and version of assemby
IAO_0000115: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community
IAO_0000119: GROUP: MIxS
in subset: GENEPIO

genome annotation algorithm
type: Class
subclass of: genomic sequencing annotation datum
metadata section: Assembly QC
term as in existing standard: Annotation Algorithm
term source: Standard Term
IAO_0000112: Prokka
IAO_0000115: Program used for annotation
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

genome annotation source
type: Class
subclass of: genomic sequencing annotation datum
metadata section: Assembly QC
term as in existing standard: Annotation Source
term source: Standard Term
IAO_0000112: annotation source description
IAO_0000115: For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
IAO_0000119: GROUP: MIxS
in subset: GENEPIO

obsolete: NCBI BioSample data item
type: Class
IAO_0000117: Damion Dooley
IAO_0000231: IAO_0000227
IAO_0100001: NCBI BioSample Pathogen.cl standard
deprecated: true

GENEPIO_0000099
type: Class
subclass of: OBI_0001616
has alternative id: CDC ID

GENEPIO_0000101
type: Class
subclass of: strain identifier
IAO_0000117: Damion Dooley

GENEPIO_0000102
type: Class
subclass of: case identifier
IAO_0000117: Damion Dooley

obsolete: NCBI BioProject data item
type: Class
IAO_0000115: An NCBI BioProject data item is a datum within the NCBI BioProject standard collection
IAO_0000117: Damion Dooley
IAO_0000231: IAO_0000227
IAO_0100001: NCBI BioProject standard
deprecated: true

obsolete: INSDC MDM standard
type: Class
IAO_0000115: The INDISC consortium "Minimum data for Matching" standard aims to define a format to capture reads and minimum metadata. It is developed by the "Repository and storage of sequence and meta-data" workgroup 2. It is used in the Global Microbial Identifier platform.
IAO_0000117: Damion Dooley
IAO_0100001: the Global Microbial Identifier Minimum Data for Matching (MDM) Standard
deprecated: true

obsolete: MIxS data item
type: Class
IAO_0000115: A MixS data item is a term or field defined in the Genomic Standards Consortium MIxS standard.
IAO_0000117: Damion Dooley
IAO_0100001: Minimum Information about any (x) Sequence (MIxS)
deprecated: true

draft data standard
type: Class
subclass of: OBI_0000658
IAO_0000114: IAO_0000428
IAO_0000115: The 'draft data standard' class contains draft representations of formal or defacto third party standards and related components. These representations may have been crafted without any involvement of related standards issuers and so no guarantee can be provided about their currency, accuracy or veracity.
IAO_0000117: Damion Dooley

obsolete: HIPPA PHI data item
type: Class
IAO_0000231: IAO_0000103
IAO_0100001: American HIPPA Protected Health Information (PHI) guidelines
deprecated: true

obsolete: PulseNet data item
type: Class
IAO_0000231: IAO_0000103
IAO_0100001: PulseNet submission standard
deprecated: true

I2B2 Data Protection role standard
type: Class
subclass of: NCIT C103180
IAO_0000114: IAO_0000428
IAO_0000115: The I2B2 Workbench Data Protection role standard is a standard which names and lists data protection roles between a user and a given dataset that define the level of detail a user has access to.
IAO_0000117: Damion Dooley
IAO_0000119: Derived from the Data Protection Track of the I2B2 Workbench software specification: https://www.i2b2.org/software/files/PDF/current/IM_Architecture.pdf

subject health status (GSCID-BRC)
type: Class
subclass of: organism datum
user interface feature: depth:1
user interface feature: order: NCIT:C115935 # healthy NCIT:C25610 # pathologic / diseased NCIT:C28554 # deceased
IAO_0000114: IAO_0000428
IAO_0000115: A description of whether a given subject organism appeared healthy, sick or deceased at the time of specimen extraction. If sick or deceased, additional details should be provided in project-specific fields.
IAO_0000117: Damion Dooley
has alternative id: CS8

GSCID-BRC Core Sample standard
type: Class
subclass of: GSCID-BRC Project and Sample Application Standard
subclass of: Restriction
  on property: is about
  some values from: OBI_0100051
IAO_0000114: IAO_0000428
IAO_0000115: The GSCID-BRC Core Sample Standard is an extension of the GMI MDM data standard
IAO_0000117: Damion Dooley
IAO_0000119: https://www.niaid.nih.gov/research/dmid-metadata-standards-core-sample

GSCID-BRC Core Project standard
type: Class
subclass of: GSCID-BRC Project and Sample Application Standard
IAO_0000114: IAO_0000428
IAO_0000115: A Core Project item is a field in the GSCID/BRC Project and Sample Application Core Project Standard.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project

specimen category
type: Class
subclass of: specimen datum
IAO_0000114: IAO_0000428
IAO_0000115: Specimen category is a categorical variable that broadly indicates the source of a specimen in order for data processing systems like NCBI's biosample submission portal to anticipate other fields related to the source. Currently this distinguishes between "clinical or host associated" specimens and "environmental/food or other pathogen" specimens.
IAO_0000117: Damion Dooley

subject age - unit
type: Class
subclass of: organism datum
IAO_0000112: day, week, month, year
IAO_0000114: IAO_0000428
IAO_0000115: Age unit of the age measurement of a subject (individual organism).
IAO_0000116: Damion Dooley Feb 20, 2017: GSCID-BRC calls for an explicit field here whereas NCBI Biosample and MIxS don't.
IAO_0000117: Damion Dooley
IAO_0000119: NIAID GSCID-BRC metadata working group

NCBI standard
type: Class
subclass of: NCIT C103180
IAO_0000115: The National Center for Biotechnology Information offers standards for submitting genomic project data to their BioProject and BioSample databases.
IAO_0000117: Damion Dooley
IAO_0000118: National Center for Biotechnology Information standard

specimen collection location - city or region
type: Class
subclass of: specimen collection site specification
subclass of: Restriction
IAO_0000114: IAO_0000122
IAO_0000115: A datum containing the city or region or more precise geographical location identifier for the site of a specimen collection event.
IAO_0000117: Damion Dooley
IAO_0000119: Adapted from NIAID GSCID-BRC metadata working group
IAO_0000600: Note that this is expressed in a particular format in some standards.

Axiom
annotated source: specimen collection location - city or region
annotated property: subClassOf
annotated target: Restriction
user interface feature: lookup

specimen collection location - country
type: Class
subclass of: specimen collection site specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: NCIT C25464
IAO_0000114: IAO_0000122
IAO_0000115: The country of the site of a given specimen collection event.
IAO_0000117: Damion Dooley
IAO_0000119: NIAID GSCID-BRC metadata working group

Darwin Core Terms
type: Class
subclass of: NCIT C103180
IAO_0000114: IAO_0000122
IAO_0000115: The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries.
IAO_0000117: Damion Dooley
IAO_0000119: http://tdwg.github.io/dwc/terms/index.htm

travel history item
type: Class
subclass of: organism location history datum
IAO_0000114: IAO_0000428
IAO_0000115: A datetime measurement related to a person's travel with respect to potential epidemilogical implications.
IAO_0000117: Damion Dooley

travel start date
type: Class
subclass of: travel history item
IAO_0000114: IAO_0000428
IAO_0000115: The date of a person's departure from their primary residence (at that time) on a journey to one or more other locations.
IAO_0000117: Damion Dooley

travel end date
type: Class
subclass of: travel history item
subclass of: Restriction
  on property: after
  some values from: travel start date
IAO_0000114: IAO_0000428
IAO_0000115: The date of a person's return to some residence from a journey originating at that residence.
IAO_0000117: Damion Dooley

infection aquired during travel
type: Class
subclass of: human exposure event - travel datum
IAO_0000114: IAO_0000428
IAO_0000115: Infection aquired during travel is a boolean datum indicating a diagnosis of a traveller's infection during a given trip.
IAO_0000117: Damion Dooley

draft pathogenic epidemiology case investigation record
type: Class
subclass of: draft data standard
IAO_0000114: IAO_0000428
IAO_0000115: This is a model of the datums involved in an epidemiology investigation.
IAO_0000117: Damion Dooley

draft pathogenic epi case exposure record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000428
IAO_0000115: The draft epi case exposure model describes datums related to the possible transmission of a pathogen between a case person and other people, places, animals etc.
IAO_0000117: Damion Dooley

draft pathogenic epi case food record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000428
IAO_0000115: A description of a food item that a case patient has come in contact with.
IAO_0000117: Damion Dooley

food brought back from travel
type: Class
subclass of: human exposure event - travel datum

epidemiology contact network model
type: Class
subclass of: contact specification
IAO_0000115: An epidemiology contact network model is a definition of the information necessary to connect pathogen transmission patterns between individuals or animals in connection with an outbreak investigation.
IAO_0000117: Damion Dooley

epi contact network model - human
type: Class
subclass of: epidemiology contact network model
IAO_0000114: IAO_0000428
IAO_0000115: An epi contact network - human is contact information about a person who may be involved in transmitting a pathogen.
IAO_0000117: Damion Dooley

epi contact network model - animal
type: Class
subclass of: epidemiology contact network model
IAO_0000114: IAO_0000428
IAO_0000115: This is a model that provides location and transportation information about an animal that may be involved in transmitting a pathogen to a human or other animal.
IAO_0000117: Damion Dooley

note
type: Class
subclass of: IAO_0000300
IAO_0000115: A note is text that provides human-readable information on one or more subjects.
IAO_0000117: Damion Dooley

draft pathogenic epi case general information record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000428
IAO_0000115: An epi case general info model contains datum specifications about an epidemiology investigation case including the person involved, contact information and their demographics.
IAO_0000117: Damion Dooley

draft pathogenic epi case isolate detail record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000428
IAO_0000115: A record of the details around how, when, and from what an isolate was extracted.
IAO_0000117: Damion Dooley

specimen source substance
type: Class
equivalent class: Class
  union of: ENVO_00010483
  union of: food specimen
  union of: subject organism
subclass of: BFO_0000040
subclass of: Restriction
  on property: located in
  some values from: specimen collection site
IAO_0000114: IAO_0000428
IAO_0000115: A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted.
IAO_0000117: Damion Dooley

isolate sequence filename
type: Class
subclass of: laboratory sequencing datum
IAO_0000114: IAO_0000428
IAO_0000115: An isolate sequence filename is the file name (http://edamontology.org/data_1050) of the contig assembly file created by a bioinformatics assembly process.
IAO_0000117: Damion Dooley

cluster identifier
type: Class
subclass of: test specification
IAO_0000114: IAO_0000428
IAO_0000115: A cluster identifier is an identifier that locates a genomic variant of an organism within a community of past or present genetically related organisms.
IAO_0000117: Damion Dooley

draft pathogenic epi case test record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000428
IAO_0000115: A laboratory test performed on a specimen from a patient with regard to potential pathogenic disease.
IAO_0000117: Damion Dooley

contact specification - lab test requester
type: Class
subclass of: contact specification - person
IAO_0000114: IAO_0000428
IAO_0000115: A lab test requestor is the individual or agency requesting that one or more tests be performed on a specimen.
IAO_0000117: Damion Dooley

food cultural origin
type: Class
subclass of: food specimen datum
IAO_0000114: IAO_0000428
IAO_0000115: A food cultural origin datum indicates the cultural origin of a food product.
IAO_0000117: Damion Dooley

draft pathogenic epi case travel record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123
IAO_0000115: A record of a patient's recent travel - departure and return, mode of travel and locations visited - as it may pertain to an outbreak pathogen transmission event.
IAO_0000117: Damion Dooley

Region (England) (entry subject to GAZ replacement)
type: Class
subclass of: subnational region

contact specification - epi network contact
type: Class
subclass of: contact specification - person
IAO_0000114: IAO_0000428
IAO_0000115: An epi network contact is a person who may have recieved or transmitted an infectious disease related to an outbreak investigation.
IAO_0000117: Damion Dooley

public health lab epidemiology contextual data standard
type: Class
subclass of: public health data standard
IAO_0000114: IAO_0000428
IAO_0000115: This model contains data type specifications for whole genome sequencing and epidemiology investigation contextual data.
IAO_0000117: Damion Dooley

draft whole genome sequencing lab test record
type: Class
subclass of: draft data standard
IAO_0000115: This is a set of datums involved in laboratory processing of whole-genome-sequenced isolates.
IAO_0000117: Damion Dooley

draft WGS lab bioinformatics process record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

draft WGS lab sequencing record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

NCBI SRA meta information standard
type: Class
subclass of: NCBI standard
IAO_0000114: IAO_0000428
IAO_0000115: An NCBI SRA meta information item is a field specification for a NCBI Sequence Read Archive record.
IAO_0000117: Damion Dooley

isolate raw read filename
type: Class
subclass of: laboratory sequencing datum
IAO_0000115: An isolate raw read filename is the file name (http://edamontology.org/data_1050) of the raw read file created by a genomic sequencing assay.

library preparation kit version
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
IAO_0000114: IAO_0000428
IAO_0000115: The version identifier of a packaged kit tailored for specific sequencing workflows.
IAO_0000117: Damion Dooley

read trimming and filtering software
type: Class
subclass of: laboratory sequencing datum
IAO_0000114: IAO_0000428
IAO_0000115: The name and version of software used in a bioinformatics workflow to improve the quality of sequencing reads.
IAO_0000117: Damion Dooley

bioinformatics pipeline name
type: Class
subclass of: laboratory sequencing datum
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

bioinformatics pipeline version
type: Class
subclass of: laboratory sequencing datum
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

bioinformatics pipeline protocol
type: Class
subclass of: laboratory sequencing datum
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

draft WGS lab sequencing quality metrics record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

draft WGS lab assembly quality metrics record
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

project data type
type: Class
subclass of: IAO_0000104
IAO_0000114: IAO_0000122
IAO_0000115: A general label indicating the primary study goal. These are only relevant for Primary submission projects (not Umbrella projects).
IAO_0000117: Damion Dooley
comment: Damion Dooley's note: According to http://trace.ddbj.nig.ac.jp/news/2014-11-12_e.html, "A BioProject record can have multiple project data types"

assembly project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Genome assembly project utilizing already existing sequence data including data that was submitted by a different group
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

clone ends project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: A sequencing project involving clone-ends
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

epigenomics project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: A sequencing project involving DNA methylation, histone modification, and/or chromatin accessibility datasets
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

exome resequencing project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Exome resequencing project
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

genome sequencing project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: A whole, or partial, genome sequencing project (with or without a genome assembly)
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

draft ReSeq Tuberculosis data platform standard
type: Class
subclass of: draft data standard
IAO_0000115: The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb.
IAO_0000117: Damion Dooley
IAO_0000119: https://platform.reseqtb.org/

test threshold measurement comparator
type: Class
subclass of: phenotypic antimicrobial drug susceptibility test datum
IAO_0000112: In expressions like: "<= 8mg/L"
IAO_0000114: IAO_0000123
IAO_0000115: The measurement comparator is a sign indicating that a measurement is above, equal to, or below a given threshold.
IAO_0000117: Damion Dooley

less than
type: Class
subclass of: test threshold measurement comparator
user interface label: <
IAO_0000114: IAO_0000428
IAO_0000115: The "less than" comparator indicates that a given substance was present at less than a given quantity or concentration.
IAO_0000117: Damion Dooley
has alternative id: <

less than or equal to
type: Class
subclass of: test threshold measurement comparator
user interface label: <=
IAO_0000114: IAO_0000428
IAO_0000115: The "less than or equal to" comparator indicates that a given substance was present at less than or equal to a given quantity or concentration.
IAO_0000117: Damion Dooley
has alternative id: <=

equal to
type: Class
subclass of: test threshold measurement comparator
user interface label: ==
IAO_0000114: IAO_0000428
IAO_0000115: The "equal to" comparator indicates that a given substance was present at the given quantity or concentration.
IAO_0000117: Damion Dooley
has alternative id: ==

greater than or equal to
type: Class
subclass of: test threshold measurement comparator
user interface label: >=
IAO_0000114: IAO_0000428
IAO_0000115: The "greater than or equal to" comparator indicates that a given substance was present at greater than or equal to a given quantity or concentration.
IAO_0000117: Damion Dooley
has alternative id: >=

greater than
type: Class
subclass of: test threshold measurement comparator
user interface label: >
IAO_0000114: IAO_0000428
IAO_0000115: The "greater than" comparator indicates that a given substance was present at greater than a given quantity or concentration.
IAO_0000117: Damion Dooley
has alternative id: >

NCBI Antibiogram standard
type: Class
subclass of: NCBI standard
user interface feature: order: OBI:0001616 # specimen identifier OBI:0001614 # GenBank ID GENEPIO:0001100 # antibiogram drug test model GENEPIO:0002062 # amr testing reference standard GENEPIO:0002045 # amr resistance testing method GENEPIO:0002047 # ... version or reagent GENEPIO:0002049 # amr testing platform GENEPIO:0002056 # ... vendor
IAO_0000114: IAO_0000428
IAO_0000115: The NCBI antibiogram standard details the reporting specifications for antimicrobial susceptibility and resistance data derived from drug resistant pathogens. This information is submitted as an antibiogram table on BioSample records.
IAO_0000117: Damion Dooley

obsolete: NCBI isolate AMR testing model
type: Class
IAO_0100001: NCBI Antibiogram standard
deprecated: true

obsolete: restaurant
type: Class
IAO_0000115: A restaurant or an eatery, is a business which prepares and serves food and drinks to customers in exchange for money.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Restaurant
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000934
deprecated: true

Canadian Integrated Public Health Information System (iPHIS) Standard
type: Class
subclass of: public health data standard
user interface label: iPHIS standard
IAO_0000114: IAO_0000428
IAO_0000115: The Canadian Integrated Public Health Information System (iPHIS) System provides a standard for holding reportable disease cases from participating jurisdictions.
IAO_0000117: Damion Dooley

MIRU24 - international standard
type: Class
subclass of: test specification
IAO_0000112: 254532233433235152213423
IAO_0000114: IAO_0000428
IAO_0000115: The MIRU24 - international standard is a mycobacterial interspersed repetitive units (MIRU) typing method that classifies Mycobacterium tuberculosis complex (MBTC) bacteria according to a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) typing scheme of counts of repeats at 24 sequence loci.
IAO_0000600: The ordering of loci is as follows: MIRU 04, MIRU 26, MIRU 40, MIRU 10, MIRU 16, MIRU 31, 424 577, 2165, 401, 3690, 4156, 2163, 1955, 4052, MIRU 02, MIRU 23, MIRU 39, MIRU 20, MIRU 24, MIRU 27, 2347, 2461, 3171

MIRU24 - Canadian standard
type: Class
subclass of: test specification
IAO_0000114: IAO_0000428
IAO_0000115: The MIRU24 - Canadian standard is a Mycobacterium tuberculosis typing method exactly like MIRU24 - international standard except that the report of the ordering of the matching loci is different.
IAO_0000117: Damion Dooley
IAO_0000600: The ordering of loci is as follows: MIRU 02, MIRU 04, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 31, MIRU 39, MIRU 40, 424, 577, 1955, 2163, 2165, 2347, 2401, 2461, 3171, 3690, 4052, 4156

spray-wading water
type: Class
subclass of: treated water - ambient temperature

pool water
type: Class
subclass of: treated water - ambient temperature

obsolete: hot tub
type: Class
IAO_0100001: ENVO_01000938
deprecated: true

obsolete: cafeteria
type: Class
IAO_0000115: A cafeteria is a type of food service location in which there is little or no waiting staff table service, whether a restaurant or within an institution such as a large office building or school.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Cafeteria
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000969
deprecated: true

obsolete: bakery
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_00003864
deprecated: true

obsolete: delicatessen
type: Class
IAO_0000115: A delicatessen or deli is a retail establishment that sells a selection of unusual or foreign prepared foods.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Delicatessen
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000970
deprecated: true

obsolete: food kiosk
type: Class
IAO_0000115: A food kiosk is a kiosk (a booth with an open window on one side) that sells food.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000974
deprecated: true

obsolete: grocery store
type: Class
IAO_0000115: A grocery store is a retail store that primarily sells food.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000984
deprecated: true

obsolete: specialty/ethnic store
type: Class
IAO_0000115: A specialty/ethnic food store is a store specializing in a particular variety of food or food of cultural / regional origin.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000988
deprecated: true

obsolete: market
type: Class
IAO_0000115: A market, or marketplace, is a location where people regularly gather for the purchase and sale of provisions, livestock, and other goods
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000987
deprecated: true

treatment history datum
type: Class
subclass of: IAO_0000416
IAO_0000114: IAO_0000428
IAO_0000115: A time measurement datum that pertains to a patient's medical treatment.
IAO_0000117: Damion Dooley

obsolete: take out restaurant
type: Class
IAO_0000115: A restaurant providing prepared meals or other food items that the purchaser intends to eat elsewhere
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Take-out
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000972
deprecated: true

treatment start date
type: Class
subclass of: treatment history datum
IAO_0000114: IAO_0000428
IAO_0000115: A treatment start date is a date/time datum which indicates the start of a particular medical treatment for a patient.
IAO_0000117: Damion Dooley

canoeing / kayaking / boating
type: Class
subclass of: human water activity

hiking
type: Class
subclass of: human general activity

camping
type: Class
subclass of: human general activity

obsolete: social gathering
type: Class
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/PCO_0000033
deprecated: true

obsolete: party
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/PCO_0000035
deprecated: true

obsolete: wedding
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/PCO_0000038
deprecated: true

obsolete: baby shower
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/PCO_0000039
deprecated: true

obsolete: potluck
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/PCO_0000037
deprecated: true

obsolete: community event
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/PCO_0000034
deprecated: true

obsolete: long term care facility
type: Class
IAO_0000115: A long term care facility provides a type of residential care. It is a place of residence for people who require continual nursing care and have significant difficulty coping with the required activities of daily living.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Nursing_home_care
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000932
deprecated: true

treatment end date
type: Class
subclass of: treatment history datum
subclass of: Restriction
  on property: after
  some values from: treatment start date
IAO_0000114: IAO_0000428
IAO_0000115: A treatment end date is a date/time datum which indicates the end of a particular medical treatment for a patient.
IAO_0000117: Damion Dooley

food related exposure event
type: Class
subclass of: infectious disease exposure event
IAO_0000117: Damion Dooley

infection-specific food detail
type: Class
subclass of: food specimen detail
IAO_0000114: IAO_0000428
IAO_0000115: Some bacteria are associated with particular foods. Need relationship
IAO_0000117: Damion Dooley

tuberculosis treatment drug
type: Class
subclass of: CHEBI_36357
IAO_0000114: IAO_0000428
IAO_0000115: A tuberculosis treatment antibiotic is an antibiotic used in the treatment of tuberculosis.
IAO_0000117: Damion Dooley
see also: “Treatment of Tuberculosis Guidelines”, WHO, Geneva, 2010, 30 www.who.int/tb/ - See more at: http://www.tbfacts.org/tb-drugs/#sthash.nibuzCLV.dpuf

vegetarian
type: Class
subclass of: dietary restriction

organism location history datum
type: Class
subclass of: IAO_0000416
IAO_0000114: IAO_0000428
IAO_0000115: A time measurement datum that pertains to an organism's physical location.
IAO_0000117: Damion Dooley

food avoidance
type: Class
subclass of: dietary restriction
comment: This will take on a sub-herarchy of food types.

special diet
type: Class
subclass of: dietary restriction

water related exposure event
type: Class
subclass of: infectious disease exposure event

municipal water
type: Class
subclass of: treated water - ambient temperature

immigration year of arrival
type: Class
subclass of: organism location history datum
IAO_0000114: IAO_0000428
IAO_0000115: A time measurement datum indicating the year a person immigrated to a given country.
IAO_0000117: Damion Dooley

bottled water
type: Class
subclass of: treated water - ambient temperature

infectious disease exposure event
type: Class
subclass of: BFO_0000011
IAO_0000115: An event (occuring at some location and for some duration of time) where
IAO_0000117: Damion Dooley

human related exposure event
type: Class
subclass of: infectious disease exposure event
IAO_0000117: Damion Dooley

animal related exposure event
type: Class
subclass of: infectious disease exposure event
IAO_0000117: Damion Dooley

NCBI BioSample isolate (human name or description)
type: Class
subclass of: IAO_0000300
IAO_0000114: IAO_0000428
IAO_0000115: Identification or description of the specific individual from which this sample was obtained
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/

obsolete: petting zoo
type: Class
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ENVO_01000923
deprecated: true

agricultural fair
type: Class
subclass of: PCO_0000033
IAO_0000117: Damion Dooley

isolate passage history datum
type: Class
subclass of: laboratory sequencing datum
IAO_0000115: An isolate passage history is a record of the cyclic growth process that led to it, including number of times its was put through the process, and the method used.
IAO_0000117: Damion Dooley
IAO_0000119: NCBI BioSample Pathogen.cl standard

NCBI pathotype
type: Class
subclass of: IAO_0000300
IAO_0000112: For Eschericia coli: STEC, UPEC
IAO_0000115: A pathotype is a common name for a group of organisms (of the same species) that have the same pathogenicity on a specified host
IAO_0000119: https://en.wiktionary.org/wiki/pathotype

pet treat
type: Class
subclass of: animal exposure event by material
IAO_0000117: Damion Dooley
IAO_0100001: FOODON_00003357

pet food (raw)
type: Class
subclass of: animal exposure event by material
IAO_0000117: Damion Dooley
IAO_0100001: FOODON_00003356

human exposure event - travel datum
type: Class
subclass of: organism datum
IAO_0000114: IAO_0000428
IAO_0000115: An epidemiology travel datum is a datum regarding a particular human's travel trip destination, mode, and motivation, with respect to an epidemiology investigation.
IAO_0000117: Damion Dooley

boat / cruise travel
type: Class
subclass of: travel mode

train travel
type: Class
subclass of: travel mode

bus travel
type: Class
subclass of: travel mode

car travel
type: Class
subclass of: travel mode

airline travel
type: Class
subclass of: travel mode

travel mode
type: Class
subclass of: human exposure event - travel datum
IAO_0000114: IAO_0000428
IAO_0000115: A travel mode is a type of transportation which a given human has used while travelling on a particular trip.
IAO_0000117: Damion Dooley

travel reason
type: Class
subclass of: human exposure event - travel datum
IAO_0000114: IAO_0000428
IAO_0000115: A travel reason is a motivation for traveling on a particular trip expressed by the traveller.
IAO_0000117: Damion Dooley

travel for pleasure
type: Class
subclass of: travel reason

business activity
type: Class
subclass of: travel reason

religious missionairy activity
type: Class
subclass of: travel reason

rural backpacking activity
type: Class
subclass of: travel for pleasure

visiting relative/friends
type: Class
subclass of: travel for pleasure

travel tour
type: Class
subclass of: travel for pleasure

unsure of travel reason
type: Class
subclass of: travel reason

draft tuberculosis - specimen contextual data standard
type: Class
subclass of: draft data standard
IAO_0000115: The tuberculosis draft standard is a GenEpiO set of draft genomic and clinical data items related to Mycobacterium tuberculosis that various agencies are using in their own reporting.

behavioural risk factor
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

obsolete: E. coli serotype part
type: Class
IAO_0100001: E. coli serotype specification
deprecated: true

O antigen
type: Class
subclass of: OBI_1110034
has db xref: Snomed: Concept 260827009

H antigen
type: Class
subclass of: OBI_1110034
has db xref: Snomed: Concept 260823008

homeless status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

serovar/serotype common name
type: Class
subclass of: test specification
IAO_0000114: IAO_0000122
IAO_0000115: A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Serotype

Salmonella serovar
type: Class
subclass of: OMP_0000207
subclass of: Restriction
  on property: is about
  some values from: NCBITaxon 590

Salmonella serovar name
type: Class
subclass of: serovar/serotype common name

Salmonella antigenic formula
type: Class
subclass of: antigenic formula
subclass of: Restriction
  on property: is about
  some values from: NCBITaxon 590

drug use status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

incarceration status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

HIV status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

HIV risk status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

A.I.D.S status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

drug abuse status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

injection drug use status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

recreational drug use status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

methadone use status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

substantial alcohol use/abuse status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

smoking status
type: Class
subclass of: behavioural risk factor
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

country of birth
type: Class
subclass of: organism datum
subclass of: Restriction
  on property: BFO_0000067
  some values from: NCIT C25155
subclass of: Restriction
  on property: is about
  some values from: NCIT C25464
IAO_0000114: IAO_0000428
IAO_0000115: A country of birth is the country that a given person (or animal) was born in.
IAO_0000117: Damion Dooley

sequence number
type: Class
subclass of: laboratory sequencing datum
IAO_0000112: Tb_1 (with respect to an Illumina SampleSheet.csv spreadsheet) 13 (with respect to a ReSeqTB SNP pipeline sample report)
IAO_0000114: IAO_0000428
IAO_0000115: A sequence number is a numeric identifier of a sequence with respect to a particular data table or dataset.

date last seen alive
type: Class
subclass of: lifespan history item
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
IAO_0000117: The 'date last seen alive' is the date that a subject (patient) was last known (seen, heard, messaged) to be alive.

second line or reserve tuberculosis drug
type: Class
subclass of: tuberculosis treatment drug

tuberculosis infection anatomical site
type: Class
subclass of: BFO_0000029

obsolete: NCBI Antibiogram model
type: Class
IAO_0100001: NCBI Antibiogram standard
deprecated: true

draft antibiogram drug test model
type: Class
subclass of: draft data standard
user interface feature: order: GENEPIO:0001187 # antimicrobial resistance test drug GENEPIO:0002112 # drug MIC GENEPIO:0002080 # drug minimum inhibitory concentration unit GENEPIO:0001001 # measurement comparator NCIT:C85539 # antimicrobial resistance phenotype GENEPIO:0002181 # antimicrobial resistance phenotype - ECOFF
IAO_0000114: IAO_0000428
IAO_0000115: This is the minimal set of parameters for drug test results for a particular antimicrobial agent.
IAO_0000117: Damion Dooley

predicted exposure start
type: Class
subclass of: exposure history item
IAO_0000115: A date-time datum that marks the predicted start of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time.
IAO_0000117: Damion Dooley

predicted exposure end
type: Class
subclass of: exposure history item
IAO_0000115: A date-time datum that marks the predicted end of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time.
IAO_0000117: Damion Dooley

map project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Map: - project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

metagenome project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Metagenome: sequence analysis of environmental samples
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

metagenome assembly project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Metagenome assembly: a genome assembly generated from sequenced environmental samples
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

other project data type
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Other: a free text description is provided to indicate Other data type
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

phenotype or genotype project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Phenotype or Genotype: project correlating phenotype and genotype
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

proteome project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Proteome: large scale proteomics experiment including mass spec. analysis
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

random survey project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Random Survey: sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

targeted locus (loci) project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Targeted locus (loci): project to sequence specific loci, such as a 16S rRNA sequencing
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

transcriptome or gene expression
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: Transcriptome or Gene expression: large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

variation project
type: Class
subclass of: project data type
IAO_0000114: IAO_0000122
IAO_0000115: A sequencing project with a primary goal of identifying large or small sequence variation across populations.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

INSDC country qualifier
type: Class
subclass of: INSDC standard
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: NCIT C25464
subclass of: Restriction
  on property: OBI_0002135
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: (Afghanistan|Albania|Algeria|American Samoa|Andorra|Angola|Anguilla|Antarctica|Antigua and Barbuda|Arctic Ocean|Argentina|Armenia|Aruba|Ashmore and Cartier Islands|Atlantic Ocean|Australia|Austria|Azerbaijan|Bahamas|Bahrain|Baltic Sea|Baker Island|Bangladesh|Barbados|Bassas da India|Belarus|Belgium|Belize|Benin|Bermuda|Bhutan|Bolivia|Borneo|Bosnia and Herzegovina|Botswana|Bouvet Island|Brazil|British Virgin Islands|Brunei|Bulgaria|Burkina Faso|Burundi|Cambodia|Cameroon|Canada|Cape Verde|Cayman Islands|Central African Republic|Chad|Chile|China|Christmas Island|Clipperton Island|Cocos Islands|Colombia|Comoros|Cook Islands|Coral Sea Islands|Costa Rica|Cote d'Ivoire|Croatia|Cuba|Curacao|Cyprus|Czech Republic|Democratic Republic of the Congo|Denmark|Djibouti|Dominica|Dominican Republic|East Timor|Ecuador|Egypt|El Salvador|Equatorial Guinea|Eritrea|Estonia|Ethiopia|Europa Island|Falkland Islands (Islas Malvinas)|Faroe Islands|Fiji|Finland|France|French Guiana|French Polynesia|French Southern and Antarctic Lands|Gabon|Gambia|Gaza Strip|Georgia|Germany|Ghana|Gibraltar|Glorioso Islands|Greece|Greenland|Grenada|Guadeloupe|Guam|Guatemala|Guernsey|Guinea|Guinea-Bissau|Guyana|Haiti|Heard Island and McDonald Islands|Honduras|Hong Kong|Howland Island|Hungary|Iceland|India|Indian Ocean|Indonesia|Iran|Iraq|Ireland|Isle of Man|Israel|Italy|Jamaica|Jan Mayen|Japan|Jarvis Island|Jersey|Johnston Atoll|Jordan|Juan de Nova Island|Kazakhstan|Kenya|Kerguelen Archipelago|Kingman Reef|Kiribati|Kosovo|Kuwait|Kyrgyzstan|Laos|Latvia|Lebanon|Lesotho|Liberia|Libya|Liechtenstein|Line Islands|Lithuania|Luxembourg|Macau|Macedonia|Madagascar|Malawi|Malaysia|Maldives|Mali|Malta|Marshall Islands|Martinique|Mauritania|Mauritius|Mayotte|Mediterranean Sea|Mexico|Micronesia|Midway Islands|Moldova|Monaco|Mongolia|Montenegro|Montserrat|Morocco|Mozambique|Myanmar|Namibia|Nauru|Navassa Island|Nepal|Netherlands|New Caledonia|New Zealand|Nicaragua|Niger|Nigeria|Niue|Norfolk Island|North Korea|North Sea|Northern M…
user interface feature: help: Consult the http://www.insdc.org/country.html country list for valid options.
IAO_0000115: The INSDC country qualifier is a textual controlled vocabulary used to indicate the country of origin of a DNA sample. It can also have the following format: country:sub_region, such as: "Canada:Vancouver".
IAO_0000117: Damion Dooley

phenotype project objective
type: Class
subclass of: OBI_0001892
user interface label: phenotype
IAO_0000114: IAO_0000122
IAO_0000115: Phenotype: phenotypic measurements for submission to dbGaP
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

genome material from specimen
type: Class
subclass of: OBI_0001882
subclass of: Restriction
  on property: is about
  some values from: SO_0001026
user interface label: genome material
IAO_0000114: IAO_0000122
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

TB lineage 7 - Ethiopia
type: Class
subclass of: Mycobacterium tuberculosis lineage

organs or organ parts
type: Class
subclass of: BFO_0000027
subclass of: Class
  intersection of: Restriction
    on property: has member
    some values from: Restriction
      on property: part of
      some values from: UBERON_0000062
  intersection of: Restriction
    on property: has member
    all values from: Restriction
      on property: part of
      some values from: UBERON_0000062
IAO_0000114: IAO_0000122
IAO_0000115: An object aggregate which has as members whole organs or parts of organs, possibly from different organisms.
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2021-04-19T23:36:25Z

travel outside Canada
type: Class
subclass of: travel destination
IAO_0000115: A travel destination which a given human has travelled to on a particular trip and is outside Canada.
IAO_0000117: https://orcid.org/0000-0002-9578-0788
date: 2021-05-27T04:35:17Z

travel outside province/territory
type: Class
subclass of: travel destination
IAO_0000115: A travel destination which a given human has travelled to on a particular trip and is outside a given province/territory of interest.
IAO_0000117: https://orcid.org/0000-0002-9578-0788
date: 2021-05-27T04:36:13Z

data field category
type: Class
subclass of: IAO_0000027
subclass of: Restriction
  on property: has member
  some values from: data field
IAO_0000112: An instance of a "data field category" that contains the "bioproject accession field", "biosample accession field", and "GISAID accession field".
IAO_0000114: IAO_0000428
IAO_0000115: A data field category which receives a range of one or more data fields.
contributor: http://orcid.org/0000-0002-9578-0788
date: 2022-11-23T00:33:27.896Z

lifespan history item
type: Class
subclass of: IAO_0000416
IAO_0000114: IAO_0000428
IAO_0000115: A livespan history item is a date-associated event pertaining to the life of a subject.
IAO_0000117: Damion Dooley

untreated water
type: Class
subclass of: water exposure by source

treated water - ambient temperature
type: Class
subclass of: water exposure by source

epidemiology investigation data item
type: Class
subclass of: awaiting ontology review

obsolete distribution event
type: Class
IAO_0000231: Unclear semantics and origin
deprecated: true

obsolete supply point / event
type: Class
deprecated: true

well water - treated
type: Class
subclass of: ENVO_01000002
subclass of: treated water - ambient temperature

Well water - untreated
type: Class
subclass of: ENVO_01000002
subclass of: untreated water

organism datum
type: Class
subclass of: IAO_0000027
subclass of: Restriction
  on property: is about
  some values from: OBI_0100026

organism role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: inheres in
  some values from: OBI_0100026
IAO_0000115: a role which inheres in an organism and is realized by the process of being alive

isolate organism role
type: Class
subclass of: organism role

animal role
type: Class
equivalent class: Class
  intersection of: organism role
  intersection of: Restriction
    on property: inheres in
    some values from: NCBITaxon_33213
subclass of: organism role

plant role
type: Class
equivalent class: Class
  intersection of: organism role
  intersection of: Restriction
    on property: inheres in
    some values from: NCBITaxon_33090
subclass of: organism role

taxonomic datum
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley

infectious disease treatment
type: Class
subclass of: patient as host datum
IAO_0000114: IAO_0000428
IAO_0000115: A course of treatment designed to resolve an infectious disease
IAO_0000117: Damion Dooley

antimicrobial resistance test drug
type: Class
equivalent class: Class
  intersection of: CHEBI_36357
  intersection of: Restriction
    on property: RO_0000087
    some values from: CHEBI_33281
subclass of: CHEBI_36357
IAO_0000114: IAO_0000428
IAO_0000115: This is a collection of drugs used to test antimicrobial resistance.
IAO_0000116: This is a class of chemicals by use. They are organized more indirectly in CHEBI via 'has role' some 'antimicrobial agent'. Note: NCBI provides special requirements for antibiotic test-selection for BETA-LACTAMASE, see https://www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/ Damion Dooley note: Used http://cts.fiehnlab.ucdavis.edu/conversion/batchConvert to convert antibiotic name to CHEBI entries. 60% match, some matches off, had to curate hits manually. Note that this is a longer list of antibiotics that we will need to incorporate, perhaps through ARO: https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/?format=txt
IAO_0000117: Damion Dooley

analytic datum
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: Judgements here are marked down after an agent's (doctor/veterenary) analysis of symptoms.

obsolete: type of illness
type: Class
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/DOID_4
deprecated: true

specimen with confirmed presence of disease agent
type: Class
subclass of: organism datum
IAO_0000114: IAO_0000428
IAO_0000115: A specimen which has been confirmed by laboratory test(s) to contain a disease-causing agent such as a pathogen
IAO_0000117: Damion Dooley

dietary restriction
type: Class
subclass of: BFO_0000016

patient type
type: Class
subclass of: NCIT C25190
IAO_0000114: IAO_0000428
IAO_0000115: A person which has a patient care role.
IAO_0000117: Damion Dooley

obsolete: mother
type: Class
IAO_0100001: NCIT C25189
deprecated: true

subject disease outcome
type: Class
subclass of: personal health datum
term source: NCBI BioSample
user interface feature: depth:1
user interface feature: lookup
IAO_0000114: IAO_0000428
IAO_0000115: A subject disease outcome is an assessment of the persistence of a given disease course in a subject (patient)
IAO_0000117: Damion Dooley
comment: Note that this is closely related to OGMS_0000063 "disease course" that lists chronic, progressive, transient and accute processes.

treated water - warm/hot
type: Class
subclass of: water exposure by source

jacuzzi water
type: Class
subclass of: treated water - warm/hot

spa water
type: Class
subclass of: treated water - warm/hot

whirlpool water
type: Class
subclass of: treated water - warm/hot

patient as host datum
type: Class
subclass of: personal health datum
subclass of: Restriction
  on property: is about
  some values from: IDO_0000531
IAO_0000114: IAO_0000428
IAO_0000115: A host datum is a datum that pertains to infection-related information about an organism (animal or human) who is likely bearing a pathogen
IAO_0000117: Damion Dooley

pregnancy history item
type: Class
subclass of: IAO_0000416

date of conception
type: Class
subclass of: pregnancy history item

lifespan history record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

obsolete: food cooking method
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/FOODON_03450002
deprecated: true

obsolete: food preservation method
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/FOODON_03470107
deprecated: true

infectious disease case datum
type: Class
subclass of: IAO_0000027

laboratory data
type: Class
subclass of: IAO_0000027

specimen record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

specimen source material category
type: Class
subclass of: CHMO_0000993
IAO_0000114: IAO_0000428
IAO_0000115: The type of material from which the specimen was obtained. Specimens are usually categorized as food, body products or tissues, or environmental material.
IAO_0000117: Damion Dooley
IAO_0000118: specimen type (host or environmental context)

symbiotic role
type: Class
subclass of: isolate organism role
IAO_0000115: Organism has a symbiotic relationship with host

obsolete: NCBI BioSample attribute package
type: Class
IAO_0100001: specimen category
deprecated: true

obsolete: host sample material
type: Class
IAO_0000117: Damion Dooley
IAO_0100001: subject anatomical site
IAO_0100001: subject body product
deprecated: true

food specimen detail
type: Class
subclass of: food specimen datum
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

patient specimen
type: Class
subclass of: human clinical specimen

environmental specimen
type: Class
subclass of: specimen source material category
has broad synonym: environmental
has db xref: NCBI Biosample: environmental (swab or sampling)

animal specimen
type: Class
subclass of: specimen source material category
IAO_0000114: IAO_0000428
IAO_0000115: A specimen extracted from an animal
IAO_0000117: Damion Dooley

built environment specimen
type: Class
subclass of: environmental specimen

food specimen
type: Class
subclass of: environmental specimen

natural environment specimen
type: Class
subclass of: environmental specimen

exposure event person
type: Class
subclass of: BFO_0000040
IAO_0000114: IAO_0000428
IAO_0000115: The type of person a patient had epidemiological (i.e. close proximity) contact with.
IAO_0000117: Damion Dooley

exposure group statistics record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: An exposure group statistics record is a sumary of disease outbreak statistics on a certain date of a group of humans or animals potentially exposed to a pathogen.

symptom history item
type: Class
subclass of: IAO_0000416
IAO_0000114: IAO_0000428

health state record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

obsolete: swab
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C17627
deprecated: true

obsolete: fluid - aspirate
type: Class
IAO_0000115: [WHICH DEFINITION?] See http://medical-dictionary.thefreedictionary.com/aspirate
IAO_0000117: Damion Dooley
IAO_0100001: NCIT C13347
deprecated: true

plant rinse
type: Class
equivalent class: Class
  intersection of: plant product
  intersection of: rinse
subclass of: rinse
IAO_0000114: IAO_0000428
IAO_0000115: Plant rinse is a rinse derived from plant material from one or more plants.
IAO_0000117: Damion Dooley

outbreak animal exposure event location
type: Class
subclass of: awaiting ontology review
IAO_0000117: Damion Dooley

animal exposure process
type: Class
subclass of: BFO_0000015
IAO_0000117: Damion Dooley

animal exposure event by material
type: Class
subclass of: investigative subject
IAO_0000117: Damion Dooley

exposure by human contact
type: Class
subclass of: human to human exposure process
IAO_0000117: Damion Dooley

obsolete: human exposure activity type
type: Class
IAO_0000117: Damion Dooley
IAO_0000231: unnecessary distinction
IAO_0100001: human to human exposure process
deprecated: true

outbreak human exposure event location
type: Class
subclass of: outbreak exposure event location
IAO_0000117: Damion Dooley

human to human exposure process
type: Class
subclass of: BFO_0000015
IAO_0000114: IAO_0000428
IAO_0000115: A process in which one or more humans may be exposed to one or more contagious human infectious disease carriers.
IAO_0000117: Damion Dooley

water exposure by source
type: Class
subclass of: investigative subject

human water activity
type: Class
subclass of: human general activity

health authority
type: Class
subclass of: OBI_0000245
comment: This list would be customized to include organizations local to an application's software installation. It is an example of a set of ontology terms that would best be organized by a central authority if federated installations need to share investigator contact info for example.

symptom record
type: Class
subclass of: draft GenEpiO component record
user interface feature: order: HP:0000118 # symptom FLU:0000976 # onset GENEPIO:0001789 # cessation GENEPIO:0001784 # duration
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

PFGE pattern
type: Class
subclass of: test specification
subclass of: Restriction
  on property: is about
  some values from: NCIT C53471
IAO_0000115: A visual pattern caused by DNA fragments concentrated in stratefied bands in a Pulsed-field gel electrophoresis (PFGE) gel plate.

phage type salmonella (DT)
type: Class
subclass of: test specification
IAO_0000114: IAO_0000428

phage type e-coli 0157 (PT)
type: Class
subclass of: test specification
IAO_0000114: IAO_0000428

sequence record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

outbreak exposure event location
type: Class
subclass of: investigative subject
IAO_0000114: IAO_0000428
IAO_0000115: A type of built structure that is suspected to be related to an outbreak investigation.
IAO_0000117: Damion Dooley

lab test history record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

obsolete: earth surface
type: Class
IAO_0100001: RBO_00000017
deprecated: true

data specification
type: Class
subclass of: OBI_0000658
IAO_0000114: IAO_0000428
IAO_0000115: A data specification is a specification of a data structure that can hold a categorical, textual or numeric variable, or that has such variables or other data structures as component parts.
IAO_0000116: A data standard, may be defined as a data specification, but a data specification isn't necessarily a formal or de-facto data standard - it would have to be sanctioned by a community of users and developers to take on that status.
IAO_0000117: Damion Dooley

specimen history item
type: Class
subclass of: specimen datum
subclass of: IAO_0000416
IAO_0000114: IAO_0000428
IAO_0000115: A specimen history item is a time-related datum about a particular specimen
IAO_0000117: Damion Dooley

diagnostic test
type: Class
subclass of: OBI_0000070
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

obsolete: sample datum
type: Class
IAO_0000117: Damion Dooley
deprecated: true

obsolete: laboratory sequencing datum
type: Class
IAO_0000115: A laboratory sequencing datum is a datum related to the sequencing assay process applied to an isolate.
IAO_0000117: Damion Dooley
IAO_0100001: laboratory sequencing datum
deprecated: true

genomic sequencing annotation datum
type: Class
subclass of: IAO_0000027

lab test record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: ISSUE: lab test results are appropriate to lab test types. Logic around that?

sequencing assembly datum
type: Class
subclass of: laboratory sequencing datum
subclass of: Restriction
  on property: is about
  some values from: NCIT C53471

container record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000115: A container id is an identifier that refers to a container object about a patient specimen. Container ids are referenced in clinical patient records reported to be suspect, or lab test results.
IAO_0000117: Damion Dooley

health care personal identifier
type: Class
subclass of: IAO_0000577
IAO_0000117: Damion Dooley
IAO_0000117: identifier of a person with the context of a health care system

strain identifier
type: Class
subclass of: IAO_0000577
subclass of: Restriction
  on property: is about
  some values from: NCIT C14419
IAO_0000114: IAO_0000428
IAO_0000115: A strain identifier is the unique microbial or eukaryotic strain name from a reference database that a sample has been matched to.
IAO_0000117: Damion Dooley

line list object
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000115: A line list is a collection of suspected or known disease outbreak cases. It may also include details about healthy patients associated with an exposure event (picnic, concert etc.) who have been interviewed in order to compare food intake, assess risk factors, etc. Note that the health status of people associated with an exposure event can change from healthy or unknown status, to ill patient.
IAO_0000117: Damion Dooley

awaiting ontology review
type: Class
subclass of: Thing
IAO_0000115: This class is a temporary holding bin for items that need a class hierarchy home, definition, and/or subclass items. Some classes have subclasses that are currently disjoint in other ontologies like ENVO, so awaiting resolution on such issues.
IAO_0000117: Damion Dooley

GENEPIO_0001433
type: Class
subclass of: user identifier
IAO_0000115: The IRIDA user ID is a user account identifier provided by the IRIDA.ca system.
IAO_0000117: Damion Dooley

exposure group healthy count
type: Class
subclass of: STATO_0000047
IAO_0000115: The count of healthy individuals or animals on a certain date/time from a group that was likely exposed to a pathogen
IAO_0000117: Damion Dooley

exposure group ill count
type: Class
subclass of: STATO_0000047
IAO_0000115: The count of ill individuals or animals on a certain date/time from a group that was likely exposed to a pathogen
IAO_0000117: Damion Dooley

human general activity
type: Class
subclass of: BFO_0000015

exposure history record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value.

isolate history record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

outbreak history record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet).

pregnancy history record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: Needs to cover the various pregnancy events

diagnosis record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: Issue: a diagnosis is a set of diseases, each of which can be marked primary or secondary "Illness causality" with respect to a particular case? Requires a relation annotation.

exposure event record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

hospitalization event record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

exposure history item
type: Class
subclass of: IAO_0000416
comment: An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value.

hospital admission date
type: Class
subclass of: hospitalization history item

exposure event end
type: Class
subclass of: exposure history item
IAO_0000115: A date-time datum that marks the end of possible human or animal exposure to a pathogen agent, directly or indirectly.
IAO_0000117: Damion Dooley

exposure event start
type: Class
subclass of: exposure history item
IAO_0000115: A date-time datum that marks the start of a human or animal exposure event to a suspected pathogen agent, directly or indirectly.
IAO_0000117: Damion Dooley
IAO_0000600: This datum is NOT predicted as a function of pathogen and first symptom date.

hospitalization history item
type: Class
subclass of: IAO_0000416

isolate history item
type: Class
subclass of: IAO_0000416

outbreak history item
type: Class
subclass of: IAO_0000416
comment: An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet).

hospital discharge date
type: Class
subclass of: hospitalization history item
subclass of: Restriction
  on property: after
  some values from: hospital admission date

notification date
type: Class
subclass of: outbreak history item
IAO_0000114: IAO_0000428
IAO_0000115: A notification date is the date that an outbreak is suspected by a laboratory or other agency and is reported per outbreak detection guidelines.
IAO_0000117: Damion Dooley

outbreak date
type: Class
subclass of: outbreak history item
IAO_0000114: IAO_0000428
IAO_0000115: An outbreak date is on which disease onset appears to have occured
IAO_0000117: Damion Dooley

outbreak over
type: Class
subclass of: outbreak history item
subclass of: Restriction
  on property: after
  some values from: outbreak date
IAO_0000114: IAO_0000428
IAO_0000115: An outbreak over date is the date on which a disease outbreak appears to have abated
IAO_0000117: Damion Dooley

test history item
type: Class
subclass of: IAO_0000416
IAO_0000114: IAO_0000428

lab test result date
type: Class
subclass of: test history item
IAO_0000114: IAO_0000428

data enumeration
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000428
IAO_0000115: A data item that is a set of entities, referenced by mention, that don't necessarily have something in common.
IAO_0000117: 0000-0002-8844-9165
IAO_0000117: 0000-0002-9578-0788
date: 2022-01-31T03:45:04Z
comment: While "enumeration" is a "data item" not everything referenced within an enumeration qualifies as a "data item". Not to be confused with "data set" which describes "data item"s of the same type that have something in common.

signs and symptoms
type: Class
subclass of: analytic datum
IAO_0000115: An analytic datum which describes the observed or detectable signs, and experienced symptomps of an illness, injury, or condition.
IAO_0000117: 0000-0002-9578-0788
IAO_0000119: https://en.wikipedia.org/wiki/Signs_and_symptoms
date: 2022-01-31T23:08:50Z
has exact synonym: signs & symptoms

food specimen datum
type: Class
subclass of: specimen datum
IAO_0000114: IAO_0000428
IAO_0000115: A particular attribute (feature, quality or process history) of a food sample.
IAO_0000117: Damion Dooley
comment: The underlying facets will be supplied from the FoodOn food ontology.

food specimen specification
type: Class
subclass of: data specification
user interface feature: order: FOODON:03411564 # food source FOODON:00002381 # food product by organism FOODON:03311737 # processed food product NCIT:C71898 # brand name
IAO_0000114: IAO_0000428
IAO_0000115: A food specimen type is a categorization of a food specimen, by the organism it is or came from, or by a class of food products.
IAO_0000117: Damion Dooley

disease cluster notification agency
type: Class
subclass of: OBI_0000245
IAO_0000114: IAO_0000428
IAO_0000115: An agency that has reported a disease cluster.
IAO_0000117: Damion Dooley

obsolete: NCBI BioProject ID
type: Class
IAO_0000115: This is a subset of OBI investigation identifier. It pertains only to NCBI Biosample projects
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/OBI_0001628
deprecated: true

exposure group unknown health status count
type: Class
subclass of: STATO_0000047
IAO_0000115: The count of individuals or animals for which no health status is available on a certain date/time from a group that was likely exposed to a pathogen.
IAO_0000117: Damion Dooley

person role
type: Class
equivalent class: Class
  intersection of: animal role
  intersection of: Restriction
    on property: inheres in
    some values from: NCBITaxon 9606
subclass of: animal role
IAO_0000114: IAO_0000428
IAO_0000115: A role which inheres in a person and is realized by the process of being in the context of civilization
IAO_0000117: Damion Dooley

exposed person role
type: Class
subclass of: person role
IAO_0000115: An exposed person role is the role a person takes on who has been exposed to a pathogen. In serious situations this may call for special treatment, e.g. quarantine.
IAO_0000117: Damion Dooley

parent-guardian role
type: Class
subclass of: person role

illness causality
type: Class
subclass of: analytic datum
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

pre-existing condition
type: Class
subclass of: illness causality

resolving health trend
type: Class
subclass of: health status trend datum
subclass of: Restriction
  on property: after
  some values from: stable health trend
IAO_0000114: IAO_0000428
IAO_0000115: To restore to the normal state after some pathologic process.
IAO_0000117: Damion Dooley
IAO_0000119: Dorland's Illustrated Medical Dictionary, 30th ed.
has exact synonym: improving
has exact synonym: recovering

close interpersonal relationship exposure
type: Class
subclass of: exposure by human contact
IAO_0000117: Damion Dooley

obsolete: household exposure
type: Class
IAO_0000117: Damion Dooley
IAO_0000231: Found to be redudant with another term, deprecrated in favor of said term.
IAO_0100001: GENEPIO_0100212
deprecated: true

exposure to individual with diarrhea
type: Class
subclass of: human to human exposure process
IAO_0000117: Damion Dooley

other human exposure
type: Class
subclass of: human to human exposure process
IAO_0000117: Damion Dooley

sexual contact exposure
type: Class
subclass of: exposure by human contact
IAO_0000117: Damion Dooley

exposure via diaper changing (human fecal)
type: Class
subclass of: human to human exposure process
IAO_0000117: Damion Dooley

container identifier
type: Class
subclass of: IAO_0000577

outbreak identifier
type: Class
subclass of: IAO_0000577
has db xref: PulseNet: Outbreak

reference genome size
type: Class
subclass of: sequencing assembly datum
subclass of: STATO_0000047
subclass of: Restriction
  on property: IAO_0000039
  some values from: UO_0000244
subclass of: Restriction
  on property: is about
  some values from: SO_0001505
in subset: GENEPIO

assembly genome size
type: Class
subclass of: assembly quality control datum
subclass of: Restriction
  on property: IAO_0000039
  some values from: UO_0000244
IAO_0000114: IAO_0000428
IAO_0000115: The assembly genome size is the sum of all lengths of a sequence assembly's contigs.
IAO_0000117: Damion Dooley
in subset: GENEPIO
comment: As noted in Quast documentation: " The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. "

reference genome identifier
type: Class
subclass of: sequencing assembly datum
subclass of: sequence identifier
subclass of: Restriction
  on property: is about
  some values from: SO_0001505
IAO_0000115: Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community
IAO_0000117: Damion Dooley
in subset: GENEPIO

genome size delta ratio
type: Class
subclass of: assembly quality control datum
metadata section: Assembly QC
IAO_0000114: IAO_0000428
IAO_0000115: The 'genome size delta ratio' is a ratio of the difference between a sample's genome assembly size and the size of a given reference genome, over the reference genome size. The formula: | (reference_genome_size - assembly_genome_size) | / reference_genome_size This yeilds a decimal / percentage ranging from 0 = exact length, to say .1 which is equivalent to a 10% variance. If the ratio is too far from a quality control ratio that depends on the species in question, this indicates a bad assembly or a mis-identified sample.
IAO_0000117: Damion Dooley
in subset: GENEPIO

genome size delta ratio QC threshold
type: Class
subclass of: assembly quality control datum
metadata section: Assembly QC
IAO_0000114: IAO_0000428
IAO_0000115: This is the upper acceptable limit of the 'genome size delta ratio' with respect to a particular species. For Salmonella a 0.10 variance in length between an assembly size and a reference genome size may be acceptable. For E-coli a more generous 0.30 or .40 variance should be allowed, given the pathogenic subspecies’ highly dynamic genome.
in subset: GENEPIO

contig N50 length QC threshold
type: Class
subclass of: contig length
metadata section: Assembly QC
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000428
IAO_0000115: The contig N50 length QC threshold is a minimum length threshold that a contig N50 length datum should be above for good QC. A lower length is indicative of assembly problems (insufficient read depth) or a mismatched reference genome.
IAO_0000117: Damion Dooley
in subset: GENEPIO

contig N99 length QC threshold
type: Class
subclass of: contig length
metadata section: Assembly QC
IAO_0000112: 2000
IAO_0000114: IAO_0000428
IAO_0000115: The contig N99 length QC threshold is the minimum length that a contig N99 or NG99 length datum can be for satisfactory QC. This threshold avoids having too many gene coding regions prematurely clipped inside short contigs. An assembly having 1% or more of its content in less than 2Kbp chunks is cause for concern. Bacterial genes are generally about 1Kbp in length.
IAO_0000117: Damion Dooley
in subset: GENEPIO

subject organism (host) taxonomic species
type: Class
subclass of: OBI_0001930
subclass of: Restriction
user interface feature: lookup
IAO_0000112: Homo sapiens
IAO_0000114: IAO_0000428
IAO_0000115: The species of the host organism from which a specimen (pathogen) organism was obtained. Use the full taxonomic name, eg, "Homo sapiens".
IAO_0000117: Damion Dooley
IAO_0000119: NCBI BioSample Pathogen.cl standard

Axiom
annotated source: subject organism (host) taxonomic species
annotated property: subClassOf
annotated target: Restriction
user interface feature: lookup

assembly quality control datum
type: Class
subclass of: sequencing assembly datum
subclass of: Restriction
  on property: is about
  some values from: SO_0000353
metadata section: Assembly QC
IAO_0000114: IAO_0000428
IAO_0000115: A single datum having to do with a metric for genomic sequence assembly quality control. A "quality control measurement" can be defined as a measurement that has some norm within a definable context, e.g. for a certain subspecies. It may be a calculated quantity. A "quality control metric" is an upper or lower bound threshold that a measurement is compared to. Surpassing the threshold may indicate an error situation. A "measure" can indicate an amount of activity, consumption, transformation, etc. but doesn't itself convey an over-stepping of bounds in the way that a metric does.
IAO_0000117: Damion Dooley
in subset: GENEPIO

clinical or host-associated pathogen
type: Class
subclass of: specimen category
subclass of: Restriction
IAO_0000117: Damion Dooley
has alternative id: GSCID-BRC:Clinical/host-associated pathogen
has alternative id: NCBI:Pathogen.cl

Clinical/host-associated pathogen
type: Axiom
annotated source: clinical or host-associated pathogen
annotated property: subClassOf
annotated target: Restriction

Pathogen.cl
type: Axiom
annotated source: clinical or host-associated pathogen
annotated property: subClassOf
annotated target: Restriction

contig N99
type: Class
subclass of: contig length
metadata section: Assembly QC
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000428
IAO_0000115: The N99 length definition is identical to the N50 definition except that the threshold for determining the contigs is 1% of the nucleotides. This contig basepair length can be compared to a minimum threshold to determine if gene annotation (where contigs greater than say 2000bp are necessary) would generally succeed.
IAO_0000117: Damion Dooley
in subset: GENEPIO

contig count QC threshold
type: Class
subclass of: contig count
metadata section: Assembly QC
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000428
IAO_0000115: The upper threshold of contig counts that are acceptable in a genome assembly. This may vary based on the overall genome length and depth of coverage. A large contig count may indicate insufficient read coverage.
IAO_0000117: Damion Dooley

project relevance
type: Class
subclass of: IAO_0000005
IAO_0000114: IAO_0000122
IAO_0000115: Indicates how the knowledge derived from the project can be applied, and to what field(s).
IAO_0000116: Damion Dooley's note: NAIAD GRCID-BRC has Project Relevance map to OBO Foundry Study Design (http://purl.obolibrary.org/obo/OBI_0500000) but this is a bit of a stretch.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project

agricultural project relevance
type: Class
subclass of: project relevance

medical knowledge relevance
type: Class
subclass of: project relevance

industrial processing relevance
type: Class
subclass of: project relevance

evolution modelling relevance
type: Class
subclass of: project relevance

environmental project relevance
type: Class
subclass of: project relevance

model organism relevance
type: Class
subclass of: project relevance

obsolete: NCBI BioProject model
type: Class
IAO_0000115: The NCBI BioProject model includes all datums associated with the current NCBI BioProject specification.
IAO_0000117: Damion Dooley
IAO_0100001: NCBI BioProject standard
deprecated: true

obsolete: NCBI SRA model
type: Class
IAO_0100001: NCBI SRA meta information standard
deprecated: true

draft NCBI BioSample model - mixed clinical and environmental/food/other
type: Class
subclass of: draft NCBI component model
term source: http://www.ncbi.nlm.nih.gov/biosample/docs/attributes/
term source: http://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/
IAO_0000114: IAO_0000428
IAO_0000116: Damion Dooley notes: NCBI doesn't quite make the distinction but it may be helpful to distinguish sample submission facilitator vs submitter/repository organization contact? So should we have a BioSample_submission_facilitator field and a BioSample_contact_information field?
IAO_0000117: Damion Dooley
comment: Damion's note: There are a few different kinds of biosample, and required fields depend on the type selected.

monoisolate sample scope
type: Class
subclass of: OBI_0001884
user interface label: monoisolate
IAO_0000114: IAO_0000122
IAO_0000115: A monoisolate sample scope involves specimens from a single animal, cultured cell-line, inbred population, or possibly a heterogeneous population when a single genome assembly is generated from a pooled sample because multiple individuals are needed to collect enough material and an inbred line is not available; however, this situation is not preferred.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/
OBI_0001886: monoisolate

multiisolate sample scope
type: Class
subclass of: OBI_0001884
user interface label: multiisolate
IAO_0000114: IAO_0000122
IAO_0000115: A multiisolate sample scope contains multiple individuals that represent distinct specimen collections, a population (representative of a species).
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/
IAO_0000600: This is often used for variation or phenotype and genotype studies. This should not be used when multiple genomes will be annotated. Eventually, multiple locus_tag prefixes will be able to be assigned to a single multiisolate genome sequencing project, but currently only a single prefix can be registered per project. Therefore, individual monoisolate projects need to be registered when more than one genome will be annotated.

multispecies sample scope
type: Class
subclass of: OBI_0001884
user interface label: multispecies
IAO_0000114: IAO_0000122
IAO_0000115: A multi-species sample scope involves a sample representing multiple species.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

environment sample scope
type: Class
subclass of: OBI_0001884
user interface label: environment
IAO_0000114: IAO_0000122
IAO_0000115: An environment sample scope indicates that the species content of the sample is not known. Generally, nucleic acid is directly isolated from an environmental sample for analysis. This is used for metagenome studies.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

synthetic sample scope
type: Class
subclass of: OBI_0001884
IAO_0000114: IAO_0000122
IAO_0000115: A synthetic sample scope involves a sample synthesized in a laboratory.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

single cell
type: Class
subclass of: OBI_0001884
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

other project objective
type: Class
subclass of: OBI_0001892
user interface label: other
IAO_0000114: IAO_0000122
IAO_0000115: Other project objective: specify an objective not listed above
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

environmental, food or other pathogen
type: Class
subclass of: specimen category
subclass of: Restriction
IAO_0000117: Damion Dooley
has alternative id: GSCID-BRC:environmental/food/other
has alternative id: NCBI:Pathogen.env

environmental/food/other
type: Axiom
annotated source: environmental, food or other pathogen
annotated property: subClassOf
annotated target: Restriction

Pathogen.env
type: Axiom
annotated source: environmental, food or other pathogen
annotated property: subClassOf
annotated target: Restriction

whole genomic data capture
type: Class
subclass of: OBI_0001899
user interface label: whole
IAO_0000114: IAO_0000122
IAO_0000115: Whole: the project makes use of the whole sample material (most common case). Use this for whole genome sequencing studies, transcriptome studies that are not targeting specific loci, epigenetic studies of a genome, and metagenomes or unbiased transcriptome studies of metagenomes.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

raw sequence read objective
type: Class
subclass of: OBI_0001892
user interface label: raw sequence reads
IAO_0000114: IAO_0000122
IAO_0000115: A raw sequence reads project objective has the goal of submission of raw reads to SRA or Trace repositories
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

sequence project objective
type: Class
subclass of: OBI_0001892
user interface label: sequence
IAO_0000114: IAO_0000122
IAO_0000115: A sequence project objective has a goal of submission of sequence data to standard archival sequence databases (yielding accession.version identifiers; e.g., whole genome shotgun, cDNA sequences, transcript shotgun assemblies)
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

analysis objective
type: Class
subclass of: OBI_0001892
user interface label: analysis
IAO_0000114: IAO_0000122
IAO_0000115: An "analysis project objective" indicates there was an other analysis not otherwise indicated, includes submission of BAM files.
IAO_0000116: This defn. could be a negation of the "not otherwise indicated".
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

assembly objective
type: Class
subclass of: OBI_0001892
user interface label: assembly
IAO_0000114: IAO_0000122
IAO_0000115: Submission of genome assembly (AGP data)
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

sequence annotation objective
type: Class
subclass of: OBI_0001892
user interface label: annotation
IAO_0000114: IAO_0000122
IAO_0000115: Sequence annotation data
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

sequence variation project objective
type: Class
subclass of: OBI_0001892
user interface label: sequence variation
IAO_0000114: IAO_0000122
IAO_0000115: Variation: identification of sequence variation data for submission to dbSNP or dbVAR
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

epigenetic markers objective
type: Class
subclass of: OBI_0001892
user interface label: epigenetic markers
IAO_0000114: IAO_0000122
IAO_0000115: DNA methylation, histone modification, chromatin accessibility datasets
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

transcript or protein expression objective
type: Class
subclass of: OBI_0001892
user interface label: expression
IAO_0000114: IAO_0000122
IAO_0000115: Expression: assays of transcript or protein existence or abundance
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

mapping objective
type: Class
subclass of: OBI_0001892
user interface label: maps
IAO_0000114: IAO_0000122
IAO_0000115: Maps: non-sequence based map data; e.g., genetic, radiation hybrid, cytogenetic, etc.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

phenotypic observation data from specimen
type: Class
subclass of: OBI_0001882
IAO_0000114: IAO_0000123
IAO_0000115: Phenotypic descriptive data.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

sequencing project method
type: Class
subclass of: OBI_0001896
user interface label: select sequence if any sequence data is generated from this project.
user interface label: sequencing
IAO_0000114: IAO_0000122
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

array project method
type: Class
subclass of: OBI_0001896
user interface label: array
IAO_0000114: IAO_0000122
IAO_0000115: Select Array if that is the primary method and no sequence data is submitted
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

mass spectrometry project method
type: Class
subclass of: OBI_0001896
user interface label: mass spectrometry
IAO_0000114: IAO_0000122
IAO_0000115: Select Mass Spectrometry if that is the primary method
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

contact specification - person
type: Class
subclass of: contact specification
user interface feature: order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C42775 # email address GENEPIO:0001756 # phone

investigation datum
type: Class
subclass of: IAO_0000109
IAO_0000115: A categorical investigation datum is a datum pertaining to some entity examined for scientific research or diagnostic purposes and which has a scope that is broader than one of the clinical, environmental or epidemiological domains.
IAO_0000117: Damion Dooley

commensal role
type: Class
subclass of: isolate organism role
IAO_0000115: An organism and its host share physical space but no evidence exists to determine if one benefits from this arrangement.

draft isolate details model
type: Class
subclass of: data specification

subject age
type: Class
subclass of: OBI_0001169
IAO_0000114: IAO_0000428
IAO_0000115: A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time.
IAO_0000117: Damion Dooley

draft NCBI component model
type: Class
subclass of: draft data standard
IAO_0000114: IAO_0000428

draft IRIDA BioSample model
type: Class
subclass of: draft IRIDA standard

draft GenEpiO epidemiology case record
type: Class
subclass of: draft GenEpiO component record
subclass of: Restriction
  on property: is about
  some values from: IDO_0000531

subject description
type: Class
subclass of: SIO_000136
subclass of: Restriction
IAO_0000115: A subject description is a field containing additional information about an organism (related to an investigation, study and/or specimen) that is not included in other defined vocabulary fields.
IAO_0000117: Damion Dooley
IAO_0000119: NCBI BioSample Pathogen.cl standard

host description
type: Axiom
annotated source: subject description
annotated property: subClassOf
annotated target: Restriction

host profile or identifers
type: Class
subclass of: SIO_000136
term source: NCBI BioSample
IAO_0000115: The host profile or identifiers text is the "identification or description of the specific individual from which this sample was obtained".
IAO_0000117: Damion Dooley
has db xref: NCBI BioSample: isolate

subject identifier
type: Class
subclass of: OBI_0001141
IAO_0000114: IAO_0000428
IAO_0000115: A subject identifier is an identifier of a subject organism within the context of a particular investigation, study, or specimen extraction event.
IAO_0000117: Damion Dooley
comment: This varies in its type (numeric or string) and its central repository depending on its context (use in a particular application/instance). Note: GSCID-BRC specification states " 'Host' is not the preferred term since some specimens may lack any detectable pathogen". In other words, a person would technically (logically) only have a host identifier AFTER they have been diagnosed as having a pathogen. A health care personal identifier, or a case identifier would be better than a more ephemeral "host id"

subject disease
type: Class
subclass of: DOID 4
subclass of: Restriction
  on property: inheres in
  some values from: subject organism
IAO_0000114: IAO_0000428
IAO_0000115: Name of disease in a subject that is related to a given investigation, study and/or specimen.
IAO_0000117: Damion Dooley
IAO_0000119: NIAID GSCID-BRC metadata working group
comment: Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067

missing
type: Class
subclass of: datum status
term source: INSDC term (top level)
IAO_0000115: A categorical choice recorded when a measurement value was known to be recorded in the past but the observed value cannot be located or retrieved for some reason.
IAO_0000119: missing-values.html
has db xref: INSDC standard
has db xref: NCBI Biosample: missing

not applicable
type: Class
subclass of: datum status
term source: INSDC term (top level)
IAO_0000112: 'not applicable' is an appropriate value for the measure of femur length for a patient with a missing limb
IAO_0000114: IAO_0000428
IAO_0000115: A categorical choice recorded when a measurable datum does not apply to a given context.
IAO_0000117: Damion Dooley
IAO_0000119: missing-values.html
has db xref: INSDC standard
has db xref: NCBI BioSample Pathogen.cl standard

not collected
type: Class
subclass of: missing
term source: INSDC term (lower level)
IAO_0000115: A categorical choice recorded when a datum was not measured with respect to some entity during some process.
IAO_0000119: missing-values.html
has db xref: INSDC standard
has db xref: NCBI Biosample: not collected

draft isolate identifier model
type: Class
subclass of: data specification

draft GenEpiO isolate testing model
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428

draft NCBI isolate source location model
type: Class
subclass of: draft NCBI component model
IAO_0000114: IAO_0000428

draft GenEpiO isolate environment model
type: Class
subclass of: draft GenEpiO component record

subject disease stage
type: Class
subclass of: personal health datum
IAO_0000115: A subject disease stage is a measure of the acuteness of a subject organism's diagnosed disease, if any, at a given time in an investigation, study or specimen extraction event.
IAO_0000117: Damion Dooley
IAO_0000119: NCBI BioSample Pathogen.cl standard

environmental datum
type: Class
subclass of: IAO_0000109

temperature of sample
type: Class
subclass of: environmental datum
subclass of: Restriction
  on property: is about
  some values from: PATO_0000146

de-novo assembly
type: Class
subclass of: assembly method
disjoint with: mapping (reference based)

obsolete: sample body source
type: Class
IAO_0000231: IAO_0000227
IAO_0100001: subject anatomical site
deprecated: true

contig length QC threshold
type: Class
subclass of: contig length
IAO_0000111: contig pre-analysis minimum length QC threshold
IAO_0000114: IAO_0000123
IAO_0000115: A 'contig length QC threshold' is an integer setting which can be applied by an algorithm to an array of assembly and annotation contig lengths to remove (filter out) all items less than the threshold value. The reduced array is used for calculation of statistics.
IAO_0000117: Damion Dooley
IAO_0000119: http://quast.bioinf.spbau.ru/manual.html
comment: QUAST specifies which of its report stats are affected by the "--min-contig" minimum contig length parameter.

contig NG50
type: Class
subclass of: contig length
IAO_0000114: IAO_0000428
IAO_0000115: The NG50 length is the same as the N50 length except that the length of the reference genome is used in the calculation rather than the assembly genome size.
IAO_0000117: Damion Dooley
comment: "Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this, the authors of the Assemblathon competition derived a new measure called NG50. The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than the N50 statistic." - wikipedia

contig length
type: Class
subclass of: assembly quality control datum
subclass of: Restriction
  on property: is about
  some values from: SO_0000149
IAO_0000114: IAO_0000123
IAO_0000115: A contig length is the count of base pairs in a given sequence assembly contig.
IAO_0000117: Damion Dooley

contig L50
type: Class
subclass of: contig count
metadata section: Assembly QC
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000428
IAO_0000115: Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation.
IAO_0000117: Damion Dooley
IAO_0000119: QUAST manual

contig LG99
type: Class
subclass of: contig count
metadata section: Assembly QC
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000428
IAO_0000115: The LG99 count is like the L99 count except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths.
IAO_0000117: Damion Dooley

obsolete: specimen from subject datum
type: Class
IAO_0000114: IAO_0000428
IAO_0000115: An organism isolate datum is any datum pertaining to an isolate organism
IAO_0000117: Damion Dooley
deprecated: true

animal body product
type: Class
subclass of: subject body product
subclass of: Restriction
  on property: RO_0003001
  some values from: OBI_0100026
IAO_0000114: IAO_0000428
IAO_0000115: A product of an animal, as in blood, feces, sputum, etc. that has no particular anatomical site
IAO_0000117: Damion Dooley

obsolete: specimen source material category
type: Class
IAO_0000115: This is the scientific role or category that the subject organism or material has with respect to an investigation.
IAO_0000117: Damion Dooley
IAO_0100001: specimen source material category
deprecated: true

draft GenEpiO general information record
type: Class
subclass of: draft GenEpiO component record

antigenic formula
type: Class
subclass of: test specification
subclass of: Restriction
  on property: is about
  some values from: CHEBI_59132
subclass of: Restriction
  on property: is about
  some values from: NCIT C53471
IAO_0000115: An antigenic formula is a string composed of codes representing categorized results of tests performed on various viral, bacterial or immune cell surface antigens.
IAO_0000117: Damion Dooley

specimen organism taxonomy (species)
type: Class
subclass of: OBI_0001930
subclass of: Restriction
  on property: OBI_0001927
  some values from: Class
    union of: NCBITaxon_10239
    union of: NCBITaxon 2
    union of: NCBITaxon 2157
    union of: NCBITaxon 2759
user interface feature: lookup
IAO_0000114: IAO_0000428
IAO_0000115: This is the taxonomic species descriptor of a specimen isolate (an organism found within a specimen.)
IAO_0000117: Damion Dooley

identifier model
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000115: An identifier moe3l indicates an identifier, the organization it has been issued by, and the status of the identifier - whether it is a primary one, active or archaic.
IAO_0000117: Damion Dooley

curator organization name
type: Class
subclass of: investigation datum
user interface feature: help:This should be populated with a selection from INSDC.org controlled vocabulary for providers: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt
IAO_0000114: IAO_0000428
IAO_0000115: The curator organization name is the name of an organization that manages a given repository of entities (samples, isolates, sequences ...)
IAO_0000117: Damion Dooley

Agriculture and Agri-Food Canada
type: Class
subclass of: OBI_0001893
has db xref: INSDC:institution_code:BRS
has db xref: IRIDA:ACK

isolate identifier
type: Class
subclass of: IAO_0000577
IAO_0000114: IAO_0000428
IAO_0000115: An isolate identifier is an identifier assigned to a given isolate by a particular agency that is handling or storing it.
IAO_0000117: Damion Dooley

identifier status
type: Class
subclass of: investigation datum
IAO_0000114: IAO_0000428
IAO_0000115: An identifier status describes the principle role of an identifier assigned to an entity by its curator or handler. An entity may have a number of identifiers assigned to it over time. An identifier may be phased-out as can happen when its content is transferred to another curator.
IAO_0000117: Damion Dooley

data protection role
type: Class
subclass of: BFO_0000023
term source: GenEpiO
IAO_0000114: IAO_0000428
IAO_0000115: A data protection role is a role (or user permission) that a user has with respect to particular data.
IAO_0000116: A data server may be able to provide a protected(modified) dataset with metadata indicating what parts have a protection role with respect to the user requesting this information. A data protection role would be inherited from a user's relation to an entitiy to the entity's components or subclasses.
IAO_0000117: Damion Dooley

original submission
type: Class
subclass of: identifier status
IAO_0000114: IAO_0000428
IAO_0000115: An identifier used in the initial submission of content to a repository.

NCBI Contributing organization / project
type: Class
subclass of: organization identifier
IAO_0000114: IAO_0000428
IAO_0000116: This was created to help define a contributing organization to a repository. However this still needs organizing. The "collected_by" field is free text but contact name AND organization could be associated with this in controlled vocabulary.

food - liquid
type: Class
subclass of: food specimen

draft NCBI BioSample identifier model
type: Class
subclass of: draft NCBI component model
IAO_0000114: IAO_0000428

INSDC institution code
type: Class
subclass of: organization identifier
IAO_0000114: IAO_0000428
IAO_0000115: An INSDC institution code is an identifier of an organization from a list of sequence repository organizations managed by INSDC.
IAO_0000117: Damion Dooley
IAO_0000119: http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier

draft IRIDA epidemiological case model
type: Class
subclass of: draft IRIDA standard

previous (archaic) identifier
type: Class
subclass of: identifier status
IAO_0000114: IAO_0000428
IAO_0000115: An identifier that had been used previously but is no longer promoted.
IAO_0000117: Damion Dooley

geographic location datum
type: Class
subclass of: IAO_0000109
IAO_0000114: IAO_0000428
IAO_0000115: A geographical location datum is a datum that refers to a real, hypothesized or fanciful spatial location
IAO_0000117: Damion Dooley

obsolete: categorical tree specification
type: Class
IAO_0000115: A categorical tree specification datum is a categorical value specification which takes its value from the ontology URI identifier of any one of its subclass items; these may be organized in a hierarchy.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/OBI_0001930
comment: A categorical tree specification datum may have its own URI identifier as its value. This could be interpreted to mean that the datum was recorded but that no particular categorical subclass distinction was observed. This in effect makes the datum act as a boolean variable.
deprecated: true

latitude and longitude coordinate (ISO 6709)
type: Class
subclass of: draft NCBI component model
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: A geographic coordinate entity composed of both latitude and longitude components.

draft NCBI BioSample geo_loc_name model
type: Class
subclass of: draft NCBI component model
subclass of: Restriction
  on property: is about
  some values from: OBI_0100051
user interface feature: order: NCIT:C25464 # country ENVO:00000005 # state / province etc.
IAO_0000114: IAO_0000428
IAO_0000115: Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"
IAO_0000117: Damion Dooley

draft GenEpiO isolate sequencing model
type: Class
subclass of: draft GenEpiO component record

case identifier
type: Class
subclass of: IAO_0000577
IAO_0000115: A case ID is a unique identifier associated with a particular episode of care for an individual or animal.
IAO_0000117: Damion Dooley

neuter
type: Class
subclass of: PATO_0001894
disjoint with: PATO_0000383
disjoint with: PATO_0000384
IAO_0000115: An animal that has had a substantial part of its reproductive organs removed surgically.
IAO_0000117: Damion Dooley
has db xref: NCBI BioSample: neuter
comment: Not a PATO phenotypic sex catigorical value.

pooled male and female
type: Class
equivalent class: Class
  union of: PATO_0000383
  union of: PATO_0000384
subclass of: PATO_0001894
term source: NCBI BioSample
IAO_0000115: 'pooled male and female' is a categorical value used when the male and female categories or levels of a factor are combined. If used to describe a single organism, then the organism will be one or the other.
IAO_0000116: Not a PATO phenotypic sex catigorical value.
IAO_0000117: Damion Dooley
has db xref: NCBI BioSample: 'pooled male and female'

in process
type: Class
subclass of: missing
IAO_0000114: IAO_0000428
IAO_0000115: A categorical choice recorded while the data for a given measurable datum has not finished being collected, is awaiting a conclusion, or has not yet been communicated.
IAO_0000117: Damion Dooley
has exact synonym: undetermined

swimming / wading
type: Class
subclass of: human water activity

infection detail datum
type: Class
subclass of: patient as host datum
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: NECESSARY? : What details are categorical and what are freehand? This item was originally too broad; moved sub-items to Treatment.

antibiotics required
type: Class
subclass of: infection detail datum
IAO_0000114: IAO_0000428
IAO_0000116: This is problematic - its not clear if this is reporting that antibiotics were administered, or whether they are recommended as a result of diagnosis.
IAO_0000117: Damion Dooley

INSDC standard
type: Class
subclass of: NCIT C103180
IAO_0000114: IAO_0000120
IAO_0000115: The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations.
IAO_0000117: Damion Dooley
IAO_0000118: International Nucleotide Database Collaboration standard
has db xref: INSDC

outcome of pregnancy associated with illness
type: Class
subclass of: awaiting ontology review
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

not provided
type: Class
subclass of: missing
term source: INSDC term (lower level)
IAO_0000115: a categorical choice indicating that information of an expected format was not given; a value may be given at the later stage.
IAO_0000119: missing-values.html
has db xref: INSDC standard

stable health status
type: Class
subclass of: subject health status (UK NHS)
subclass of: Restriction
  on property: after
  some values from: serious health status
subclass of: Restriction
  on property: RO_0002083
  some values from: fair health status
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

induced abortion
type: Class
subclass of: outcome of pregnancy associated with illness

live birth
type: Class
subclass of: outcome of pregnancy associated with illness
IAO_0000114: IAO_0000428

obsolete: gestation duration (weeks)
type: Class
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/VT_0002292
deprecated: true

date of pregnancy outcome
type: Class
subclass of: pregnancy history item
subclass of: Restriction
  on property: after
  some values from: date of conception

contact specification - physician
type: Class
subclass of: contact specification - person
subclass of: Restriction
  on property: is about
  some values from: NCIT C25741
subclass of: Restriction
  on property: has component
  some values from: contact specification - address
IAO_0000114: IAO_0000428

obsolete: matrix - solid
type: Class
deprecated: true

contact specification - parent/guardian
type: Class
subclass of: contact specification - person
subclass of: Restriction
  on property: is about
  some values from: parent-guardian role
IAO_0000114: IAO_0000428

contact specification - patient
type: Class
subclass of: contact specification - person
subclass of: Restriction
  on property: is about
  some values from: OBI_0000093
subclass of: Restriction
  on property: has component
  some values from: contact specification - address
IAO_0000114: IAO_0000428

draft GenEpiO case epidemiology record
type: Class
subclass of: draft GenEpiO component record

contact specification - address
type: Class
subclass of: contact specification
user interface feature: order: NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision aka state/province/territory/region (via GenEpiO -> GAZ ) NCIT:C80234 # Municipality (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address NCIT:C25621 # postal code
IAO_0000114: IAO_0000428
IAO_0000115: The address component of a contact specification.

obsolete: draft IRIDA model
type: Class
IAO_0000114: IAO_0000428
IAO_0100001: GENEPIO_0001829
deprecated: true

laboratory sequencing datum
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000428
IAO_0000115: A datum related to the sequencing assay process applied to an isolate.
IAO_0000117: Damion Dooley

host illness associated with
type: Class
subclass of: awaiting ontology review
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

draft subject demographic specification
type: Class
subclass of: draft GenEpiO component record

E. coli K antigen specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: CHEBI_73772
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: string

other antigen specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: CHEBI_59132
subclass of: Restriction
  on property: OBI_0002135
  qualified cardinality: 1
  on data range: Datatype
    on datatype: string
    with restrictions:
      max length: 6

E. coli serotype specification
type: Class
subclass of: serotype specification
IAO_0000114: IAO_0000428

Salmonella serovar specification
type: Class
subclass of: serotype specification
IAO_0000114: IAO_0000428
comment: Damion's note: This will be converted to a categorical tree specification list of serovars by name or id asap.

test specification
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000115: A lab test specification indicates the inputs and outputs (results / conclusions) of a test.
IAO_0000117: Damion Dooley

listeria antigen
type: Class
subclass of: OBI_0001933
subclass of: Restriction
  on property: OBI_0001927
  some values from: CHEBI_59132
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: string
    with restrictions:
      pattern: (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7)

obsolete: matrix - fluid
type: Class
deprecated: true

listeria serotype 1/2a
type: Class
subclass of: listeria antigen

listeria serotype 1/2b
type: Class
subclass of: listeria antigen

listeria serotype 1/2c
type: Class
subclass of: listeria antigen

listeria serotype 1/2
type: Class
subclass of: listeria antigen

listeria serotype 3a
type: Class
subclass of: listeria antigen

listeria serotype 3b
type: Class
subclass of: listeria antigen

listeria serotype 4a
type: Class
subclass of: listeria antigen

listeria serotype 4b
type: Class
subclass of: listeria antigen

listeria serotype 4c
type: Class
subclass of: listeria antigen

listeria serotype 4d
type: Class
subclass of: listeria antigen

listeria serotype 4e
type: Class
subclass of: listeria antigen

non-monocytogenes listeria antigen
type: Class
subclass of: listeria antigen

listeria serotype 3c
type: Class
subclass of: listeria antigen

textual test result
type: Class
subclass of: IAO_0000300

obsolete: draft GenEpiO BioProject standard
type: Class
IAO_0000115: This is an organizational category for grouping parameters relevant to biomedical research projects.
IAO_0000117: Damion Dooley
IAO_0000231: IAO_0000103
deprecated: true

NCBI BioSample collection code
type: Class
subclass of: collection identifier
IAO_0000117: Damion Dooley
has db xref: NCBI BioSample: collection_code

draft NCBI BioSample host model
type: Class
subclass of: draft NCBI component model
subclass of: Restriction
  on property: is about
  some values from: IDO_0000531
IAO_0000114: IAO_0000428

food - solid
type: Class
subclass of: food specimen

lab test datum
type: Class
subclass of: IAO_0000027

Xbal
type: Class
subclass of: primary enzyme (LMAAI)

Ascl
type: Class
subclass of: primary enzyme (LMAAI)

Smal
type: Class
subclass of: primary enzyme (LMAAI)

Blnl
type: Class
subclass of: secondary enzyme (LMACI)

Apal
type: Class
subclass of: secondary enzyme (LMACI)

Kpnl
type: Class
subclass of: secondary enzyme (LMACI)

subgroup
type: Class
subclass of: test specification
IAO_0000114: IAO_0000122
IAO_0000115: Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate.
IAO_0000117: Damion Dooley
IAO_0000119: NCBI Biosample

viral subtype
type: Class
subclass of: test specification
user interface feature: help:This is an optional additional subtype classification as per organism convention
IAO_0000114: IAO_0000428
IAO_0000115: A viral subtype is a classification name for a virus according to some protocol.
IAO_0000117: Damion Dooley
IAO_0000119: NCBI BioSample

serotype specification
type: Class
subclass of: test specification
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: E. coli serotype specification
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: Salmonella serovar specification
IAO_0000114: IAO_0000428

phage type specification
type: Class
subclass of: test specification
term source: IRIDA
IAO_0000114: IAO_0000428
IAO_0000115: An integer and character referring to a pattern of opaque or confluent lysis caused by a panel of bacteriophage infections e.g. 14a.
IAO_0000117: Damion Dooley
has db xref: SNOMED: http://www.snomedbrowser.com/Codes/Details/272405002

obsolete: swab - food contact surface
type: Class
IAO_0000231: IAO_0000229
deprecated: true

NCBI culture collection
type: Class
subclass of: culture identifier
IAO_0000112: ATCC:26370
IAO_0000115: An NCBI culture collection is a composite identifier containing “institution code:collection code”.
IAO_0000600: Annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier.

NCBI specimen voucher
type: Class
subclass of: OBI_0001616
IAO_0000112: UAM:Mamm:52179
IAO_0000115: The NCBI specimen voucher is an identifier composed of “institution code:collection code:specimen id” parts. In addition to a specimen identifier, it includes an institution-code (and optional collection-code) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides.
has db xref: INSDC:specimen_voucher

culture identifier
type: Class
subclass of: IAO_0000577

subject organism common name
type: Class
subclass of: NCIT C42614
subclass of: Restriction
  on property: IAO_0000219
  some values from: OBI_0100026
IAO_0000112: human; dog; horse
IAO_0000115: The natural language (non-taxonomic) name of the type of organism (human or animal) that is the subject of a given investigation, study and/or specimen.
IAO_0000116: Damion Dooley's note: as of 2017 this is a problematic field for NCBI Biosample because it is slotted into "host" field, yet field is listed as "host common name" which does not fit with requirement that scientific name be provided.
IAO_0000117: Person: Damion Dooley

temperature of air - average daily
type: Class
subclass of: environmental datum
subclass of: Restriction
  on property: is about
  some values from: ENVO_00002005
subclass of: Restriction
  on property: is about
  some values from: PATO_0000146

obsolete: swab - inanimate object surface
type: Class
IAO_0000231: IAO_0000229
deprecated: true

obsolete: swab - meat
type: Class
IAO_0000231: IAO_0000229
deprecated: true

obsolete: swab - rectal swab
type: Class
IAO_0000231: IAO_0000229
deprecated: true

obsolete: swab - tissue
type: Class
IAO_0000231: IAO_0000229
deprecated: true

unknown source
type: Class
subclass of: CHMO_0002743

human clinical specimen
type: Class
subclass of: CHMO_0002743
subclass of: specimen source material category
IAO_0000118: patient sample

obsolete: environmental (swab or sampling)
type: Class
IAO_0000116: "environment (swab or sampling)" is a specific response for NCBI BioSample that could be mapped or unified with "environment sample" used elsewhere in GenEpiO
IAO_0000117: Damion Dooley
IAO_0100001: environmental specimen
deprecated: true

avian - wild
type: Class
subclass of: animal specimen

avian - domesticated
type: Class
subclass of: animal specimen

human clinical specimen - invasive
type: Class
subclass of: human clinical specimen

pH measurement
type: Class
subclass of: environmental datum
IAO_0000115: In chemistry, pH is a numeric scale used to specify the acidity or basicity(alkalinity) of an aqueous solution
IAO_0000117: Damion Dooley
IAO_0000119: Wikipedia
comment: Normally falls within the bounds of 0 - 14

precipitation
type: Class
subclass of: environmental datum

assembly and annotation project objective
type: Class
subclass of: sequencing assembly datum
IAO_0000114: IAO_0000428
IAO_0000115: The assembly and annotation objective is the set of objectives that assembly and annotation techniques (including instruments and software platforms) applied to a sample are meant to satisfy. This impacts on the quality control thresholds applied to the sequencing project.
IAO_0000117: Damion Dooley

line list row record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

draft GenEpiO component record
type: Class
subclass of: draft data standard
IAO_0000114: IAO_0000428
IAO_0000115: This class contains components under development for fulfilling GenEpiO and other standard data specifications. Components are relevant to epidemiological, laboratory, clinical or environmental pathogen sample data collection and analysis.
IAO_0000117: Damion Dooley

subnational region
type: Class
subclass of: ENVO_00000005
disjoint with: NCIT C25632
disjoint with: NCIT C87194
disjoint with: NCIT C89811
user interface label: region
user interface feature: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
IAO_0000114: IAO_0000428
IAO_0000115: A subnational region is a type of subnational entity similar to a nation's state, province, or territory.
IAO_0000117: Damion Dooley

public health data standard
type: Class
subclass of: NCIT C103180
IAO_0000114: IAO_0000428
IAO_0000115: A data standard related to public health research and service delivery.
IAO_0000117: Damion Dooley

GENEPIO_0001744
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

reagent derived material from specimen
type: Class
subclass of: OBI_0001882
IAO_0000114: IAO_0000122
IAO_0000115: Reagent: material studied was obtained by chemical reaction, precipitation.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

transcriptome data from specimen
type: Class
subclass of: OBI_0001882
user interface label: transcriptome
IAO_0000114: IAO_0000122
IAO_0000115: Transcriptome: transcript and/or expression data.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

proteome data derived from specimen
type: Class
subclass of: OBI_0001882
user interface label: proteome
IAO_0000114: IAO_0000122
IAO_0000115: Proteome material is protein or peptide sequences.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

purified chromosome from specimen
type: Class
subclass of: OBI_0001882
user interface label: purified chromosome
IAO_0000114: IAO_0000122
IAO_0000115: Purified chromosome: one or more chromosomes or replicons were experimentally purified.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

Targeted Locus Loci data capture
type: Class
subclass of: OBI_0001899
user interface label: targeted locus/loci
IAO_0000114: IAO_0000122
IAO_0000115: TargetedLocusLoci: capturing specific loci (gene, genomic region, bar code standard).
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

clone end data capture
type: Class
subclass of: OBI_0001899
user interface label: clone ends
IAO_0000114: IAO_0000122
IAO_0000115: CloneEnds: capturing clone end data.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

exome specific data capture
type: Class
subclass of: OBI_0001899
user interface label: exome
IAO_0000114: IAO_0000122
IAO_0000115: Exome: capturing exon-specific data.
IAO_0000117: Damion Dooley
IAO_0000119: NCBI BioSample
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

random survey data capture
type: Class
subclass of: OBI_0001899
user interface label: random survey
IAO_0000114: IAO_0000122
IAO_0000115: Sequences generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material
IAO_0000116: Is this with respect to an isolate or a specimen derived culture?
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54364/

contact specification
type: Class
subclass of: data specification
IAO_0000114: IAO_0000428
IAO_0000115: This is a collection of various human (and animal contact location) contact information specifications used in data standards.
IAO_0000117: Damion Dooley

contact specification - phone
type: Class
subclass of: contact specification
user interface feature: order: NCIT:C40978 # phone GENEPIO:0001896 # phone type
IAO_0000114: IAO_0000428

millimetres per day
type: Class
subclass of: UO_0000060
IAO_0000114: IAO_0000125
IAO_0000117: Damion Dooley

obsolete: millisiemens
type: Class
IAO_0100001: UO_0010002
deprecated: true

millisiemens per centimetre
type: Class
subclass of: UO_0000000
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

cubic metre per second
type: Class
subclass of: UO_0000000
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

micromole per kilogram
type: Class
subclass of: UO_0000051
user interface label: umol/kg
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

micromole per litre
type: Class
subclass of: UO_0000051
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

quality control record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

1 - standard draft
type: Class
subclass of: assembly status
IAO_0000115: Standard draft: describing the minimum information needed for submission to a public database.
IAO_0000117: Damion Dooley

2 - high quality draft
type: Class
subclass of: assembly status
IAO_0000115: High quality draft: describing sequences with little to no manual review.
IAO_0000117: Damion Dooley

3 - improved high quality draft
type: Class
subclass of: assembly status
IAO_0000115: Improved high quality draft: in which data is either reviewed by people or machines to some extent to indicate that most of the genetic data is assembled correctly, but some errors may still be present.
IAO_0000117: Damion Dooley

4 - annotation-directed improvement
type: Class
subclass of: assembly status
IAO_0000115: Annotation-directed improvement: in which genetic information in various gene regions is represented as accurately as possible.
IAO_0000117: Damion Dooley

5 - non-contiguous finished
type: Class
subclass of: assembly status
IAO_0000115: Non-contiguous finished: which includes sequences that have been reviewed by both people and machines and would be considered complete except for “recalcitrant regions” that are proving problematic for genome closure.
IAO_0000117: Damion Dooley

6 - finished
type: Class
subclass of: assembly status
IAO_0000115: Finished: which describes un-gapped complete sequences that have minimal errors, if any. The biology of the microbe will determine whether this finished genome consists of more than one chromosome.
IAO_0000117: Damion Dooley

contig NG99
type: Class
subclass of: contig length
metadata section: Assembly QC
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000428
IAO_0000115: The NG99 length is the same as the N99 length except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths.
IAO_0000117: Damion Dooley
in subset: GENEPIO

contig LG50
type: Class
subclass of: contig count
metadata section: Assembly QC
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000428
IAO_0000115: Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation.
IAO_0000117: Damion Dooley

contig L99
type: Class
subclass of: contig count
metadata section: Assembly QC
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000428
IAO_0000115: Contig L99 is the number of contigs equal to or longer than contig N99. The length of the assembly itself is used in the calculation.
IAO_0000117: Damion Dooley

subject age at time of specimen collection
type: Class
subclass of: subject age
IAO_0000114: IAO_0000428
IAO_0000115: A subject age at time of specimen extraction is the age (since birth) of the organism at the time a given specimen was extracted.
IAO_0000117: Damion Dooley

pathogen specific data standard
type: Class
subclass of: public health lab epidemiology contextual data standard
IAO_0000114: IAO_0000428
IAO_0000117: A public health related data standard involving a particular species of pathogen.
IAO_0000117: Damion Dooley

draft tuberculosis contextual data standard
type: Class
subclass of: draft data standard
IAO_0000114: IAO_0000123
IAO_0000115: The draft tuberculosis contextual data standard is a data standard for the collection of contextual information of a given tuberculosis case that pertain to typing, clinical treatment, and potential research questions.
IAO_0000117: Damion Dooley

draft PulseNet Canada Salmonella submission standard
type: Class
subclass of: draft data standard
subclass of: Restriction
  on property: has component
  qualified cardinality: 1
  on class: Class
    intersection of: string value specification
    intersection of: Restriction
      on property: OBI_0001927
      some values from: outbreak identifier
    intersection of: Restriction
      on property: exactMatch
      has value: PulseNet:Outbreak
    intersection of: Restriction
      on property: type uri
      some values from: string
    intersection of: Restriction
      on property: name
      has value: PulseNet:Outbreak
IAO_0000114: IAO_0000428
IAO_0000115: The PulseNet Canada Salmonella submission standard details the fields required in a PuseNet Canada pathogen submission report for Salmonella in spreadsheet format
IAO_0000117: Damion Dooley

PFGE Xbal pattern
type: Class
subclass of: PFGE pattern
subclass of: Restriction
  on property: is about
  some values from: Xbal
IAO_0000115: A PFGE pattern resulting from DNA fragmentation induced by the Xbal enzyme.
IAO_0000117: http://orcid.org/0000-0002-8844-9165

PFGE Blnl pattern
type: Class
subclass of: PFGE pattern
subclass of: Restriction
  on property: is about
  some values from: Blnl
IAO_0000115: A PFGE pattern resulting from DNA fragmentation induced by the Blnl enzyme.
IAO_0000117: http://orcid.org/0000-0002-8844-9165

National Laboratory for Enteric Pathogens Identifier
type: Class
subclass of: OBI_0001616
user interface label: NLEP ID
IAO_0000115: An NLEP ID is a unique identifier code for a sample registered with the Canadian "National Laboratory for Enteric Pathogens" (NLEP)
IAO_0000117: Damion Dooley
IAO_0000119: Pulsenet Canada spreadsheet.

upload modified date
type: Class
subclass of: isolate history item
subclass of: Restriction
  on property: after
  some values from: isolate upload date
term source: PulseNet spreadsheet
IAO_0000115: Date an uploaded sample was re-uploaded or had its metadata modified.
IAO_0000117: Damion Dooley
has db xref: PulseNet: UploadModifiedDate

travel destination
type: Class
subclass of: human exposure event - travel datum
IAO_0000114: IAO_0000428
IAO_0000115: A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip.
IAO_0000117: Damion Dooley

symptom duration
type: Class
subclass of: symptom history item
subclass of: EFO_0000433
IAO_0000114: IAO_0000428
IAO_0000115: A symptom duration is a date-time entity which is the duration (in hours or days or weeks etc.) that one or more symptoms persist for in a particular human or animal
IAO_0000117: Damion Dooley
comment: This may be a calculated field if symptoms are reported to cease on a particular date. Often however symptom duration is reported more generally as a date or time range since cesation date is less certain.

specimen collection location - city
type: Class
subclass of: specimen collection site specification
subclass of: Restriction
IAO_0000114: IAO_0000428
IAO_0000115: The city where a specimen was collected (taken) from a subject or environment
IAO_0000117: Damion Dooley

Axiom
annotated source: specimen collection location - city
annotated property: subClassOf
annotated target: Restriction
user interface feature: lookup

obsolete: sample city
type: Class
IAO_0000117: Damion Dooley
IAO_0000231: IAO_0000227
IAO_0100001: specimen collection location - city
deprecated: true

genus of pathogen
type: Class
subclass of: taxonomic datum
subclass of: Restriction
  on property: is about
  some values from: NCBITaxon genus
IAO_0000114: IAO_0000428
IAO_0000115: This is the genus-level taxonomic name of an organism playing a pathogen role
IAO_0000117: Damion Dooley

species of pathogen
type: Class
subclass of: taxonomic datum
subclass of: Restriction
  on property: is about
  some values from: NCBITaxon species
IAO_0000114: IAO_0000428
IAO_0000115: This is the species-level taxonomic name of an organism playing a pathogen role
IAO_0000117: Damion Dooley

symptom cessation date
type: Class
subclass of: symptom history item
IAO_0000114: IAO_0000428
IAO_0000115: A symptom cessation date is a date-time entity that marks the end of one or more reported symptoms pertaining to an episode of human or animal illness
IAO_0000117: Damion Dooley

specimen datum
type: Class
subclass of: IAO_0000027
subclass of: Restriction
  on property: is about
  some values from: OBI_0100051
IAO_0000115: This is a catch-all category for listing specimen related terms
IAO_0000117: Damion Dooley

isolate identifier specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: isolate identifier
IAO_0000114: IAO_0000428

data obfuscated
type: Class
subclass of: data protection role
IAO_0000114: IAO_0000428
IAO_0000115: The 'data obfuscated' role between a user and given data entails that the user is authorized to see particular fields that have been transformed consistently such that statistics performed on those fields would yeild the same results as statistics applied to the un-obfuscated data. The purpose of obfuscation is to prevent related individuals or organizations from being identified.
IAO_0000117: Damion Dooley

data aggregated
type: Class
subclass of: data protection role
IAO_0000114: IAO_0000122
IAO_0000115: The 'data aggregated' role between a user and given data entails that the user is authorized to see aggregated results (like the patient count) via preset reports, queries or views. The results are not obfuscated.
IAO_0000117: Damion Dooley

limited data set
type: Class
subclass of: data protection role
IAO_0000114: IAO_0000122
IAO_0000115: A 'limited data set' role between a user and given data entails that a user is authorized to see some of the fields but the remainder are withheld (or encrypted).
IAO_0000117: Damion Dooley

de-identified data
type: Class
subclass of: data protection role
user interface feature: help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users.
IAO_0000114: IAO_0000428
IAO_0000115: A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them.
IAO_0000116: Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature.
IAO_0000117: Damion Dooley
IAO_0000600: Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/

data protected
type: Class
subclass of: data protection role
IAO_0000114: IAO_0000122
IAO_0000115: A 'data protected' role between a user and given data entails that a user must be authorized in order to view that data.
IAO_0000117: Damion Dooley

specimen collector
type: Class
subclass of: specimen datum
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: Class
    intersection of: string value specification
    intersection of: Restriction
      on property: OBI_0001927
      some values from: NCIT C25191
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: Class
    intersection of: string value specification
    intersection of: Restriction
      on property: OBI_0001927
      some values from: NCIT C93874
IAO_0000114: IAO_0000122
IAO_0000115: A datum containing the name of persons or institute who collected a given specimen.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/

NCBI BioSample culture identifier
type: Class
subclass of: culture identifier
IAO_0000117: IAO_0000123
IAO_0000117: Damion Dooley

user identifier
type: Class
subclass of: IAO_0000577
IAO_0000115: A user identifier is an identifier provided as part of an authentication process of a client (user) to a service (server). User identifiers normally persist over time, in contrast to session identifiers which are temporary.
IAO_0000117: Damion Dooley

sequence identifier
type: Class
subclass of: IAO_0000577

metagenomic species identification
type: Class
subclass of: assembly and annotation project objective

document citation identifier
type: Class
subclass of: IAO_0000577
IAO_0000115: Note: REPLACE WITH Citation: SIO_000174 ????

organization identifier
type: Class
subclass of: IAO_0000577

collection identifier
type: Class
subclass of: IAO_0000577

variant calling / pathogen identification and clustering
type: Class
subclass of: assembly and annotation project objective

isolate (pathogen) identification
type: Class
subclass of: assembly and annotation project objective

obsolete: NCBI BioSample ID -
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/OBI_0001616
deprecated: true

specimen title
type: Class
subclass of: specimen datum
IAO_0000112: 1) Escherichia coli O104:H4 str. C227-11 clinical isolate 2010_333_NC-6 2) CD8+ T cells from female TSG6-knockout BALB/c mouse 3) Human metagenome isolated from urine of healthy female
IAO_0000114: IAO_0000428
IAO_0000115: A specimen (or sample) title should be short and informative. Each specimen title must be unique in a submission.
IAO_0000116: NCBI BioSample record documentation refers to a "BioSample title", stating that it is "auto-generated if one is not supplied by the submitter." This is distinct from any assigned BioSession accession, or other "external sample identifier" that may have been issued by the source database or repository.
IAO_0000117: Damion Dooley

draft GenEpiO isolate source context
type: Class
subclass of: draft GenEpiO component record

restricted access
type: Class
subclass of: missing
term source: INSDC term (lower level)
IAO_0000114: IAO_0000120
IAO_0000115: A categorical choice recorded when the data for a given measurable datum is available but not shared publicly because of information privacy concerns.
IAO_0000119: missing-values.html
has db xref: INSDC standard

State (United States of America)
type: Class
subclass of: NCIT C87194

health status trend datum
type: Class
subclass of: organism datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: OBI_0100026
    intersection of: Restriction
      on property: RO_0000087
      some values from: OBI_0000093
IAO_0000114: IAO_0000428
IAO_0000115: A health status trend is a short-term prognosis about whether health is improving, worsening or unchanging
IAO_0000117: Damion Dooley

ITIS
type: Class
subclass of: source database
term source: http://www.itis.gov
IAO_0000114: IAO_0000428
IAO_0000115: The Integrated Taxonomic Information System (ITIS) contains authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world.
IAO_0000117: Damion Dooley
IAO_0000118: Integrated Taxonomic Information System
has db xref: ITIS

MESH
type: Class
subclass of: source database
term source: https://www.nlm.nih.gov/mesh/meshhome.html
IAO_0000114: IAO_0000428
IAO_0000115: MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity.
IAO_0000117: Damion Dooley
IAO_0000118: Medical Subject Headings
has db xref: MSH

NCIT
type: Class
subclass of: source database
term source: https://ncit.nci.nih.gov/ncitbrowser/
IAO_0000114: IAO_0000120
IAO_0000115: The National Cancer Institute Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities.
IAO_0000117: Damion Dooley
IAO_0000118: National Cancer Institude Thesaurus
has db xref: NCI_Thesaurus
has db xref: NCIt

NIFSTD
type: Class
subclass of: source database
IAO_0000114: IAO_0000123
IAO_0000115: The NIFSTD ontology of the Neuroscience Information Framework is composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction.
IAO_0000117: Damion Dooley
IAO_0000119: https://wiki.nci.nih.gov/display/VKC/NIFSTD+Ontology

SNOMEDCT
type: Class
subclass of: source database
IAO_0000114: IAO_0000123
IAO_0000115: SNOMED CT is a large clinical health terminology product owned and distributed by SNOMED International.
IAO_0000117: Damion Dooley
IAO_0000119: http://www.snomed.org/snomed-ct
has db xref: SNOMEDCT

ASFIS
type: Class
subclass of: source database
term source: http://www.fao.org/fishery/collection/asfis/en
IAO_0000114: IAO_0000120
IAO_0000115: ASFIS is a database curated by the United Nations Food And Agriculture Organization (FAO) Fisheries and Aquaculture Statistics and Information Branch (FIPS). It contains over 12,700 species items selected according to their interest or relation to fisheries and aquaculture.
IAO_0000117: Damion Dooley
IAO_0000118: UN FAO Fisheries and Aquaculture Statistics and Information Branch database
has db xref: FAO ASFIS

FTT
type: Class
subclass of: source database
IAO_0000114: IAO_0000123

TGN
type: Class
subclass of: source database
IAO_0000114: IAO_0000123

Wikipedia
type: Class
subclass of: source database
IAO_0000114: IAO_0000122
IAO_0000115: Wikipedia is a free online encyclopedia that aims to allow anyone to edit articles.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Wikipedia

SWEETRealm
type: Class
subclass of: source database
IAO_0000114: IAO_0000123

Geonames
type: Class
subclass of: source database
IAO_0000114: IAO_0000428
IAO_0000115: The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.
IAO_0000117: Damion Dooley
IAO_0000119: http://www.geonames.org/

EcoLexicon
type: Class
subclass of: source database
term source: http://ecolexicon.ugr.es/en/index.htm
IAO_0000114: IAO_0000428
IAO_0000115: EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada.
IAO_0000117: Damion Dooley

draft IRIDA standard
type: Class
subclass of: draft data standard
IAO_0000114: IAO_0000120
IAO_0000115: A standard established for use by the Integrated Rapid Infectious Disease Analysis (IRIDA) project, which is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology.
IAO_0000117: Damion Dooley
IAO_0000119: http://www.irida.ca/

ISO3166-1
type: Class
subclass of: NCIT C103180
IAO_0000114: IAO_0000120
IAO_0000115: ISO 3166-1 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for the names of countries, dependent territories, and special areas of geographical interest.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/ISO_3166-2

ISO3166-2
type: Class
subclass of: NCIT C103180
IAO_0000114: IAO_0000120
IAO_0000115: ISO 3166-2 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for identifying the principal subdivisions (e.g., provinces or states) of all countries coded in ISO 3166-1.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/ISO_3166-1

ANSI INCITS 38
type: Class
subclass of: NCIT C103180
IAO_0000114: IAO_0000122
IAO_0000115: Information Technology – Codes For The Identification Of The States And Equivalent Areas Within The United States, Puerto Rico, And The Insular Areas
IAO_0000117: Damion Dooley
IAO_0000119: American National Standards Institute

GNISID
type: Class
subclass of: source database
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
IAO_0000117: The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical.
IAO_0000119: https://nhd.usgs.gov/gnis.html

LTER
type: Class
subclass of: source database
IAO_0000114: IAO_0000123

NCBI BioSample Pathogen.cl standard
type: Class
subclass of: NCBI standard
subclass of: Restriction
  on property: is about
  some values from: OBI_0100051
user interface feature: order: OBI:0001628 # investigation identifier OBI:0001616 # specimen identifier GENEPIO:0001808 # specimen title GENEPIO:0000113 # specimen category sep:00196 # specimen description OBI:0001479 # specimen from organism GENEPIO:0001640 # specimen organism taxonomy (species) GENEPIO:0000027 # specimen source context GENEPIO:0001722 # NCBI specimen voucher GENEPIO:0001429 # strain identifier GENEPIO:0001798 # NCBI BioSample culture identifier GENEPIO:0001717 # viral subtype OMP:0000207 # serotype phenotype SO:0001027 # genotype GENEPIO:0001079 # serovar GENEPIO:0001716 # subgroup GENEPIO:0001055 # NCBI pathotype GENEPIO:0001054 # isolate passage history GENEPIO:0001656 # latitude and longitude coordinate GENEPIO:0001657 # NCBI BioSample geo_loc_name model GENEPIO:0001051 # NCBI BioSample isolate (human name or description) GENEPIO:0001648 # NCBI Contributing organization / project GENEPIO:0001797 # specimen collector OBI:0001619 # specimen collection date OBI:0001888 # sequencing facility contact person GENEPIO:0001651 # INSDC institution code GENEPIO:0001721 # NCBI culture collection GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0001724 # subject organism common name GENEPIO:0001775 # subject age at time of specimen collection GENEPIO:0000026 # subject health status at time of specimen extraction GENEPIO:0000031 # subject sex GENEPIO:0001614 # subject description GENEPIO:0001617 # subject disease GENEPIO:0001625 # subject disease stage GENEPIO:0001212 # subject disease outcome
IAO_0000114: IAO_0000120
IAO_0000115: A National Center for Biotechnology Information BioSample specification defines fields and terms that provide "descriptions of biological source materials used in experimental assays".
IAO_0000117: Damion Dooley
IAO_0000119: http://www.ncbi.nlm.nih.gov/biosample/

NCBI BioProject standard
type: Class
subclass of: NCBI standard
subclass of: Restriction
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: sequencing facility name specification
subclass of: Restriction
  on property: has component
  max qualified cardinality: 1
  on class: Class
    intersection of: OBI_0001930
    intersection of: Restriction
      on property: OBI_0001927
      some values from: project data type
IAO_0000114: IAO_0000120
IAO_0000115: The National Center for Biotechnology Information BioProject standard is a collection of datums that describe biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.
IAO_0000117: Damion Dooley
IAO_0000119: http://www.ncbi.nlm.nih.gov/bioproject/
comment: NCBI lists project data type and other controlled vocabulary fields at : https://www.ncbi.nlm.nih.gov/books/NBK54364/

Restriction
on property: has component
qualified cardinality: 1
on class: Class
  intersection of: OBI_0001930
  intersection of: Restriction
    on property: OBI_0001927
    some values from: OBI_0001892

Restriction
on property: has component
max qualified cardinality: 1
on class: investigation identifier specification

Restriction
on property: has component
max qualified cardinality: 1
on class: Class
  intersection of: OBI_0001930
  intersection of: Restriction
    on property: OBI_0001927
    some values from: OBI_0001896

Objective
type: Axiom
annotated source: NCBI BioProject standard
annotated property: subClassOf
annotated target: Restriction

Project Accession
type: Axiom
annotated source: NCBI BioProject standard
annotated property: subClassOf
annotated target: Restriction
comment: The format of the BioProject Accession is five alpha-letters followed by one to six numbers. For example PRJNA43021

Methodology
type: Axiom
annotated source: NCBI BioProject standard
annotated property: subClassOf
annotated target: Restriction

AHA HIPPA standard
type: Class
subclass of: public health data standard
term source: http://www.aha.org/content/00-10/overview0302.pdf
term source: http://www.webcitation.org/5VBWPbFgY
IAO_0000114: IAO_0000120
IAO_0000115: The American Hospital Association has issued HIPAA Updated Guidelines for Releasing Information on the Condition of Patients
IAO_0000117: Damion Dooley
IAO_0000118: American Hospital Association HIPAA Standard
has db xref: AHA HIPPA

PubMed
type: Class
subclass of: source database
term source: http://www.ncbi.nlm.nih.gov/pubmed/
IAO_0000114: IAO_0000120
IAO_0000115: PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
IAO_0000118: NCBI PubMed
has db xref: PMID

PulseNet submission standard
type: Class
subclass of: public health data standard
term source: www.pulsenetinternational.org
IAO_0000114: IAO_0000123
IAO_0000115: PulseNet, a national and international surveillance system used to identify and respond to foodborne disease outbreaks, has a standardized laboratory method and data submission standard for pathogen isolate typing test results and related isolate contextual data. From this information clusters of disease can be identified that might represent unrecognized outbreaks.
IAO_0000118: Pulse Net International BioSample Metadata
has db xref: PulseNet

good health status
type: Class
subclass of: ExO_0000038
subclass of: subject health status (AHA)
subclass of: Restriction
  on property: after
  some values from: progressing well health status
subclass of: Restriction
  on property: RO_0002083
  some values from: NCIT C115935
term source: AHA HIPPA: http://www.aha.org/content/00-10/overview0302.pdf
IAO_0000114: IAO_0000120
IAO_0000115: Good - Vital signs are stable and within normal limits. Patient is conscious and comfortable. Indicators are excellent.
IAO_0000117: Damion Dooley
has db xref: AHA HIPPA standard
has db xref: NHS standard
has db xref: AHA Hippa: Good

Good
type: Axiom
annotated source: good health status
annotated property: hasDbXref
annotated target: AHA HIPPA standard

satisfactory
type: Axiom
annotated source: good health status
annotated property: hasDbXref
annotated target: NHS standard

fair health status
type: Class
subclass of: ExO_0000038
subclass of: subject health status (AHA)
subclass of: Restriction
  on property: after
  some values from: stable health status
subclass of: Restriction
  on property: RO_0002083
  some values from: satisfactory health status
IAO_0000114: IAO_0000120
IAO_0000115: Fair - Vital signs are stable and within normal limits. Patient is conscious, but may be uncomfortable. Indicators are favorable.
IAO_0000117: Damion Dooley
has db xref: NHS standard

fair
type: Axiom
annotated source: fair health status
annotated property: subClassOf
annotated target: subject health status (AHA)

Stable
type: Axiom
annotated source: fair health status
annotated property: hasDbXref
annotated target: NHS standard

serious health status
type: Class
subclass of: ExO_0000038
subclass of: subject health status (AHA)
subclass of: Restriction
  on property: after
  some values from: critical but stable health status
subclass of: Restriction
  on property: RO_0002083
  some values from: stable health status
IAO_0000114: IAO_0000120
IAO_0000115: Serious - Vital signs may be unstable and not within normal limits. Patient is acutely ill. Indicators are questionable.
IAO_0000117: Damion Dooley
has db xref: AHA HIPPA standard

Serious
type: Axiom
annotated source: serious health status
annotated property: hasDbXref
annotated target: AHA HIPPA standard

health status history datum
type: Class
subclass of: organism datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: OBI_0100026
    intersection of: Restriction
      on property: RO_0000087
      some values from: OBI_0000093
IAO_0000114: IAO_0000428
IAO_0000115: A health status history datum is a record of the longer-term pattern or presence of a given patient's health status.
IAO_0000117: Damion Dooley

origin
subclass of: SIO_000507
IAO_0000112: (0,0) is the origin of the cartesian coordinate system.
IAO_0000115: "In mathematics, the origin of a Euclidean space is a special point, usually denoted by the letter O, used as a fixed point of reference for the geometry of the surrounding space. In physical problems, the choice of origin is often arbitrary, meaning any choice of origin will ultimately give the same answer. This allows one to pick an origin point that makes the mathematics as simple as possible, often by taking advantage of some kind of geometric symmetry."
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Origin_(mathematics)

NHS standard
type: Class
subclass of: NCIT C103180
term source: https://en.wikipedia.org/wiki/Medical_state
IAO_0000115: United Kingdom National Health Service trusts, boards, etc. have some terminology in common for public disclosure of patient health conditions.
IAO_0000117: Damion Dooley
IAO_0000118: National Health Service terminology

critical but stable health status
type: Class
subclass of: ExO_0000038
subclass of: subject health status (UK NHS)
subclass of: Restriction
  on property: after
  some values from: critical health status
subclass of: Restriction
  on property: RO_0002083
  some values from: serious health status
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley
comment: Damion Dooley's note: This is a contentious term. AHA calls for it never to be used, since the common phrase "critical but stable" is misleading by the very nature of "critical". The NHS however has it as one of its central terms. The use of "stable" also points to a health trend, rather than a state. A separate "health status trend datum" has been set up to capture this.

critical but stable
type: Axiom
annotated source: critical but stable health status
annotated property: subClassOf
annotated target: subject health status (UK NHS)

comfortable health status
type: Class
subclass of: ExO_0000038
subclass of: subject health status (UK NHS)
subclass of: Restriction
  on property: after
  some values from: satisfactory health status
subclass of: Restriction
  on property: RO_0002083
  some values from: progressing well health status
term source: NHS Terms: https://en.wikipedia.org/wiki/Medical_state
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

Comfortable
type: Axiom
annotated source: comfortable health status
annotated property: subClassOf
annotated target: subject health status (UK NHS)

progressing well health status
type: Class
subclass of: ExO_0000038
subclass of: subject health status (UK NHS)
subclass of: Restriction
  on property: after
  some values from: comfortable health status
subclass of: Restriction
  on property: RO_0002083
  some values from: good health status
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

progressing well
type: Axiom
annotated source: progressing well health status
annotated property: subClassOf
annotated target: subject health status (UK NHS)

discharged from hospital
type: Class
subclass of: host hospital service status
subclass of: subject health status (UK NHS)
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: Damion Dooley note: This term (weakly) implies that the patient is recovered enough to be released from hospital. Technically this isn't a health status though, it is a patient medical service state.

discharged
type: Axiom
annotated source: discharged from hospital
annotated property: subClassOf
annotated target: subject health status (UK NHS)

datum status
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000428
IAO_0000115: A data item which is about the collection state of a datum at some point in time.
IAO_0000116: Damion Dooley note: We'll need to incorporate NIAID GSCID-BRC Sample data standards mention: Unknown/Not Applicable/Censored Allowed Unknown/not applicable/not available/ available upon request
IAO_0000117: Damion Dooley
comment: A given datum's datum status value is metadata, i.e. a statement about a particular datum, often when no actual data entry or categorical choice for that datum has been made.
see also: INSDC missing value reporting terms: http://www.ebi.ac.uk/ena/about/missing-values-reporting

recorded
type: Class
subclass of: datum status
IAO_0000114: IAO_0000428
IAO_0000115: A categorical choice indicating that a datum is available for retrieval.
IAO_0000117: Damion Dooley
comment: In theory any datum that has a recorded value has 'recorded' for its datum status.

undetermined health status - awaiting assessment
type: Class
subclass of: ExO_0000038
subclass of: subject health status (AHA)
IAO_0000114: IAO_0000428
IAO_0000115: Patient is awaiting physician and/or assessment.
IAO_0000116: Very similar to 'datum status' 'in process' status.
IAO_0000117: Damion Dooley
has db xref: AHA HIPPA standard

worsening health trend
type: Class
subclass of: health status trend datum
subclass of: Restriction
  on property: RO_0002083
  some values from: stable health trend
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
has exact synonym: deteriorating

GENEPIO_0001859
subclass of: BFO_0000141
IAO_0000114: IAO_0000428
IAO_0000115: This covers the description of data and abstract structure in n-dimensional space. Within space there are coordinate systems, coordinates, and entities made up of coordinates.
IAO_0000117: Damion Dooley

GENEPIO_0001862
subclass of: OBI_0001931
subclass of: Restriction
  on property: OBI_0001927
  some values from: OBI_0001620
user interface regular epression normalize: /^[N+](:<lat>\d(\.\d+)?)$/, $lat /^S(:<lat>\d(\.\d+)?)$/, '-' + $lat
user interface regular expression validate: /^(:<lat>[-S+N])?(:<degree>[1-8]?[0-9](:<decimal>\.\d{1,6})?)$/, $lat$degree.$decimal /^(:<lat>[-S+N])?(:<degree>90(:<decimal>\.0{1,6})?))$/, $lat$degree.$decimal
user interface regular expression display format: /^(\d(\.\d+)?)$/, '+\1'
IAO_0000114: IAO_0000428
IAO_0000115: A decimal latitude measurement in degrees in conformance with the ISO 6709 standard.
IAO_0000116: This is failing Hermit reasoner since it rejects totalDigits, and fractionDigits: 'has primitive data type' exactly 1 xsd:decimal[>= -90.0 , <= 90.0 , totalDigits 8 , fractionDigits 6]'
IAO_0000117: Damion Dooley

GENEPIO_0001863
subclass of: OBI_0001931
subclass of: Restriction
  on property: OBI_0001927
  some values from: OBI_0001621
user interface regular expression validate: /^(:<long>[-W+E])?(:<degree>(1[0-7]|[1-9])?[0-9])(:<decimal>\.\d{1,6})?)$/, $long$degree.$decimal /^(:<long>[-W+E])?(:<degree>180(:<decimal>\.0{1,6})?)$,$long$degree.$decimal
IAO_0000114: IAO_0000428
IAO_0000115: A decimal longitude measurement in degrees in conformance with the ISO 6709 standard.
IAO_0000117: Damion Dooley

GENEPIO_0001864
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001865
IAO_0000114: IAO_0000428
IAO_0000115: A 2D coordinate system is a coordinate system in 2 dimensional space. Each coordinate is composed of an offset from the origin of each dimension
IAO_0000117: Damion Dooley

GENEPIO_0001866
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001867
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

datetime range intermediate
subclass of: datetime range item
subclass of: Restriction
  on property: after
  some values from: datetime range start
subclass of: Restriction
  on property: RO_0002083
  some values from: datetime range end
IAO_0000115: A datetime range intermediate datum is a datetime item grouped under a process, and occuring after some process start and before some process end.
IAO_0000117: Damion Dooley

datetime range item
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

datetime range end
subclass of: datetime range item
subclass of: Restriction
  on property: BFO_0000062
  some values from: datetime range start
comment: The ending date of a process

datetime range start
subclass of: datetime range item
subclass of: Restriction
  on property: BFO_0000063
  some values from: datetime range end
IAO_0000117: Damion Dooley
comment: The starting date of a process

GENEPIO_0001884
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001885
subclass of: Restriction
  on property: BFO_0000051
  some values from: 2D boundary
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001886
subclass of: BFO_0000029
IAO_0000114: IAO_0000428
IAO_0000114: A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time.
IAO_0000117: Damion Dooley

GENEPIO_0001888
disjoint with: NCIT C25720
IAO_0000114: IAO_0000428
IAO_0000115: A Canadian postal code is a postal code that pertains to a geographic region of Canada.
IAO_0000116: Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account.

obsolete: US postal code
type: Class
IAO_0000115: A "USA zip code" is a five digit (Zone Improvement Plan) or 9 digit postal code pertaining to a region of the United States of America. The optional trailing 4 digits of a 9 digit zip code provide greater granularity of delivery target.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C25720
deprecated: true

entity history record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

generic range history record
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001900
subclass of: BFO_0000141
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: A set does not have a direct distance metric between its members.

GENEPIO_0001904
subclass of: NCIT C40978
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001907
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001911
subclass of: GENEPIO_0001919
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001919
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

sequencing instrument model
type: Class
subclass of: OBI_0000832
IAO_0000114: IAO_0000428
IAO_0000115: A product name and model number of a manufacturer's genomic (dna) sequencer.
IAO_0000117: Damion Dooley

circle
type: Class
subclass of: 2D entity
subclass of: 2D boundary
subclass of: SIO_000608
subclass of: Restriction
  on property: has component
  qualified cardinality: 1
  on class: centre point
subclass of: Restriction
  on property: has component
  qualified cardinality: 1
  on class: PATO_0002390
IAO_0000114: IAO_0000428
IAO_0000115: A circle is a simple closed shape in Euclidean geometry. It is the set of all points in a plane that are at a given distance from a given point, the centre; equivalently it is the curve traced out by a point that moves so that its distance from a given point is constant.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Circle

Illumina platform
type: Class
subclass of: sequencing platform (brand)
has db xref: NCBI SRA: ILLUMINA

Complete Genomics platform
type: Class
subclass of: sequencing platform (brand)
has db xref: NCBI SRA: COMPLETE_GENOMICS
comment: Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: "Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010)."

earth area boundary census
type: Class
subclass of: APOLLO SV 00000173
subclass of: Restriction
  on property: has component
  min qualified cardinality: 0
  on class: geospatial name
subclass of: Restriction
  on property: has component
  qualified cardinality: 1
  on class: 2D boundary
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

Roche LS454 platform
type: Class
subclass of: sequencing platform (brand)
has db xref: NCBI SRA: LS454

PacBio platform
type: Class
subclass of: sequencing platform (brand)
has db xref: NCBI SRA: PACBIO_SMRT

SOLiD 4hq System
type: Class
subclass of: OBI_0000696
has db xref: NCBI SRA: AB SOLiD 4hq

SOLiD 5500
type: Class
subclass of: OBI_0000696
has db xref: NCBI SRA: AB SOLiD 5500

SOLiD 5500xl
type: Class
subclass of: OBI_0000696
has db xref: NCBI SRA: AB SOLiD 5500xl

SOLiD PI System
type: Class
subclass of: OBI_0000696
has db xref: NCBI SRA: AB SOLiD PI System

SOLiD System 2.0
type: Class
subclass of: OBI_0000696
has db xref: NCBI SRA: AB SOLiD System 2.0

SOLiD System 3.0
type: Class
subclass of: OBI_0000696
has db xref: NCBI SRA: AB SOLiD System 3.0

2D entity
type: Class
subclass of: GENEPIO_0001884
IAO_0000114: IAO_0000428
IAO_0000115: A two dimensional entity is an entity composed of one or more points on a two dimensional surface.
IAO_0000117: Damion Dooley

GENEPIO_0001935
type: Class
has db xref: NCBI SRA: Ion Torrent PGM

454 Genome Sequencer FLX Titanium
type: Class
subclass of: 454 Genome Sequencer
has db xref: NCBI SRA: 454 GS FLX Titanium

454 Genome Sequencer
type: Class
subclass of: sequencing instrument model
subclass of: OBI_0400103
has db xref: NCBI SRA: 454 GS

454 Genome Sequencer Junior
type: Class
subclass of: 454 Genome Sequencer
has db xref: NCBI SRA: 454 GS Junior

library selection
type: Class
subclass of: laboratory sequencing datum
term source: https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/
IAO_0000115: Whether any method was used to select for or against, enrich, or screen the material being sequenced.
IAO_0000117: Damion Dooley
has db xref: NCBI SRA: LIBRARY_SELECTION

5-methylcytidine antibody method
type: Class
subclass of: library selection
IAO_0000115: Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).
has db xref: NCBI SRA: 5-methylcytidine antibody

CAGE method
type: Class
subclass of: library selection
IAO_0000115: Cap-analysis gene expression.
has db xref: NCBI SRA: CAGE

CF-H method
type: Class
subclass of: library selection
IAO_0000115: Cot-filtered highly repetitive genomic DNA
has db xref: NCBI SRA: CF-H

CF-M method
type: Class
subclass of: library selection
IAO_0000115: Cot-filtered moderately repetitive genomic DNA
has db xref: NCBI SRA: CF-M

CF-S method
type: Class
subclass of: library selection
IAO_0000115: Cot-filtered single/low-copy genomic DNA
has db xref: NCBI SRA: CF-S

CF-T method
type: Class
subclass of: library selection
IAO_0000115: Cot-filtered theoretical single-copy genomic DNA
has db xref: NCBI SRA: CF-T

ChIP method
type: Class
subclass of: library selection
IAO_0000115: Chromatin immunoprecipitation
has db xref: NCBI SRA: ChIP

DNAse method
type: Class
subclass of: library selection
IAO_0000115: Deoxyribonuclease (MNase) digestion
has db xref: NCBI SRA: DNAse

HMPR method
type: Class
subclass of: library selection
IAO_0000115: Hypo-methylated partial restriction digest
has db xref: NCBI SRA: HMPR

Hybrid Selection method
type: Class
subclass of: library selection
IAO_0000115: Selection by hybridization in array or solution.
has db xref: NCBI SRA: Hybrid Selection

MBD2 protein methyl-CpG binding domain method
type: Class
subclass of: library selection
IAO_0000115: Enrichment by methyl-CpG binding domain.
has db xref: NCBI SRA: MBD2 protein methyl-CpG binding domain

MF method
type: Class
subclass of: library selection
IAO_0000115: Methyl Filtrated
has db xref: NCBI SRA: MF

MNase method
type: Class
subclass of: library selection
IAO_0000115: Micrococcal Nuclease (MNase) digestion
has db xref: NCBI SRA: MNase

MSLL method
type: Class
subclass of: library selection
IAO_0000115: Methylation Spanning Linking Library
has db xref: NCBI SRA: MSLL

PCR method
type: Class
subclass of: library selection
IAO_0000115: Source material was selected by designed primers.
has db xref: NCBI SRA: PCR

RACE method
type: Class
subclass of: library selection
IAO_0000115: Rapid Amplification of cDNA Ends.
has db xref: NCBI SRA: RACE

RANDOM PCR method
type: Class
subclass of: library selection
IAO_0000115: Source material was selected by randomly generated primers.
has db xref: NCBI SRA: RANDOM PCR

RANDOM method
type: Class
subclass of: library selection
IAO_0000115: Random selection by shearing or other method.
has db xref: NCBI SRA: RANDOM

RT-PCR method
type: Class
subclass of: library selection
IAO_0000115: Source material was selected by reverse transcription PCR
has db xref: NCBI SRA: RT-PCR

Reduced Representation method
type: Class
subclass of: library selection
IAO_0000115: Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling.
has db xref: NCBI SRA: Reduced Representation

Restriction Digest method
type: Class
subclass of: library selection
IAO_0000115: DNA fractionation using restriction enzymes.
has db xref: NCBI SRA: Restriction Digest

cDNA method
type: Class
subclass of: library selection
IAO_0000115: PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA.
has db xref: NCBI SRA: cDNA

size fractionation method
type: Class
subclass of: library selection
IAO_0000115: Physical selection of size appropriate targets.
has db xref: NCBI SRA: size fractionation

other library method
type: Class
subclass of: library selection
IAO_0000115: Other library enrichment, screening, or selection process.
has db xref: NCBI SRA: other

library source
type: Class
subclass of: laboratory sequencing datum
term source: https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/
IAO_0000115: The library source specifies the type of source material that is being sequenced.
IAO_0000117: Damion Dooley

genomic source
type: Class
subclass of: library source
IAO_0000115: Genomic DNA (includes PCR products from genomic DNA).
IAO_0000117: Damion Dooley
has db xref: NCBI SRA: GENOMIC

metagenomic source
type: Class
subclass of: library source
IAO_0000115: Mixed material from metagenome.
IAO_0000117: Damion Dooley
has db xref: NCBI SRA: METAGENOMIC

metatranscriptomic source
type: Class
subclass of: library source
IAO_0000115: Transcription products from community targets
IAO_0000117: Damion Dooley
has db xref: NCBI SRA: METATRANSCRIPTOMIC

other library source
type: Class
subclass of: library source
IAO_0000115: Other, unspecified, or unknown library source material.
IAO_0000117: Damion Dooley
has db xref: NCBI SRA: OTHER

synthetic source
type: Class
subclass of: library source
IAO_0000115: Synthetic DNA.
IAO_0000117: Damion Dooley
has db xref: NCBI SRA: SYNTHETIC

transcriptomic source
type: Class
subclass of: library source
IAO_0000115: Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
IAO_0000117: Damion Dooley
has db xref: NCBI SRA: TRANSCRIPTOMIC

viral RNA source
type: Class
subclass of: library source
IAO_0000115: Viral RNA.
IAO_0000117: Damion Dooley
has db xref: NCBI SRA: VIRAL RNA

library strategy
type: Class
subclass of: laboratory sequencing datum
IAO_0000115: Sequencing technique intended for this library.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/

amplicon strategy
type: Class
subclass of: library strategy
IAO_0000115: Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA
has db xref: NCBI SRA: AMPLICON

Bisulfite-Seq strategy
type: Class
subclass of: library strategy
IAO_0000115: MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status.
has db xref: NCBI SRA: Bisulfite-Seq

clone end strategy
type: Class
subclass of: library strategy
IAO_0000115: Clone end (5', 3', or both) sequencing.
has db xref: NCBI SRA: CLONEEND

clone strategy
type: Class
subclass of: library strategy
IAO_0000115: Genomic clone based (hierarchical) sequencing.
has db xref: NCBI SRA: CLONE

CTS strategy
type: Class
subclass of: library strategy
IAO_0000115: Concatenated Tag Sequencing
has db xref: NCBI SRA: CTS

ChIP-Seq strategy
type: Class
subclass of: library strategy
IAO_0000115: Direct sequencing of chromatin immunoprecipitates.
has db xref: NCBI SRA: ChIP-Seq

DNase-Hypersensitivity strategy
type: Class
subclass of: library strategy
IAO_0000115: Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI.
has db xref: NCBI SRA: DNase-Hypersensitivity

EST strategy
type: Class
subclass of: library strategy
IAO_0000115: Single pass sequencing of cDNA templates
has db xref: NCBI SRA: EST

finishing strategy
type: Class
subclass of: library strategy
IAO_0000115: Sequencing intended to finish (close) gaps in existing coverage.
has db xref: NCBI SRA: FINISHING

FL-cDNA strategy
type: Class
subclass of: library strategy
IAO_0000115: Full-length sequencing of cDNA templates
has db xref: NCBI SRA: FL-cDNA

MBD-Seq strategy
type: Class
subclass of: library strategy
IAO_0000115: Direct sequencing of methylated fractions sequencing strategy.
has db xref: NCBI SRA: MBD-Seq

MNase-Seq strategy
type: Class
subclass of: library strategy
IAO_0000115: Direct sequencing following MNase digestion.
has db xref: NCBI SRA: MNase-Seq

MRE-Seq strategy
type: Class
subclass of: library strategy
IAO_0000115: Methylation-Sensitive Restriction Enzyme Sequencing strategy.
has db xref: NCBI SRA: MRE-Seq

MeDIP-Seq strategy
type: Class
subclass of: library strategy
IAO_0000115: Methylated DNA Immunoprecipitation Sequencing strategy.
has db xref: NCBI SRA: MeDIP-Seq

other library strategy
type: Class
subclass of: library strategy
IAO_0000115: Library strategy not listed.
has db xref: NCBI SRA: OTHER

pool clone strategy
type: Class
subclass of: library strategy
IAO_0000115: Shotgun of pooled clones (usually BACs and Fosmids).
has db xref: NCBI SRA: POOLCLONE

RNA-Seq strategy
type: Class
subclass of: library strategy
IAO_0000115: Random sequencing of whole transcriptome.
has db xref: NCBI SRA: RNA-Seq

WCS strategy
type: Class
subclass of: library strategy
IAO_0000115: Random sequencing of a whole chromosome or other replicon isolated from a genome.
has db xref: NCBI SRA: WCS

WGS strategy
type: Class
subclass of: library strategy
IAO_0000115: Random sequencing of the whole genome.
has db xref: NCBI SRA: WGS

WXS strategy
type: Class
subclass of: library strategy
IAO_0000115: Random sequencing of exonic regions selected from the genome.
has db xref: NCBI SRA: WXS

library construction protocol
type: Class
subclass of: laboratory sequencing datum
IAO_0000115: Free form text describing the protocol by which the sequencing library was constructed.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/

library name
type: Class
subclass of: laboratory sequencing datum
subclass of: IAO_0000300
IAO_0000115: The submitter's name for this library.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/
has db xref: NCBI SRA: LIBRARY_NAME

2D boundary
type: Class
subclass of: GENEPIO_0001884
IAO_0000114: IAO_0000428
IAO_0000115: A two dimensional boundary is a continuous path (loop) defined on a two dimensional surface.
IAO_0000117: Damion Dooley

colony forming unit per 100 milliliter
type: Class
subclass of: UO_0000212
user interface label: cfu/100mL
IAO_0000114: IAO_0000428
IAO_0000115: A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid.
IAO_0000116: Should this be deprecated? Need to find working examples that actually use / 100mL.
IAO_0000117: Damion Dooley

decimal quantity unit
type: Class
subclass of: GENEPIO_0001909
IAO_0000114: IAO_0000428
IAO_0000115: A multiplier in the decimal number system that has been applied to an accompanying number or set of numbers often to simplfy their appearance. Numbers described by multipliers may have lost significant digits through rounding or trimming.
IAO_0000117: Damion Dooley

draft tuberculosis - dataset features and provenance
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123

draft tuberculosis - case specimen characteristics
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123

draft tuberculosis - case subject characteristics
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123

draft tuberculosis - case risk factors
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123

draft tuberculosis - case clinical presentation
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123

draft tuberculosis - case laboratory testing
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123

draft tuberculosis - case medication
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123

draft isolate whole genome sequencing model
type: Class
subclass of: draft data standard
IAO_0000114: IAO_0000123

draft tuberculosis - case model
type: Class
subclass of: data specification
IAO_0000114: IAO_0000123

Mycobacterium tuberculosis lineage
type: Class
subclass of: organism datum
IAO_0000114: IAO_0000428
IAO_0000115: A Mycobacterium tuberculosis lineage is a named family of strains of tuberculosis, named usually with reference to their shared geographic origin.
IAO_0000117: Damion Dooley
see also: A TB-Lineage identification tool using spoligotypes and MIRU data: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
see also: Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans http://www.nature.com/ng/journal/v45/n10/full/ng.2744.html

TB lineage 2 - East-Asian, includes Bejing
type: Class
subclass of: Mycobacterium tuberculosis lineage

TB lineage 3 - East-African Indian, includes CAS/Delhi
type: Class
subclass of: Mycobacterium tuberculosis lineage

TB lineage 4 - Euro-American, includes Haarlem, LAM3, X, T, F11, H37Rv
type: Class
subclass of: Mycobacterium tuberculosis lineage

TB lineage 1 - Indo-Oceanic
type: Class
subclass of: Mycobacterium tuberculosis lineage

TB lineage 5 - West African 1
type: Class
subclass of: Mycobacterium tuberculosis lineage

TB lineage 6 - West African 2
type: Class
subclass of: Mycobacterium tuberculosis lineage

isolate preparation facility
type: Class
subclass of: OBI_0000245
IAO_0000114: IAO_0000122
IAO_0000117: Damion Dooley
comment: An isolate preparation facility is a type of organization that provides the service of isolating organisms of interest from provided specimens.

plant product
type: Class
subclass of: subject body product

geospatial name
type: Class
subclass of: NCIT C42614
subclass of: Restriction
  on property: is about
  some values from: GENEPIO_0001886

personal health datum
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000428
IAO_0000115: A personal health datum is a datum that pertains to the health situation or history of an individual.
IAO_0000116: Personal health datum covers the following information 'has member' some 'analytic datum' 'has member' some 'behavioural risk factor' 'has member' some 'country of birth' 'has member' some 'dietary restrictions' 'has member' some 'Disease Attributes' 'has member' some 'health status history datum' 'has member' some 'health status trend datum' 'has member' some 'host hospital service status' 'has member' some 'subject disease stage' 'has member' some 'subject health status' 'has member' some 'subject health status (AHA)' 'has member' some 'subject health status (GSCID-BRC)' 'has member' some 'subject health status (NCIT)' 'has member' some 'subject health status (UK NHS)' 'has member' some 'subject health status at time of specimen extraction' 'has member' some 'tuberculosis disease anatomical site' 'has member' some comorbidity 'has member' some disease 'has member' some symptom
IAO_0000117: Damion Dooley

host hospital service status
type: Class
subclass of: organism datum
IAO_0000115: A host hospital service status indicates the state of a host's interaction with hospital medical services.
IAO_0000117: Damion Dooley

admitted to hospital
type: Class
subclass of: host hospital service status
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

treated and released (not admitted to hospital)
type: Class
subclass of: host hospital service status
IAO_0000114: IAO_0000428
IAO_0000115: Received treatment but not admitted.
has db xref: AHA HIPPA standard

Treated and Released
type: Axiom
annotated source: treated and released (not admitted to hospital)
annotated property: hasDbXref
annotated target: AHA HIPPA standard

treated and transferred
type: Class
subclass of: host hospital service status
IAO_0000114: IAO_0000428
IAO_0000115: Received treatment. Transferred to a different facility.
has db xref: AHA HIPPA standard

Treated and Transferred
type: Axiom
annotated source: treated and transferred
annotated property: hasDbXref
annotated target: AHA HIPPA standard

satisfactory health status
type: Class
subclass of: ExO_0000038
subclass of: subject health status (UK NHS)
subclass of: Restriction
  on property: after
  some values from: fair health status
subclass of: Restriction
  on property: RO_0002083
  some values from: comfortable health status
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

satisfactory
type: Axiom
annotated source: satisfactory health status
annotated property: subClassOf
annotated target: subject health status (UK NHS)

subject health status (UK NHS)
type: Class
subclass of: organism datum
user interface feature: depth:1

subject health status (AHA)
type: Class
subclass of: organism datum
user interface feature: depth:1

stable health trend
type: Class
subclass of: health status trend datum
subclass of: Restriction
  on property: after
  some values from: worsening health trend
subclass of: Restriction
  on property: RO_0002083
  some values from: resolving health trend

obsolete: ordinal variable
type: Class
IAO_0000115: An ordinal variable is a categorical variable whose values have sequential order, but no distance metric between them.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/STATO_0000228
deprecated: true

mapping (reference based)
type: Class
subclass of: assembly method

data protection item
type: Class
subclass of: IAO_0000027

subject provided consent
type: Class
subclass of: consent datum

ordinal value specification
type: Class
subclass of: OBI_0001930
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: An ordinal tree specification is a value specification entity whose subclasses each represent a possible value selection, and which have a linear order with respect to their siblings.

consent datum
type: Class
subclass of: data protection item

agency provided consent
type: Class
subclass of: consent datum

draft ISO sequence repository field
type: Class
subclass of: OBI_0000658
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2019-11-17T00:43:00Z

centre point
type: Class
subclass of: SIO_000507
IAO_0000112: Centre of circle, ellipse or parabola; centre of mass.
IAO_0000114: IAO_0000428
IAO_0000115: A centre point is a point used in the description of an n-dimentional entity from which other (given) aspects of the entity are most efficienty described. A point of symmetry. The entity must have only one such point.
IAO_0000116: Probably a better formal math defn?
IAO_0000117: Damion Dooley

phenotypic antimicrobial drug susceptibility test datum
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000428
IAO_0000116: This covers the following entities: 'has member' some 'antimicrobial phenotype' 'has member' some 'antimicrobial resistance test drug' 'has member' some 'antimicrobial resistance test platform' 'has member' some 'antimicrobial resistance testing method' 'has member' some 'antimicrobial resistance testing method version or reagent' 'has member' some 'antimicrobial resistance testing reference standard' 'has member' some 'antimicrobial resistance testing reference standard version' 'has member' some 'antimicrobial resistance tissue specificity' 'has member' some 'antimicrobial resistant plasmid type' 'has member' some 'automated testing platform vendor' 'has member' some 'draft antibiogram drug test model' 'has member' some 'in-vitro microbial susceptibility test' 'has member' some 'measurement comparator' 'has member' some 'MIC unit' 'has member' some 'MIC value' 'has member' some 'Minimum Inhibitory Concentration Test' 'has member' some 'test drug maximum concentration' 'has member' some 'test drug minimum concentration' 'has member' some 'tuberculosis treatment drug'
IAO_0000117: Damion Dooley
IAO_0000117: This is a collection of antibiotic resistance process parameters and outputs

obsolete: antimicrobial resistance phenotype
type: Class
IAO_0000115: The resistance phenotype of an isolate represents the interpretation of an MIC value with regard to some breakpoint threshold e.g. resistant (R), sensitive (S), intermediate (I), wild type (WT), or non-wild type (NWT)
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C85539
deprecated: true

obsolete: antibiotic intermediate resistance (I)
type: Class
IAO_0000115: Intermediate resistance indicates that an isolate is observed to offer an intermediate level of resistance to a given antibiotic.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C85560
deprecated: true

obsolete: antibiotic nonsensitive (high resistance)
type: Class
IAO_0000115: Non-susceptible indicates that an isolate is observed to offer complete resistance to a given antibiotic.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C85561
deprecated: true

antibiotic resistance not defined
type: Class
subclass of: ARO_3004299
IAO_0000114: IAO_0000428
IAO_0000115: A not defined resistance indicates that an isolate was not tested against a given antibiotic, or the result of the test was inconclusive.
IAO_0000116: Damion Dooley note: Is this the same as "indeterminate"?
IAO_0000117: Damion Dooley
has alternative id: N
has alternative id: ND

obsolete: antibiotic resistant (R)
type: Class
IAO_0000115: Resistant indicates that an isolate is observed to offer a greater than intermediate level of resistance to a given antibiotic.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C85562
deprecated: true

obsolete: antibiotic sensitive (S)
type: Class
IAO_0000115: Susceptible indicates that an isolate is observed to offer a detectable but less than intermediate level of resistance to a given antibiotic.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C85563
deprecated: true

obsolete: sensitive - dose dependent
type: Class
IAO_0000115: Susceptible - dose dependent indicates that an isolate is observed to offer resistance to a given antibiotic when a sufficient dose is given.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C85559
deprecated: true

MIC dilution measurement datum
type: Class
subclass of: IAO_0000032
subclass of: Restriction
  on property: is about
  some values from: NCIT C128985
IAO_0000114: IAO_0000428
IAO_0000115: A MIC test measurement resulting from a laboratory dilution method.
IAO_0000116: Damion Dooley's note: is this still useful? Currently "MIC dilution measurement specification' refers directly via 'is about' to "broth dilution method" but that may be too specific.
IAO_0000117: Damion Dooley

obsolete: antimicrobial resistance testing method
type: Class
IAO_0000115: The type of assay used to determine the minimum inhibitory concentration.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C85540
deprecated: true

obsolete: agar dilution evidence
type: Class
IAO_0000114: IAO_0000123
IAO_0100001: http://purl.obolibrary.org/obo/NCIT_C85555
deprecated: true

antimicrobial resistance testing method device or reagent
type: Class
subclass of: OBI_0000968
IAO_0000114: IAO_0000428
IAO_0000115: The commercial kit or product used to determine the MIC e.g. E-Test. If a commercial product was not used, include the type of media used.
IAO_0000117: Damion Dooley

antimicrobial resistant plasmid type
type: Class
subclass of: phenotypic antimicrobial drug susceptibility test datum
IAO_0000114: IAO_0000428

obsolete: antimicrobial resistance testing platform
type: Class
IAO_0000115: The instrumentation used to determine minimum inhibitory concentration values.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004390
deprecated: true

obsolete: Microscan
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004400
deprecated: true

obsolete: Phoenix
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004401
deprecated: true

obsolete: Sensititre
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004402
deprecated: true

obsolete: Vitek
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004403
deprecated: true

obsolete: Trek
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004409
deprecated: true

obsolete: manual - noncommercial
type: Class
IAO_0100001: ARO_3004399
deprecated: true

obsolete: antimicrobial resistance testing platform vendor
type: Class
IAO_0000115: The manufacturer of an antibiotic resistance lab typing platform
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004404
deprecated: true

obsolete: Siemens
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004407
deprecated: true

obsolete: Biomérieux
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004406
deprecated: true

obsolete: Becton Dickinson
type: Class
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004405
deprecated: true

Etest (device)
type: Class
subclass of: antimicrobial resistance testing method device or reagent
IAO_0000114: IAO_0000122
IAO_0000115: A manual in vitro diagnostic device used by laboratories to determine the MIC (Minimum Inhibitory Concentration) and whether or not a specific strain of bacterium or fungus is susceptible to the action of a specific antimicrobial.
IAO_0000117: Damion Dooley
IAO_0000119: Etest
has exact synonym: E-Test
has exact synonym: Epsilometer test

GM-NEG
type: Class
subclass of: antimicrobial resistance testing method device or reagent
IAO_0000114: IAO_0000123

obsolete: antimicrobial resistance testing reference standard
type: Class
IAO_0000115: The clinical and laboratory guidelines or standards that prescribe the threshold values for determining resistance phenotypes.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004360
deprecated: true

obsolete: British Society for Antimicrobial Chemotherapy (BSAC)
type: Class
IAO_0000115: BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership
IAO_0000117: Damion Dooley
IAO_0100001: ARO_3004365
has alternative id: BSAC
deprecated: true

obsolete: Clinical and Laboratory Standards Institute (CLSI)
type: Class
IAO_0000115: The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards
IAO_0000117: Damion Dooley
IAO_0000118: NCCLS
IAO_0000119: http://clsi.org
IAO_0100001: ARO_3004366
has alternative id: CLSI
comment: On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI
deprecated: true

obsolete: German Institute for Standardization (DIN)
type: Class
IAO_0000115: DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations. @de
IAO_0000117: Damion Dooley
IAO_0000119: http://www.din.de/en/din-and-our-partners/din-e-v
IAO_0100001: ARO_3004367
has alternative id: DIN
label: Deutsches Institut für Normung @de
deprecated: true

obsolete: European Committe on Antimicrobial Susceptibility Testing (EUCAST)
type: Class
IAO_0000115: EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in vitro antimicrobial susceptibility testing.
IAO_0000117: Damion Dooley
IAO_0000119: http://www.eucast.org/
IAO_0100001: ARO_3004368
has alternative id: EUCAST
deprecated: true

obsolete: National Committee on Clinical Laboratory Standards (NCCLS)
type: Class
IAO_0000117: Damion Dooley
IAO_0100001: ARO_3004366
has alternative id: NCCLS
deprecated: true

obsolete: Société Française de Microbiologie (SFM)
type: Class
IAO_0000115: La SFM a vocation à rassembler les microbiologistes de France et des pays francophones, travaillant dans les différents domaines de la microbiologie médicale, industrielle, et environnementale, en physiologie, génétique, taxonomie, hygiène, agents antimicrobiens, ...concernant les bactéries, virus, champignons et parasites. @fr
IAO_0000115: The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents.
IAO_0000116: This isn't at moment considered a valid EBI antibiogram choice?
IAO_0000117: Damion Dooley
IAO_0000119: http://www.sfm-microbiologie.org/
IAO_0100001: ARO_3004369
has alternative id: SFM
deprecated: true

obsolete: SIR
type: Class
IAO_0000231: Replaced by domain appropriate term created in the Comprehensive Antibiotic Resistance Database (CARD).
IAO_0100001: ARO_3007397
deprecated: true

obsolete: WRG
type: Class
IAO_0000231: Replaced by domain appropriate term created in the Comprehensive Antibiotic Resistance Database (CARD).
IAO_0100001: ARO_3007398
deprecated: true

first line tuberculosis drug
type: Class
subclass of: tuberculosis treatment drug

last resort antibiotic
type: Class
subclass of: antimicrobial resistance test drug

National Institute of Allergy and Infectious Disease standard
type: Class
subclass of: NCIT C103180
user interface label: NIAID standard
IAO_0000114: IAO_0000120
IAO_0000115: NIAID provides The GSCID/BRC Project and Sample Application Standard. It is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards

RefSeq accession identifier
type: Class
subclass of: sequence accession
IAO_0000115: A RefSeq accession identifier is an accession identifier for selected NCBI-curated genomic, transcript and protein sequences. These identifiers are distinct from DDBJ/EMBL/GenBank identifiers.
IAO_0000117: Damion Dooley

Genomic Standards Consortium (GSC) standard
type: Class
subclass of: NCIT C103180
IAO_0000115: A Genomic Standards Consortium standard is an international, community-driven standard to facilitate genomic data integration, discovery and comparison.
IAO_0000117: Damion Dooley

specimen collection site - geographic feature
type: Class
subclass of: data specification
IAO_0000114: IAO_0000428
IAO_0000115: A landform, biome or built environment at site that a given specimen was collected from.
IAO_0000117: Damion Dooley

subject organism
type: Class
subclass of: investigative subject
subclass of: Restriction
  on property: RO_0000086
  some values from: OBI_0001169
IAO_0000112: A particular human patient, or a given animal or plant.
IAO_0000114: IAO_0000122
IAO_0000115: An investigative subject which is an organism.
IAO_0000117: Damion Dooley

number of passages
type: Class
subclass of: isolate passage history datum
subclass of: STATO_0000047
user interface feature: help=The number of passages should be expressed as a numerical value.
IAO_0000114: IAO_0000122
IAO_0000115: The number of serial iterations that an isolate is grown in one environment.
IAO_0000117: Damion Dooley

passage protocol
type: Class
subclass of: isolate passage history datum
subclass of: SIO_000136
user interface feature: help:The passage protocol should include, when applicable, inoculum size, media type, temperature and duration of incubation.
IAO_0000115: A passage protocol should detail the number of serial iterations that an isolate is grown in one environment, and the conditions of that environment.
IAO_0000117: Damion Dooley

obsolete: drug minimum inhibitory concentration unit
type: Class
IAO_0000115: The unit provided for an antibiotic drug test dosage.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004372
deprecated: true

draft sequence repository data - specimen collection
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0001237 # specimen type (host or environmental context) OBI:0001619 # specimen collection date OBI:0000659 # specimen collection process GENEPIO:0002094 # specimen collection device GENEPIO:00001600 # draft sequence repository data - geographic location ENVO:00010483 # environmental material ENVO:00002297 # environmental feature GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0000110 # subject health status GENEPIO:0001617 # subject disease GENEPIO:0000028 # subject body product GENEPIO:0000025 # specimen source anatomical site FOODON:03411564 # draft sequence repository data - food processing
IAO_0000114: IAO_0000428

contact specification - specimen related organization
type: Class
subclass of: contact specification
user interface feature: order: GENEPIO:0002105 # Specimen processing organization role NCIT:C93874 # organization name NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision -> GAZ state/province/territory/region) NCIT:C80234 # Municipality” (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address
IAO_0000114: IAO_0000428
IAO_0000115: Contact information for an organization related to specimen collection, processing or storage.
IAO_0000117: Damion Dooley

draft sequence repository contextual data standard
type: Class
subclass of: draft data standard
user interface feature: dateFormat:ISO 8601
user interface feature: order: GENEPIO:0002082 # specimen related organization GENEPIO:0002081 # specimen collection GENEPIO:0002086 # geographic location GENEPIO:0002084 # isolate GENEPIO:0002087 # isolate history GENEPIO:0002106 # food specimen GENEPIO:0002088 # antibiogram GENEPIO:0002085 # sequencing GENEPIO:0002090 # sequencing QC GENEPIO:0002089 # virulence GENEPIO:0002092 # submission to EBI GENEPIO:0002091 # submission to NCBI/DDBJ
IAO_0000114: IAO_0000428
IAO_0000115: This draft specification provides a collection of fields related to the contextual data of a specimen, its genomic sequencing, and its pathogenic epidemiology.
IAO_0000117: Damion Dooley

draft sequence repository data - isolate
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0001640 # specimen taxonomy GENEPIO:0001429 # strain identifier GENEPIO:0001644 # isolate identifier OBI:0000079 # culture medium GENEPIO:0002107 # isolation medium
IAO_0000114: IAO_0000428

draft sequence repository data - sequencing
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0000069 # sequencing date OBI:0000079 # culture medium” (via MicrO, yields a list of formulas). GENEPIO:0002093 # sequencing dna extraction method EFO:0000683 # replicate GENEPIO:0000085 # library preparation kit GENEPIO:0000149 # library preparation kit version GENEPIO:0000075 # sequencing chemistry GENEPIO:0001921 # sequencing instrument model GENEPIO:0000150 # read trimming and filtering software GENEPIO:0000084 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000090 # assembly method GENEPIO:0000151 # bioinformatics pipeline name GENEPIO:0000153 # bioinformatics pipeline protocol GENEPIO:0000152 # bioinformatics pipeline version GENEPIO:0000095 # genome annotation algorithm
IAO_0000114: IAO_0000428

draft sequence repository data - geographic location
type: Class
subclass of: data specification
user interface feature: order: GENEPIO_0001656 # latitude and longitude ISO 6709 GENEPIO:0000118 # specimen collection country GENEPIO:0002097 # specimen collection state/prov/ter/region GENEPIO:0001785 # specimen collection city
IAO_0000114: IAO_0000428
IAO_0000115: The geographical origin of the sample by city, region, country or latitude and logitude.
IAO_0000117: Damion Dooley

draft sequence repository data - isolate passage history
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0002078 # number of passages GENEPIO:0002079 # passage protocol
IAO_0000114: IAO_0000428

draft sequence repository data - antibiogram
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0001100 # antimicrobial drug tests GENEPIO:0002101 # test drug minimum concentration GENEPIO:0002100 # test drug maximum concentration GENEPIO:0002045 # antimicrobial resistance testing method GENEPIO:0002047 # antimicrobial testing method version or reagent GENEPIO:0002062 # antimicrobial resistance testing reference standard GENEPIO:0002049 # antimicrobial resistance testing platform
IAO_0000114: IAO_0000428
IAO_0000115: A dataset of the minimal inhibitory concentrations (value, unit, sign (<,>, =)) and resistance phenotypes (resistant, sensitive or undetermined) of the sequenced isolate against different antibiotics tested.
IAO_0000117: Damion Dooley

draft sequence repository data - virulence
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0002130 # Virulence factor name GENEPIO:0002131 # Virulence testing protocol GENEPIO:0002132 # detection limit
IAO_0000114: IAO_0000428
IAO_0000115: The virulence factors determined to be present in the sequenced isolate by phenotypic or target amplification methods e.g. Shiga toxins, hemolysins.
IAO_0000117: Damion Dooley

draft sequence repository data - sequencing quality control
type: Class
subclass of: data specification
user interface feature: order: OBI:0001941 # N50 GENEPIO_0000092 # sequencing depth / read coverage
IAO_0000114: IAO_0000428
IAO_0000115: Measurements or calculated quantities used to assess the extent and success of the sequence assembly process. Metric thresholds are species-specific.
IAO_0000117: Damion Dooley

draft sequence repository data - submission to NCBI/DDBJ
type: Class
subclass of: data specification
user interface feature: order: OBI:0001616 # specimen identifier GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0001657 # geo_loc_name GENEPIO:0001656 # latitude and longitude coord GENEPIO:0000027 # specimen source context GENEPIO:0001567 # subject organism taxonomy GENEPIO:0001724 # subject organism common name GENEPIO:0001617 # subject disease
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

draft sequence repository data - submission to EBI
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0001079 # serovar GENEPIO:0002135 # EBI environmental feature GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0002086 # geographic location GENEPIO:0000027 # specimen source context GENEPIO:0002076 # geographic feature GENEPIO:0001567 # subject taxonomy GENEPIO:0000110 # subject health status
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

sequencing dna extraction method datum
type: Class
subclass of: laboratory sequencing datum
IAO_0000114: IAO_0000428
IAO_0000115: The procedure used to obtain genomic DNA from a sample through chemical, physical or mechanical means.
IAO_0000117: Damion Dooley

obsolete: specimen collection device
type: Class
IAO_0000231: Moved term to OBI, deprecated in favour of the OBI version.
IAO_0100001: OBI_0002814
deprecated: true

read paired-end merging software
type: Class
subclass of: laboratory sequencing datum
IAO_0000115: The name and version of the software used to merge paired-end reads before assembly.

read adapter trimming software
type: Class
subclass of: laboratory sequencing datum
metadata section: Sequencing
IAO_0000115: The name and version of the software product used for removal of adapter sequences from demultiplexed data reads
IAO_0000119: GROUP: IRIDA Ontology (Emma)
in subset: GENEPIO

specimen collection location - state/province/territory/region
type: Class
subclass of: specimen collection site specification
subclass of: Restriction
IAO_0000114: IAO_0000122
IAO_0000115: An ontology identifier or textual name of the most precise geographical location available for the site of a specimen collection event.
IAO_0000117: Damion Dooley
IAO_0000119: Adapted from NIAID GSCID-BRC metadata working group
IAO_0000600: Note that this is expressed in a particular format in some standards.

Axiom
annotated source: specimen collection location - state/province/territory/region
annotated property: subClassOf
annotated target: Restriction
user interface feature: lookup

obsolete: wild type (WT)
type: Class
IAO_0000115: A wild type (WT) resistance phenotype indicates a bacterial pathogen belongs to a "Naïve", susceptible wild-type population with respect to a given antimicrobial. No acquired or mutational resistance mechanisms are present to the antimicrobial in question.
IAO_0000117: Damion Dooley
IAO_0000119: https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004432
deprecated: true

obsolete: non-wild type (NWT)
type: Class
IAO_0000115: A non-wild type (WT) resistance phenotype indicates a bacterial pathogen has an acquired or mutational resistance mechanism present with respect to the antimicrobial in question. The bacteria has a reduced susceptibility to this agent.
IAO_0000117: Damion Dooley
IAO_0000119: https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004433
deprecated: true

test drug maximum concentration
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000428
IAO_0000115: This is the maximum concentration of a drug applied during an an assay.
IAO_0000117: Damion Dooley

test drug minimum concentration
type: Class
subclass of: IAO_0000027
IAO_0000114: IAO_0000428
IAO_0000115: This is the minimum concentration of a drug applied during an an assay.
IAO_0000117: Damion Dooley

obsolete: antimicrobial resistance tissue specificity
type: Class
IAO_0000115: The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results.
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004430
deprecated: true

subject health status (NCIT)
type: Class
subclass of: organism datum
user interface feature: depth:1
user interface feature: order: NCIT:C115935 # healthy NCIT:C126054 # non-pathalogical NCIT:C25610 # pathologic NCIT:C82508 # life threatening NCIT:C28554 # deceased

contact specification - professional role
type: Class
subclass of: contact specification
user interface feature: order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone

specimen processing organization type
type: Class
subclass of: OBI_0000245
IAO_0000114: IAO_0000428
IAO_0000115: An organization related to the collection, isolate production, sequencing or storage of specimen material or data.
IAO_0000117: Damion Dooley

draft sequence repository data - food specimen
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0001533 # food specimen type FOODON:03450002 # food cooking method FOODON:03440011 # extent of heat treatment FOODON:03430113 # physical state, shape or form FOODON:03470107 # food preservation method FOODON:03490100 # container or wrapping FOODON:03480020 # food packing medium FOODON:03500010 # food contact surface GENEPIO:0000139 # food cultural origin FOODON:03460111 # treatment applied to food
IAO_0000115: This specification offers food source, product type, packaging and processing attributes relevant to describing a food specimen.

isolation medium
type: Class
subclass of: OBI_0000079
IAO_0000114: IAO_0000428
IAO_0000115: An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment.
IAO_0000116: Chris has proposed this term for OBI as "enrichment culture medium"
IAO_0000117: Damion Dooley

draft travel log specification
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0000121 # start date GENEPIO:0000122 # end date GENEPIO:0001783 # travel destination GENEPIO:0001064 # travel mode GENEPIO:0001065 # travel reason
IAO_0000114: IAO_0000428
IAO_0000115: This record details a person's travel movement and duration for epidemiological analysis.
IAO_0000117: Damion Dooley

draft EBI antimicrobial susceptibility test V. 2017-08-30
type: Class
subclass of: draft data standard
user interface feature: order: OBI:0001616 # BioSample_ID GENEPIO:0001640 # Species GENEPIO:0001187 # Antibiotic_Name GENEPIO:0002062 # AST_Standard GENEPIO:0002111 # Breakpoint_version NCIT:C85540 # Laboratory_typing_method GENEPIO:0002112 # Measurement GENEPIO:0002080 # Measurement_units GENEPIO:0001001 # Measurement_sign NCIT:C85539 # Resistance_phenotype GENEPIO:0002181 # Resistance_phenotype - ECOFF GENEPIO:0002049 # Platform
IAO_0000114: IAO_0000428
IAO_0000115: A standard for European Bioinformatics Institute (EBI) antibiogram data submission
IAO_0000117: Damion Dooley

MIC diffusion measurement datum
type: Class
subclass of: IAO_0000032
subclass of: Restriction
  on property: is about
  some values from: NCIT C128985
IAO_0000114: IAO_0000428
IAO_0000115: A MIC test measurement resulting from a laboratory diffusion method.
IAO_0000116: Damion Dooley's note: is this still useful? Currently "MIC diffusion measurement specification' refers directly via 'is about' to "Disk Diffusion Method".
IAO_0000117: Damion Dooley

antimicrobial resistance testing reference standard version
type: Class
subclass of: IAO_0000300
IAO_0000114: IAO_0000428
IAO_0000115: The version of the antimicrobial reistance testing reference standard protocol used in assessing an isolate.
IAO_0000117: Damion Dooley

draft sequence repository data - antibiogram MIC measurement
type: Class
subclass of: data specification
IAO_0000115: This is a component of an antibiogram that enables a choice of MIC measurements based on either the diffusion or dilution method. These methods call for different numeric input ranges and units.

time value specification
type: Class
subclass of: OBI_0001931
subclass of: Restriction
  on property: IAO_0000039
  max qualified cardinality: 1
  on class: UO_0000003
subclass of: Restriction
  on property: OBI_0002135
  some values from: dateTime

feces collection
type: Class
subclass of: OBI_0600005
IAO_0000114: IAO_0000122
IAO_0000115: The process of collecting a portion of feces from an organism.
IAO_0000117: Emma Griffiths
has exact synonym: stool collection

sputum collection
type: Class
subclass of: OBI_0600005
IAO_0000114: IAO_0000122
IAO_0000115: The process of collecting a portion of urine from an organism.
IAO_0000117: Emma Griffiths

rinsing for specimen collection
type: Class
subclass of: OBI_0600005
IAO_0000114: IAO_0000122
IAO_0000115: The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids.
IAO_0000117: Emma Griffiths

swabbing for specimen collection
type: Class
subclass of: OBI_0600005
IAO_0000114: IAO_0000122
IAO_0000115: The process of collecting specimen material using a swab collection device.
IAO_0000117: Emma Griffiths

exudate collection
type: Class
subclass of: OBI_0600005
IAO_0000114: IAO_0000122
IAO_0000115: The process of collecting bodily fluids that have been discharged from blood vessels usually arising from inflammation or injury.
IAO_0000117: Emma Griffiths

vacuuming for specimen collection
type: Class
subclass of: OBI_0600005
IAO_0000114: IAO_0000122
IAO_0000115: The removal or collection of specimen material through the use of suction.
IAO_0000117: Emma Griffiths

tube containing media or preservative
type: Class
subclass of: NCIT C41277
IAO_0000114: IAO_0000122
IAO_0000117: Emma Griffiths
IAO_0000600: NOTE: there are different types of tubes with coloured caps indicating different preservatives etc.

tube containing antimicrobial
type: Class
subclass of: NCIT C41277
IAO_0000117: Emma Griffiths
IAO_0000600: NOTE: there are different types of tubes with coloured caps indicating different preservatives etc.

Whirlpak sampling bag
type: Class
subclass of: NCIT C43167
IAO_0000114: IAO_0000122
IAO_0000115: A sterilized sampling bag that is puncture proof tabs for protection from damage due to wire-end protrusion and leak-proof closures.
IAO_0000117: Emma Griffiths

spoon
type: Class
subclass of: NCIT C43167
IAO_0000114: IAO_0000122
IAO_0000117: Emma Griffiths

fork
type: Class
subclass of: NCIT C43167
IAO_0000114: IAO_0000122
IAO_0000117: Emma Griffiths

hand scoop
type: Class
subclass of: NCIT C43167
IAO_0000114: IAO_0000122
IAO_0000115: A shovel-like utensil that has a deep curved dish and a short handle and is used for digging into a soft substance for lifting out a portion.
IAO_0000117: Emma Griffiths
contributor: https://orcid.org/0000-0002-1107-9135
date: 2023-06-21T13:54:32Z

trier
type: Class
subclass of: NCIT C43167
IAO_0000117: Emma Griffiths

vaccum device
type: Class
subclass of: OBI_0002814
IAO_0000114: IAO_0000122
IAO_0000115: A device which generates a vacuum to provide suction of material.
IAO_0000117: Emma Griffiths
IAO_0000119: https://orcid.org/0000-0002-9578-0788

investigation identifier specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: OBI_0001628

draft Enterobase contextual data standard
type: Class
subclass of: draft data standard
user interface feature: order: GENEPIO:0001640 # taxonomy GENEPIO:0002086 # geographic location GENEPIO:0002076 # geographic feature GENEPIO:0002106 # food FOODON:03510136 # food consumer GENEPIO:0002094 # specimen collection device GENEPIO:0000025 # anatomical site GENEPIO:0000028 # body product GENEPIO:0001724 # host organism common name GENEPIO:0001567 # host taxonomy UBERON:0000105 # life cycle GENEPIO:0001639 # antigenic formula GENEPIO:0001718 # serotype specification GENEPIO:0000045 # PFGE test specification
IAO_0000114: IAO_0000428
IAO_0000115: This is a draft (under development) collection of fields for capturing the contextual data for Enterobase (https://enterobase.warwick.ac.uk/) records.
IAO_0000117: Damion Dooley

virulence factor name
type: Class
subclass of: IAO_0000300
subclass of: Restriction
  on property: is about
  some values from: IDO_0000547
IAO_0000114: IAO_0000428
IAO_0000115: The name of the virulence factor molecule produced by a pathogen that specifically causes disease, or that influences the host's function to allow the pathogen to thrive.
IAO_0000117: Emma Griffiths

virulence testing protocol name
type: Class
subclass of: IAO_0000300
subclass of: Restriction
  on property: is about
  some values from: IDO_0000547
user interface feature: help:The protocol for determining virulence should include, when applicable, inoculum preparation, platforms and instrumentation, conditions, cell lines and animal models.
IAO_0000114: IAO_0000428
IAO_0000115: The laboratory protocol used to determine virulence phenotypes and markers.
IAO_0000117: Emma Griffiths

detection limit
type: Class
subclass of: IAO_0000300
subclass of: Restriction
  on property: is about
  some values from: IDO_0000547
user interface feature: help:Detection limits should include the numerical cut-off (threshold) value and units for determining positive results e.g. qPCR value, CFUs.
IAO_0000115: The detection limit denotes the smallest measure that can be detected with reasonable certainty for a given analytical procedure.
IAO_0000117: Emma Griffiths

disease cluster
type: Class
subclass of: IAO_0000100
IAO_0000114: IAO_0000122
IAO_0000115: A disease cluster is an unusually high incidence of a particular disease or disorder occurring in close proximity in terms of both time and geography.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Disease_cluster

infectious disease cluster
type: Class
subclass of: disease cluster
IAO_0000114: IAO_0000122
IAO_0000114: IAO_0000428
IAO_0000115: A disease cluster in which two or more cases have been linked by an infectious disease transmission process.
IAO_0000117: Damion Dooley

EBI ENA Webin environmental feature
type: Class
subclass of: specimen datum
user interface feature: help:used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier
IAO_0000115: Identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture).
has alternative id: ENA Webin:environmental_feature

EBI European Nucleotide Archive Webin
type: Class
subclass of: NCIT C103180
IAO_0000114: IAO_0000122
IAO_0000115: The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Webin is an ENA interface and standard for sequence submissions.
IAO_0000119: https://www.ebi.ac.uk/ena

breadth of coverage
type: Class
subclass of: assembly quality control datum
user interface feature: help:Breadth of coverage should be reported as a percentage value (e.g. 95%) to a fold of coverage (e.g. 10X).
IAO_0000112: Eighty percent of the reference genome was covered by sequence fragments with a coverage depth of 4X; therefore, the breadth of coverage was 80% (4:5).
IAO_0000114: IAO_0000428
IAO_0000115: A data item which is the amount of a reference sequence covered by a sequence of interest.
IAO_0000119: Emma Griffiths
contributor: https://orcid.org/0000-0002-1107-9135
contributor: https://orcid.org/0000-0002-9578-0788
has db xref: OBI:0002879

mean contig length
type: Class
subclass of: assembly quality control datum
subclass of: IAO_0000032
IAO_0000115: The mean contig length is the count of base pairs in the average size contig of the sequence assembly.
IAO_0000117: Emma Griffiths

raw sequence data processing datum
type: Class
subclass of: data specification
user interface feature: order: GENEPIO:0000084 # read adapter trimming (y/n) GENEPIO:0002096 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000150 # read trimming and filtering software
IAO_0000114: IAO_0000428
IAO_0000115: The procedures used to remove adapters from raw sequence reads, trim low quality bases and where applicable, merge paired-end reads.
IAO_0000117: Emma Griffiths

specimen strain or isolate identifier
type: Class
subclass of: data specification
IAO_0000114: IAO_0000122
IAO_0000115: Name of strain from which sample was obtained OR name of isolate from which sample was obtained.
IAO_0000117: Damion Dooley

latitude and longitude coordinate (NCBI BioSample format)
type: Class
subclass of: IAO_0000300
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: string
    with restrictions:
      pattern: \s*(\d(.\d{1,4})?|[1-8]\d(.\d{1,4})?|90(.0{1,4})?)\s*[WEwe]\s*(\d(.\d{1,4})?|[1-9]\d(.\d{1,4})?|1[0-7]\d(.\d{1,4})?|180(.0{1,4})?)\s*[NSns]\s*
IAO_0000114: IAO_0000428
IAO_0000115: The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/

decimal value specification
type: Class
subclass of: OBI_0001933
subclass of: Restriction
  on property: OBI_0002135
  some values from: decimal

floating point value specification
type: Class
subclass of: OBI_0001933
subclass of: Restriction
  on property: OBI_0002135
  some values from: float

unsigned integer value specification
type: Class
subclass of: unsigned long integer value specification
subclass of: Restriction
  on property: OBI_0002135
  some values from: unsignedInt
user interface label: unsigned integer
IAO_0000115: A 32 bit number having a range 0 - 4294967295.

date value specification
type: Class
subclass of: OBI_0001933
subclass of: Restriction
  on property: IAO_0000039
  qualified cardinality: 1
  on class: Class
    union of: UO_0000033
    union of: UO_0000034
    union of: UO_0000035
    union of: UO_0000036
subclass of: Restriction
  on property: IAO_0000039
  max qualified cardinality: 1
  on class: UO_0000003
subclass of: Restriction
  on property: OBI_0002135
  all values from: dateTime

assembly genome size specification
type: Class
subclass of: decimal value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: assembly genome size
subclass of: Restriction
  on property: IAO_0000039
  qualified cardinality: 1
  on class: Class
    union of: UO_0000244
    union of: UO_0000328
    union of: UO_0000329
IAO_0000115: A specification for the size of an assembled genome as measured in base pairs.
IAO_0000116: This is a decimal because the megabasepair unit may involve a fractional component.

sequencing facility name specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: OBI_0001891

date value specification (ISO 8601)
type: Class
subclass of: date value specification
user interface label: date (ISO 8601)
IAO_0000115: A date should be recorded as YYYY-MM-DD according to ISO 8601. HOWEVER ... OWL 2.0 does not include xsd:date as a permitted data type, so this value specification only accepts xsd:dateTime

strain identifier specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: strain identifier

MIC diffusion measurement specification
type: Class
subclass of: OBI_0001931
subclass of: Restriction
  on property: is about
  some values from: ARO_3004391
subclass of: Restriction
  on property: OBI_0001927
  some values from: ARO_3004371
subclass of: Restriction
  on property: IAO_0000039
  qualified cardinality: 1
  on class: UO_0000016
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: positiveInteger
    with restrictions:
      min exclusive: 5
    with restrictions:
      max exclusive: 100
IAO_0000115: A MIC test measurement resulting from a laboratory diffusion method.
IAO_0000117: Damion Dooley

unsigned short integer value specification
type: Class
subclass of: unsigned integer value specification
subclass of: Restriction
  on property: OBI_0002135
  some values from: unsignedShort
user interface label: unsigned short
IAO_0000115: A 16 bit integer ranging from 0 - 65535

genomic sequence length specification
type: Class
subclass of: decimal value specification
subclass of: Restriction
  on property: IAO_0000039
  qualified cardinality: 1
  on class: Class
    union of: UO_0000244
    union of: UO_0000329

MIC dilution measurement specification
type: Class
subclass of: OBI_0001931
subclass of: Restriction
  on property: is about
  some values from: ARO_3004397
subclass of: Restriction
  on property: OBI_0001927
  some values from: ARO_3004371
subclass of: Restriction
  on property: IAO_0000039
  qualified cardinality: 1
  on class: Class
    union of: UO_0000273
    union of: UO_0000274
subclass of: Restriction
  on property: OBI_0002135
  all values from: Datatype
    on datatype: float
    with restrictions:
      min inclusive: 0.01
    with restrictions:
      max inclusive: 2048.0
IAO_0000115: A MIC test measurement resulting from a laboratory dilution method.
IAO_0000117: Damion Dooley

specimen collection date (ISO 8601)
type: Class
subclass of: date value specification (ISO 8601)
subclass of: Restriction
  on property: OBI_0001927
  some values from: OBI_0001619
comment: The date on which a specimen was collected, in ISO 8601 format.

date of diagnosis (ISO 8601)
type: Class
subclass of: date value specification (ISO 8601)
subclass of: Restriction
  on property: OBI_0001927
  some values from: EFO_0004953

subject age specification
type: Class
subclass of: duration specification
subclass of: Restriction
  on property: is about
  some values from: subject organism
subclass of: Restriction
  on property: OBI_0001927
  some values from: OBI_0001169
subclass of: Restriction
  on property: IAO_0000039
  max qualified cardinality: 1
  on class: Class
    union of: UO_0000033
    union of: UO_0000034
    union of: UO_0000035
    union of: UO_0000036
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: decimal
    with restrictions:
      min inclusive: 0
IAO_0000115: A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time.
IAO_0000117: Damion Dooley

subject age at time of specimen collection specification
type: Class
subclass of: subject age specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: subject age at time of specimen collection

boolean value specification
type: Class
subclass of: OBI_0001933
subclass of: Restriction
  on property: is about
  some values from: STATO_0000090
subclass of: Restriction
  on property: OBI_0002135
  qualified cardinality: 1
  on data range: boolean
user interface label: boolean
IAO_0000114: IAO_0000428
IAO_0000115: A boolean value specification indicates a presence (true value) or absence (false value) of a given feature.
IAO_0000117: Damion Dooley

specimen identifier specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: OBI_0001616

email address specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: NCIT C42775
subclass of: Restriction
  on property: OBI_0002135
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: [A-Za-z0-9]+([_.\-][A-Za-z0-9]+)*\@[A-Za-z0-9]+([.\-][A-Za-z0-9]+){1,3}

region, province, state or territory specification
type: Class
subclass of: OBI_0001930
subclass of: Restriction
  on property: OBI_0001927
  some values from: Class
    union of: subnational region
    union of: NCIT C25632
    union of: NCIT C87194
    union of: NCIT C89811

specimen collection site specification
type: Class
subclass of: OBI_0001930
subclass of: Restriction
  on property: OBI_0001927
  some values from: SIO_000415
IAO_0000115: A specification for a geographic location that a specimen was collected at.

subject organism common name specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: subject organism common name

subject identifier specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: subject identifier
IAO_0000115: A subject identifier specification is a specification including datatype pertaining to a given standard's subject identifier field.
IAO_0000117: Damion Dooley

subject disease specification
type: Class
subclass of: OBI_0001930
subclass of: Restriction
  on property: is about
  some values from: subject disease
subclass of: Restriction
  on property: OBI_0001927
  some values from: DOID 4
IAO_0000115: Name of disease in a subject that is related to a given investigation, study and/or specimen.
IAO_0000117: Damion Dooley
IAO_0000119: NIAID GSCID-BRC metadata working group
comment: Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067

unsigned long integer value specification
type: Class
subclass of: decimal value specification
subclass of: Restriction
  on property: OBI_0002135
  some values from: unsignedLong
user interface label: unsigned long integer
IAO_0000115: A 64 bit integer ranging from 0 - 18446744073709551615

specimen collection site
type: Class
subclass of: GENEPIO_0001886
subclass of: Class
  union of: ENVO_00000005
  union of: NCIT C25464
  union of: NCIT C80234
IAO_0000114: IAO_0000428
IAO_0000115: The physical location that a specimen was collected at. The location may be described by geographic coordinates, city or other geopolitical entity, biome, etc.
IAO_0000117: Damion Dooley

drug MIC unit specification
type: Class
subclass of: data specification
subclass of: Restriction
  on property: is about
  some values from: ARO_3004372
IAO_0000115: The unit provided for an antibiotic drug test dosage.
IAO_0000117: Damion Dooley

test drug maximum concentration specification
type: Class
subclass of: decimal value specification
subclass of: Restriction
  on property: IAO_0000039
  some values from: Class
    union of: UO_0000016
    union of: UO_0000274
subclass of: Restriction
  on property: OBI_0001927
  some values from: test drug maximum concentration
IAO_0000117: Damion Dooley
IAO_0000598: A datum specification for the maximum concentration of a drug applied during an an assay.

test drug minimum concentration specification
type: Class
subclass of: decimal value specification
subclass of: Restriction
  on property: IAO_0000039
  some values from: Class
    union of: UO_0000016
    union of: UO_0000274
subclass of: Restriction
  on property: OBI_0001927
  some values from: test drug minimum concentration
IAO_0000115: This is the minimum concentration of a drug applied during an an assay.
IAO_0000117: Damion Dooley

listeria antigen specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: listeria antigen
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: string
    with restrictions:
      pattern: (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7)

URL specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: SIO_000811
subclass of: Restriction
  on property: OBI_0002135
  qualified cardinality: 1
  on data range: Datatype
    on datatype: string
    with restrictions:
      pattern: url

travel destination specification
type: Class
subclass of: OBI_0001930
subclass of: Restriction
  on property: is about
  some values from: travel destination
subclass of: Restriction
  on property: OBI_0001927
  some values from: Class
    union of: NCIT C25160
    union of: NCIT C25464
    union of: NCIT C25632
    union of: NCIT C80234
    union of: NCIT C87194
    union of: NCIT C89811
IAO_0000115: A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip.
IAO_0000117: Damion Dooley

specimen source substance specification
type: Class
subclass of: data specification
subclass of: Restriction
  on property: is about
  some values from: specimen source substance
IAO_0000115: A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted.
IAO_0000117: Damion Dooley

specimen from organism specification
type: Class
subclass of: data specification
subclass of: Restriction
  on property: is about
  some values from: OBI_0001479
IAO_0000116: Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy".

duration specification
type: Class
subclass of: decimal value specification
subclass of: Restriction
  on property: IAO_0000039
  qualified cardinality: 1
  on class: UO_0000003
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: decimal
    with restrictions:
      min inclusive: 0

obsolete: field specification
type: Class
subclass of: OBI_0000658
IAO_0000115: A field specification is the specification of a data field used in a data standard or database table. This includes at least a database field name, and optionally display name, description, and data type (binary blob, numeric, categorical, textual or cross-reference).
IAO_0000117: Damion Dooley
IAO_0100001: SlotDefinition
date: 2019-04-17T23:04:53Z
deprecated: true

obsolete: antimicrobial resistance phenotype - epidemiological cut-off values
type: Class
IAO_0000117: Damion Dooley
IAO_0100001: http://purl.obolibrary.org/obo/ARO_3004431
deprecated: true

PulseNet Canada field
type: Class
subclass of: OBI_0000658
IAO_0000117: Damion Dooley
date: 2019-04-17T23:41:35Z

PulseNet Canada Salmonella field
type: Class
subclass of: PulseNet Canada field
IAO_0000117: Damion Dooley
date: 2019-04-17T23:41:56Z

specimen collection service
type: Class
subclass of: specimen related service
IAO_0000117: Damion Dooley
date: 2019-05-03T02:44:38Z

bioinformatics analysis service
type: Class
subclass of: specimen related service
IAO_0000117: Damion Dooley
date: 2019-05-03T02:49:24Z

isolate preparation service
type: Class
subclass of: specimen related service
IAO_0000115: An isolate preparation service prepares isolates for molecular sequencing.
IAO_0000117: Damion Dooley
date: 2019-05-03T02:51:51Z
label: IAO_0000428

specimen related service
type: Class
subclass of: OBI_0001173
user interface feature: order: GENEPIO:0002222 # specimen collection service GENEPIO:0002226 # specimen repository/biobank service GENEPIO:0002224 # isolate preparation service OBI:0001904 # sequencing service OBI:0000992 # DNA sequencing service GENEPIO:0002223 # bioinformatics analysis service
IAO_0000117: Damion Dooley
date: 2019-05-03T02:52:19Z

specimen repository/biobank service
type: Class
subclass of: specimen related service
IAO_0000117: Damion Dooley
date: 2019-05-03T03:24:33Z

critical health status
type: Class
subclass of: ExO_0000038
subclass of: subject health status (UK NHS)
subclass of: subject health status (AHA)
subclass of: Restriction
  on property: RO_0002083
  some values from: critical but stable health status
IAO_0000114: IAO_0000122
IAO_0000115: Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable.
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2019-11-19T22:17:43Z
has broad synonym: grave

critical
type: Axiom
annotated source: critical health status
annotated property: subClassOf
annotated target: subject health status (UK NHS)

critical
type: Axiom
annotated source: critical health status
annotated property: subClassOf
annotated target: subject health status (AHA)

Salmonella subspecies
type: Class
subclass of: organism datum
IAO_0000115: A datum indicating one of six defined subspecies of Salmonella.
IAO_0000117: http://orcid.org/0000-0002-8844-9165
IAO_0000119: Salmonella
date: 2019-11-25T08:45:41Z

PFGE Spel pattern
type: Class
subclass of: PFGE pattern
IAO_0000115: A PFGE pattern resulting from DNA fragmentation induced by the Spel enzyme.
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2019-11-25T09:07:26Z

fecal indicator
type: Class
subclass of: PCO_0000000
IAO_0000114: IAO_0000122
IAO_0000115: A collection of organisms that is indicative of faecal contamination.
IAO_0000117: http://orcid.org/0000-0002-8844-9165
IAO_0000119: iwachap13.pdf
date: 2020-02-08T20:15:43Z
comment: Fecal indicator organism collections include bacterial groups such as thermotolerant coliforms or E. coli. Hence, they only infer that pathogens may be present

food isolate
type: Class
equivalent class: Class
  intersection of: FOODON_00002403
  intersection of: NCIT C53471
subclass of: NCIT C53471
IAO_0000114: IAO_0000122
IAO_0000115: An isolate derived from a food sample.
IAO_0000117: Damion Dooley
date: 2019-06-28T23:41:26Z

microbial 16S RNA typing
type: Class
subclass of: diagnostic test
IAO_0000114: IAO_0000428
IAO_0000115: A method for typing The RNA component of the small (30S) subunit of prokaryotic ribosomes.
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2020-04-24T19:06:05Z

E. coli H antigen specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: H antigen
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: string
    with restrictions:
      pattern: h(1|2|3|4|5|6|7|8|9|10|11|12|14|15|16|17|18|19|21|23|24|26|27|28|29|30|31|32|33|34|35|36|37|38|39|40|41|42|43|44|45|46|47|48|49|51|52|53|54|55|56)

E. coli O antigen specification
type: Class
subclass of: string value specification
subclass of: Restriction
  on property: OBI_0001927
  some values from: O antigen
subclass of: Restriction
  on property: OBI_0002135
  some values from: Datatype
    on datatype: string
    with restrictions:
      pattern: O([1-9][0-9][0-9])

string value specification
type: Class
subclass of: OBI_0001933
subclass of: Restriction
  on property: OBI_0002135
  qualified cardinality: 1
  on data range: string
user interface label: string

Helicos platform
type: Class
subclass of: sequencing platform (brand)
IAO_0000115: A sequencing platform brand provided by Helicos corporation (now defunct).
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2020-04-24T22:50:49Z

Ion Torrent platform
type: Class
subclass of: sequencing platform (brand)
IAO_0000115: A sequencing platform provided by the Ion Torrent company.
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2020-04-24T22:54:06Z

SOLiD sequening platform
type: Class
subclass of: sequencing platform (brand)
IAO_0000115: A sequencing platform provided by Life Technologies Corporation
IAO_0000117: http://orcid.org/0000-0002-8844-9165
IAO_0000118: Sequencing by Oligonucleotide Ligation and Detection
date: 2020-04-24T22:55:31Z

obsolete: drag swab
type: Class
IAO_0100001: OBI_0002822
deprecated: true

rinse
type: Class
equivalent class: Restriction
  on property: output of
  some values from: rinsing for specimen collection
subclass of: OBI_0100051
IAO_0000114: IAO_0000122
IAO_0000115: Rinse is the liquid output of rinsing plant, animal or other material with liquid with the objective of extracting specimen material from that liquid.
IAO_0000117: Damion Dooley
date: 2019-06-28T20:07:25Z

animal rinse
type: Class
equivalent class: Class
  intersection of: animal body product
  intersection of: rinse
subclass of: rinse
IAO_0000115: Animal rinse is a rinse derived from animal material of one or more animals.
IAO_0000117: Damion Dooley
date: 2019-06-28T20:11:45Z

obsolete: surface wipe
type: Class
IAO_0100001: OBI_0002824
deprecated: true

culture plate
type: Class
subclass of: OBI_0000047
IAO_0000115: A low flat-bottomed laboratory container for growing a layer of organisms such as bacteria, molds, and cells on a thin layer of nutrient medium.
IAO_0000119: https://en.wikipedia.org/wiki/Culture_plate
date: 2022-09-23T10:59:09Z

fluid from meat rinse
type: Class
subclass of: animal rinse
IAO_0000115: A fluid that is obtained from rinsing meat for the purpose of collecting materials and organisms that are on its surface.
contributor: https://orcid.org/0000-0002-1107-9135
date: 2022-09-23T11:24:53Z

BGI Genomics platform
type: Class
subclass of: sequencing platform (brand)
IAO_0000115: A sequencing platform provided by the BGI Genomics company.
IAO_0000119: https://en.wikipedia.org/wiki/BGI_Group
contributor: https://orcid.org/0000-0001-5275-8866
date: 2022-09-23T11:41:23Z

MGI platform
type: Class
subclass of: sequencing platform (brand)
IAO_0000115: A sequencing platform provided by the MGI company.
IAO_0000119: https://en.wikipedia.org/wiki/MGI_(company)
contributor: https://orcid.org/0000-0001-5275-8866
date: 2022-09-23T11:43:21Z

fecal grab
type: Class
subclass of: feces collection
IAO_0000115: A fecal specimen collection method in which feces is obtained by inserting the collection device into the anus of the host, or the feces is captured as it is excreted.
IAO_0000119: Emma J Griffiths
contributor: https://orcid.org/0000-0002-1107-9135
date: 2022-09-23T11:47:33Z

Illumina NextSeq 1000
type: Class
subclass of: GENEPIO_0100126
IAO_0000114: IAO_0000428
IAO_0000115: A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.
IAO_0000116: Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term.
contributor: https://orcid.org/0000-0001-5275-8866
contributor: https://orcid.org/0000-0002-1107-9135
date: 2023-06-21T12:33:56Z

Oxford Nanopore Flongle
type: Class
subclass of: GENEPIO_0100140
IAO_0000114: IAO_0000428
IAO_0000115: An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells.
IAO_0000116: Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term.
IAO_0000119: https://store.nanoporetech.com/flongle.html
contributor: https://orcid.org/0000-0001-5275-8866
contributor: https://orcid.org/0000-0002-1107-9135
date: 2023-06-21T13:02:13Z

host health complications at time of specimen collection
type: Class
subclass of: personal health datum
subclass of: Restriction
  on property: is about
  some values from: NCIT C2959
subclass of: Restriction
  on property: is about
  some values from: OBI_0001619
IAO_0000114: IAO_0000428
IAO_0000115: A personal health datum which specifies host health complications at time of specimen collection.
IAO_0000117: 0000-0002-9578-0788
date: 2022-01-31T23:52:14Z

pre-existing conditions and risk factors at time of specimen collection
type: Class
subclass of: personal health datum
subclass of: Restriction
  on property: is about
  some values from: pre-existing condition
subclass of: Restriction
  on property: is about
  some values from: OBI_0001619
IAO_0000114: IAO_0000428
IAO_0000115: A personal health datum which specifies host pre-existing conditions and risk factors at time of specimen collection.
IAO_0000117: 0000-0002-9578-0788
date: 2022-01-31T23:52:41Z

signs and symptoms at time of specimen collection
type: Class
subclass of: personal health datum
subclass of: Restriction
  on property: is about
  some values from: signs and symptoms
subclass of: Restriction
  on property: is about
  some values from: OBI_0001619
IAO_0000114: IAO_0000428
IAO_0000115: A personal health datum which specifies host signs and symptoms at time of specimen collection.
IAO_0000117: 0000-0002-9578-0788
date: 2022-01-31T23:53:13Z

environmental testing sampling strategy
type: Class
subclass of: GENEPIO_0100219
IAO_0000115: A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work.
contributor: https://orcid.org/0000-0001-5275-8866

clinical trial sampling strategy
type: Class
subclass of: GENEPIO_0100219
IAO_0000115: A sampling strategy in which individuals are sampled in the context of experiments or observations performed as part of clinical research.
contributor: https://orcid.org/0000-0001-5275-8866
date: 2022-09-23T11:08:21Z

field experiment sampling strategy
type: Class
subclass of: GENEPIO_0100219
IAO_0000115: A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work.
IAO_0000119: https://en.wikipedia.org/wiki/Field_experiment
contributor: https://orcid.org/0000-0001-5275-8866
date: 2022-09-23T11:12:34Z

Environmental Pathogen Attribute Package (Pathogen.env)
type: Class
subclass of: NCBI standard
IAO_0000115: A collection of contextual data attributes pertaining to a pathogen in an environmental sample, as specified by the International Nucleotide Sequence Database Collaboration (INSDC).
contributor: https://orcid.org/0000-0002-1107-9135
date: 2022-09-23T10:54:21Z

survey study sampling strategy
type: Class
subclass of: GENEPIO_0100219
IAO_0000115: A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes.
contributor: https://orcid.org/0000-0001-5275-8866
date: 2022-09-23T11:04:13Z

data field
type: Class
subclass of: IAO_0000027
IAO_0000112: The "specimen collector sample ID" is where one can store sample identifiers given by the specimen collector.
IAO_0000114: IAO_0000428
IAO_0000115: A data item which is a location for a predetermined type of data.
IAO_0000119: https://analystanswers.com/what-is-a-data-field-definition-types-examples/
contributor: http://orcid.org/0000-0002-9578-0788
date: 2022-11-23T00:33:27.896Z
has exact synonym: data slot

State or Province or Territory
type: Class
equivalent class: Class
  union of: NCIT C25632
  union of: NCIT C87194
  union of: NCIT C89811
subclass of: NCIT C16632
IAO_0000114: IAO_0000428
IAO_0000116: This "or" class is just to represent an equivalency with a commonly used classification, it should not have subclasses under it. (2022-12-22)
contributor: http://orcid.org/0000-0002-9578-0788
date: 2022-12-22T22:56:03.687Z

GEO_000000788
subclass of: GENEPIO_0001866
subclass of: GENEPIO_0001867
subclass of: Restriction
  on property: aligned with
  some values from: RBO_00000017
subclass of: Restriction
  on property: has component
  qualified cardinality: 1
  on class: GENEPIO_0001907

HP_0000118
subclass of: BFO_0000019
user interface label: symptom
has db xref: http://purl.obolibrary.org/obo/SYMP_0000462

HP_0012830
type: Class
subclass of: BFO_0000019
user interface label: position of phenotype abnormality

IAO_0000416
comment: Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards

IAO_0000577
comment: Damion notes: Subclasses can actually have two components - the identifier, and the agency it is associated with. Under the general concept of "postal code" one can place particular national postal code systems like the US Postal code.

pregnant woman
type: Class
subclass of: patient type
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2020-04-24T22:38:17Z

source database
type: Class
subclass of: IAO_0000577
term source: http://www.ontobee.org/ontology/MI
user interface label: data source
IAO_0000114: IAO_0000122
IAO_0000115: Database that originally provided the interaction record for exchange purposes.
has db xref: PMID:14755292
comment: Damion Dooley's note: GenEpiO is using members of this class for the first part of the hasDbXref relation. This is where we are keeping the mapping between a code and its source database. Depending on its context, hasDbXref annotations may point directly to metadata field names in the target database, and may be annotated with additional information that guides any additional specifications that impact on data conversion of these fields.

necropsy
type: Class
subclass of: OBI_0600005
user interface label: tissue collection (necropsy)
IAO_0000115: A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. [database_cross_reference: Merriam-Webster:Merriam-Websters_Online_Dictionary--11th_Ed]

NCBITaxon 2157
IAO_0000114: IAO_0000122
IAO_0000115: The Archaea constitute a domain and kingdom of single-celled microorganisms
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Archaea

subspecies
type: Class
subclass of: taxonomic rank

NCIT C105370
type: Class
subclass of: CHEBI_33697
IAO_0000116: Damion Dooley's note: this term was mistakenly placed in a list of GenEpiO diagnostic tests; in fact it references a material entity

NCIT C115935
type: Class
subclass of: ExO_0000038
subclass of: subject health status at time of specimen collection
subclass of: subject health status (GSCID-BRC)
subclass of: subject disease outcome
subclass of: subject health status (NCIT)
subclass of: Restriction
  on property: after
  some values from: good health status
user interface label: healthy

NCIT C128985
type: Class
subclass of: OBI_0000070
IAO_0000116: NCIT offers this alternate definition which GenEpiO intends: "A measurement that specifies the minimum concentration of the agent at which organism growth was inhibited."
has alternative id: MIC
see also: Clinical and Laboratory Standards Institute MIC antimicrobial testing standards at http://em100.edaptivedocs.info/GetDoc.aspx?doc=CLSI%20M100%20S27:2017&scope=user

NCIT C17627
type: Class
subclass of: OBI_0002814
user interface definition: A portion of an absorbent material attached to one end of a small stick for the purpose of applying or collecting material.
IAO_0000114: IAO_0000122
IAO_0000117: Emma Griffiths

NCIT C25610
type: Class
subclass of: subject health status at time of specimen collection
subclass of: subject health status (GSCID-BRC)
subclass of: subject health status (NCIT)
user interface label: diseased
has exact synonym: sick

NCIT C25632
type: Class
subclass of: ENVO_00000005
disjoint with: NCIT C87194
disjoint with: NCIT C89811
user interface feature: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
IAO_0000114: IAO_0000428

NCIT C25720
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: BFO_0000029
      intersection of: Restriction
        on property: located in
        some values from: GAZ_00002459
  intersection of: Restriction
    on property: OBI_0001927
    some values from: NCIT C25621
subclass of: Restriction
  on property: OBI_0002135
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: [A-Za-z0-9]+([_.\-][A-Za-z0-9]+)*\@[A-Za-z0-9]+([.\-][A-Za-z0-9]+){1,3}
user interface regular expression validate: /^(:<zip>\d{5}(-\d{4})?)/, $zip

NCIT C28554
type: Class
subclass of: ExO_0000038
subclass of: subject health status at time of specimen collection
subclass of: subject health status (GSCID-BRC)
subclass of: subject disease outcome
subclass of: subject health status (UK NHS)
subclass of: subject health status (AHA)
subclass of: subject health status (NCIT)
subclass of: SIO_010057
subclass of: Restriction
  on property: RO_0002083
  some values from: critical health status
disjoint with: NCIT C37987
user interface label: deceased

deceased
type: Axiom
annotated source: NCIT C28554
annotated property: subClassOf
annotated target: subject health status (UK NHS)

NCIT C40978
subclass of: IAO_0000577
user interface label: phone

NCIT C41277
type: Class
subclass of: OBI_0002814
user interface definition: A hollow cylinder, especially one for holding or conveying liquids.
IAO_0000117: Damion Dooley

NCIT C42775
IAO_0000116: Damion Dooley's note: It can also be used as an authorization token in some identification processes.
has exact synonym: IAO_0000429

NCIT C45910
type: Class
subclass of: PATO_0000047
IAO_0000114: IAO_0000122
IAO_0000116: Damion Dooley's note: here "sample" means more than one specimen merged together.
has exact synonym: pooled

NCIT C68615
type: Class
subclass of: lifespan history item
subclass of: pregnancy history item
subclass of: Restriction
  on property: after
  some values from: date of conception
IAO_0000114: IAO_0000122
IAO_0000117: Damion Dooley

NCIT C70810
type: Class
subclass of: lifespan history item
IAO_0000114: IAO_0000122
IAO_0000117: Damion Dooley

NCIT C71898
type: Class
subclass of: IAO_0000300
user interface label: brand name

investigative subject
type: Class
subclass of: BFO_0000040
IAO_0000115: An entity, either biologic or otherwise, of interest in an investigation. [def-source: NCI]
IAO_0000117: Damion Dooley
IAO_0000119: NCIT Thesaurus

NCIT C80234
type: Class
subclass of: ENVO_00000062
subclass of: SIO_000415
user interface feature: lookup:http://purl.obolibrary.org/obo/GAZ_00000448

NCIT C85540
type: Class
subclass of: OBI_0000011
user interface label: antimicrobial resistance testing method

NCIT C85596
type: Class
subclass of: NCIT C85540
user interface label: E-test (Epsilometry)

NCIT C87194
subclass of: ENVO_00000005
disjoint with: NCIT C89811
user interface feature: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
IAO_0000114: IAO_0000428

NCIT C89811
type: Class
subclass of: ENVO_00000005
user interface feature: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
IAO_0000114: IAO_0000428

NCIT C93874
type: Class
subclass of: NCIT C42614
user interface label: organization name
IAO_0000114: IAO_0000122
IAO_0000117: Damion Dooley
IAO_0000119: NCI Thesaurus

antibiotic treatment
type: Class
subclass of: infectious disease treatment

OAE_0002678
type: Class
subclass of: outcome of pregnancy associated with illness
user interface label: fetal death (miscarriage/still birth)

OBI_0000689
subclass of: 454 Genome Sequencer
has db xref: NCBI SRA: 454 GS 20

OBI_0000696
subclass of: sequencing instrument model
has db xref: NCBI SRA: AB SOLiD System

OBI_0000702
subclass of: 454 Genome Sequencer
has db xref: NCBI SRA: 454 GS FLX

OBI_0000703
subclass of: sequencing instrument model
has db xref: NCBI SRA: Illumina Genome Analyzer II

OBI_0000717
subclass of: sequencing instrument model
has db xref: NCBI SRA: Helicos HeliScope

pathogen role
type: Class
subclass of: isolate organism role

OBI_0000925
equivalent class: Class
  intersection of: OBI_0100026
  intersection of: Restriction
    on property: RO_0002451
    some values from: transmission of infection
comment: Note: testing use of 'transmitted by' relation; issue to be resolved is whether appropriate domain and range are involved. This use would place 'transmitted by' as a subclass of 'participates in'

OBI_0001479
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: RO_0001000
    some values from: Class
      union of: subject anatomical site
      union of: subject body product
IAO_0000116: Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy".

OBI_0001614
subclass of: sequence accession
user interface regular expression validate: ^SAM[NED](\w)?\d+$

OBI_0001615
subclass of: SIO_000136
subclass of: Restriction
  on property: inheres in
  some values from: OBI_0000066
in subset: NCBI BioProject

Project Description
type: Axiom
annotated source: OBI_0001615
annotated property: subClassOf
annotated target: Restriction

Description*
type: Axiom
annotated source: OBI_0001615
annotated property: subClassOf
annotated target: Restriction

OBI_0001616
has synonym: sample identifier

OBI_0001619
subclass of: specimen history item
user interface label: specimen collection date

OBI_0001620
subclass of: geographic location datum
user interface feature: help:Latitude should not be abstracted to the centre of a city, province/state or country as this may falsely implicate an existing location.
IAO_0000116: Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises.
comment: See http://www.csgnetwork.com/gpscoordconv.html See http://www.geomidpoint.com/latlon.html See http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0001621 See http://www.w3.org/2003/01/geo/wgs84_pos

OBI_0001622
subclass of: NCIT C42614
subclass of: Restriction
  on property: inheres in
  some values from: OBI_0000066
in subset: NCBI BioProject
in subset: NIAID GSCID-BRC

OBI_0001627
subclass of: geospatial name
subclass of: Restriction
  on property: inheres in
  some values from: NCIT C25464
comment: Damion Dooley's note: A 'sovereign state' entity should have attribute or relationships to measurables - population, size, name, etc. So e.g. " 'country name' inheres in some 'sovereign state/country'". Also note historical name issue (Myanmar vs Burma) and diplomatic name issue (Taiwan vs "Republic of China"). Both point to needing a single entity with multiple names.

OBI_0001882
user interface label: target material
has exact synonym: NCBI BioProject: Material
comment: Used in NCBI BioProject specifcation

OBI_0001884
user interface label: specimen sample scope

OBI_0001891
type: Class
user interface label: sequencing facility

OBI_0001892
type: Class
user interface label: project objective
has exact synonym: NCBI BioProject: Objective

OBI_0001896
user interface label: project method

OBI_0001903
subclass of: specimen datum
user interface label: specimen provider PI email

OBI_0001930
subclass of: Restriction
  on property: is about
  some values from: STATO_0000252
subclass of: Restriction
  on property: OBI_0002135
  qualified cardinality: 1
  on data range: anyURI
user interface label: categorical

OBI_0001931
user interface label: scalar

OBI_0001933
comment: Damion Dooley's note: Often a value specification may need to allow for a "data item state" that indicates that a given datum doesn't have a recorded or observed or retrievable value, and the general reason for this state.

OBI_0001941
type: Class
subclass of: contig length
metadata section: Assembly QC
IAO_0000117: Damion Dooley
IAO_0000119: http://www.nature.com/nature/journal.../409860a0.html
in subset: GENEPIO

OBI_0002003
subclass of: sequencing instrument model
has db xref: NCBI SRA: Illumina MiSeq

OBI_0002012
subclass of: sequencing instrument model
has db xref: NCBI SRA: PacBio RS

OBI_0002021
subclass of: sequencing instrument model
has db xref: NCBI SRA: Illumina NextSeq

OBI_0100051
subclass of: Restriction
  on property: RO_0001000
  some values from: specimen source substance
has exact synonym: sample

diagnosis
type: Class
subclass of: analytic datum
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2019-09-08T23:41:09Z

extended organism
type: Class
subclass of: UBERON_0000465
IAO_0000115: An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.

OMIABIS_0001008
type: Class
subclass of: diagnosis
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
has db xref: National Institute of Allergy and Infectious Disease standard
has db xref: NIAID: Comorbidity
has narrow synonym: complications

Comorbidity
type: Axiom
annotated source: OMIABIS_0001008
annotated property: hasDbXref
annotated target: National Institute of Allergy and Infectious Disease standard

OMIT_0017096
type: Class
subclass of: OMIT_0020789
IAO_0000115: Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable.
IAO_0000117: Damion Dooley
has broad synonym: grave

Shiga toxin 1
type: Class
subclass of: NCIT C1225
IAO_0000114: IAO_0000122
IAO_0000115: A type of Shiga toxin found in E. coli
IAO_0000117: Damion Dooley
IAO_0000118: Stx1
IAO_0000119: PMC4270005
IAO_0000412: http://snomed.info/sct/900000000000207008

Shiga toxin 2
type: Class
subclass of: NCIT C1225
IAO_0000114: IAO_0000122
IAO_0000115: A type of Shiga toxin found in E. coli which is antigenically distinct from Shiga toxin 1
IAO_0000117: Damion Dooley
IAO_0000118: Stx2
IAO_0000119: PMC4270005
IAO_0000412: http://snomed.info/sct/900000000000207008

OMIT_0027406
type: Class
subclass of: test specification
user interface label: MLST typing

physician role
type: Class
subclass of: person role
IAO_0000114: IAO_0000428
IAO_0000115: A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.

PATO_0000146
type: Class
comment: Damion's Note: Future use might prefer: CMO_0000015 body temperature.

PATO_0000383
type: Class
has db xref: NCBI BioSample: female

PATO_0000384
type: Class
has db xref: NCBI BioSample: male

PATO_0001894
type: Class
IAO_0000115: Phenotypic sex refers to an individual's sex as determined by their internal and external genitalia, expression of secondary sex characteristics, and behavior.
IAO_0000116: Note that NCBI Biosample has these values allowed: male | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected
IAO_0000119: NCBI: http://www.ncbi.nlm.nih.gov/books/NBK10943/

PATO_0002390
IAO_0000114: IAO_0000428
comment: Damion Dooley's note: We can't say radius is a subclass of "linear coordinate" because length is considered a quality/specifically dependent continuant, which is disjoint with immaterial entity/independent continuant . I.e. "length" as quality unfortunately can't pertain to abstract entities, only "real" ones.

PCO_0000033
type: Class
subclass of: human general activity
user interface label: social gathering

SO_0000149
subclass of: sequencing assembly datum
subclass of: Restriction
  on property: IAO_0000039
  some values from: UO_0000244
subclass of: Restriction
  on property: member of
  some values from: SO_0001462
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

SO_0000353
type: Class
subclass of: sequencing assembly datum
subclass of: Restriction
  on property: is about
  some values from: OBI_0100026
subclass of: Restriction
  on property: has component
  qualified cardinality: 1
  on class: SO_0001462
user interface label: sequence assembly
has exact synonym: http://purl.obolibrary.org/obo/OBI_0000973 - 'sequence data'
has exact synonym: http://edamontology.org/data_0925

SO_0001026
type: Class
subclass of: BFO_0000027
IAO_0000114: IAO_0000122
IAO_0000117: Damion Dooley

STATO_0000047
subclass of: IAO_0000109
IAO_0000116: Damion Dooley's note: Unfortunately an IAO "count" cannot be a subclass of immaterial entity "linear coordinate" as this leads to disjoint conflict.
comment: Damion Dooley's note: A count datum often implicity carries a date range for which the count is ascertained, or estimated, or simulated for.
comment: Damion Dooley's note: The result of the act of counting is a scalar number whose unit is a description of the thing being counted. One can count 10 oranges and compare that to a count of 5 oranges. One can generalize that a count of 5 oranges is a count of pieces of fruit. One can then compare 5 oranges and 5 apples, fruitfully!

STATO_0000258
type: Class
subclass of: IAO_0000030
user interface label: variable type

transmission of infection
type: Class
equivalent class: Class
  intersection of: GO_0008150
  intersection of: Restriction
    on property: has input
    some values from: IDO_0000659
  intersection of: Restriction
    on property: has output
    some values from: OBI_0000925
  intersection of: Restriction
    on property: RO_0002404
    some values from: IDO_0000495
subclass of: GO_0008150
IAO_0000115: A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
IAO_0000119: https://www.ebi.ac.uk/ols/ontologies/trans
comment: TRANS follows the CDC Epidemiology model of transmission between two hosts, a reservoir and host or other non-host, non-reservoir entities (e.g), a needle and a host.

direct transmission
type: Class
subclass of: transmission of infection
IAO_0000115: Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission.
IAO_0000119: https://www.ebi.ac.uk/ols/ontologies/trans

indirect transmission
type: Class
subclass of: transmission of infection
IAO_0000115: Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles.
IAO_0000119: https://www.ebi.ac.uk/ols/ontologies/trans

congenital
type: Class
subclass of: direct transmission
IAO_0000115: Congenital transmission is a direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth.
IAO_0000119: https://www.ebi.ac.uk/ols/ontologies/trans

contact
type: Class
subclass of: direct transmission
user interface label: contact transmission
IAO_0000115: Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen.
IAO_0000119: https://www.ebi.ac.uk/ols/ontologies/trans

droplet spread
type: Class
subclass of: direct transmission
IAO_0000115: Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking.
IAO_0000119: https://www.ebi.ac.uk/ols/ontologies/trans

vehicle-born ingestion
type: Class
subclass of: indirect transmission
IAO_0000115: Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products.
IAO_0000119: https://www.ebi.ac.uk/ols/ontologies/trans

UBERON_0000463
subclass of: Restriction
  on property: RO_0003001
  some values from: OBI_0100026
user interface label: organism body product

UBERON_0008291
subclass of: animal body product
user interface label: poultry fluff
IAO_0000116: Damion Dooley's note: Poultry fluff is both an 'anatomical structure' and a body product when it is shed.

UO_0000000
subclass of: BFO_0000141
comment: Damion Dooley's note: Need to build this out further with reference to http://unitsofmeasure.org/trac and other unit ontologies: [1] R. Hodgson and P. J. Keller, "QUDT-quantities, units, dimensions and data types in OWL and XML." Online (September 2011) http://www. qudt.org [2] M. van Assem, H. Rijgersberg, and J. Top, "Ontology of units of measure and related concepts." Semantic Web 4, no. 1 (2013): 3-13. [3] G. V. Gkoutos, P. N. Schofield, and R. Hoehndorf, "The Units Ontology: a tool for integrating units of measurement in science." Database2012 (2012): bas033.

UO_0000016
has alternative id: mm

UO_0000274
has alternative id: µg/ml

XCO_0000412
type: Class
subclass of: outcome of pregnancy associated with illness
subclass of: host illness associated with
user interface label: ongoing pregnancy

ancestral group
type: Class
subclass of: organism datum

sep_00196
subclass of: specimen datum
IAO_0000114: IAO_0000122
IAO_0000117: Damion Dooley

host role at time of specimen collection
type: Class
subclass of: personal health datum
subclass of: Restriction
  on property: is about
  some values from: IDO_0000629
subclass of: Restriction
  on property: is about
  some values from: OBI_0001619
IAO_0000114: IAO_0000428
IAO_0000115: A personal health datum which specifies host role at time of specimen collection.
IAO_0000117: 0000-0002-9578-0788
date: 2022-01-31T23:53:59Z

MLVA
type: Class
subclass of: test specification
user interface label: MLVA typing
IAO_0000114: IAO_0000428

SIO_000503
subclass of: Restriction
  on property: aligned with
  some values from: SIO_000505
comment: Damion Dooley's comment: On spheroids a polygon can be minimally defined by latitude and longitude coordinates, however technically this is ambiguous whether the larger or smaller area is being referred to. Unambiguously, such a polygon could be defined by an epicenter, and a latitude width and longitude height.

SIO_000505
subclass of: 2D entity
subclass of: 2D boundary
IAO_0000115: In elementary geometry, a polygon is a plane figure that is bounded by a finite chain of straight line segments closing in a loop to form a closed chain or circuit.
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Polygon

SIO_000729
subclass of: IAO_0000577
has db xref: PulseNet: Key

medical health record (history / timeline)
type: Class
subclass of: draft GenEpiO component record
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

SIO_010057
equivalent class: Class
  union of: NCIT C28554
  union of: NCIT C37987
subclass of: organism datum
user interface feature: depth:1
user interface feature: lookup

Bacterial bacteriophage typing
type: Class
subclass of: OBI_0000070
IAO_0000412: http://snomed.info/sct/900000000000207008

obsolete: ancestral group
type: Class
IAO_0100001: ancestral group
deprecated: true

EFO_0001799
type: Class
subclass of: OBI_0000181
subclass of: Restriction
  on property: has member
  some values from: NCBITaxon 9606
IAO_0000600: A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)

Thing
comment: Welcome to the GenEpiO ontology! The "information content entity" class has many GenEpiO terms. "data item > measurement data item" has many datum terms; see "data representational model" for collections of terms set up for compatibility with 3rd party sources. Note that this file contains examples of cities, provinces, states, territories, and soverign nations from around the world; customization of this geographical content would be expected for particular regional use.

Definition
type: Class
subclass of: Element
IAO_0000115: Base class for definitions.

Element
type: Class
subclass of: OBI_0000658
IAO_0000115: A named element in the model.

Example
type: Class
subclass of: Element
IAO_0000115: Usage example and description.

LocalName
type: Class
subclass of: Element
IAO_0000115: An attributed label.

PermissibleValue
type: Class
subclass of: Element
IAO_0000115: A permissible value, accompanied by intended text and an optional mapping to a concept URI.

SchemaDefinition
type: Class
subclass of: Definition
IAO_0000115: A collection of subset, type, slot and class definitions.

SlotDefinition
type: Class
subclass of: Definition
IAO_0000115: The definition of a property or a slot.

GENEPIO_0001367
type: NamedIndividual
type: health authority
located in: GAZ_00002562
has member: GENEPIO_0001368
has member: GENEPIO_0001369
has member: GENEPIO_0001370
has member: GENEPIO_0001372
has member: GENEPIO_0001373
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
comment: Damion Dooley's note: Here we are exploring the use of individuals/instances to describe local picklists for GenEpiO driven software.

United Nations
type: NamedIndividual

MSH
type: NamedIndividual

NCI_Thesaurus
type: NamedIndividual

NIFSTD
type: NamedIndividual

GENEPIO_0001897
type: NamedIndividual
user interface label: home

_test_individual
type: NamedIndividual

PulseNet:LabID
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: LabID assigned by NLEP
IAO_0000117: Damion Dooley
date: 2019-04-17T23:31:44Z

SourceCountry
type: NamedIndividual
IAO_0000115: Country where isolate was collected
IAO_0000117: Damion Dooley
date: 2019-04-17T23:32:45Z

PulseNet:SourceCountry
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Country where isolate was collected
IAO_0000116: Currently not used for PulseNet Canada
IAO_0000117: Damion Dooley
date: 2019-04-17T23:37:19Z

PulseNet:SourceState
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: (Province for PNC) where isolate was collected.
IAO_0000117: Damion Dooley
date: 2019-04-17T23:38:09Z

PulseNet:SourceCity
type: NamedIndividual
type: PulseNet Canada field
IAO_0000117: Damion Dooley
date: 2019-04-17T23:40:57Z

PulseNet:SourceSite
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Site of the source type where isolate was collected, e.g. blood, CSF, etc.
IAO_0000117: Damion Dooley
date: 2019-04-17T23:47:10Z

PulseNet:SourceType
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: The source type of the isolate, e.g. human, environmental, etc.
IAO_0000117: Damion Dooley
date: 2019-04-17T23:48:49Z

PulseNet:Traveled_To
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: Other countries where the patient traveled
IAO_0000117: Damion Dooley
date: 2019-04-17T23:49:47Z

PulseNet:TypeDetails
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Further description of the source type, e.g. bovine, chicken
IAO_0000117: Damion Dooley
date: 2019-04-17T23:51:02Z

PulseNet:SubmittedNumber
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Submitted isolate # (if diff. From Key #), NLEP will enter Prov. Submitted # if sample was sent to NLEP for PFGE
IAO_0000117: Damion Dooley
date: 2019-04-17T23:52:01Z

PulseNet:OtherStateIsolate
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: (Province for PNC) additional number used to identify the isolate
IAO_0000117: Damion Dooley
date: 2019-04-17T23:53:47Z

PulseNet:PatientAge
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Age of patient when isolate was collected
IAO_0000117: Damion Dooley
date: 2019-04-17T23:54:24Z

PulseNet:PatientSex
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Sex of patient when isolate was collected
IAO_0000117: Damion Dooley
date: 2019-04-17T23:55:04Z

PulseNet:IsolatDate
type: NamedIndividual
type: date value specification (ISO 8601)
type: PulseNet Canada field
IAO_0000115: Date of collection
IAO_0000117: Damion Dooley
date: 2019-04-17T23:56:33Z

PulseNet:UploadModifiedDate
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Date the isolate is uploaded to the national database after initial upload
IAO_0000117: Damion Dooley
date: 2019-04-18T00:21:46Z

PulseNet:AntigenForm
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: Antigenic Formula
IAO_0000117: Damion Dooley
date: 2019-04-18T00:23:18Z

PulseNet:Subspecies
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: Subspecies, I - VI (roman numerals)
IAO_0000117: Damion Dooley
date: 2019-04-18T00:24:11Z

PulseNet:OGroup
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: O polysaccharide (LPS) Group
IAO_0000117: Damion Dooley
date: 2019-04-18T00:24:53Z

PulseNet:Serotype
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: Serotype of isolate
IAO_0000117: Damion Dooley
date: 2019-04-18T00:25:22Z

PulseNet:Outbreak
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Code issued by CDC; see: 'Naming of outbreaks…' on WebBoard. (format YYMMLabIDLITScode-#)
IAO_0000116: Currently not used for PulseNet Canada
IAO_0000117: Damion Dooley
date: 2019-04-18T00:27:08Z

PulseNet:cdc_id
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Number issued by CDC if isolate is run at CDC (Key will be # issued by NLEP if isolate run at NLEP)
IAO_0000117: Damion Dooley
date: 2019-04-18T00:28:01Z

PulseNet:ListMember
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Enzyme name present if part of that national list.
IAO_0000117: Damion Dooley
date: 2019-04-18T00:28:35Z

PulseNet:Phagetype
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Phage type
IAO_0000117: Damion Dooley
date: 2019-04-18T00:29:20Z

PulseNet:TEMP
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Provides LabID, gel and lane information
IAO_0000117: Damion Dooley
date: 2019-04-18T00:29:58Z

PulseNet:Status
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Status of the isolate; this is only confirmed once CDC runs it.
IAO_0000116: Currently not used for PulseNet Canada
IAO_0000117: Damion Dooley
date: 2019-04-18T00:30:44Z

PulseNet:NARMS-EB
type: NamedIndividual
type: PulseNet Canada field
IAO_0000116: Currently not used for PulseNet Canada
IAO_0000116: checked if the isolate is part of NARMS.
IAO_0000117: Damion Dooley
date: 2019-04-18T00:35:55Z

PulseNet:FoodNet
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Checked if the isolate is part of FoodNet.
IAO_0000116: Currently not used for PulseNet Canada
IAO_0000117: Damion Dooley
date: 2019-04-18T00:36:39Z

PulseNet:PFGE-XbaI-file
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: XbaI gel where the isolate is located, lane of gel
IAO_0000117: Damion Dooley
date: 2019-04-18T00:38:57Z

PulseNet:PFGE-XbaI-pattern
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: XbaI pattern assigned by CDC (format XXXXXX.####)
IAO_0000117: Damion Dooley
date: 2019-04-18T00:39:23Z

PulseNet:PFGE-XbaI-rundate
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: The date the XbaI gel is run
IAO_0000117: Damion Dooley
date: 2019-04-18T00:40:05Z

PulseNet:PFGE-XbaI-status
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: Once the XbaI pattern is named, the status is confirmed by CDC
IAO_0000117: Damion Dooley
date: 2019-04-18T00:41:39Z

PulseNet:PFGE-BlnI-file
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: BlnI gel where the isolate is located, lane of gel
IAO_0000117: Damion Dooley
date: 2019-04-18T00:42:11Z

PulseNet:PFGE-BlnI-pattern
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: BlnI pattern assigned by CDC (format XXXXXX.####).
IAO_0000117: Damion Dooley
date: 2019-04-18T00:42:42Z

PulseNet:PFGE-BlnI-rundate
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: The date the BlnI gel is run
IAO_0000117: Damion Dooley
date: 2019-04-18T00:43:50Z

PulseNet:PFGE-BlnI-status
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: Once the BlnI pattern is named, the status is confirmed by CDC
IAO_0000117: Damion Dooley
date: 2019-04-18T00:44:44Z

PulseNet:PFGE-SpeI-file
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: SpeI gel where the isolate is located, lane of gel.
IAO_0000117: Damion Dooley
date: 2019-04-18T00:45:15Z

PulseNet:PFGE-SpeI-pattern
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: SpeI pattern assigned by CDC (format XXXXXX.####).
IAO_0000117: Damion Dooley
date: 2019-04-18T00:45:41Z

PulseNet:PFGE-SpeI-rundate
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: The date the SpeI gel is run.
IAO_0000117: Damion Dooley
date: 2019-04-18T00:46:21Z

PulseNet:PFGE-SpeI-status
type: NamedIndividual
type: PulseNet Canada Salmonella field
IAO_0000115: Once the SpeI pattern is named, the status is confirmed by CDC.
IAO_0000117: Damion Dooley
date: 2019-04-18T00:47:00Z

PulseNet:ReceivedDate
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Date WHICH (PH?) lab received isolate.
IAO_0000117: Damion Dooley
date: 2019-04-18T00:57:28Z

ISO_23418.organization_contact.service
type: NamedIndividual
type: draft ISO sequence repository field
IAO_0000117: http://orcid.org/0000-0002-8844-9165
date: 2019-11-17T00:54:44Z

PulseNet:UploadDate
type: NamedIndividual
type: PulseNet Canada field
IAO_0000115: Date the isolate uploaded to the national database.
IAO_0000117: Damion Dooley
date: 2019-04-17T22:47:51Z

University of Manitoba (UM)
type: NamedIndividual
type: OBI_0000245
IAO_0000115: A Canadian public research university in the province of Manitoba.
IAO_0000119: umanitoba.ca
contributor: https://orcid.org/0000-0001-5275-8866
date: 2023-06-21T14:22:42Z

Public Health Agency of Canada (PHAC)
type: NamedIndividual
type: OBI_0000245
IAO_0000115: The Public Health Agency of Canada is an agency of the Government of Canada that is responsible for public health, emergency preparedness and response, and infectious and chronic disease control and prevention.
IAO_0000117: https://orcid.org/0000-0001-5275-8866
IAO_0000119: https://en.wikipedia.org/wiki/Public_Health_Agency_of_Canada
date: 2022-09-23T10:10:13Z
has exact synonym: PHAC

Canadian Food Inspection Agency (CFIA)
type: NamedIndividual
type: OBI_0000245
IAO_0000115: The Canadian Food Inspection Agency is a regulatory agency that is dedicated to the safeguarding of food, plants, and animals in Canada
IAO_0000117: https://orcid.org/0000-0001-5275-8866
IAO_0000119: https://en.wikipedia.org/wiki/Canadian_Food_Inspection_Agency
date: 2022-09-23T10:23:42Z
has exact synonym: CFIA

Agriculture and Agri-Food Canada (AAFC)
type: NamedIndividual
type: OBI_0000245
IAO_0000115: Agriculture and Agri-Food Canada is the department of the Government of Canada responsible for the federal regulation of agriculture, including policies governing the production, processing, and marketing of all farm, food, and agri-based products.
IAO_0000117: https://orcid.org/0000-0001-5275-8866
IAO_0000119: https://en.wikipedia.org/wiki/Agriculture_and_Agri-Food_Canada
date: 2022-09-23T10:29:32Z
has exact synonym: AAFC

Health Canada
type: NamedIndividual
type: OBI_0000245
IAO_0000115: Health Canada is the department of the Government of Canada responsible for national health policy.
IAO_0000117: https://orcid.org/0000-0001-5275-8866
IAO_0000119: https://en.wikipedia.org/wiki/Health_Canada
date: 2022-09-23T10:33:24Z
has exact synonym: HC

Environment and Climate Change Canada (ECCC)
type: NamedIndividual
type: OBI_0000245
IAO_0000115: Environment and Climate Change Canada, is the department of the Government of Canada, that is responsible for coordinating environmental policies and programs, as well as preserving and enhancing the natural environment and renewable resources. It is also colloquially known by its former name, Environment Canada.
IAO_0000117: https://orcid.org/0000-0001-5275-8866
IAO_0000119: https://en.wikipedia.org/wiki/Environment_and_Climate_Change_Canada
date: 2022-09-23T10:38:21Z
has exact synonym: ECCC
has exact synonym: Environment Canada

Fisheries and Oceans Canada (DFO)
type: NamedIndividual
type: OBI_0000245
IAO_0000115: Fisheries and Oceans Canada, is a department of the Government of Canada that is responsible for developing and implementing policies and programs in support of Canada's economic, ecological and scientific interests in oceans and inland waters.
IAO_0000117: https://orcid.org/0000-0001-5275-8866
IAO_0000119: https://en.wikipedia.org/wiki/Fisheries_and_Oceans_Canada
date: 2022-09-23T10:42:12Z
has exact synonym: DFO

qualified cardinality: 2

qualified cardinality: 2

ARO_3004300
user interface label: intermediate
has alternative id: I

ARO_3004301
user interface label: resistant
has alternative id: R

ARO_3004302
user interface label: susceptible
has alternative id: S
has exact synonym: sensitive

ARO_3004303
user interface label: nonsusceptible
has alternative id: NS
has exact synonym: nonsensitive

ARO_3004304
user interface label: susceptible - dose dependent
has alternative id: SSD
has exact synonym: sensitive - dose dependent

ARO_3004365
has alternative id: BSAC

ARO_3004367
has alternative id: DIN

ARO_3004368
has alternative id: EUCAST

ARO_3004369
has alternative id: SFM

BFO_0000008
comment: Damion Dooley's note: this BFO class is incompatible with "immaterial entity" "n-dimensional concept".

CHEBI_33290
user interface label: food role

ENVO_00000002
user interface label: constructed feature

ENVO_00000450
has exact synonym: irrigation pond

ENVO_00002003
has exact synonym: stool

ENVO_00002191
has narrow synonym: straw bedding

ENVO_01000753
deprecated: true

ENVO_01000922
has narrow synonym: chicken cage

ERO_0001642
has db xref: NCBI SRA: ION_TORRENT

FOODON_03412612
has synonym: asian tiger shrimp
has synonym: black tiger shrimp

FOODON_03530153
has synonym: gathered
has synonym: wild

GENEPIO_0000098
IAO_0000117: Damion Dooley

GENEPIO_0000116
IAO_0000114: IAO_0000428
IAO_0000115: This is a catch-all category for Gazetteer items that have "located in" relations but not an imported GAZETTEER class parent in GenEpiO.
IAO_0000117: Damion Dooley

obsolete: has primitive data type
IAO_0000117: Damion Dooley
IAO_0100001: type uri
deprecated: true

GENEPIO_0001854
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001855
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001856
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001857
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001858
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001860
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001861
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001868
IAO_0000114: IAO_0000428
IAO_0000116: Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises with "immaterial entity"
IAO_0000117: Damion Dooley

GENEPIO_0001869
IAO_0000117: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001870
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001871
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001872
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001874
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001875
IAO_0000116: This seems to be covered by 'datetime range intermediate'
IAO_0000117: Damion Dooley

GENEPIO_0001879
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001880
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001881
IAO_0000114: IAO_0000428
IAO_0000115: A datetime set item is a datetime that has been grouped semantically under a given type of process
IAO_0000117: Damion Dooley

GENEPIO_0001882
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001883
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001887
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001889
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001894
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001895
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001898
user interface label: mobile

GENEPIO_0001899
user interface label: work

GENEPIO_0001901
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001902
IAO_0000114: IAO_0000428
IAO_0000115: An unordered set is a set of elements which have no intrinsic (semantic) order with respect to each other. The set of all living people is not intrinsically ordered; an ordering can only be provided by looking at some partiular feature of the given set elements.
IAO_0000117: Damion Dooley

GENEPIO_0001903
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001905
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001906
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

GENEPIO_0001908
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley
IAO_0000119: https://en.wikipedia.org/wiki/Plane_(geometry)

GENEPIO_0001910
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

NCBITaxon 6447
IAO_0000118: clam, squid, octopus

OBI_0000697
has db xref: NCBI SRA: HELICOS

OBI_0000706
has db xref: NCBI SRA: ABI_SOLID

OBI_0000973
IAO_0000115: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.

OBI_0001880
user interface label: specimen provider PI organization

OBI_0002000
has db xref: NCBI SRA: Illumina Genome Analyzer IIx

OBI_0002007
has db xref: NCBI SRA: AB SOLiD 3 Plus System

OBI_0002024
has db xref: NCBI SRA: AB SOLiD 4 System

OBI_0002027
has db xref: NCBI SRA: Illumina Genome Analyzer IIe

OGMS_0000031
user interface label: disease (OGMS)

PATO_0001340
has db xref: NCBI BioSample: hermaphrodite

PATO_0001827
IAO_0000116: This value is not present in NCBI BioSample host sex.

derives into

starts during

happens during

starts with

ends with

input of

STATO_0000010
user interface label: n-dimensional coordinate system
comment: Damion Dooley's note:Damion Dooley's note: Outstanding issue: How to attach units to each dimension? This depends on the instance of the problem involving a dimension? Linear offset can be decimal or integer or complex, or a count. - Can have a unit: meter, kilometer, foot, light-year, oranges, apples, fruit Angular offset can be radians or degrees.

UBERON_0001052
has synonym: rectal

UBERON_0001359
user interface label: cerebrospinal fluid (CSF)

UO_0000213
user interface label: cfu/mL
IAO_0000114: IAO_0000428
IAO_0000117: Damion Dooley

SIO_000546
IAO_0000114: IAO_0000123
IAO_0000117: Damion Dooley