Health Surveillance Ontology (HSO)
type: Ontology
version IRI: hso.owl
contributor: Crawford Revie
contributor: Eva Blomqvist
contributor: Karl Hammar
contributor: Matthias Filter
contributor: Patrick Lambrix
contributor: Taras Günther
license: http://creativecommons.org/licenses/by/3.0/
creator: Fernanda Dórea
description: An ontology to support semantic interoperability among domains involved in health surveillance (animal health, public health and food safety). More details at http://datadrivensurveillance.org.
comment: This is an ontology to support (one) health surveillance, focused on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc.

BFO OWL specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator note: Really of interest to developers only
sub property of: label

BFO CLIF specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only
sub property of: label

SSD_catalogue
type: AnnotationProperty
description: From the European Food Safety Agency (EFSA): https://zenodo.org/record/344473#.WzvvyvkzYkV The Data Collection Framework (DCF) application is constituted of an interactive web-based application that aims at facilitating data exchange, data extraction and data reusability. A harmonized terminology is used to collect and analyse data in a coherent way with the aim to support scientific research. DCF_catalogues file contains all the valid catalogues published in the DCF. The SSD2 file contains the controlled terminologies based on the standard description of samples and analytical results (Standard Sample Description Extension), extended to cover additional data collection domains, such as zoonotic agents in food and animals, antimicrobial resistance and food additives. This annotation points to the specific catalague, within SSD2, form which terms were imported.
sub property of: European Food Safety Agency Standard Sample Description Framework - EFSA SSD

SSD_termCode
type: AnnotationProperty
description: "This annotation gives the specific code for the concept include din the ontology. Look for this code in the specific catalogue via the annotation property ""SSD_catalogue"". Full names are stored in the property ""SSD_termExtendedName""."
sub property of: European Food Safety Agency Standard Sample Description Framework - EFSA SSD

SSD_termExtendedName
type: AnnotationProperty
description: This annotation gives the specific term name for the concept include din the ontology. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode".
sub property of: European Food Safety Agency Standard Sample Description Framework - EFSA SSD

SSD_termScopeNote
type: AnnotationProperty
description: This annotation gives any additional notes. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode".
sub property of: European Food Safety Agency Standard Sample Description Framework - EFSA SSD

One-Health Consensus Reference Annotation Checklist (OH-CRAC)
type: AnnotationProperty
definition: A collection of annotations which refer to all the annotation steps in the One Health Consensus Reporting Annotation Checklist (OH-CRAC). OH-CRAC is part of the One Health Codex - https://oh-surveillance-codex.readthedocs.io/en/latest/5-the-reporting-principle.html.
domain: Surveillance Activity

CRAC 1.1 Motivation / cause
type: AnnotationProperty
definition: This section provides information on what "caused" the surveillance activity and what is expected from the surveillance activity. It may be triggered by a new law or feedback from previous surveillance activities. It might even be initiated by practices in other (national and international) organisations.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 1.2. Requirement analysis
type: AnnotationProperty
definition: This section documents the results of consultation activities between the surveillance "actor" with its customers / stakeholders to identify/confirm the needs of the surveillance activity. Specifically, it documents what is agreed to be delivered by this surveillance activity, when, how and why. It also documents whether previously identified needs have changed.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 1.3. Surveillance objective and constraints
type: AnnotationProperty
definition: This section documents what surveillance objectives (e.g. prevalence estimation, case detection, early detection, disease freedom) and their quality criteria are defined to meet the needs of the end-users / stakeholders. It also describes existing legal or practical constraints, e.g. confidentiality, resources etc.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.1. Framework design
type: AnnotationProperty
definition: This section gives an overview on all designed outputs, products and services related to the surveillance activity. This includes the output of the surveillance activity, but also related work, as e.g. preparation of systems and tools for dissemination, disclosure control methods etc.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.2. Variable specifications
type: AnnotationProperty
definition: This section describes which variables / measurements were planned to be collected / taken and which metadata set / standard were used. It further specifies if measured values were planned to be grouped or classified, how this was planned to be done. It also specifies if new variables derive from the original ones (see section 4.5, New variable/unit derivation). It may overlap with the description requested for section 2.3 (Surveillance methods/strategy)
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.3. Surveillance methods/strategy
type: AnnotationProperty
definition: This section describes the developed "collection strategy" (collection strategy in this context means, e.g. active or passive surveillance). It also describes the collection instruments (survey, data extraction methods etc.) and collection units (e.g. individuals, herds, food batch etc.). It may overlap with the surveillance variables specification described in section 2.2 (Variable specifications)
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.4. Sampling plan
type: AnnotationProperty
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.4.1. Sampled population
type: AnnotationProperty
definition: "This sub-section specifies the population(s) that were sampled. "
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.4.2. Sampling schema
type: AnnotationProperty
definition: This sub-section describes the design process followed for the sampling plan generation and the sampling criteria.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.4.3. Sample collection
type: AnnotationProperty
definition: This sub-section describes the sample collection approach carried out including information on the practical handling, storage and labeling of taken samples by different actors (e.g. storage temperature, labeling with unique IDs).
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.4.4. Sample preparation
type: AnnotationProperty
definition: This sub-section details the processing of the samples prior to the analytical processing.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.4.5. Analytical procedures
type: AnnotationProperty
definition: This sub-section reports on the analytical procedures applied to the different sets of samples.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 2.5. Data processing/analysis
type: AnnotationProperty
definition: This section describes the methods used for the data processing including analysis of bioinformatics, trends, modelling, statistical tests, etc. This section also includes design of specifications for data integration from multiple data sources, validation of data and estimation.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 3.1. Practical aspects on sample selection
type: AnnotationProperty
definition: This section describes how the specific sampling units were chosen based on the sampling plan that is described in section 2.4 (Sampling plan). In contrast to the information given in 2.4, this section should describe how the real "implementation" of the sampling plan took place, as sometimes the "field work" is done by other actors than the planning.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 3.2. Practical support activities
type: AnnotationProperty
definition: "This section describes the activies undertaken to ensure that the people, processes and technology (e.g. web-based applications, GPS system) were ready to collect data and metadata. It includes the strategy, planning and training activities in preparation for the specific sampling activity. This description might include information on: - Preparing a sample storage and / or shipment strategy; - Training staff how to collect samples, e.g. physician; - Training staff how to analyze selected samples in the lab, e.g. perform ring trials - Provisioning of collection resources (e.g. laptops, collection apps, central data or sample repositories, questionnaires, information leaflets or letters, required lab material); - Agreements with intermediate collection bodies, (e.g. sub-contractors); - How security and confidentiality of data to be collected and data transmission was guaranteed"
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 3.3. Practical aspects on field and lab work
type: AnnotationProperty
definition: This section describes how the execution / implementation of the sample collection worked out, e.g. if there were corrective actions taken along the sampling period. This should include reports on quality control activities carried out by labs and actors involved in sample collection.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 3.4. Practical aspects on information handling
type: AnnotationProperty
definition: "This section describes how the collected lab data and metadata were loaded into a suitable electronic environment for further processing. It may include a description of manual or automatic data capture processes that were applied to extract e.g. metadata from paper questionnaires, or converting the formats of files or encoding the variables received. It may also include analysis of the metadata and paradata associated with collection to ensure the collection activities have met requirements. It might also describe how physical samples or related material (questionnaires) will be archived. When software is used for data collection the version and software archiving should be described."
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 4.1. Data integration
type: AnnotationProperty
definition: "This section describes any activity related to data integration or data fusion. The data collection could be a combination of new and historical data, from external or internal sources, from a variety of collection instruments etc. For example the data collection could be enriched by information from official (governmental) or non-official sources. It could further include a description on: - Data pooling, with the aim of increasing the effective number of observations of some phenomena; - Mapping or record linkage routines, with the aim of linking different data sources that use different encoding schemas; - Prioritising, when two or more sources contain data for the same variable, with potentially different values. - Data anonymization, e.g. if identifiers such as name and address are stripped to help to protect confidentiality."
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 4.2. Data classification / encoding
type: AnnotationProperty
definition: "This section describes if data/variables were classified and/or encoded. Examples: - Automatic coding routines that assign numeric codes to text responses according to a pre-determined statistical classification. - Classification based on analytical results (e.g. MLST pattern), bioinformatics analysis (e.g. phylogenetic trees) or mathematical models (PCA, SVM / ANN)"
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 4.3. Data validation
type: AnnotationProperty
definition: This section describes activities carried out to detect and localise actual or potential errors and discrepancies such as outliers, item non-response and miscoding (input data validation).
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 4.4. Data cleansing and correction
type: AnnotationProperty
definition: "This section describes what action was taken for incorrect, missing, unreliable or outdated data. For example new values may have been inserted or outdated data may have been removed. It should describe whether data were added or changed, the method used, and the flags used to mark them as changed. "
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 4.5. New variable/unit derivation
type: AnnotationProperty
definition: This section describes if new data were derived from variables/units that were not explicitly provided in the data collection but were needed to deliver the required outputs. Examples include deriving variables on households where the collection units are persons or deriving variables on enterprises where the collection units are legal units.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 4.6. Weighing of records
type: AnnotationProperty
definition: This section describes if weights for unit data records were created according to the methodology developed in sub-process 2.5 (Data processing/analysis). For example, weights might have been used to "gross-up" data to make them representative of the target population (e.g. for sample surveys or extracts from scanner data), or to adjust for non-response in total enumerations. In other situations, variables might have needed weighting for normalisation purpose or for benchmarking indicators (e.g. known population totals).
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 4.7. Data aggregation
type: AnnotationProperty
definition: This section describes how aggregate data and population totals were generated from the data collection or lower-level aggregates. It includes summing data for records sharing certain characteristics (e.g. aggregation of data by demographic or geographic classifications), determining measures of average and dispersion, and applying weights from sub-process 4.6 (Weighting of records) to derive appropriate totals. In the case of statistical outputs, which use sample surveys, sampling errors corresponding to relevant aggregates may also be calculated in this section.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 5.1. Surveillance output generation
type: AnnotationProperty
definition: This section describes how data from section 4.7 (Data aggregation) were transformed into surveillance statistics outputs such as indexes, seasonally adjusted statistics, e.g. trend, cycle, seasonal and irregular components, accessibility measures, etc., as well as the recording of quality characteristics such as coefficients of variation. The preparation of maps, GIS outputs and geo-statistical services can be included to maximise the value and capacity to analyse the statistical information.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 5.2. Surveillance output validation
type: AnnotationProperty
definition: "This section describes how the quality of the generated surveillance statistical outputs were validated, in accordance with a general quality framework and with expectations. Validation activities can include: - Checking that the population coverage and response rates are as required; - Comparing the statistics with previous cycles (if applicable); - Checking that the associated metadata, paradata and quality indicators are present and in line with expectations; - Checking geospatial consistency of the data; - Confronting the statistics against other relevant data (both internal and external); - Investigating inconsistencies in the statistics; - Performing macro editing; - Validating the statistics against expectations and domain intelligence."
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 5.3. Surveillance output statistical analysis
type: AnnotationProperty
definition: This section describes performed in-depth statistical analyses such as time-series analysis, consistency and comparability analysis, revision analysis (analysis of the differences between preliminary and revised estimates), analysis of asymmetries (discrepancies in mirror statistics) etc.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

CRAC 5.4. Surveillance disclosure control
type: AnnotationProperty
definition: This section describes activities carried out to ensure that the data (and metadata) to be disseminated do not breach the appropriate rules on confidentiality according to either organisation policies and rules, or to the process-specific methodology created in section 2.5 (Data processing/analysis plan). This may include checks for primary and secondary disclosure, as well as the application of data suppression or perturbation techniques and output checking. The degree and method of statistical disclosure control may vary for different types of outputs. For example, the approach used for microdata sets for research purposes will be different to that for published tables, finalised outputs of geospatial statistics or visualisations on maps.
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

European Food Safety Agency Standard Sample Description Framework - EFSA SSD
type: AnnotationProperty
definition: annotations created to map specific entities to their origin in the Standard Sample Description, a terminology catalogue maintained by the European Foos Safety Agency (EFSA). https://www.efsa.europa.eu/en/efsajournal/pub/3424

surveillance output
type: AnnotationProperty
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

discussion
type: AnnotationProperty
sub property of: One-Health Consensus Reference Annotation Checklist (OH-CRAC)

additional information
type: AnnotationProperty
definition: Annotation property created to be a "catch all" property for information given about a surveillance activity, and not recognized as any specific entity in the ontology when using automated RDF conversion/import tools.

editor preferred term
type: AnnotationProperty

example of usage
type: AnnotationProperty

definition
type: AnnotationProperty

editor note
type: AnnotationProperty

term editor
type: AnnotationProperty

alternative term
type: AnnotationProperty

definition source
type: AnnotationProperty

curator note
type: AnnotationProperty

imported from
type: AnnotationProperty

elucidation
type: AnnotationProperty

has associated axiom(nl)
type: AnnotationProperty

has associated axiom(fol)
type: AnnotationProperty

has axiom label
type: AnnotationProperty

has_rank
type: AnnotationProperty
definition: A metadata relation between a class and its taxonomic rank (eg species, family)
has_obo_namespace: ncbi_taxonomy
comment: This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored

has_alternative_id
type: AnnotationProperty

has broad synonym
type: AnnotationProperty
label: has_broad_synonym
sub property of: has synonym

database_cross_reference
type: AnnotationProperty

has exact synonym
type: AnnotationProperty
label: has_exact_synonym
sub property of: has synonym

has narrow synonym
type: AnnotationProperty
label: has_narrow_synonym
sub property of: has synonym

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has synonym
type: AnnotationProperty

part of
type: ObjectProperty
equivalent property:
  inverse of: has part
inverse of: has part
type: TransitiveProperty
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
imported from: obi.owl
imported from: uberon.owl
RO_0001900: RO_0001901
database_cross_reference: BFO:0000050
has_obo_namespace: uberon
id: part_of
shorthand: part_of

has part
type: ObjectProperty
equivalent property:
  inverse of: part of
type: TransitiveProperty
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative term: has_part
imported from: obi.owl
imported from: uberon.owl
RO_0001900: RO_0001901
database_cross_reference: BFO:0000051
has_obo_namespace: uberon
id: has_part
shorthand: has_part

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
inverse of: realizes
domain: realizable entity
range: process
editor preferred term: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
imported from: obi.owl
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
equivalent property:
  inverse of: realized in
domain: process
range: realizable entity
editor preferred term: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
imported from: obi.owl
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

preceded_by
type: ObjectProperty
type: TransitiveProperty
definition: X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
imported from: uberon.owl
database_cross_reference: BFO:0000062
has exact synonym: is preceded by
has exact synonym: takes place after
has_obo_namespace: uberon
id: preceded_by
shorthand: preceded_by

precedes
type: ObjectProperty
type: TransitiveProperty
imported from: uberon.owl
database_cross_reference: BFO:0000063
has_obo_namespace: uberon
id: precedes
shorthand: precedes

anterior_to
type: ObjectProperty
type: TransitiveProperty
definition: x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
imported from: uberon.owl
created by: cjm
creation date: 2009-07-31T02:15:46Z
database_cross_reference: BSPO:0000096
has_obo_namespace: uberon
id: anterior_to
shorthand: anterior_to

distal_to
type: ObjectProperty
definition: x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
imported from: uberon.owl
database_cross_reference: BSPO:0000097
has_obo_namespace: uberon
id: distal_to
shorthand: distal_to

dorsal_to
type: ObjectProperty
inverse of: ventral_to
type: TransitiveProperty
definition: x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
imported from: uberon.owl
database_cross_reference: BSPO:0000098
has_obo_namespace: uberon
id: dorsal_to
shorthand: dorsal_to

posterior_to
type: ObjectProperty
type: TransitiveProperty
definition: x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
imported from: uberon.owl
database_cross_reference: BSPO:0000099
has narrow synonym: caudal_to
has_obo_namespace: uberon
id: posterior_to
shorthand: posterior_to

ventral_to
type: ObjectProperty
type: TransitiveProperty
definition: x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
imported from: uberon.owl
database_cross_reference: BSPO:0000102
has_obo_namespace: uberon
id: ventral_to
shorthand: ventral_to

deep_to
type: ObjectProperty
type: TransitiveProperty
definition: Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
imported from: uberon.owl
database_cross_reference: BSPO:0000107
has_obo_namespace: uberon
id: deep_to
shorthand: deep_to

superficial_to
type: ObjectProperty
definition: Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
imported from: uberon.owl
database_cross_reference: BSPO:0000108
has_obo_namespace: uberon
id: superficial_to
shorthand: superficial_to

in_left_side_of
type: ObjectProperty
sub property of: in_lateral_side_of
definition: X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
imported from: uberon.owl
database_cross_reference: BSPO:0000120
has_obo_namespace: uberon
id: in_left_side_of
shorthand: in_left_side_of

in_right_side_of
type: ObjectProperty
sub property of: in_lateral_side_of
definition: X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
imported from: uberon.owl
database_cross_reference: BSPO:0000121
has_obo_namespace: uberon
id: in_right_side_of
shorthand: in_right_side_of

in_anterior_side_of
type: ObjectProperty
sub property of: part of
definition: X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
imported from: uberon.owl
database_cross_reference: BSPO:0000123
has_obo_namespace: uberon
id: in_anterior_side_of
shorthand: in_anterior_side_of

in_proximal_side_of
type: ObjectProperty
sub property of: part of
inverse of: in_distal_side_of
definition: X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
imported from: uberon.owl
database_cross_reference: BSPO:0000124
has_obo_namespace: uberon
id: in_proximal_side_of
shorthand: in_proximal_side_of

in_distal_side_of
type: ObjectProperty
sub property of: part of
definition: X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
imported from: uberon.owl
database_cross_reference: BSPO:0000125
has_obo_namespace: uberon
id: in_distal_side_of
shorthand: in_distal_side_of

in_lateral_side_of
type: ObjectProperty
sub property of: part of
property disjoint with: in_central_side_of
definition: X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
imported from: uberon.owl
database_cross_reference: BSPO:0000126
has_obo_namespace: uberon
id: in_lateral_side_of
shorthand: in_lateral_side_of

proximalmost_part_of
type: ObjectProperty
sub property of: in_proximal_side_of
definition: X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
imported from: uberon.owl
database_cross_reference: BSPO:0001106
has_obo_namespace: uberon
id: proximalmost_part_of
shorthand: proximalmost_part_of

distalmost_part_of
type: ObjectProperty
sub property of: in_distal_side_of
definition: X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
imported from: uberon.owl
database_cross_reference: BSPO:0001108
has_obo_namespace: uberon
id: distalmost_part_of
shorthand: distalmost_part_of

isSubSpeciesOf
type: ObjectProperty
domain: organism
range: organism

isSerotypeOf
type: ObjectProperty
domain: organism
range: organism

has datum
type: ObjectProperty
domain: material entity
range: information content entity

has specimen datum
type: ObjectProperty
sub property of: topObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: specimen collection protocol
  union of: specimen
range: specimen datum

has matrix type
type: ObjectProperty
sub property of: has specimen datum
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: specimen collection protocol
  union of: specimen
range: matrix type
property chain axiom: follows surveillance protocol
property chain axiom: has sample collection protocol
property chain axiom: sampled specimen

sampled from
type: ObjectProperty
domain: specimen
range: material entity

sampled from anatomical entity
type: ObjectProperty
sub property of: sampled from
domain: specimen
range: anatomical entity
property chain axiom: follows surveillance protocol
property chain axiom: has sample collection protocol
property chain axiom: sampled specimen

sampled from organism
type: ObjectProperty
sub property of: sampled from
domain: specimen
range: organism
property chain axiom: follows surveillance protocol
property chain axiom: has sample collection protocol
property chain axiom: sampled specimen

has specimen from organism type
type: ObjectProperty
sub property of: has specimen datum
domain: specimen
range: specimen from organism type
property chain axiom: follows surveillance protocol
property chain axiom: has sample collection protocol
property chain axiom: sampled specimen

follows surveillance protocol
type: ObjectProperty
inverse of: excuted in surveillance activity
domain: Surveillance Activity
range: surveillance protocol

excuted in surveillance activity
type: ObjectProperty
domain: surveillance protocol
range: Surveillance Activity

has legal basis
type: ObjectProperty
inverse of: is legal basis of
domain: Surveillance Activity
range: legislative specification

is legal basis of
type: ObjectProperty
domain: legislative specification
range: Surveillance Activity

has surveillance objective
type: ObjectProperty
domain: Surveillance Activity
range: surveillance objective

has surveillance purpose
type: ObjectProperty
domain: Surveillance Activity
range: surveillance purpose

has surveillance actions
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
range: surveillance methods specification
property chain axiom: follows surveillance protocol

has sampling design
type: ObjectProperty
sub property of: has surveillance actions
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
range: sampling design protocol
property chain axiom: follows surveillance protocol

has reporting protocol
type: ObjectProperty
sub property of: has surveillance actions
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
range: reporting protocol
property chain axiom: follows surveillance protocol

has sample collection protocol
type: ObjectProperty
sub property of: has surveillance actions
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
range: specimen collection protocol
property chain axiom: follows surveillance protocol

has diagnostic protocol
type: ObjectProperty
sub property of: has surveillance actions
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
range: diagnostic protocol
property chain axiom: follows surveillance protocol

has surveillance context
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
range: surveillance context
property chain axiom: follows surveillance protocol

target population
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: sampling design protocol
range: entity

target geographical area
type: ObjectProperty
sub property of: target population
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: sampling design protocol
range: subnational region
property chain axiom: follows surveillance protocol
property chain axiom: has sampling design

target country
type: ObjectProperty
sub property of: target population
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: sampling design protocol
range: Country
property chain axiom: follows surveillance protocol
property chain axiom: has sampling design

target host species
type: ObjectProperty
sub property of: target population
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: sampling design protocol
range: organism
property chain axiom: follows surveillance protocol
property chain axiom: has sampling design
property chain axiom: target host sector

target host sector
type: ObjectProperty
sub property of: target population
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: sampling design protocol
range: livestock farming system
property chain axiom: follows surveillance protocol
property chain axiom: has sampling design

target pathogen
type: ObjectProperty
domain: Surveillance Activity
range: organism
alternative term: Mixed outbreaks
preferred label: causative agent

susceptible species
type: ObjectProperty
domain: Surveillance Activity
range: organism

applies sampling strategy
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: sampling design protocol
range: sampling strategy
property chain axiom: follows surveillance protocol
property chain axiom: has sampling design
definition: Specification of the type of sampling strategy planned within a surveillance protocol, and ultimately executed in a surveillance activity.

has sampling unit
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: sampling design protocol
range: sampling unit
property chain axiom: follows surveillance protocol
property chain axiom: has sampling design

has sampler type
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: specimen collection protocol
range: surveillance executor type
property chain axiom: follows surveillance protocol
property chain axiom: has sample collection protocol

sampling stage
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: specimen collection protocol
range: organization
property chain axiom: follows surveillance protocol
property chain axiom: has sample collection protocol

sampled specimen
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: specimen collection protocol
range: specimen
property chain axiom: follows surveillance protocol
property chain axiom: has sample collection protocol

employs assay
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: diagnostic protocol
range: assay
property chain axiom: follows surveillance protocol
property chain axiom: has diagnostic protocol

has diagnostic test type
type: ObjectProperty
sub property of: has assay datum
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: diagnostic protocol
  union of: assay
range: diagnostic test type
property chain axiom: follows surveillance protocol
property chain axiom: has diagnostic protocol
property chain axiom: employs assay
definition: property assigning specific datum to diagnostic tests which allows identification of their type

has assay datum
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: diagnostic protocol
  union of: assay
range: assay datum
definition: assignment of data available as information content to assays

reporting country
type: ObjectProperty
sub property of: target population
domain: Surveillance Activity
range: Country

origin country
type: ObjectProperty
sub property of: target population
domain: Surveillance Activity
range: Country

contains information about
type: ObjectProperty
inverse of: documented in dataset
domain: Dataset
example of usage: this property allows metadata documentation to link a dataset to specific entities within each and vice-versa, as long as these entitites ave unique URI, even when the dataset is not itself available as linked data
definition: this property allows a dataset to be explictly linked to any entities within it which can be referred to with an unique ID.

documented in dataset
type: ObjectProperty
range: Dataset
example of usage: this property allows metadata documentation to link a dataset to specific entities within each and vice-versa, as long as these entitites ave unique URI, even when the dataset is not itself available as linked data
definition: Links an entityt to a specific dataset that contains information about it.

reporting country
type: ObjectProperty
domain: Surveillance Activity
range: Country
definition: this property specifies specifically whic country is responsible for the documentation about a specific surveillance activity

available in language
type: ObjectProperty
domain: Surveillance Activity
domain: Dataset
range: language

place of exposure
type: ObjectProperty
domain: Surveillance Activity
range: organization

place of origin of the problem
type: ObjectProperty
domain: Surveillance Activity
range: organization

hazard status context
type: ObjectProperty
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
range: status of hazard presence in a geographical region

is about
type: ObjectProperty
domain: information content entity
example of usage: This document is about information artifacts and their representations
IAO_0000114: IAO_0000125
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: obi.owl

has material basis in
type: ObjectProperty

is_supported_by_data
type: ObjectProperty
domain: conclusion based on data
range: data item
example of usage: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
IAO_0000114: IAO_0000122
definition: The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
term editor: OBI
definition source: OBI
definition source: Philly 2011 workshop

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
editor preferred term: has_specified_input
example of usage: see is_input_of example_of_usage
IAO_0000114: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred term: is_specified_input_of
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
IAO_0000114: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
inverse of: is_specified_output_of
domain: planned process
editor preferred term: has_specified_output
IAO_0000114: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
range: planned process
editor preferred term: is_specified_output_of
IAO_0000114: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred term: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
IAO_0000114: IAO_0000120
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred term: objective_achieved_by
IAO_0000114: IAO_0000122
definition: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
term editor: OBI
definition source: OBI

inheres in
type: ObjectProperty
inverse of: bearer of
editor preferred term: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
RO_0001900: RO_0001901

bearer of
type: ObjectProperty
equivalent property:
  inverse of: inheres in
range: specifically dependent continuant
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer_of
alternative term: is bearer of
RO_0001900: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred term: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative term: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
inverse of: concretizes
domain: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
imported from: obi.owl

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
imported from: obi.owl

function of
type: ObjectProperty
sub property of: inheres in
inverse of: RO_0000085
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of

quality of
type: ObjectProperty
sub property of: inheres in
inverse of: RO_0000086
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of

role of
type: ObjectProperty
sub property of: inheres in
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of

has role
type: ObjectProperty
equivalent property:
  inverse of: role of
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role

disposition of
type: ObjectProperty
sub property of: inheres in

derives from
type: ObjectProperty
equivalent property:
  inverse of: RO_0001001
sub property of: topObjectProperty
inverse of: RO_0001001
domain: independent continuant
range: independent continuant
editor preferred term: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
IAO_0000114: IAO_0000125
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative term: derives_from
imported from: ro.owl

location_of
type: ObjectProperty
imported from: uberon.owl
database_cross_reference: RO:0001015
has_obo_namespace: uberon
id: location_of
shorthand: location_of

located in
type: ObjectProperty
sub property of: topObjectProperty
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
imported from: uberon.owl
database_cross_reference: RO:0001025
has_obo_namespace: uberon
id: RO:0001025
id: located_in
shorthand: located_in
label: located_in

has boundary
type: ObjectProperty
imported from: uberon.owl
database_cross_reference: RO:0002002
has_obo_namespace: uberon
id: has_boundary
shorthand: has_boundary

bounding layer of
type: ObjectProperty
sub property of: part of
imported from: uberon.owl
database_cross_reference: RO:0002007
has_obo_namespace: uberon
id: bounding_layer_of
shorthand: bounding_layer_of
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.

simultaneous_with
type: ObjectProperty
sub property of: starts
sub property of: ends
definition: Relation between occurrents, shares start and end boundaries.
imported from: uberon.owl
database_cross_reference: RO:0002082
has exact synonym: coincides_with
has exact synonym: is_equal_to
has_obo_namespace: uberon
id: simultaneous_with
shorthand: simultaneous_with

immediately_preceded_by
type: ObjectProperty
sub property of: preceded_by
definition: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
imported from: uberon.owl
UBPROP_0000001: A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
database_cross_reference: RO:0002087
has exact synonym: directly preceded by
has exact synonym: is directly preceded by
has exact synonym: is immediately preceded by
has exact synonym: starts_at_end_of
has_obo_namespace: uberon
id: immediately_preceded_by
shorthand: immediately_preceded_by

continuous_with
type: ObjectProperty
type: SymmetricProperty
imported from: uberon.owl
database_cross_reference: RO:0002150
has_obo_namespace: uberon
id: continuous_with
shorthand: continuous_with

connected to
type: ObjectProperty
sub property of: transitively_connected to
definition: Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
imported from: uberon.owl
database_cross_reference: RO:0002170
has_obo_namespace: uberon
id: connected_to
shorthand: connected_to
comment: Connection does not imply overlaps.

connects
type: ObjectProperty
definition: Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
editor note: this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
imported from: uberon.owl
database_cross_reference: RO:0002176
has_obo_namespace: uberon
id: connects
shorthand: connects

supplies
type: ObjectProperty
sub property of: connected to
definition: relation between an artery and the structure is supplies with blood.
imported from: uberon.owl
database_cross_reference: RO:0002178
has exact synonym: arterial supply of
has_obo_namespace: uberon
id: supplies
shorthand: supplies
comment: source: FMA

develops_from
type: ObjectProperty
sub property of: has developmental contribution from
inverse of: develops_into
type: TransitiveProperty
imported from: uberon.owl
database_cross_reference: RO:0002202
has_obo_namespace: uberon
id: develops_from
shorthand: develops_from

develops_into
type: ObjectProperty
sub property of: has potential to develop into
imported from: uberon.owl
database_cross_reference: RO:0002203
has_obo_namespace: uberon
id: develops_into
shorthand: develops_into

surrounded_by
type: ObjectProperty
inverse of: surrounds
definition: x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
imported from: uberon.owl
database_cross_reference: RO:0002219
has_obo_namespace: uberon
id: surrounded_by
shorthand: surrounded_by

adjacent_to
type: ObjectProperty
type: SymmetricProperty
definition: x adjacent_to y iff: x and y share a boundary
imported from: uberon.owl
database_cross_reference: RO:0002220
has_obo_namespace: uberon
id: adjacent_to
shorthand: adjacent_to

surrounds
type: ObjectProperty
definition: inverse of surrounded_by
imported from: uberon.owl
database_cross_reference: RO:0002221
has_obo_namespace: uberon
id: surrounds
shorthand: surrounds

starts
type: ObjectProperty
sub property of: part of
inverse of: starts with
definition: Relation between occurrents, shares a start boundary with.
imported from: uberon.owl
database_cross_reference: RO:0002223
has_obo_namespace: uberon
id: starts
shorthand: starts

starts with
type: ObjectProperty
sub property of: has part
type: TransitiveProperty
imported from: uberon.owl
database_cross_reference: RO:0002224
has_obo_namespace: uberon
id: starts_with
shorthand: starts_with

ends
type: ObjectProperty
sub property of: part of
definition: Relation between occurrents, shares an end boundary with.
imported from: uberon.owl
database_cross_reference: RO:0002229
has exact synonym: finishes
has_obo_namespace: uberon
id: ends
shorthand: ends

ends with
type: ObjectProperty
sub property of: has part
type: TransitiveProperty
imported from: uberon.owl
database_cross_reference: RO:0002230
has_obo_namespace: uberon
id: ends_with
shorthand: ends_with

has developmental contribution from
type: ObjectProperty
type: TransitiveProperty
imported from: uberon.owl
database_cross_reference: RO:0002254
has_obo_namespace: uberon
id: has_developmental_contribution_from
shorthand: has_developmental_contribution_from

developmentally_induced_by
type: ObjectProperty
definition: t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
imported from: uberon.owl
database_cross_reference: RO:0002256
has_obo_namespace: uberon
id: developmentally_induced_by
shorthand: developmentally_induced_by
comment: sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)

developmentally preceded by
type: ObjectProperty
imported from: uberon.owl
database_cross_reference: RO:0002258
has_obo_namespace: uberon
id: developmentally_preceded_by
shorthand: developmentally_preceded_by

developmentally_replaces
type: ObjectProperty
imported from: uberon.owl
database_cross_reference: RO:0002285
has_obo_namespace: uberon
id: developmentally_replaces
shorthand: developmentally_replaces

has member
type: ObjectProperty
sub property of: has part
imported from: uberon.owl
database_cross_reference: RO:0002351
has_obo_namespace: uberon
id: has_member
shorthand: has_member

has potential to developmentally contribute to
type: ObjectProperty
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
imported from: uberon.owl
database_cross_reference: RO:0002385
has_obo_namespace: uberon
id: has_potential_to_developmentally_contribute_to
shorthand: has_potential_to_developmentally_contribute_to

has potential to develop into
type: ObjectProperty
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
imported from: uberon.owl
database_cross_reference: RO:0002387
has_obo_namespace: uberon
id: has_potential_to_develop_into
shorthand: has_potential_to_develop_into

contributes to morphology of
type: ObjectProperty
imported from: uberon.owl
database_cross_reference: RO:0002433
has_obo_namespace: uberon
id: contributes_to_morphology_of
shorthand: contributes_to_morphology_of

composed primarily of
type: ObjectProperty
sub property of: has part
definition: x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
imported from: uberon.owl
database_cross_reference: RO:0002473
has_obo_namespace: uberon
id: composed_primarily_of
shorthand: composed_primarily_of

existence starts during
type: ObjectProperty
sub property of: existence starts during or after
definition: Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
imported from: uberon.owl
database_cross_reference: RO:0002488
has exact synonym: begins_to_exist_during
has_obo_namespace: uberon
id: existence_starts_during
shorthand: existence_starts_during

existence starts with
type: ObjectProperty
sub property of: existence starts during
domain: anatomical entity
definition: Relation between continuant and occurrent, such that c comes into existence at the start of p.
imported from: uberon.owl
database_cross_reference: RO:0002489
has_obo_namespace: uberon
id: existence_starts_with
shorthand: existence_starts_with

existence ends during
type: ObjectProperty
sub property of: existence ends during or before
definition: Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
imported from: uberon.owl
database_cross_reference: RO:0002492
has exact synonym: ceases_to_exist_during
has_obo_namespace: uberon
id: existence_ends_during
shorthand: existence_ends_during

existence ends with
type: ObjectProperty
sub property of: existence ends during
domain: anatomical entity
definition: Relation between continuant and occurrent, such that c ceases to exist at the end of p.
imported from: uberon.owl
database_cross_reference: RO:0002493
has_obo_namespace: uberon
id: existence_ends_with
shorthand: existence_ends_with

transformation of
type: ObjectProperty
sub property of: develops_from
type: TransitiveProperty
imported from: uberon.owl
database_cross_reference: RO:0002494
has exact synonym: transforms from
has_obo_namespace: uberon
id: transformation_of
shorthand: transformation_of

immediate transformation of
type: ObjectProperty
sub property of: transformation of
imported from: uberon.owl
database_cross_reference: RO:0002495
has exact synonym: direct_transformation_of
has exact synonym: immediately transforms from
has_obo_namespace: uberon
id: immediate_transformation_of
shorthand: immediate_transformation_of

existence starts during or after
type: ObjectProperty
imported from: uberon.owl
database_cross_reference: RO:0002496
has_obo_namespace: uberon
id: existence_starts_during_or_after
shorthand: existence_starts_during_or_after

existence ends during or before
type: ObjectProperty
imported from: uberon.owl
database_cross_reference: RO:0002497
has_obo_namespace: uberon
id: existence_ends_during_or_before
shorthand: existence_ends_during_or_before

has skeleton
type: ObjectProperty
sub property of: has part
inverse of: skeleton of
definition: A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
imported from: uberon.owl
database_cross_reference: RO:0002551
has_obo_namespace: uberon
has_related_synonym: has sekeletal support
has_related_synonym: has supporting framework
id: has_skeleton
shorthand: has_skeleton

luminal space of
type: ObjectProperty
sub property of: part of
imported from: uberon.owl
database_cross_reference: RO:0002572
has_obo_namespace: uberon
id: luminal_space_of
shorthand: luminal_space_of

skeleton of
type: ObjectProperty
sub property of: part of
imported from: uberon.owl
database_cross_reference: RO:0002576
has_obo_namespace: uberon
id: skeleton_of
shorthand: skeleton_of

produces
type: ObjectProperty
imported from: uberon.owl
database_cross_reference: RO:0003000
has_obo_namespace: uberon
id: produces
shorthand: produces

produced_by
type: ObjectProperty
imported from: uberon.owl
database_cross_reference: RO:0003001
has_obo_namespace: uberon
id: produced_by
shorthand: produced_by

channel for
type: ObjectProperty
domain: anatomical conduit
range: organism substance
imported from: uberon.owl
has broad synonym: carries
has_obo_namespace: uberon
id: channel_for

channels_from
type: ObjectProperty
type: TransitiveProperty
imported from: uberon.owl
has_obo_namespace: uberon
id: channels_from

channels_into
type: ObjectProperty
type: TransitiveProperty
imported from: uberon.owl
has_obo_namespace: uberon
id: channels_into

conduit for
type: ObjectProperty
definition: x is a conduit for y iff y passes through the lumen of x.
imported from: uberon.owl
has_obo_namespace: uberon
id: conduit_for

existence starts and ends during
type: ObjectProperty
sub property of: existence starts during
sub property of: existence ends during
domain: anatomical entity
imported from: uberon.owl
has_obo_namespace: uberon
id: existence_starts_and_ends_during

extends_fibers_into
type: ObjectProperty
sub property of: connected to
type: SymmetricProperty
imported from: uberon.owl
has_obo_namespace: uberon
id: extends_fibers_into

filtered through
type: ObjectProperty
definition: Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
imported from: uberon.owl
has_obo_namespace: uberon
id: filtered_through
comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed

in_central_side_of
type: ObjectProperty
sub property of: part of
definition: X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
imported from: uberon.owl
has_obo_namespace: uberon
id: in_central_side_of

protects
type: ObjectProperty
imported from: uberon.owl
has_obo_namespace: uberon
id: protects

proximally connected to
type: ObjectProperty
sub property of: distal_to
sub property of: connected to
sub property of: transitively proximally connected to
definition: x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
imported from: uberon.owl
has_obo_namespace: uberon
id: proximally_connected_to

subdivision of
type: ObjectProperty
imported from: uberon.owl
has_obo_namespace: uberon
id: subdivision_of
comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B

transitively_connected to
type: ObjectProperty
type: TransitiveProperty
imported from: uberon.owl
has_obo_namespace: uberon
id: transitively_connected_to

transitively proximally connected to
type: ObjectProperty
type: TransitiveProperty
definition: .
imported from: uberon.owl
has_obo_namespace: uberon
id: transitively_proximally_connected_to

surveillance activity history item
type: DatatypeProperty
domain: Surveillance Activity

surveillance activity start date
type: DatatypeProperty
sub property of: surveillance activity history item
domain: Surveillance Activity
range: date

surveillance activity end date
type: DatatypeProperty
sub property of: surveillance activity history item
domain: Surveillance Activity
range: date

Number of units tested
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Surveillance Activity
range: integer

Number of PSU tested
type: DatatypeProperty
sub property of: Number of units tested
domain: Surveillance Activity
range: integer

Number of SSU tested
type: DatatypeProperty
sub property of: Number of units tested
domain: Surveillance Activity
range: integer

Number of units positive
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Surveillance Activity
range: integer

Number of PSU positive
type: DatatypeProperty
sub property of: Number of units positive
domain: Surveillance Activity
range: integer

Number of SSU positive
type: DatatypeProperty
sub property of: Number of units positive
domain: Surveillance Activity
range: integer

Number of units negative
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Surveillance Activity
range: integer

Number of PSU negative
type: DatatypeProperty
sub property of: Number of units negative
domain: Surveillance Activity
range: integer

Number of SSU negative
type: DatatypeProperty
sub property of: Number of units negative
domain: Surveillance Activity
range: integer

Number of specimen tested
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Surveillance Activity
range: integer

Number of specimen negative
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Surveillance Activity
range: integer

calculated sample size
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: specimen collection protocol
range: integer
definition: The sample size calculated for a surveillance activity in order to achieve its specific surveillance purpose or goal, and considering its declared epidemiological unit.

calculated number of PSU
type: DatatypeProperty
sub property of: calculated sample size
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: specimen collection protocol
range: integer
example of usage: The number of herds to be sampled in a survey targetting livestock animals, which are kept in herds.
definition: In a sampling process targetting clustered units, this refers to the number of PRIMARY SAMPLING UNITS to be sampled, according to the plan designed for a surveillance activity in order to achieve its specific surveillance purpose or goal.

calculated number of SSU
type: DatatypeProperty
sub property of: calculated sample size
domain: Class
  union of: Surveillance Activity
  union of: surveillance protocol
  union of: specimen collection protocol
range: integer
example of usage: The number of animals to be sampled within each herd.
definition: In a sampling process targetting clustered units, this refers to the number of SECONDARY SAMPLING UNITS to be sampled, according to the plan designed for a surveillance activity in order to achieve its specific surveillance purpose or goal.

Number of specimen positive
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Surveillance Activity
range: integer

Percentage of units positive
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Surveillance Activity
range: Datatype
  on datatype: double
  with restrictions:
    min inclusive: 0.0
  with restrictions:
    max inclusive: 100.0

Percentage of PSU positive
type: DatatypeProperty
sub property of: Percentage of units positive
domain: Surveillance Activity
range: Datatype
  on datatype: double
  with restrictions:
    min inclusive: 0.0
  with restrictions:
    max inclusive: 100.0

Percentage of SSU positive
type: DatatypeProperty
sub property of: Percentage of units positive
domain: Surveillance Activity
range: Datatype
  on datatype: double
  with restrictions:
    min inclusive: 0.0
  with restrictions:
    max inclusive: 100.0

percentage of specimen positive
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Surveillance Activity
range: Datatype
  on datatype: double
  with restrictions:
    min inclusive: 0.0
  with restrictions:
    max inclusive: 100.0

surveillance activity aggregated results
type: DatatypeProperty
domain: Surveillance Activity
definition: a collection of properties used to assign numeric results to a surveillance activity

surveillance activity year
type: DatatypeProperty
sub property of: surveillance activity history item
domain: Surveillance Activity
range: integer

year started
type: DatatypeProperty
sub property of: surveillance activity history item
domain: Surveillance Activity
range: integer

Number of cases
type: DatatypeProperty
sub property of: surveillance activity aggregated results
domain: Surveillance Activity
range: integer

Number of domestic cases
type: DatatypeProperty
sub property of: Number of cases
domain: Surveillance Activity
range: integer

Number of imported cases
type: DatatypeProperty
sub property of: Number of cases
domain: Surveillance Activity
range: integer

specimen weight
type: DatatypeProperty
domain: Class
  intersection of: Surveillance Activity
  intersection of: specimen
range: double
definition: the weight of a specific collected specimen. use sub-properties to specify weight units

sampling weight in grams
type: DatatypeProperty
sub property of: specimen weight
domain: Class
  union of: Surveillance Activity
  union of: specimen
range: double
definition: the weight of a specific collected specimen, in grams

sampling weight in millilitre
type: DatatypeProperty
sub property of: specimen weight
domain: Class
  union of: Surveillance Activity
  union of: specimen
range: double
definition: the weight of a specific collected specimen, in mililitres

Case fatality rate
type: DatatypeProperty
sub property of: surveillance activity aggregated results
definition: The case-fatality rate is the proportion of persons with a particular condition (cases) who die from that condition. It is a measure of the severity of the condition.
definition source: https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section3.html

Hospitalized cases
type: DatatypeProperty
sub property of: surveillance activity aggregated results

Notification rate
type: DatatypeProperty
sub property of: surveillance activity aggregated results

Notification rate in domestic cases
type: DatatypeProperty
sub property of: Notification rate

Number of deaths
type: DatatypeProperty
sub property of: surveillance activity aggregated results

case definition
type: DatatypeProperty
domain: Surveillance Activity
range: Literal

entity
type: Class
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
imported from: obi.owl
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
disjoint with: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: obi.owl
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: elucidation
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: elucidation
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

spatial region
type: Class
subclass of: immaterial entity
disjoint with: site
disjoint with: continuant fiat boundary
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: elucidation
annotated target: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(nl)
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

temporal region
type: Class
subclass of: occurrent
disjoint with: spatiotemporal region
disjoint with: process
disjoint with: process boundary
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
elucidation: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: elucidation
annotated target: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

two-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

Axiom
annotated source: two-dimensional spatial region
annotated property: elucidation
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

Axiom
annotated source: two-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

spatiotemporal region
type: Class
subclass of: occurrent
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

Axiom
annotated source: spatiotemporal region
annotated property: elucidation
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

process
type: Class
subclass of: occurrent
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
imported from: obi.owl
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

Axiom
annotated source: process
annotated property: definition
annotated target: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
imported from: obi.owl
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

Axiom
annotated source: realizable entity
annotated property: elucidation
annotated target: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

zero-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

Axiom
annotated source: zero-dimensional spatial region
annotated property: elucidation
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

Axiom
annotated source: zero-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

Axiom
annotated source: quality
annotated property: elucidation
annotated target: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: elucidation
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

fiat object part
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object-part
BFO CLIF specification label: FiatObjectPart
example of usage: or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
elucidation: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has associated axiom(fol): (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]

Axiom
annotated source: fiat object part
annotated property: elucidation
annotated target: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

Axiom
annotated source: fiat object part
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

one-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
annotated source: one-dimensional spatial region
annotated property: elucidation
annotated target: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

Axiom
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
definition source: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
elucidation: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has associated axiom(fol): (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
annotated source: object aggregate
annotated property: definition source
annotated target: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated source: object aggregate
annotated property: elucidation
annotated target: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
annotated source: object aggregate
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

Axiom
annotated source: three-dimensional spatial region
annotated property: elucidation
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

Axiom
annotated source: three-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
imported from: envo.owl
imported from: obi.owl
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
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.

Axiom
annotated source: site
annotated property: elucidation
annotated target: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

Axiom
annotated source: site
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])

Axiom
annotated source: object
annotated property: elucidation
annotated target: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
imported from: obi.owl
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: elucidation
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

process boundary
type: Class
subclass of: occurrent
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

Axiom
annotated source: process boundary
annotated property: definition
annotated target: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
annotated source: process boundary
annotated property: has associated axiom(nl)
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
annotated source: one-dimensional temporal region
annotated property: elucidation
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

Axiom
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

Axiom
annotated source: material entity
annotated property: elucidation
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

continuant fiat boundary
type: Class
subclass of: immaterial entity
BFO OWL specification label: cf-boundary
BFO CLIF specification label: ContinuantFiatBoundary
definition: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
editor note: BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
editor note: BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
editor note: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
has associated axiom(fol): (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]

Axiom
annotated source: continuant fiat boundary
annotated property: definition
annotated target: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated source: continuant fiat boundary
annotated property: editor note
annotated target: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

Axiom
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
elucidation: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

process profile
type: Class
subclass of: process
disjoint with: history
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
example of usage: One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
example of usage: The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
definition: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has associated axiom(fol): (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

Axiom
annotated source: process profile
annotated property: definition
annotated target: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

Axiom
annotated source: process profile
annotated property: elucidation
annotated target: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: a marriage bond, an instance of love, an obligation between one person and another.
definition: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has associated axiom(fol): (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]

Axiom
annotated source: relational quality
annotated property: definition
annotated target: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
annotated source: relational quality
annotated property: has associated axiom(fol)
annotated target: (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
elucidation: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
elucidation: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
annotated target: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative term: temporal instant.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
annotated source: zero-dimensional temporal region
annotated property: elucidation
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

Axiom
annotated source: zero-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
elucidation: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])

Axiom
annotated source: history
annotated property: elucidation
annotated target: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

portion of material
type: Class
subclass of: material entity
definition: An independent material continuant that is self-connected and retains its identity over time.
imported from: chmo.owl

matrix
type: Class
subclass of: portion of material
GENEPIO_0000006: specimen extraction matrix
definition: Those components of a sample that are not measured by an experiment.
imported from: chmo.owl
comment: "This observable is important where process of capturing sample can affect dna extraction."

primary bacterial infectious disease
type: Class
subclass of: bacterial infectious disease
definition: A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread.
has_obo_namespace: disease_ontology
id: DOID:0050338
in subset: DO FlyBase slim

Axiom
annotated source: primary bacterial infectious disease
annotated property: definition
annotated target: A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread.
type: ECO_0007638
database_cross_reference: url:http://en.wikipedia.org/wiki/Infectious_disease

salmonellosis
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease caused by the bacteria of the genus Salmonella. It has sypmtoms diarrhea, fever, vomiting, and abdominal cramps 12 to 72 hours after infection. In most cases, the illness lasts four to seven days, and most people recover without treatment.
database_cross_reference: ICD10CM:A02.0
database_cross_reference: ICD9CM:003.0
has exact synonym: Salmonella infection
has_obo_namespace: disease_ontology
id: DOID:0060859

Axiom
annotated source: salmonellosis
annotated property: definition
annotated target: A primary bacterial infectious disease caused by the bacteria of the genus Salmonella. It has sypmtoms diarrhea, fever, vomiting, and abdominal cramps 12 to 72 hours after infection. In most cases, the illness lasts four to seven days, and most people recover without treatment.
type: ECO_0007637
database_cross_reference: url:https://www.cdc.gov/salmonella/general/index.html
database_cross_reference: url:https://www.foodsafety.gov/poisoning/causes/bacteriaviruses/salmonella

bacterial infectious disease
type: Class
equivalent class: Class
  intersection of: disease
  intersection of: Restriction
    on property: has material basis in
    some values from: Bacteria
definition: A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
database_cross_reference: ICD10CM:A49.9
database_cross_reference: MESH:D001424
database_cross_reference: NCI:C2890
database_cross_reference: SNOMEDCT_US_2020_03_01:87628006
database_cross_reference: UMLS_CUI:C0004623
has_obo_namespace: disease_ontology
id: DOID:104
in subset: DO AGR slim
in subset: DO FlyBase slim
in subset: NCIthesaurus

Axiom
annotated source: bacterial infectious disease
annotated property: definition
annotated target: A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
type: ECO_0007638
database_cross_reference: url:http://en.wikipedia.org/wiki/Pathogenic_bacteria

campylobacteriosis
type: Class
subclass of: bacterial infectious disease
subclass of: gastroenteritis
subclass of: Restriction
  on property: has material basis in
  some values from: Campylobacter jejuni
subclass of: Restriction
  on property: located in
  some values from: alimentary part of gastrointestinal system
definition: A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Campylobacter jejuni, which is transmitted_by ingestion of contaminated food or water or transmitted_by contact with infected people or animals. The infection has_symptom diarrhea or has_symptom dysentery, has_symptom abdominal cramps and pain, and has_symptom fever.
has_alternative_id: DOID:13621
database_cross_reference: MESH:D002169
database_cross_reference: SNOMEDCT_US_2020_03_01:86500004
database_cross_reference: UMLS_CUI:C0006818
has exact synonym: Campylobacteriosis
has_obo_namespace: disease_ontology
id: DOID:13622
in subset: gram-negative bacterial infectious disease

Axiom
annotated source: campylobacteriosis
annotated property: definition
annotated target: A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Campylobacter jejuni, which is transmitted_by ingestion of contaminated food or water or transmitted_by contact with infected people or animals. The infection has_symptom diarrhea or has_symptom dysentery, has_symptom abdominal cramps and pain, and has_symptom fever.
type: ECO_0007638
database_cross_reference: url:http://en.wikipedia.org/wiki/Campylobacteriosis
database_cross_reference: url:http://www.health.state.ny.us/diseases/communicable/campylobacteriosis/fact_sheet.htm

gastroenteritis
type: Class
subclass of: gastrointestinal system disease
definition: A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen.
has_alternative_id: DOID:4094
has_alternative_id: DOID:5269
database_cross_reference: ICD10CM:K52.9
database_cross_reference: MESH:D005759
database_cross_reference: NCI:C34632
database_cross_reference: SNOMEDCT_US_2020_03_01:154278002
database_cross_reference: UMLS_CUI:C0017160
has exact synonym: cholera morbus
has exact synonym: infectious colitis, enteritis and gastroenteritis
has_obo_namespace: disease_ontology
id: DOID:2326
in subset: NCIthesaurus

Axiom
annotated source: gastroenteritis
annotated property: definition
annotated target: A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen.
type: ECO_0007637
database_cross_reference: url:http://www.merck.com/mmhe/sec09/ch122/ch122a.html

disease
type: Class
subclass of: disposition
definition: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
database_cross_reference: MESH:D004194
database_cross_reference: NCI:C2991
database_cross_reference: SNOMEDCT_US_2020_03_01:64572001
database_cross_reference: UMLS_CUI:C0012634
has_obo_namespace: disease_ontology
id: DOID:4
in subset: NCIthesaurus

Axiom
annotated source: disease
annotated property: definition
annotated target: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
type: ECO_0007645
database_cross_reference: url:http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

disease of anatomical entity
type: Class
subclass of: disease
definition: A disease that manifests in a defined anatomical structure.
has_alternative_id: DOID:1
has_alternative_id: DOID:2
has_alternative_id: DOID:5
has_alternative_id: DOID:71
has_alternative_id: DOID:72
has_alternative_id: DOID:8
has_obo_namespace: disease_ontology
id: DOID:7

Axiom
annotated source: disease of anatomical entity
annotated property: definition
annotated target: A disease that manifests in a defined anatomical structure.
type: ECO_0007643
database_cross_reference: url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic

gastrointestinal system disease
type: Class
equivalent class: Class
  intersection of: disease
  intersection of: Restriction
    on property: located in
    some values from: digestive system
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the gastrointestinal tract.
has_alternative_id: DOID:27
has_alternative_id: DOID:944
database_cross_reference: ICD10CM:K92.9
database_cross_reference: ICD9CM:520-579.99
database_cross_reference: MESH:D004066
database_cross_reference: SNOMEDCT_US_2020_03_01:53619000
database_cross_reference: UMLS_CUI:C0012242
has exact synonym: GIT disease
has exact synonym: Gastroenteropathy
has exact synonym: alimentary system disease
has exact synonym: digestive system disorder
has exact synonym: gastrointestinal disease
has exact synonym: gastrointestinal disorder
has_obo_namespace: disease_ontology
id: DOID:77
in subset: DO AGR slim
in subset: DO GXD slim
in subset: DO MGI slim

Axiom
annotated source: gastrointestinal system disease
annotated property: definition
annotated target: A disease of anatomical entity that is located_in the gastrointestinal tract.
type: ECO_0007638
database_cross_reference: url:http://en.wikipedia.org/wiki/Human_gastrointestinal_tract

administrative region
type: Class
subclass of: site
imported from: envo.owl
database_cross_reference: FTT:1242
database_cross_reference: FTT:1252
database_cross_reference: FTT:15
database_cross_reference: FTT:16
database_cross_reference: FTT:18
database_cross_reference: FTT:19
database_cross_reference: FTT:21
database_cross_reference: FTT:22
database_cross_reference: FTT:23
database_cross_reference: FTT:24
database_cross_reference: FTT:25
database_cross_reference: FTT:26
database_cross_reference: FTT:27
database_cross_reference: FTT:28
database_cross_reference: FTT:29
database_cross_reference: FTT:37
database_cross_reference: SWEETRealm:AdministrativeRegion
database_cross_reference: TGN:80001
database_cross_reference: TGN:81099
database_cross_reference: TGN:81123
database_cross_reference: https://en.wikipedia.org/wiki/Administrative_region
has exact synonym: administrative area

first-order administrative region
type: Class
subclass of: administrative region
subclass of: geopolitical region
subclass of: Restriction
  on property: located in
  some values from: Country
GENEPIO_0000006: state / province / territory / region
GENEPIO_0001763: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
definition: A primary administrative division of a country, such as a state in the United States.
imported from: envo.owl
database_cross_reference: FTT:414
database_cross_reference: FTT:569
database_cross_reference: Geonames:A.ADM1
database_cross_reference: TGN:81100

national geopolitical entity
type: Class
subclass of: political entity
definition: A political association with effective dominion over a geographic area.
imported from: envo.owl
database_cross_reference: FTT:424
database_cross_reference: FTT:566
database_cross_reference: FTT:567
database_cross_reference: FTT:571
database_cross_reference: SWEETRealm:Country
database_cross_reference: SWEETRealm:State
database_cross_reference: TGN:80006
database_cross_reference: TGN:81010
database_cross_reference: TGN:81011
database_cross_reference: TGN:81102
database_cross_reference: https://en.wikipedia.org/wiki/Nation
has exact synonym: Country
has exact synonym: nation
has narrow synonym: independent nation
has narrow synonym: independent political entity
has narrow synonym: independent sovereign nation

populated place
type: Class
subclass of: environmental zone
definition: Place or area with clustered or scattered buildings and a permanent human population.
imported from: envo.owl
imported from: gaz.owl
has broad synonym: place
database_cross_reference: FTT:1097
database_cross_reference: FTT:33
database_cross_reference: Geonames:P.PPL
database_cross_reference: Geonames:P.PPLS
database_cross_reference: TGN:22201
database_cross_reference: TGN:83002
database_cross_reference: https://en.wikipedia.org/wiki/Populated_place
has exact synonym: inhabited place
has exact synonym: populated place
has exact synonym: populated places
has exact synonym: settlement

political entity
type: Class
subclass of: administrative region
definition: A geographical region whose affairs and population are administered by an authority.
imported from: envo.owl
database_cross_reference: FTT:1093
database_cross_reference: Geonames:A.PCL
database_cross_reference: TGN:80002

city
type: Class
subclass of: dense settlement
definition: Incorporated populated place.
imported from: envo.owl
imported from: gaz.owl
has broad synonym: urban area
database_cross_reference: EcoLexicon:city
database_cross_reference: FTT:430
database_cross_reference: FTT:483
database_cross_reference: FTT:484
database_cross_reference: FTT:485
database_cross_reference: SWEETRealm:City
database_cross_reference: TGN:83020
database_cross_reference: TGN:83040
database_cross_reference: TGN:83043
database_cross_reference: https://en.wikipedia.org/wiki/City
has exact synonym: Municipality

environmental zone
type: Class
subclass of: site
definition: A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
definition: An environmental zone is an environmental feature whose extent is determined by the presence or influence of one or more material entities or processes. An environmental zone may, itself, assume the role of an environmental feature.
imported from: envo.owl
imported from: gaz.owl
in subset: envoPolar
comment: For example, a intertidal zone is that part of a coast which is exposed to air and water due to tidal processes. It determines the intertidal zone environment. This class is experimental and not suitable for annotation! "Zone" is likely to become some form of BFO:site. It is intended to capture entities from both physiography and human geography.
comment: Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.

dense settlement
type: Class
subclass of: populated place
definition: A settlement with a high density of buildings and inhabitants.
imported from: envo.owl
imported from: gaz.owl
comment: The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request.

geographic location
type: Class
subclass of: designated area on Earth
definition: A reference to a place on the Earth, by its name or by its geographical location.
imported from: gaz.owl
has_alternative_id: GAZ:00000467
has exact synonym: geographic region {alternative name}

subnational region
type: Class
subclass of: first-order administrative region
disjoint with: Province
disjoint with: State
disjoint with: Territory
GENEPIO_0000006: region
GENEPIO_0001763: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
IAO_0000114: IAO_0000428
definition: A subnational region is a type of subnational entity similar to a nation's state, province, or territory.
term editor: Damion Dooley

specimen datum
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: specimen
definition: This is a catch-all category for listing specimen related terms
term editor: Damion Dooley

designated area on Earth
type: Class
subclass of: site
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.
term editor: Damion Dooley

Surveillance Activity
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: surveillance protocol
subclass of: planned process
definition: a planned process which systematically, continuously or repeatedly measures, collected, collates, analyses, interprets and disseminates health and welfare related data from defined populations.
description: A specific surveillance activity that is planned and has (or will have) associated results. A surveillance component or a surveillance system could both be a surveillance activity. Ideally, every activity would have unique attributes for methods - for instance, only one sampling stage. If samples are collected in a slaughterhouse AND in farms, these would ideally be modeled as two different activities, and the appropriate properties used to declare them as linked. But since activities are not defined the same in every health surveillance sector, nor do all data support such a granularity, the class is able to model methods and results for any surveillance activity declared. One surveillance activity should have an unique identifier, to which results are linked. The act of being a "planned activity" is used in the context of OBI, where his implies the existence of a protocol for action. Therefore, surveillance activities such as outbreak investigations, are also considered a planned process (even if the outbreak itself is not a planned occurrence, the response to one is planned for).

livestock farming system
type: Class
subclass of: role
definition: a role given to a specific herd of domesticated animals, specifying that they are raised in an agricultural setting with a specific purpose.

product oriented farming type
type: Class
subclass of: livestock farming system
definition: Classification of livstock farming systems based on the type of commodity produced. Sub-classes are not mutually exclusive.

egg production
type: Class
subclass of: product oriented farming type
HSO_0000002: MTX
HSO_0000003: A0C7P
HSO_0000005: Animals farmed for egg production purposes

meat production
type: Class
subclass of: product oriented farming type
HSO_0000002: MTX
HSO_0000003: A0C7G
HSO_0000005: Animals farmed for meat production purposes

milk production
type: Class
subclass of: product oriented farming type
HSO_0000002: MTX
HSO_0000003: A0C7N
HSO_0000005: Animals farmed for milk production purposes
HSO_0000005: milk production

reproducer
type: Class
subclass of: product oriented farming type
HSO_0000002: MTX
HSO_0000003: A0C7G
HSO_0000005: Animals farmed for breeding purposes

supra-national geopolitical entity
type: Class
subclass of: political entity

NUTS region
type: Class
subclass of: subnational region

language
type: Class
subclass of: quality

matrix type
type: Class
subclass of: specimen datum
definition: A directive information that qualifies/classifies specimens.
comment: Can be inferred if enough information about the specimen is given, but can also be assigned directly when the source of information only specifies the type of speciment (for instance when using the SSD2 terminology, catalog MTXTYP).

whole organism
type: Class
subclass of: matrix from organism

matrix from organism
type: Class
equivalent class: Restriction
  on property: sampled from
  some values from: organism
subclass of: specimen
definition: a specimen collected from an organism.
comment: inferred categorization of specimens based on the informaiton provided in matrix type and/or regarding the anatomical entity targetted

fluid specimen
type: Class
subclass of: matrix from organism

organ/tissue specimen
type: Class
equivalent class: Restriction
  on property: sampled from anatomical entity
  some values from: anatomical structure
subclass of: matrix from organism

swab specimen
type: Class
subclass of: matrix from organism

excreta specimen
type: Class
equivalent class: Restriction
  on property: sampled from anatomical entity
  some values from: excreta
subclass of: matrix from organism

surveillance context
type: Class
subclass of: objective specification
definition: A directive information that describes the context for data collection in support to a specificsurveillance objective.
definition source: https://github.com/SVA-SE/AHSURED/wiki

surveillance executor type
type: Class
subclass of: information content entity
definition: A directive information used to describe the type of agent who carries out the data collection in a surveillance activity
alternative term: surveillance sampler type
HSO_0000002: SAMPLR

sampling strategy
type: Class
subclass of: directive information entity
definition: A directive information that describes how population units will be chosen for sample/data collection in a surveillance activity.
definition source: https://github.com/SVA-SE/AHSURED/wiki/Description-of-surveillance-items-in-the-checklist
definition source: https://www.fp7-risksur.eu/terminology/glossary
comment: Describe how units have been planned to be sampled Sampling at the primary sampling unit (PSU) level Describe the information used to calculate sample size at the PSU level, e.g. the number of PSU in the population (see section 6 also), (between−herd) design prevalence, desired confidence, desired power, sensitivity, specificity. If recommended parameters from international standards are used, indicate the source of such standards (e.g. OIE) Sampling at the secondary sampling unit (SSU) level Describe the information used to calculate sample size at the SSU level, e.g. the number of SSU in the population (see section 6 also), (within−herd) design prevalence, desired confidence, desired power, sensitivity, specificity.

sampling unit
type: Class
subclass of: directive information entity
definition: A sampling unit is one of the units into which an aggregate is divided for the purpose of sampling, each unit being regarded as individual and indivisible when the selection is made.
definition source: https://stats.oecd.org/glossary/index.htm

assay datum
type: Class
subclass of: information content entity
definition: Information about an assay which can be used to find of qualify/classify assays.

diagnostic test type
type: Class
subclass of: assay datum
example of usage: Known diagnostic tests can be classified into groups here so that information such as whether they are an antibody detection or pathogen identification information can be associated to the test, even if this information is not detailed in the data source. As an example, diagnostic tests classifications contained in existing terminologies (such as EFSA SSD2, https://www.efsa.europa.eu/en/efsajournal/pub/3424) can be used to create specific test catehories here.
definition: A test category used to group diagnostic tests based on generla characteristics, such as the target for detection (antigen or antibody).
comment: Categorization of diagnostic tests used in health surveillance. This information can be assigned to a test, or inferred from test characteristics if enough information is given about it.

specimen from organism type
type: Class
subclass of: specimen datum
example of usage: fecal swab versus a fecal specimen will both have anatomical entity feces, but one will be a swab specimen and the other will be a excreta specimen.
definition: A specimen datum used, in conjunction with information about the target sampled anatomical location, in order to specify _how_ the anatomical entity was sampled

whole organism specimen
type: Class
subclass of: specimen from organism type

fluid specimen
type: Class
subclass of: specimen from organism type

organ/tissue specimen
type: Class
subclass of: specimen from organism type

excreta specimen
type: Class
subclass of: specimen from organism type

swab specimen
type: Class
subclass of: specimen from organism type

specimen by origin
type: Class
subclass of: specimen
definition: s specimen categorization which described the type of entity from which the specimen was collected
comment: inferred categorization of specimens based on the matrix type informaiton provided regarding their source

animal specimen
type: Class
subclass of: specimen by origin

food specimen
type: Class
subclass of: specimen by origin

environmental specimen
type: Class
subclass of: specimen by origin

surveillance protocol
type: Class
subclass of: plan specification
definition: A collection of all directive information associated with a surveillance activity, such as the surveillance objectives, the action specifications and legislative specification. Everything about a surveillance activity that is related to its planning and methodology.
comment: A surveillance activity is then a specific execution of a surveillance protocol, which generates specific results. A surveillance protocol exists efore a surveillance activity is carried out, and can exist even in the absence of a surveillance activity - for instance there cna be a surveillance protocol for outbreak investigations, but the exucition of a surveillance activity and associated results will only be available if an outbreak is detected.

legislative specification
type: Class
subclass of: directive information entity
definition: A directive information that details the legislative body that supports a specific surveillance activity, or the specific obligations prescried in these legislation.
elucidation: All the laws or regulations of a country or region which are related to the obligations or permissions associated with a specific surveillance activity.

surveillance objective
type: Class
subclass of: objective specification
definition: A directive information that described those goal(s) that when met will result in the collection and analysis of data in order to achieve the purpose of the system
definition source: OIE (2014a). Guide to terrestrial animal health surveillance. Paris, France, OIE.
definition source: https://www.fp7-risksur.eu/terminology/glossary

surveillance purpose
type: Class
subclass of: objective specification
definition: A directive information that describes why surveillance is necessary and what it will accomplish.
definition source: https://github.com/SVA-SE/AHSURED/wiki/
definition source: https://www.fp7-risksur.eu/terminology/glossary

case detection
type: Class
subclass of: surveillance objective
definition: A surveillance objective to search for any animals affected, clinically or not, by the hazard under surveillance.
definition source: https://github.com/SVA-SE/AHSURED/wiki
comment: This objective is appropriate if the hazard is present, regardless of whether the hazard occurrence is endemic, epidemic or sporadic, and action will be taken to control disease whenever it is detected.

demonstration of disease freedom
type: Class
subclass of: surveillance objective
definition: A surveillance objective to gather evidence that can demonstrate, with a given confidence level, that a specific hazard is not present in a given population.
definition source: https://github.com/SVA-SE/AHSURED/wiki
comment: This objective is appropriate if the target hazard is thought to be absent in the territory to be covered and the aim is to demonstrate disease freedom for trade or non−trade purposes (e.g. improve public health, to decide when to stop an eradication programme and to eliminate production losses and control costs due to endemic disease). This may apply to diseases which a) have been historically absent, b) have been eradicated and official freedom has been confirmed or c) are thought to be eradicated, but official freedom has not yet been confirmed.

early detection
type: Class
subclass of: surveillance objective
definition: A surveillance objective to detect any hazard cases as soon as possible.
definition source: https://github.com/SVA-SE/AHSURED/wiki
comment: This objective is appropriate for a situation where the disease is currently absent in the country or region. It may be applied to surveillance for an unknown disease or a known disease considered to pose a non−negligible risk of incursion or emergence. It may also apply to the early stages of an outbreak.

prevalence estimation
type: Class
subclass of: surveillance objective
definition: A surveillance objective focusedon gathering data to estimate the true or apparent prevalence of a hazard in a given population.
definition source: https://github.com/SVA-SE/AHSURED/wiki
comment: This objective is appropriate if the target hazard is (thought to be) present in the territory to be covered, and an assessment of the prevalence and or changes in prevalence over time is needed.

verify health intervention success purpose
type: Class
subclass of: surveillance purpose
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: verify success

maintaining hazard freedom purpose
type: Class
subclass of: surveillance purpose
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: maintain freedom

detect hazard introduction purpose
type: Class
subclass of: surveillance purpose
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: detect introduction

outbreak control purpose
type: Class
subclass of: surveillance purpose
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: control outbreak

informing health intervention purpose
type: Class
subclass of: surveillance purpose
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: inform intervention

detect changes in hazard occurrence purpose
type: Class
subclass of: surveillance purpose
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: detect changes

hazard control purpose
type: Class
subclass of: surveillance purpose
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: control

hazard erradication purpose
type: Class
subclass of: surveillance purpose
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: eradicate

sampling design protocol
type: Class
subclass of: surveillance methods specification
example of usage: This includes for instance the calculated sample size (which can include primary and secondary sampling units in case of clustered units), the frequency of sampling, etc.
definition: A sampling scheme design to meet a specific surveillance objective and/or purpose of a surveillance activity.

reporting protocol
type: Class
subclass of: surveillance methods specification
definition: A reporting protocol, generally used within a surveillance activity, detailing what are the reporting obligations associated with a specific surveillance target in a specific area, the reporting chain (who is obliged to report and how is the information flow from reporting), and any eventual incentives for reporting.

specimen collection protocol
type: Class
subclass of: surveillance methods specification
definition: A protocol detailing how specimens will be collected as part of the data gathering phase of a surveillance activity.
alternative term: sample collection protocol
comment: This does not include the definition of how many samples will collected, but specifically how they will be collected - where, by whom, etc.

diagnostic protocol
type: Class
subclass of: surveillance methods specification
definition: A protocol that describes which diagnostic test or tests will be used to identify animals (or another epidemiological unit) infected with a specific pathogen, possibly in more than one round of screening.
definition: A protocol to be used within a surveillance activity to classify epidemiological units according to a specific outcome.

surveillance methods specification
type: Class
subclass of: action specification
definition: An action specification for specific actions to be taken as part of a health surveillance activity.

Continuous data collection
type: Class
subclass of: surveillance context
definition: A surveillance context in which sampling in done continuously, triggered by the existing of cases of interest, for instance reporting of confirmed cases or collection of samples from every slaughter batch.
definition source: https://github.com/SVA-SE/AHSURED/wiki

Sentinel surveillance
type: Class
subclass of: surveillance context
definition: A surveillance context in which data are repeated collected from the same selected sites or groups of animals to identify changes in the health status of a specified population over time.
definition source: https://github.com/SVA-SE/AHSURED/wiki
definition source: https://www.fp7-risksur.eu/terminology/glossary
comment: Surveillance sentinels should act as a proxy for the larger population of interest; they may be selected on the basis of risk but can also be selected randomly or on the basis of convenience or compliance.

Participatory surveillance
type: Class
subclass of: surveillance context
definition: A surveillance context which explores traditional information networks by using participatory rural appraisal methods.
definition source: https://github.com/SVA-SE/AHSURED/wiki
definition source: https://www.fp7-risksur.eu/terminology/glossary
comment: Participatory surveillance explores traditional information networks by using participatory rural appraisal methods such as ranking, scoring and visualisation techniques to conduct risk-based, hazard-specific surveillance. The approach uses semi-structured interviews with key informants. This enables communities to provide their knowledge regarding health events, risks, impacts and control opportunities by gathering qualitative health data from defined populations. The analysis of participatory data emphasises the comparison of information obtained from multiple informants; the method uses a variety of techniques to obtain the most likely interpretation of events. The objective is to enhance sensitivity by identifying cases based on a clinical case definition; these may then be evaluated and confirmed using either rapid tests in the field or laboratory diagnostics. Conventional epidemiological investigation techniques can be used to evaluate and confirm outbreaks detected by participatory surveillance as part of trace-back and trace-forwards activities.

Indicator−based surveillance
type: Class
subclass of: surveillance context
definition: A surveillance context in which data are generated through the identification of cases based on agreed-upon definitions.
definition source: https://github.com/SVA-SE/AHSURED/wiki
definition source: https://www.fp7-risksur.eu/terminology/glossary
comment: Traditional disease surveillance which relies on the collection of data about the occurrence of pre-defined diseases or conditions and which uses agreed-upon case definitions; these data are analysed to produce indicators that point towards the existence of a threat. Indicator-based surveillance may be hazard-specific or general and includes the use of clinical or other data for syndromic surveillance

Syndromic surveillance
type: Class
subclass of: surveillance context
definition: A surveillance context in which health-related information (clinical signs or other data) that might precede or substitute for formal diagnosis are used as indicators of spatio-temporal trends in hazard occurrence.
definition source: https://github.com/SVA-SE/AHSURED/wiki
definition source: https://www.fp7-risksur.eu/terminology/glossary#group-S
comment: Information collected through syndromic surveillance may be used to indicate a sufficient probability of a change in the health of the population to deserve further investigation or to enable a timely assessment of the impact of health threats which may require action. This type of surveillance is not usually focused on a particular hazard so can be used to detect a variety of diseases or pathogens including new (emerging) diseases. This type of surveillance is particularly applicable for early warning surveillance.

census sampling
type: Class
subclass of: sampling strategy
definition source: https://github.com/SVA-SE/AHSURED/wiki

convenience sampling
type: Class
subclass of: sampling strategy
definition source: https://github.com/SVA-SE/AHSURED/wiki

simple random sampling
type: Class
subclass of: objective sampling
definition: A sampling strategy in which population units are selected such that each possible unit has a fixed and known or equal probability of selection.
definition source: "Random Sample" (p.238) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated.
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: simple random

systematic random sampling
type: Class
subclass of: objective sampling
definition source: https://github.com/SVA-SE/AHSURED/wiki
preferred label: systematic random

risk-based sampling
type: Class
subclass of: targeted sampling
definition source: https://github.com/SVA-SE/AHSURED/wiki

purposeful sampling
type: Class
subclass of: sampling strategy
definition source: https://github.com/SVA-SE/AHSURED/wiki

objective sampling
type: Class
subclass of: sampling strategy
definition source: https://github.com/SVA-SE/AHSURED/wiki

outbreak investigation
type: Class
subclass of: surveillance context
definition: A surveillance context in which activities are specifically triggered by the detection of an outbreak

food-borne outbreak investigation
type: Class
subclass of: outbreak investigation
definition: a type of outbreak investigation that focus specifically on foodborne agents/vehicles

FBO investigation
type: Class
equivalent class: Class
  intersection of: Surveillance Activity
  intersection of: Restriction
    on property: has surveillance context
    some values from: food-borne outbreak investigation
subclass of: Cluster/Outbreak investigation
definition: a surveillance activity with the specific surveillance context of investigating a foodborne outbreak

Cluster/Outbreak investigation
type: Class
equivalent class: Class
  intersection of: Surveillance Activity
  intersection of: Restriction
    on property: has surveillance context
    some values from: outbreak investigation
subclass of: Surveillance Activity
definition: A sampling strategy in which population units are chosen for investigation into a disease cluster or outbreak.
definition: a specific type of surveillance activity which has as surveillance context an outbreak investigation

outbreak investigation datum
type: Class
subclass of: information content entity
definition: A directive information that described specific detailsgathered during an outbreak investigation.

Food vehicle of outbreak
type: Class
subclass of: outbreak investigation datum
preferred label: Food vehicle

Nature of evidence in an outbreak
type: Class
subclass of: outbreak investigation datum
preferred label: Nature of evidence

Outbreak contributory factors
type: Class
subclass of: outbreak investigation datum
preferred label: Contributory factors

Extent of outbreak
type: Class
subclass of: outbreak investigation datum

reporting obligations
type: Class
subclass of: legislative specification
definition: A directive information that described the manadatory actions that follow on specific agents upon suspicion or confirmation of specific hazards under surveillance.

notifiable upon diagnosis
type: Class
subclass of: reporting obligations
definition: A directive information used to identify diseases which, by law, must be reported to public health authorities upon diagnosis.

notifiable upon suspicion
type: Class
subclass of: reporting obligations
definition: A directive information used to identify diseases which, by law, must be reported to public health authorities upon suspicion

status of hazard presence in a geographical region
type: Class
subclass of: quality
definition: a quality that specifies the known status of a hazard occurrence in a given geograhial region.

historically absent
type: Class
subclass of: status of hazard presence in a geographical region

absent (eradicated)
type: Class
subclass of: status of hazard presence in a geographical region

sporadic travel-related cases
type: Class
subclass of: status of hazard presence in a geographical region
definition: Single cases without a specific temporal pattern, but also without geographical pattern or other associations and where import to location is related to travel.

endemic
type: Class
subclass of: status of hazard presence in a geographical region
definition: The state of a disease, infection or other condition being maintained in a population without the need of external outputs. The population involved and their geographical location should be specified when defining an endemic state. Present in a community or common among a group of people; said of a disease prevailing continually in a region

unknown status
type: Class
subclass of: status of hazard presence in a geographical region

stratified random sampling
type: Class
subclass of: objective sampling

targeted sampling
type: Class
subclass of: sampling strategy
definition: A surveillance sampling strategy in which an aspired outcome is explicity stated.
definition source: "Target" (p.279) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated.

Baseline surveillance
type: Class
subclass of: Surveillance Activity
definition: A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling.

Targeted surveillance
type: Class
subclass of: Surveillance Activity
definition: A surveillance sampling strategy in which an aspired outcome is explicity stated.

Screening for Variants of Concern (VoC)
type: Class
subclass of: Targeted surveillance
definition: A targeted surveillance strategy in which the aim is early detection of variants of concern (VoC) in individuals.

Longitudinal surveillance
type: Class
subclass of: Targeted surveillance
definition: A priority surveillance strategy in which subsets of a defined population can be identified who are, have been, or in the future may be exposed or not exposed - or exposed in different degrees - to a disease of interest and are selected to under go repeat sampling over a defined period of time.

Re-infection surveillance
type: Class
subclass of: Targeted surveillance
definition: A priority surveillance strategy in which a population that previously tested positive for a disease of interest, and since confirmed to have recovered via a negative test, are monitored for positive test indication of re-infection with the disease of interest within a defined period of time.

Vaccine escape surveillance
type: Class
subclass of: Targeted surveillance
definition: A priority surveillance strategy in which population units are monitored for investigation into vaccine escape, i.e., identifying variants that contain mutations that counteracted the immunity provided by vaccine(s) of interest.

Travel-associated surveillance
type: Class
subclass of: Targeted surveillance
definition: A priority surveillance strategy in which population units are selected if they have a travel history outside of the reporting region within a specified number of days before onset of symptoms.

Domestic travel surveillance
type: Class
subclass of: Travel-associated surveillance
definition: A travel-associated surveillance strategy in which population units are selected if they have an intranational travel history within a specified number of days before onset of symptoms.

Interstate/ interprovincial travel surveillance
type: Class
subclass of: Domestic travel surveillance
definition: A domestic travel-associated surveillance strategy in which population units are selected if they have a travel history between states or provinces within a specified number of days before onset of symptoms.

Intra-state/ intra-provincial travel surveillance
type: Class
subclass of: Domestic travel surveillance
definition: A domestic travel-associated surveillance strategy in which population units are selected if they have a travel history in a state or province within a specified number of days before onset of symptoms.

International travel surveillance
type: Class
subclass of: Travel-associated surveillance
definition: A travel-associated surveillance strategy in which population units are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms.

Surveillance of international border crossing by air travel or ground transport
type: Class
subclass of: International travel surveillance
definition: An international travel-associated surveillance strategy in which population units are selected if they have a travel history of crossing an international border via air travel or ground transport.

Surveillance of international border crossing by air travel
type: Class
subclass of: Surveillance of international border crossing by air travel or ground transport
definition: An international travel-associated surveillance strategy in which population units are selected if they have a travel history of crossing an international border via air travel.

Surveillance of international border crossing by ground transport
type: Class
subclass of: Surveillance of international border crossing by air travel or ground transport
definition: An international travel-associated surveillance strategy in which population units are selected if they have a travel history of crossing an international border via ground transport.

Surveillance from international worker testing
type: Class
subclass of: International travel surveillance
definition: A travel-associated surveillance strategy in which population units are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms.

Multi-jurisdictional outbreak investigation
type: Class
subclass of: Cluster/Outbreak investigation
definition: An outbreak investigation sampling strategy in which population units are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions.

Intra-jurisdictional outbreak investigation
type: Class
subclass of: Cluster/Outbreak investigation
definition: An outbreak investigation sampling strategy in which population units are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction.

genetic epidemiology surveillance datum
type: Class
subclass of: awaiting ontology review/placement

objective specification
type: Class
subclass of: directive information entity
editor preferred term: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
IAO_0000114: IAO_0000122
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: obi.owl

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
IAO_0000114: IAO_0000122
definition: a directive information entity that describes an action the bearer will take
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
imported from: obi.owl

data item
type: Class
subclass of: information content entity
editor preferred term: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
IAO_0000114: IAO_0000125
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data
imported from: obi.owl

information content entity
type: Class
subclass of: generically dependent continuant
editor preferred term: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
IAO_0000114: IAO_0000122
definition: A generically dependent continuant that is about some thing.
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: obi.owl

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: IAO_0000039
  min cardinality: 1
subclass of: Restriction
  on property: IAO_0000004
  min cardinality: 1
example of usage: 10 feet. 3 ml.
IAO_0000114: IAO_0000120
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
IAO_0000114: IAO_0000122
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
imported from: obi.owl

data set
type: Class
subclass of: data item
editor preferred term: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
IAO_0000114: IAO_0000125
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
editor note: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor preferred term: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
IAO_0000114: IAO_0000122
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: obi.owl
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

measurement datum
type: Class
subclass of: data item
editor preferred term: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
IAO_0000114: IAO_0000125
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
term editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI

document
type: Class
subclass of: information content entity
editor preferred term: document
example of usage: A journal article, patent application, laboratory notebook, or a book
IAO_0000114: IAO_0000120
definition: A collection of information content entities intended to be understood together as a whole
term editor: PERSON: Lawrence Hunter

time measurement datum
type: Class
subclass of: scalar measurement datum
IAO_0000114: IAO_0000123
definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: document
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
IAO_0000114: IAO_0000125
definition: A planned process in which a document is created or added to by including the specified input in it.
editor note: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
term editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: IAO_0000581
    some values from: time measurement datum
  intersection of: Restriction
    on property: IAO_0000583
    some values from: measurement datum
IAO_0000114: IAO_0000123

Campylobacter volucris
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:580032
has_alternative_id: NCBITaxon:580034
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19767353
has_obo_namespace: ncbi_taxonomy

Campylobacter sputorum biovar faecalis
type: Class
subclass of: Campylobacter sputorum
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
has exact synonym: Campylobacter sputorum bv. faecalis
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Campylobacter sputorum biovar fecalis
has_related_synonym: Campylobacter sputorum bv. fecalis

Escherichia coli O157
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O157
imported from: ncbitaxon.owl

Escherichia coli O111
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O111
imported from: ncbitaxon.owl

Escherichia coli O103
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O103
imported from: ncbitaxon.owl

Escherichia coli O113:H21
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O113:H21
imported from: ncbitaxon.owl

Escherichia coli O45:H2
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O45:H2
imported from: ncbitaxon.owl

Salmonella enterica subsp. enterica serovar Newport
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred term: Salmonella enterica subsp. enterica serovar Newport
imported from: ncbitaxon.owl

Escherichia coli O18
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O18
imported from: ncbitaxon.owl

Campylobacter faecalis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: 'Campylobacter faecalis'

Proteobacteria
type: Class
subclass of: Bacteria
editor preferred term: Proteobacteria
alternative term: purple bacteria
alternative term: purple bacteria and relatives
alternative term: purple non-sulfur bacteria
alternative term: purple photosynthetic bacteria
alternative term: purple photosynthetic bacteria and relatives
imported from: ncbitaxon.owl

Escherichia coli O103:H11
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O103:H11
imported from: ncbitaxon.owl

Campylobacter iguaniorum
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:1244530
has_alternative_id: NCBITaxon:1442825
has_alternative_id: NCBITaxon:1442826
has_alternative_id: NCBITaxon:1442827
database_cross_reference: GC_ID:11
database_cross_reference: PMID:25574036
has_obo_namespace: ncbi_taxonomy

Escherichia coli 151_06
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli 151_06
imported from: ncbitaxon.owl

Campylobacter jejuni X
type: Class
subclass of: Campylobacter jejuni
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Boreoeutheria
type: Class
subclass of: Amniota
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11743200
database_cross_reference: PMID:11791233
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Boreotheria

Campylobacter corcagiensis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:1448858
has_alternative_id: NCBITaxon:1448859
database_cross_reference: GC_ID:11
database_cross_reference: PMID:24744327
database_cross_reference: PMID:24876239
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Campylobacter sp. CIT045
has_related_synonym: Campylobacter sp. CIT056
has_related_synonym: Campylobacter sp. CIT058

Salmonella enterica subsp. enterica serovar Hadar
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred term: Salmonella enterica subsp. enterica serovar Hadar
imported from: ncbitaxon.owl

Salmonella enterica subsp. enterica serovar Enteritidis
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred term: Salmonella enterica subsp. enterica serovar Enteritidis
imported from: ncbitaxon.owl

Campylobacter fetus subsp. testudinum
type: Class
subclass of: Campylobacter fetus
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
database_cross_reference: PMID:24336365
database_cross_reference: PMID:24899653
has_obo_namespace: ncbi_taxonomy

Campylobacter pinnipediorum subsp. pinnipediorum
type: Class
subclass of: Campylobacter pinnipediorum
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
has_alternative_id: NCBITaxon:1660068
has_alternative_id: NCBITaxon:1660069
has_alternative_id: NCBITaxon:1886620
has_alternative_id: NCBITaxon:1886621
has_alternative_id: NCBITaxon:1886668
has_alternative_id: NCBITaxon:1886669
has_alternative_id: NCBITaxon:1886671
database_cross_reference: GC_ID:11
database_cross_reference: PMID:28629508
has_obo_namespace: ncbi_taxonomy

Campylobacter geochelonis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:1780361
has_alternative_id: NCBITaxon:1780363
database_cross_reference: GC_ID:11
database_cross_reference: PMID:27266587
has_obo_namespace: ncbi_taxonomy

Campylobacter hepaticus
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:27498969
has_obo_namespace: ncbi_taxonomy

Campylobacter ornithocola
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:28126040
has_obo_namespace: ncbi_taxonomy

Campylobacter pinnipediorum subsp. caledonicus
type: Class
subclass of: Campylobacter pinnipediorum
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
has_alternative_id: NCBITaxon:1660070
has_alternative_id: NCBITaxon:1660071
database_cross_reference: GC_ID:11
database_cross_reference: PMID:28629508
has_obo_namespace: ncbi_taxonomy

Salmonella enterica subsp. enterica serovar Stanley
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred term: Salmonella enterica subsp. enterica serovar Stanley
imported from: ncbitaxon.owl

Campylobacter
type: Class
subclass of: material entity
editor preferred term: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11542086
database_cross_reference: PMID:12361288
database_cross_reference: PMID:16627635
database_cross_reference: PMID:1704793
database_cross_reference: PMID:19801389
database_cross_reference: PMID:29034857
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Ampylobacter

Campylobacter coli
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:2172530
has_alternative_id: NCBITaxon:2340791
has_alternative_id: NCBITaxon:28078
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
database_cross_reference: PMID:11411703
database_cross_reference: PMID:7857809
database_cross_reference: PMID:8590689
database_cross_reference: PMID:9336905
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Campylobacter hyoilei
has_related_synonym: Vibrio coli

Campylobacter fetus
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
database_cross_reference: PMID:1354478
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Spirillum fetus
has_related_synonym: Vibrio fetus

Campylobacter pinnipediorum
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:28629508
has_obo_namespace: ncbi_taxonomy

Campylobacter jejuni
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:2172531
has_alternative_id: NCBITaxon:2182326
has_alternative_id: NCBITaxon:2201165
has_alternative_id: NCBITaxon:2211407
has_alternative_id: NCBITaxon:2211408
has_alternative_id: NCBITaxon:2211409
has_alternative_id: NCBITaxon:2293848
has_alternative_id: NCBITaxon:2293849
has_alternative_id: NCBITaxon:2293850
has_alternative_id: NCBITaxon:2303571
has_alternative_id: NCBITaxon:2305452
has_alternative_id: NCBITaxon:2305453
has_alternative_id: NCBITaxon:2305454
has_alternative_id: NCBITaxon:2305455
has_alternative_id: NCBITaxon:2305456
has_alternative_id: NCBITaxon:2305457
has_alternative_id: NCBITaxon:2305458
has_alternative_id: NCBITaxon:2305459
has_alternative_id: NCBITaxon:2340789
has_alternative_id: NCBITaxon:2478524
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Ampylobacter jejuni
has_related_synonym: Campylobacter fetus subsp. jejuni
has_related_synonym: Vibrio hepaticus
has_related_synonym: Vibrio jejuni

Campylobacter hyointestinalis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425776
database_cross_reference: PMID:3998100
database_cross_reference: PMID:7547297
has_obo_namespace: ncbi_taxonomy

Campylobacter concisus
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:28729281
has_obo_namespace: ncbi_taxonomy

Bacteria
type: Class
subclass of: organism
editor preferred term: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl

Campylobacter curvus
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:1704793
database_cross_reference: PMID:1854636
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Wolinella curva

Campylobacter lari
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19406805
database_cross_reference: PMID:2223613
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Campylobacter laridis

Campylobacter mucosalis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
database_cross_reference: PMID:4614347
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Campylobacter sputorum mucosalis
has_related_synonym: Campylobacter sputorum subsp. mucosalis

Campylobacter rectus
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:1704793
database_cross_reference: PMID:1854636
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Wolinella recta

Campylobacter showae
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:7694633
has_obo_namespace: ncbi_taxonomy

Campylobacter blaseri
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:2044588
database_cross_reference: GC_ID:11
database_cross_reference: PMID:29624164
has_obo_namespace: ncbi_taxonomy

Campylobacter sp.
type: Class
subclass of: unclassified Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Campylobacter sputorum
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
database_cross_reference: PMID:9542089
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Vibrio sputorum

Campylobacter jejuni-like bacterium
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Escherichia coli O128:H2
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O128:H2
imported from: ncbitaxon.owl

Escherichia coli O26:H11
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O26:H11
imported from: ncbitaxon.owl

unclassified Campylobacter
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Campylobacter insulaenigrae
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:15545485
has_obo_namespace: ncbi_taxonomy

Eukaryota
type: Class
subclass of: organism
imported from: ncbitaxon.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
has exact synonym: eucaryotes
has exact synonym: eukaryotes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
has_related_synonym: Eukaryotae
has_related_synonym: eukaryotes

Campylobacter mucosalis-like bacterium
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Campylobacter mucosalis-like sp.

Campylobacter upsaliensis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: CNW group
has_related_synonym: catalase-negative or weak group of campylobacteria

Campylobacter helveticus
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:1479353
has_obo_namespace: ncbi_taxonomy

Salmonella enterica
type: Class
subclass of: Salmonella
editor preferred term: Salmonella enterica
imported from: ncbitaxon.owl

Campylobacter lawrenceae
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has exact synonym: Campylobacter lawrenci
has_obo_namespace: ncbi_taxonomy
has_related_synonym: 'Campylobacter lawrenceae '

Campylobacter fetus subsp. fetus
type: Class
subclass of: Campylobacter fetus
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
database_cross_reference: PMID:12508904
has exact synonym: Campylobacter fetus fetus
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Vibrio fetus subsp. intestinalis

Campylobacter fetus subsp. venerealis
type: Class
subclass of: Campylobacter fetus
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
has exact synonym: Campylobacter fetus subsp. venereus
has exact synonym: Campylobacter fetus venerealis
has exact synonym: Vibrio foetus venerealis
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Vibrio fetus subsp. venerealis

Campylobacter jejuni subsp. doylei
type: Class
subclass of: Campylobacter jejuni
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
has exact synonym: Campylobacter jejuni doylei
has_obo_namespace: ncbi_taxonomy

Campylobacter jejuni subsp. jejuni
type: Class
subclass of: Campylobacter jejuni
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
has exact synonym: Campylobacter jejuni jejuni
has_obo_namespace: ncbi_taxonomy

Campylobacter sputorum subsp. bubulus
type: Class
subclass of: Campylobacter sputorum
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
has exact synonym: Campylobacter sputorum bubulus
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Campylobacter bubulus
has_related_synonym: Vibrio bubulus

Campylobacter sputorum biovar sputorum
type: Class
subclass of: Campylobacter sputorum
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321120
database_cross_reference: PMID:9542089
has exact synonym: Campylobacter sputorum bv. sputorum
has exact synonym: Campylobacter sputorum sputorum
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Campylobacter sputorum subsp. sputorum

Amniota
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has exact synonym: amniotes
has_obo_namespace: ncbi_taxonomy

Salmonella enterica subsp. enterica serovar Javiana
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred term: Salmonella enterica subsp. enterica serovar Javiana
imported from: ncbitaxon.owl

Campylobacter cuniculorum
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:525139
has_alternative_id: NCBITaxon:525140
has_alternative_id: NCBITaxon:525141
has_alternative_id: NCBITaxon:525142
has_alternative_id: NCBITaxon:525143
has_alternative_id: NCBITaxon:525144
has_alternative_id: NCBITaxon:525145
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19542108
has_obo_namespace: ncbi_taxonomy

Escherichia coli O103:H2
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O103:H2
imported from: ncbitaxon.owl

Escherichia coli O142:H6
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O142:H6
imported from: ncbitaxon.owl

Escherichia coli O26:NM
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O26:NM
imported from: ncbitaxon.owl

Escherichia coli O26
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O26
imported from: ncbitaxon.owl

Campylobacter canadensis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:2703845
database_cross_reference: GC_ID:11
database_cross_reference: PMID:17978232
has_obo_namespace: ncbi_taxonomy

Salmonella enterica subsp. enterica serovar Virchow
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred term: Salmonella enterica subsp. enterica serovar Virchow
imported from: ncbitaxon.owl

Campylobacter lari subsp. concheus
type: Class
subclass of: Campylobacter lari
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19406805
has_obo_namespace: ncbi_taxonomy

Campylobacter peloridis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19406805
has_obo_namespace: ncbi_taxonomy

Campylobacter subantarcticus
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19661523
has_obo_namespace: ncbi_taxonomy

Campylobacter avium
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:522483
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19620353
has_obo_namespace: ncbi_taxonomy

Enterobacteriaceae
type: Class
subclass of: Proteobacteria
editor preferred term: Enterobacteriaceae
imported from: ncbitaxon.owl

Salmonella bongori
type: Class
subclass of: Salmonella
editor preferred term: Salmonella bongori
imported from: ncbitaxon.owl

Escherichia coli
type: Class
subclass of: Enterobacteriaceae
editor preferred term: Escherichia coli
alternative term: E. coli
alternative term: Escherichia/Shigella coli
imported from: ncbitaxon.owl

Salmonella
type: Class
subclass of: Enterobacteriaceae
editor preferred term: Salmonella
imported from: ncbitaxon.owl

Salmonella enterica subsp. enterica
type: Class
subclass of: Salmonella enterica
editor preferred term: Salmonella enterica subsp. enterica
imported from: ncbitaxon.owl

Campylobacter sputorum biovar paraureolyticus
type: Class
subclass of: Campylobacter sputorum
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
has exact synonym: Campylobacter sputorum bv. paraureolyticus
has_obo_namespace: ncbi_taxonomy

Salmonella enterica subsp. enterica serovar Infantis
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred term: Salmonella enterica subsp. enterica serovar Infantis
imported from: ncbitaxon.owl

Salmonella enterica subsp. enterica serovar Heidelberg
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred term: Salmonella enterica subsp. enterica serovar Heidelberg
imported from: ncbitaxon.owl

Campylobacter lari subsp. lari
type: Class
subclass of: Campylobacter lari
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19406805
has_obo_namespace: ncbi_taxonomy

Campylobacter troglodytis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:535089
has_alternative_id: NCBITaxon:654364
has_alternative_id: NCBITaxon:654365
database_cross_reference: GC_ID:11
database_cross_reference: PMID:21278267
has_obo_namespace: ncbi_taxonomy

Campylobacter lanienae
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10758898
has_obo_namespace: ncbi_taxonomy

Campylobacter hominis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321111
database_cross_reference: PMID:7857801
database_cross_reference: PMID:8123559
database_cross_reference: PMID:9720027
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Candidatus Campylobacter hominis

Campylobacter gracilis
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:1854636
database_cross_reference: PMID:26383656
database_cross_reference: PMID:7857794
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacteroides gracilis

Campylobacter ureolyticus
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:1854636
database_cross_reference: PMID:19801389
database_cross_reference: PMID:7857794
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacteroides corrodens
has_related_synonym: Bacteroides ureolyticus

Gallus gallus
type: Class
subclass of: Amniota
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has exact synonym: bantam
has exact synonym: chicken
has exact synonym: chickens
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Gallus domesticus
has_related_synonym: Gallus gallus domesticus

Salmonella enterica subsp. enterica serovar Typhimurium
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred term: Salmonella enterica subsp. enterica serovar Typhimurium
imported from: ncbitaxon.owl

Campylobacter hyointestinalis subsp. hyointestinalis
type: Class
subclass of: Campylobacter hyointestinalis
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425776
database_cross_reference: PMID:7547297
has_obo_namespace: ncbi_taxonomy

Campylobacter hyointestinalis subsp. lawsonii
type: Class
subclass of: Campylobacter hyointestinalis
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425776
database_cross_reference: PMID:7547297
has_obo_namespace: ncbi_taxonomy

Cetartiodactyla
type: Class
subclass of: Boreoeutheria
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has exact synonym: whales, hippos, ruminants, pigs, camels etc.
has_obo_namespace: ncbi_taxonomy
has_related_synonym: even-toed ungulates

Homo sapiens
type: Class
subclass of: Boreoeutheria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has exact synonym: human
has exact synonym: man
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Home sapiens
has_related_synonym: Homo sampiens
has_related_synonym: Homo sapeins
has_related_synonym: Homo sapian
has_related_synonym: Homo sapians
has_related_synonym: Homo sapien
has_related_synonym: Homo sapience
has_related_synonym: Homo sapiense
has_related_synonym: Homo sapients
has_related_synonym: Homo sapines
has_related_synonym: Homo spaiens
has_related_synonym: Homo spiens
has_related_synonym: Humo sapiens

Sus scrofa
type: Class
subclass of: Cetartiodactyla
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has exact synonym: pig
has exact synonym: pigs
has exact synonym: swine
has exact synonym: wild boar
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Sus scrofus

Campylobacter cf. lanienae UB 992
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Campylobacter cf. lanienae UB 994
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Bos taurus
type: Class
subclass of: Cetartiodactyla
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:272461
database_cross_reference: GC_ID:1
has exact synonym: bovine
has exact synonym: cattle
has exact synonym: cow
has exact synonym: dairy cow
has exact synonym: domestic cattle
has exact synonym: domestic cow
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bos Tauurus
has_related_synonym: Bos bovis
has_related_synonym: Bos primigenius taurus

Escherichia coli O103:H25
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O103:H25
imported from: ncbitaxon.owl

Escherichia coli O121:H19
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O121:H19
imported from: ncbitaxon.owl

Escherichia coli O145:NM
type: Class
subclass of: Escherichia coli
editor preferred term: Escherichia coli O145:NM
imported from: ncbitaxon.owl

Country
type: Class
subclass of: geopolitical region
definition: A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states.
imported from: ncit.owl
has exact synonym: COUNTRY
has exact synonym: Country

Province
type: Class
subclass of: first-order administrative region
disjoint with: State
disjoint with: Territory
GENEPIO_0001763: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
IAO_0000114: IAO_0000428
definition: A region, district or division of a country; a tract; a portion a state, especially one remote from the capital.
imported from: ncit.owl
has exact synonym: Province

Municipality
type: Class
subclass of: populated place
subclass of: geopolitical region
GENEPIO_0001763: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
definition: A political unit, such as a city, town, or village, incorporated for local self-government.
imported from: ncit.owl
has exact synonym: Municipality

State
type: Class
subclass of: first-order administrative region
disjoint with: Territory
GENEPIO_0001763: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
IAO_0000114: IAO_0000428
definition: A constituent administrative district of a nation.
imported from: ncit.owl
has exact synonym: State
has exact synonym: Territory

Territory
type: Class
subclass of: first-order administrative region
GENEPIO_0001763: lookup:http://purl.obolibrary.org/obo/GAZ_00000448
IAO_0000114: IAO_0000428
definition: A geographical area under the jurisdiction of a sovereign state and marked off for administrative or other purposes.
imported from: ncit.owl
has exact synonym: Territory

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred term: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
IAO_0000114: IAO_0000122
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: obi.owl

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has_specified_output
      some values from: study design
editor preferred term: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
IAO_0000114: IAO_0000122
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
term editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl
OBI_0001847: study

assay
type: Class
subclass of: planned process
disjoint with: planning
editor preferred term: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
IAO_0000114: IAO_0000122
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
term editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: obi.owl
OBI_0001847: study assay
OBI_9991118: any method

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred term: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
IAO_0000114: IAO_0000122
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
term editor: GROUP: Role Branch
definition source: OBI

organization
type: Class
subclass of: material entity
editor preferred term: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
IAO_0000114: IAO_0000122
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI

plan
type: Class
subclass of: realizable entity
editor preferred term: plan
example of usage: The plan of researcher X to perform an experiment according to a protocol.
IAO_0000114: IAO_0000125
definition: A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
editor note: This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
term editor: AR, BP, JM, MC, PRS
definition source: branch derived

protocol
type: Class
subclass of: plan specification
editor preferred term: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
IAO_0000114: IAO_0000122
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
OBI_0001847: study protocol

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion based on data
editor preferred term: interpreting data
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
IAO_0000114: IAO_0000122
definition: A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters

planning
type: Class
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has participant
    some values from: plan specification
editor preferred term: planning
example of usage: The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
IAO_0000114: IAO_0000122
definition: a process of creating or modifying a plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
term editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: study design
subclass of: planned process
editor preferred term: study design execution
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
IAO_0000114: IAO_0000122
definition: a planned process that carries out a study design
editor note: removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
definition source: branch derived
curator note: 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
imported from: obi.owl

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
editor preferred term: specimen collection process
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
IAO_0000114: IAO_0000122
definition: A planned process with the objective of collecting a specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
term editor: Bjoern Peters
alternative term: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop

specimen collection objective
type: Class
subclass of: objective specification
editor preferred term: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
IAO_0000114: IAO_0000122
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
term editor: Bjoern Peters
definition source: Bjoern Peters

hospital
type: Class
subclass of: organization
editor preferred term: hospital
example of usage: human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660]
IAO_0000114: IAO_0000120
definition: A medical organization at which sick or injured people are given clinical care
term editor: Person:Alan Ruttenberg
term editor: Person:Helen Parkinson
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
definition source: modified from the wording of the wordnet definition
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
example of usage: The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
IAO_0000114: IAO_0000122
definition: An information content entity that is inferred from data.
editor note: In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
term editor: Group:2013 Philly Workshop group
definition source: Group:2013 Philly Workshop group

surveillance process
type: Class
subclass of: Surveillance Activity
subclass of: investigation
editor preferred term: surveillance process
definition: An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity.
term editor: Chris Stoeckert
definition source: Shane Babcock, OBI
IAO_0000233: https://github.com/obi-ontology/obi/issues/1181
IAO_0000234: IDO, VEuPathDB

organism
type: Class
subclass of: material entity
editor preferred term: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
IAO_0000114: IAO_0000122
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: obi.owl

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
editor preferred term: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
IAO_0000114: IAO_0000122
definition: A material entity that has the specimen role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
term editor: PERSON: James Malone
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
editor preferred term: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
IAO_0000114: IAO_0000122
definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
term editor: PERSON: Chris Stoeckert
alternative term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

exocrine pancreas
type: Class
subclass of: serous gland
subclass of: endoderm-derived structure
subclass of: trunk region element
subclass of: Restriction
  on property: part of
  some values from: pancreas
subclass of: Restriction
  on property: contributes to morphology of
  some values from: pancreas
definition: The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO].
imported from: uberon.owl
UBPROP_0000001: The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]
UBPROP_0000001: The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]
UBPROP_0000003: In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
database_cross_reference: Exocrine component of pancreas
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0553695
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/248202004
database_cross_reference: AAO:0010407
database_cross_reference: BTO:0000434
database_cross_reference: CALOHA:TS-1241
database_cross_reference: EMAPA:35328
database_cross_reference: EV:0100093
database_cross_reference: FMA:16017
database_cross_reference: MA:0002415
database_cross_reference: NCIT:C32546
database_cross_reference: TAO:0001249
database_cross_reference: UMLS:C0553695
database_cross_reference: VHOG:0000048
database_cross_reference: XAO:0000137
database_cross_reference: ZFA:0001249
has exact synonym: exocrine pancreas
has exact synonym: pars exocrina pancreatis
has_obo_namespace: uberon
has_related_synonym: exocrine component of pancreas
has_related_synonym: exocrine part of pancreas
id: UBERON:0000017
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

sense organ
type: Class
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: sensory system
definition: An organ that is capable of transducing sensory stimulus to the nervous system.
imported from: uberon.owl
contributor: cmungall
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0935626
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/244485009
database_cross_reference: AEO:0000094
database_cross_reference: BSA:0000121
database_cross_reference: BTO:0000202
database_cross_reference: CALOHA:TS-2043
database_cross_reference: EHDAA2:0001824
database_cross_reference: EHDAA:500
database_cross_reference: EMAPA:35955
database_cross_reference: FBbt:00005155
database_cross_reference: GAID:63
database_cross_reference: HAO:0000930
database_cross_reference: MA:0000017
database_cross_reference: MESH:D012679
database_cross_reference: NCIT:C33224
database_cross_reference: UMLS:C0935626
database_cross_reference: VHOG:0001407
database_cross_reference: WBbt:0006929
has exact synonym: organ of sense organ system
has exact synonym: organ of sensory organ system
has exact synonym: organ of sensory system
has exact synonym: sense organ system organ
has exact synonym: sensory organ
has exact synonym: sensory organ system organ
has exact synonym: sensory system organ
has narrow synonym: sensillum
has_obo_namespace: uberon
has_related_synonym: Sinnesorgan
has_related_synonym: sensor
id: UBERON:0000020
in subset: uberon slim

lymph node
type: Class
subclass of: immune organ
subclass of: Restriction
  on property: part of
  some values from: lymphoid system
subclass of: Restriction
  on property: has part
  some values from: lymph
definition: Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
imported from: uberon.owl
UBPROP_0000003: Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]
database_cross_reference: Lymph node
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0024204
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181756000
database_cross_reference: BTO:0000784
database_cross_reference: CALOHA:TS-0579
database_cross_reference: EFO:0000872
database_cross_reference: EMAPA:35523
database_cross_reference: EV:0100050
database_cross_reference: FMA:5034
database_cross_reference: GAID:947
database_cross_reference: MA:0000139
database_cross_reference: MAT:0000442
database_cross_reference: MESH:D008198
database_cross_reference: NCIT:C12745
database_cross_reference: NCIT:C33027
database_cross_reference: OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA
database_cross_reference: TAO_RETIRED:0005318
database_cross_reference: UMLS:C0024204
database_cross_reference: VHOG:0001273
database_cross_reference: ZFA_RETIRED:0005318
database_cross_reference: galen:Lymphnode
has_obo_namespace: uberon
has_related_synonym: lymph gland
has_related_synonym: nodus lymphaticus
id: UBERON:0000029
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

large intestine
type: Class
subclass of: subdivision of digestive tract
subclass of: digestive system element
subclass of: Restriction
  on property: part of
  some values from: intestine
subclass of: Restriction
  on property: contributes to morphology of
  some values from: intestine
definition: A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
UBPROP_0000003: Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
database_cross_reference: Large intestine (anatomy)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0021851
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181254001
database_cross_reference: AAO:0010396
database_cross_reference: BTO:0000706
database_cross_reference: CALOHA:TS-1306
database_cross_reference: EFO:0000840
database_cross_reference: EMAPA:19252
database_cross_reference: EV:0100077
database_cross_reference: FMA:7201
database_cross_reference: GAID:306
database_cross_reference: MA:0000333
database_cross_reference: MESH:A03.492.411.495
database_cross_reference: MIAA:0000046
database_cross_reference: NCIT:C12379
database_cross_reference: OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0021851
database_cross_reference: VHOG:0000054
database_cross_reference: XAO:0000131
database_cross_reference: galen:LargeIntestine
has_obo_namespace: uberon
has_related_synonym: intestinum crassum
id: UBERON:0000059
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim

Axiom
annotated source: large intestine
annotated property: subClassOf
annotated target: subdivision of digestive tract
source: cjm

Axiom
annotated source: large intestine
annotated property: definition
annotated target: A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
database_cross_reference: Large intestine (anatomy)
database_cross_reference: ISBN10:0073040584

Axiom
annotated source: large intestine
annotated property: UBPROP_0000003
annotated target: Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000054
ontology: VHOG
source: bgee.unil.ch
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566

Axiom
annotated source: large intestine
annotated property: database_cross_reference
annotated target: UMLS:C0021851
source: ncithesaurus:Large_Intestine

Axiom
annotated source: large intestine
annotated property: has_related_synonym
annotated target: intestinum crassum
database_cross_reference: BTO:0000706

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
imported from: uberon.owl
database_cross_reference: AnatomicalStructure
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362889002
database_cross_reference: AAO:0010825
database_cross_reference: AEO:0000003
database_cross_reference: BILA:0000003
database_cross_reference: CARO:0000003
database_cross_reference: EHDAA2:0003003
database_cross_reference: EMAPA:0
database_cross_reference: FBbt:00007001
database_cross_reference: FMA:305751
database_cross_reference: FMA:67135
database_cross_reference: GAID:781
database_cross_reference: HAO:0000003
database_cross_reference: MA:0003000
database_cross_reference: MESH:D000825
database_cross_reference: TAO:0000037
database_cross_reference: TGMA:0001823
database_cross_reference: VHOG:0001759
database_cross_reference: XAO:0003000
database_cross_reference: ZFA:0000037
has exact synonym: biological structure
has exact synonym: connected biological structure
has_obo_namespace: uberon
id: UBERON:0000061
in subset: upper level

organ
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: anatomical system
definition: Anatomical structure that performs a specific function or group of functions [WP].
imported from: uberon.owl
UBPROP_0000001: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
UBPROP_0000012: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
database_cross_reference: Organ (anatomy)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0178784
database_cross_reference: birnlex 4
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/272625005
database_cross_reference: CARO:0020004
database_cross_reference: EFO:0000634
database_cross_reference: EMAPA:35949
database_cross_reference: ENVO:01000162
database_cross_reference: FMA:67498
database_cross_reference: MA:0003001
database_cross_reference: NCIT:C13018
database_cross_reference: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
database_cross_reference: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0178784
database_cross_reference: WBbt:0003760
has_obo_namespace: uberon
has_related_synonym: anatomical unit
has_related_synonym: body organ
has_related_synonym: element
id: UBERON:0000062
in subset: upper level

organ part
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: organ
definition: A multicellular structure that is a part of an organ.
curator note: currently defined in a very broad sense, may be replaced by more specific classes in the future
imported from: uberon.owl
database_cross_reference: birnlex 16
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/113343008
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/91717005
database_cross_reference: AAO:0011124
database_cross_reference: EFO:0000635
database_cross_reference: FMA:82472
has exact synonym: cardinal organ part
has_obo_namespace: uberon
has_related_synonym: regional part of organ
id: UBERON:0000064
in subset: efo slim
in subset: non informative
in subset: upper level

zona pellucida
type: Class
subclass of: acellular anatomical structure
definition: A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.
imported from: uberon.owl
UBPROP_0000003: Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]
has broad synonym: zona pellucida - vitelline membrane
database_cross_reference: Zona pellucida
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0043519
database_cross_reference: BTO:0003135
database_cross_reference: EHDAA2:0002220
database_cross_reference: EHDAA:31
database_cross_reference: EHDAA:62
database_cross_reference: EMAPA:16035
database_cross_reference: FMA:18674
database_cross_reference: GAID:410
database_cross_reference: MA:0001715
database_cross_reference: MESH:D015044
database_cross_reference: NCIT:C33896
database_cross_reference: TAO:0001111
database_cross_reference: UMLS:C0043519
database_cross_reference: VHOG:0000720
database_cross_reference: ZFA:0001111
has_obo_namespace: uberon
has_related_synonym: oolemma
has_related_synonym: pellucid zone
has_related_synonym: striated membrane
has_related_synonym: vitelline envelope
has_related_synonym: vitelline membrane
has_related_synonym: zona radiata
has_related_synonym: zona striata
id: UBERON:0000086
in subset: pheno slim
in subset: vertebrate core

membrane organ
type: Class
subclass of: organ
definition: Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
imported from: uberon.owl
created by: cjm
creation date: 2009-07-30T05:19:13Z
has broad synonym: membrane
database_cross_reference: FMA:7145
has exact synonym: membrane of organ
has_obo_namespace: uberon
id: UBERON:0000094

intestine
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: part of
  some values from: alimentary part of gastrointestinal system
subclass of: Restriction
  on property: contributes to morphology of
  some values from: digestive system
definition: Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
editor note: This class is probably too inclusive
UBPROP_0000001: Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
UBPROP_0000001: The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBPROP_0000007: intestinal
UBPROP_0000008: In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
database_cross_reference: Intestine
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0021853
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/256876008
database_cross_reference: AAO:0000246
database_cross_reference: ANISEED:1235303
database_cross_reference: BSA:0000093
database_cross_reference: BTO:0000648
database_cross_reference: CALOHA:TS-0490
database_cross_reference: EFO:0000834
database_cross_reference: EMAPA:32874
database_cross_reference: EV:0100071
database_cross_reference: FMA:7199
database_cross_reference: GAID:295
database_cross_reference: MA:0000328
database_cross_reference: MA:0001524
database_cross_reference: MESH:A03.492.411
database_cross_reference: MIAA:0000043
database_cross_reference: NCIT:C12736
database_cross_reference: TAO:0001338
database_cross_reference: UMLS:C0021853
database_cross_reference: VHOG:0000056
database_cross_reference: WBbt:0005772
database_cross_reference: XAO:0000129
database_cross_reference: ZFA:0001338
database_cross_reference: galen:Intestine
has exact synonym: bowel
has_obo_namespace: uberon
has_related_synonym: intestinal tract
id: UBERON:0000160
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: intestine
annotated property: subClassOf
annotated target: subdivision of digestive tract
source: cjm

Axiom
annotated source: intestine
annotated property: definition
annotated target: Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
database_cross_reference: Intestine
database_cross_reference: GOC:GO

Axiom
annotated source: intestine
annotated property: UBPROP_0000001
annotated target: Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000246
ontology: AAO
source: AAO:EJS

Axiom
annotated source: intestine
annotated property: UBPROP_0000001
annotated target: The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000056
ontology: VHOG
source: bgee.unil.ch

Axiom
annotated source: intestine
annotated property: database_cross_reference
annotated target: UMLS:C0021853
source: ncithesaurus:Intestine

pair of lungs
type: Class
equivalent class: Class
  intersection of: anatomical collection
  intersection of: Restriction
    on property: has member
    some values from: right lung
  intersection of: Restriction
    on property: has member
    some values from: left lung
subclass of: anatomical collection
subclass of: Class
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 1
    on class: right lung
  intersection of: Restriction
    on property: has member
    max qualified cardinality: 1
    on class: right lung
subclass of: Class
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 1
    on class: left lung
  intersection of: Restriction
    on property: has member
    max qualified cardinality: 1
    on class: left lung
subclass of: Restriction
  on property: has member
  some values from: right lung
subclass of: Restriction
  on property: has member
  some values from: left lung
definition: The pair of anatomical structures comprised of a left lung and right lung.
imported from: uberon.owl
database_cross_reference: FMA:68877
database_cross_reference: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
has exact synonym: lungs
has exact synonym: lungs pair
has exact synonym: pulmones
has exact synonym: set of lungs
has_obo_namespace: uberon
id: UBERON:0000170
in subset: pheno slim

respiration organ
type: Class
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: respiratory system
definition: Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
imported from: uberon.owl
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/272626006
database_cross_reference: EMAPA:17607
database_cross_reference: SPD:0000428
database_cross_reference: TGMA:0001247
has exact synonym: apparatus respiratorius organ
has exact synonym: breathing organ
has exact synonym: organ of apparatus respiratorius
has exact synonym: organ of respiratory system
has exact synonym: respiratory organ
has exact synonym: respiratory system organ
has_obo_namespace: uberon
has_related_synonym: gas exchange organ
id: UBERON:0000171
in subset: functional classification
in subset: organ slim

excreta
type: Class
subclass of: organism substance
definition: A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity
imported from: uberon.owl
has_alternative_id: UBERON:0000324
has_alternative_id: UBERON:0007550
database_cross_reference: AEO:0000184
database_cross_reference: BTO:0000491
database_cross_reference: EHDAA2_RETIRED:0003184
database_cross_reference: ENVO:02000022
database_cross_reference: FMA:9674
database_cross_reference: galen:Excretion
has exact synonym: excreted substance
has exact synonym: portion of excreted substance
has exact synonym: waste substance
has_obo_namespace: uberon
has_related_synonym: excretion
id: UBERON:0000174

blood
type: Class
subclass of: haemolymphatic fluid
subclass of: Restriction
  on property: part of
  some values from: hematopoietic system
subclass of: Restriction
  on property: has part
  some values from: blood plasma
definition: A fluid that is composed of blood plasma and erythrocytes.
curator note: This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
imported from: uberon.owl
UBPROP_0000001: A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
UBPROP_0000001: Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
UBPROP_0000002: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
UBPROP_0000003: Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
contributor: cmungall
contributor: tmeehan
database_cross_reference: Blood
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0005767
database_cross_reference: AAO:0000046
database_cross_reference: BTO:0000089
database_cross_reference: CALOHA:TS-0079
database_cross_reference: EFO:0000296
database_cross_reference: EHDAA2:0000176
database_cross_reference: EHDAA:418
database_cross_reference: EMAPA:16332
database_cross_reference: ENVO:02000027
database_cross_reference: EV:0100047
database_cross_reference: FMA:9670
database_cross_reference: GAID:965
database_cross_reference: MA:0000059
database_cross_reference: MESH:D001769
database_cross_reference: MIAA:0000315
database_cross_reference: NCIT:C12434
database_cross_reference: OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000007
database_cross_reference: UMLS:C0005767
database_cross_reference: VHOG:0000224
database_cross_reference: XAO:0000124
database_cross_reference: ZFA:0000007
database_cross_reference: galen:Blood
has exact synonym: portion of blood
has exact synonym: vertebrate blood
has_obo_namespace: uberon
has_related_synonym: whole blood
id: UBERON:0000178
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

haemolymphatic fluid
type: Class
equivalent class: Class
  intersection of: organism substance
  intersection of: Restriction
    on property: part of
    some values from: hemolymphoid system
subclass of: bodily fluid
subclass of: Restriction
  on property: part of
  some values from: hemolymphoid system
definition: Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
imported from: uberon.owl
created by: cjm
creation date: 2009-04-08T04:38:19Z
database_cross_reference: CARO:0000081
has_obo_namespace: uberon
has_related_synonym: blood or blood analog
has_related_synonym: circulating fluid
id: UBERON:0000179

late embryo
type: Class
subclass of: embryo
definition: An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
editor note: TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus.
imported from: uberon.owl
UBPROP_0000001: Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919].
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0015965
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/83418008
database_cross_reference: BTO:0000449
database_cross_reference: CALOHA:TS-0360
database_cross_reference: EFO:0001323
database_cross_reference: FBbt:00005333
database_cross_reference: FMA:63919
database_cross_reference: GAID:552
database_cross_reference: MESH:D005333
database_cross_reference: NCIT:C13235
database_cross_reference: OpenCyc:Mx4rvZfC2ZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0015965
has narrow synonym: fetus
has_obo_namespace: uberon
has_related_synonym: embryo late growth stage
has_related_synonym: embryo late stage
id: UBERON:0000323
in subset: efo slim
in subset: pheno slim

gastric gland
type: Class
subclass of: exocrine gland
subclass of: gland of foregut
definition: The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
imported from: uberon.owl
database_cross_reference: BTO:0000503
database_cross_reference: EMAPA:27181
database_cross_reference: FMA:14919
has_obo_namespace: uberon
id: UBERON:0000325
in subset: organ slim
in subset: pheno slim

serous gland
type: Class
subclass of: exocrine gland
subclass of: Restriction
  on property: produces
  some values from: secretion of serous gland
definition: A gland in which the principal secretory cells are serous secreting cells.
imported from: uberon.owl
UBPROP_0000001: glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
database_cross_reference: Serous gland
database_cross_reference: BTO:0001837
database_cross_reference: EMAPA:37950
database_cross_reference: FMA:62889
has_obo_namespace: uberon
id: UBERON:0000409
in subset: organ slim
in subset: pheno slim

mucous gland
type: Class
subclass of: exocrine gland
subclass of: Restriction
  on property: produces
  some values from: mucus
definition: A gland in which the principal secretory cells are mucus secreting cells.
imported from: uberon.owl
UBPROP_0000008: In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]
database_cross_reference: Mucous gland
database_cross_reference: AAO:0010601
database_cross_reference: BTO:0001979
database_cross_reference: EMAPA:37913
database_cross_reference: FMA:62888
has exact synonym: glandula mucosa
has_obo_namespace: uberon
has_related_synonym: muciparous gland
has_related_synonym: mucous secreting gland
has_related_synonym: mucus gland
has_related_synonym: mucus-secreting gland
id: UBERON:0000414
in subset: organ slim

secretion of exocrine gland
type: Class
equivalent class: Class
  intersection of: organism substance
  intersection of: Restriction
    on property: produced_by
    some values from: exocrine gland
subclass of: organism substance
subclass of: Restriction
  on property: produced_by
  some values from: exocrine gland
definition: A portion of organism substance that is produced by exocrine glands.
imported from: uberon.owl
UBPROP_0000012: BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
has_alternative_id: UBERON:0006540
has broad synonym: secretion
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1516992
database_cross_reference: AEO:0001005
database_cross_reference: BTO:0002977
database_cross_reference: BTO:0002979
database_cross_reference: EMAPA:36535
database_cross_reference: FMA:9675
database_cross_reference: MA:0002504
database_cross_reference: MESH:D012634
database_cross_reference: NCIT:C34062
database_cross_reference: UMLS:C1516992
database_cross_reference: galen:Secretion
has exact synonym: bodily secretion
has exact synonym: exocrine gland fluid/secretion
has exact synonym: secreted substance
has_obo_namespace: uberon
has_related_synonym: exocrine gland fluid
has_related_synonym: exocrine gland fluid or secretion
has_related_synonym: exocrine gland secretion
has_related_synonym: external secretion
id: UBERON:0000456

organism substance
type: Class
subclass of: material anatomical entity
subclass of: Restriction
  on property: part of
  some values from: multicellular organism
definition: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
imported from: uberon.owl
database_cross_reference: AAO:0010839
database_cross_reference: AEO:0000004
database_cross_reference: BILA:0000004
database_cross_reference: CALOHA:TS-2101
database_cross_reference: CARO:0000004
database_cross_reference: EHDAA2:0003004
database_cross_reference: EMAPA:35178
database_cross_reference: FBbt:00007019
database_cross_reference: FMA:9669
database_cross_reference: HAO:0000004
database_cross_reference: MA:0002450
database_cross_reference: NCIT:C13236
database_cross_reference: SPD:0000008
database_cross_reference: TAO:0001487
database_cross_reference: TGMA:0001824
database_cross_reference: VHOG:0001726
database_cross_reference: XAO:0004001
database_cross_reference: ZFA:0001487
database_cross_reference: galen:BodySubstance
has exact synonym: body fluid or substance
has exact synonym: body substance
has exact synonym: organism substance
has exact synonym: portion of body substance
has exact synonym: portion of organism substance
has_obo_namespace: uberon
id: UBERON:0000463
in subset: pheno slim
in subset: upper level

material anatomical entity
type: Class
subclass of: anatomical entity
definition: Anatomical entity that has mass.
imported from: uberon.owl
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FBbt:00007016
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721
has_obo_namespace: uberon
id: UBERON:0000465
in subset: upper level

anatomical system
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: multicellular organism
subclass of: Restriction
  on property: has part
  some values from: organ
definition: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
imported from: uberon.owl
has broad synonym: system
database_cross_reference: Organ system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0460002
database_cross_reference: birnlex 14
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/278195005
database_cross_reference: AAO:0000007
database_cross_reference: AEO:0000011
database_cross_reference: BILA:0000011
database_cross_reference: BSA:0000049
database_cross_reference: CALOHA:TS-2088
database_cross_reference: CARO:0000011
database_cross_reference: EHDAA2:0003011
database_cross_reference: EHDAA:392
database_cross_reference: EMAPA:16103
database_cross_reference: EV:0100000
database_cross_reference: FBbt:00004856
database_cross_reference: FMA:7149
database_cross_reference: HAO:0000011
database_cross_reference: MA:0000003
database_cross_reference: NCIT:C12919
database_cross_reference: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
database_cross_reference: TAO:0001439
database_cross_reference: TGMA:0001831
database_cross_reference: UMLS:C0460002
database_cross_reference: VHOG:0001725
database_cross_reference: WBbt:0005746
database_cross_reference: WBbt:0005763
database_cross_reference: XAO:0003002
database_cross_reference: ZFA:0001439
database_cross_reference: galen:AnatomicalSystem
has exact synonym: body system
has exact synonym: connected anatomical system
has exact synonym: organ system
has_obo_namespace: uberon
has_related_synonym: anatomical systems
id: UBERON:0000467
in subset: pheno slim
in subset: uberon slim
in subset: upper level

multicellular organism
type: Class
subclass of: multicellular anatomical structure
definition: Anatomical structure that is an individual member of a species and consists of more than one cell.
editor note: TODO - split body and mc organism? body continues after death stage
imported from: uberon.owl
UBPROP_0000007: organismal
has broad synonym: organism
database_cross_reference: Multi-cellular organism
database_cross_reference: birnlex 18
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/243928005
database_cross_reference: AAO:0010026
database_cross_reference: AEO:0000191
database_cross_reference: BILA:0000012
database_cross_reference: BSA:0000038
database_cross_reference: BTO:0000042
database_cross_reference: CARO:0000012
database_cross_reference: EFO:0002906
database_cross_reference: EHDAA2:0003103
database_cross_reference: EHDAA2:0003191
database_cross_reference: EHDAA:1
database_cross_reference: EMAPA:25765
database_cross_reference: EV:0100016
database_cross_reference: FBbt:00000001
database_cross_reference: FMA:256135
database_cross_reference: HAO:0000012
database_cross_reference: NCIT:C13041
database_cross_reference: TADS:0000001
database_cross_reference: TAO:0001094
database_cross_reference: TGMA:0001832
database_cross_reference: VHOG:0000671
database_cross_reference: WBbt:0007833
database_cross_reference: XAO:0003004
database_cross_reference: ZFA:0001094
database_cross_reference: galen:Organism
database_cross_reference: ncithesaurus:Whole_Organism
has exact synonym: multi-cellular organism
has narrow synonym: animal
has_obo_namespace: uberon
has_related_synonym: Koerper
has_related_synonym: body
has_related_synonym: whole body
has_related_synonym: whole organism
id: UBERON:0000468
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: upper level

female reproductive system
type: Class
subclass of: reproductive system
definition: The organs and associated structures associated with bearing offspring in a female animal.
imported from: uberon.owl
UBPROP_0000003: By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
database_cross_reference: Female genitalia
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0700038
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/361386004
database_cross_reference: BTO:0000083
database_cross_reference: CALOHA:TS-1303
database_cross_reference: EFO:0000969
database_cross_reference: EHDAA2:0000506
database_cross_reference: EHDAA:8116
database_cross_reference: EMAPA:17959
database_cross_reference: EV:0100110
database_cross_reference: FBbt:00004864
database_cross_reference: FMA:45663
database_cross_reference: GAID:364
database_cross_reference: HAO:0000324
database_cross_reference: MA:0000381
database_cross_reference: MESH:D005836
database_cross_reference: MIAA:0000028
database_cross_reference: NCIT:C12402
database_cross_reference: OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA
database_cross_reference: TGMA:0000635
database_cross_reference: UMLS:C0700038
database_cross_reference: VHOG:0000726
database_cross_reference: WBbt:0006748
database_cross_reference: WikipediaCategory:Female_reproductive_system
database_cross_reference: XAO:0000156
has exact synonym: female organism genitalia
has exact synonym: female organism reproductive system
has exact synonym: genitalia of female organism
has exact synonym: reproductive system of female organism
has_obo_namespace: uberon
has_related_synonym: female genital system
has_related_synonym: female genital tract
has_related_synonym: female genitalia
has_related_synonym: female genitals
has_related_synonym: female reproductive tract
has_related_synonym: gynaecological tissue
has_related_synonym: systema genitale femininum
id: UBERON:0000474
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

acellular anatomical structure
type: Class
subclass of: anatomical structure
definition: Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
imported from: uberon.owl
database_cross_reference: AAO:0010268
database_cross_reference: AEO:0000040
database_cross_reference: BILA:0000040
database_cross_reference: CARO:0000040
database_cross_reference: EHDAA2:0003040
database_cross_reference: FBbt:00007013
database_cross_reference: FMA:63863
database_cross_reference: HAO:0000040
database_cross_reference: TAO:0000382
database_cross_reference: TGMA:0001841
database_cross_reference: XAO:0003162
database_cross_reference: ZFA:0000382
has_obo_namespace: uberon
has_related_synonym: acellular anatomical structures
id: UBERON:0000476
in subset: vertebrate core

tissue
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: multicellular organism
definition: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
editor note: changed label and definition to reflect CARO2
imported from: uberon.owl
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0040300
database_cross_reference: birnlex 19
database_cross_reference: AAO:0000607
database_cross_reference: AAO:0010054
database_cross_reference: AEO:0000043
database_cross_reference: BILA:0000043
database_cross_reference: CALOHA:TS-2090
database_cross_reference: CARO:0000043
database_cross_reference: EHDAA2:0003043
database_cross_reference: EMAPA:35868
database_cross_reference: FBbt:00007003
database_cross_reference: FMA:9637
database_cross_reference: HAO:0000043
database_cross_reference: MA:0003002
database_cross_reference: MESH:D014024
database_cross_reference: NCIT:C12801
database_cross_reference: TAO:0001477
database_cross_reference: TGMA:0001844
database_cross_reference: UMLS:C0040300
database_cross_reference: VHOG:0001757
database_cross_reference: WBbt:0005729
database_cross_reference: XAO:0003040
database_cross_reference: ZFA:0001477
database_cross_reference: galen:Tissue
has exact synonym: portion of tissue
has exact synonym: tissue portion
has narrow synonym: simple tissue
has_obo_namespace: uberon
id: UBERON:0000479
in subset: pheno slim
in subset: upper level

multi-tissue structure
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: has part
  some values from: tissue
definition: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
imported from: uberon.owl
database_cross_reference: AAO:0010048
database_cross_reference: AEO:0000055
database_cross_reference: BILA:0000055
database_cross_reference: CARO:0000055
database_cross_reference: EHDAA2:0003055
database_cross_reference: FBbt:00007010
database_cross_reference: HAO:0000055
database_cross_reference: TAO:0001488
database_cross_reference: TGMA:0001847
database_cross_reference: VHOG:0001762
database_cross_reference: XAO:0003037
database_cross_reference: ZFA:0001488
has_obo_namespace: uberon
has_related_synonym: multi-tissue structures
id: UBERON:0000481
in subset: upper level

cavitated compound organ
type: Class
subclass of: compound organ
definition: Compound organ that contains one or more macroscopic anatomical spaces.
curator note: this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
imported from: uberon.owl
database_cross_reference: AAO:0010016
database_cross_reference: AEO:0000072
database_cross_reference: BILA:0000072
database_cross_reference: CARO:0000072
database_cross_reference: EHDAA2:0003072
database_cross_reference: FMA:55671
database_cross_reference: HAO:0000072
database_cross_reference: TAO:0001490
database_cross_reference: TGMA:0001857
database_cross_reference: VHOG:0001730
database_cross_reference: XAO:0003165
database_cross_reference: ZFA:0001490
has exact synonym: cavitated organ
has_obo_namespace: uberon
has_related_synonym: cavitated compound organs
id: UBERON:0000489
in subset: organ slim
in subset: upper level

mucus
type: Class
subclass of: secretion of exocrine gland
subclass of: bodily fluid
definition: Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
imported from: uberon.owl
UBPROP_0000007: mucoid
UBPROP_0000007: mucous
database_cross_reference: Mucus
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0026727
database_cross_reference: CALOHA:TS-2144
database_cross_reference: ENVO:02000040
database_cross_reference: FMA:66938
database_cross_reference: GAID:1164
database_cross_reference: MESH:D009093
database_cross_reference: NCIT:C13259
database_cross_reference: OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0026727
database_cross_reference: galen:Mucus
has_obo_namespace: uberon
id: UBERON:0000912

interstitial fluid
type: Class
subclass of: organism substance
subclass of: Restriction
  on property: part of
  some values from: tissue
definition: Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
imported from: uberon.owl
database_cross_reference: Interstitial fluid
database_cross_reference: ENVO:02000042
database_cross_reference: FMA:9673
database_cross_reference: NCIT:C120839
has exact synonym: intercellular fluid
has exact synonym: tissue fluid
has_obo_namespace: uberon
id: UBERON:0000913
in subset: pheno slim

embryo
type: Class
subclass of: multicellular organism
definition: Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
imported from: uberon.owl
UBPROP_0000007: embryonic
UBPROP_0000012: Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
database_cross_reference: Embryo
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0013935
database_cross_reference: Category:Embryonic organism
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/57991002
database_cross_reference: AAO:0011035
database_cross_reference: AEO:0000169
database_cross_reference: BILA:0000056
database_cross_reference: BSA:0000039
database_cross_reference: BTO:0000379
database_cross_reference: CALOHA:TS-0229
database_cross_reference: EFO:0001367
database_cross_reference: EHDAA2:0000002
database_cross_reference: EHDAA2_RETIRED:0003236
database_cross_reference: EHDAA:38
database_cross_reference: EMAPA:16039
database_cross_reference: FBbt:00000052
database_cross_reference: FMA:69068
database_cross_reference: GAID:963
database_cross_reference: MAT:0000226
database_cross_reference: MESH:D004622
database_cross_reference: MIAA:0000019
database_cross_reference: NCIT:C28147
database_cross_reference: OGEM:000001
database_cross_reference: OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0013935
database_cross_reference: VHOG:0001766
database_cross_reference: XAO:0000113
database_cross_reference: ZFA:0000103
has exact synonym: embryonic organism
has_obo_namespace: uberon
has_related_synonym: developing organism
has_related_synonym: developmental tissue
id: UBERON:0000922
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

stomach
type: Class
subclass of: subdivision of digestive tract
subclass of: food storage organ
subclass of: Restriction
  on property: contributes to morphology of
  some values from: digestive system
definition: An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
UBPROP_0000001: Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
UBPROP_0000003: It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
UBPROP_0000008: We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
database_cross_reference: Stomach
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0038351
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181246003
database_cross_reference: AAO:0000579
database_cross_reference: ANISEED:1235297
database_cross_reference: BTO:0001307
database_cross_reference: CALOHA:TS-0980
database_cross_reference: EFO:0000837
database_cross_reference: EHDAA2:0001915
database_cross_reference: EHDAA:2993
database_cross_reference: EMAPA:17021
database_cross_reference: EV:0100070
database_cross_reference: FMA:7148
database_cross_reference: GAID:293
database_cross_reference: MA:0000353
database_cross_reference: MAT:0000051
database_cross_reference: MESH:A03.492.766
database_cross_reference: MIAA:0000051
database_cross_reference: NCIT:C12391
database_cross_reference: OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0002121
database_cross_reference: UMLS:C0038351
database_cross_reference: VHOG:0000408
database_cross_reference: XAO:0000128
database_cross_reference: galen:Stomach
has narrow synonym: stomach chamber
has_obo_namespace: uberon
has_related_synonym: anterior intestine
has_related_synonym: gaster
has_related_synonym: mesenteron
has_related_synonym: ventriculus
id: UBERON:0000945
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: stomach
annotated property: subClassOf
annotated target: subdivision of digestive tract
source: cjm

Axiom
annotated source: stomach
annotated property: subClassOf
annotated target: food storage organ
source: cjm

Axiom
annotated source: stomach
annotated property: definition
annotated target: An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
database_cross_reference: Stomach
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: ISBN10:0073040584

Axiom
annotated source: stomach
annotated property: UBPROP_0000001
annotated target: Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000579
ontology: AAO
source: AAO:EJS

Axiom
annotated source: stomach
annotated property: UBPROP_0000003
annotated target: It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000408
ontology: VHOG
source: bgee.unil.ch
source: DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)

Axiom
annotated source: stomach
annotated property: UBPROP_0000008
annotated target: We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
source: WP:Stomach#In_other_animals

Axiom
annotated source: stomach
annotated property: database_cross_reference
annotated target: UMLS:C0038351
source: ncithesaurus:Stomach

Axiom
annotated source: stomach
annotated property: has_related_synonym
annotated target: gaster
database_cross_reference: BTO:0001307

Axiom
annotated source: stomach
annotated property: has_related_synonym
annotated target: ventriculus
database_cross_reference: Stomach
has synonym type: LATIN

endocrine system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: composed primarily of
  some values from: endocrine gland
definition: Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
imported from: uberon.owl
UBPROP_0000001: Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
UBPROP_0000003: Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
UBPROP_0000007: endocrine
database_cross_reference: Endocrine system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0014136
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/278876000
database_cross_reference: AAO:0010279
database_cross_reference: CALOHA:TS-1301
database_cross_reference: EFO:0002969
database_cross_reference: EHDAA2:0002224
database_cross_reference: EMAPA:35306
database_cross_reference: EV:0100128
database_cross_reference: FBbt:00005068
database_cross_reference: FMA:9668
database_cross_reference: GAID:439
database_cross_reference: MA:0000012
database_cross_reference: MESH:D004703
database_cross_reference: NCIT:C12705
database_cross_reference: TAO:0001158
database_cross_reference: UMLS:C0014136
database_cross_reference: VHOG:0000098
database_cross_reference: XAO:0000158
database_cross_reference: ZFA:0001158
has exact synonym: endocrine glandular system
has exact synonym: endocrine system
has exact synonym: systema endocrinum
has_obo_namespace: uberon
id: UBERON:0000949
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

brain
type: Class
subclass of: organ
subclass of: ectoderm-derived structure
subclass of: Restriction
  on property: in_anterior_side_of
  some values from: multicellular organism
subclass of: Restriction
  on property: contributes to morphology of
  some values from: nervous system
definition: The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
editor note: requires review for applicability to invertebrate structures, e.g. synganglion
imported from: uberon.owl
UBPROP_0000001: Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
UBPROP_0000001: Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
UBPROP_0000001: The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
UBPROP_0000003: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
contributor: cmungall
database_cross_reference: http://braininfo.rprc.washington.edu/centraldirectory.aspx
database_cross_reference: Brain
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0006104
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1269537
database_cross_reference: birnlex 796
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/258335003
database_cross_reference: AAO:0010478
database_cross_reference: ABA:Brain
database_cross_reference: BAMS:Br
database_cross_reference: BAMS:Brain
database_cross_reference: BILA:0000135
database_cross_reference: BTO:0000142
database_cross_reference: CALOHA:TS-0095
database_cross_reference: DHBA:10155
database_cross_reference: EFO:0000302
database_cross_reference: EHDAA2:0000183
database_cross_reference: EHDAA:2641
database_cross_reference: EHDAA:6485
database_cross_reference: EMAPA:16894
database_cross_reference: EV:0100164
database_cross_reference: FBbt:00005095
database_cross_reference: FMA:50801
database_cross_reference: GAID:571
database_cross_reference: HBA:4005
database_cross_reference: MA:0000168
database_cross_reference: MAT:0000098
database_cross_reference: MBA:8
database_cross_reference: MBA:997
database_cross_reference: MESH:D001921
database_cross_reference: MIAA:0000098
database_cross_reference: NCIT:C12439
database_cross_reference: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
database_cross_reference: PBA:3999
database_cross_reference: TAO:0000008
database_cross_reference: UMLS:C0006104
database_cross_reference: UMLS:C1269537
database_cross_reference: VHOG:0000157
database_cross_reference: XAO:0000010
database_cross_reference: ZFA:0000008
database_cross_reference: galen:Brain
has_obo_namespace: uberon
has_related_synonym: encephalon
has_related_synonym: suprasegmental levels of nervous system
has_related_synonym: suprasegmental structures
has_related_synonym: synganglion
has_related_synonym: the brain
id: UBERON:0000955
in subset: cumbo
in subset: efo slim
in subset: major organ
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

reproductive system
type: Class
subclass of: anatomical system
definition: Anatomical system that has as its parts the organs concerned with reproduction.
editor note: consider splitting genitalia from reproductive system
imported from: uberon.owl
UBPROP_0000001: Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
UBPROP_0000003: Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
UBPROP_0000202: FMA_75572
database_cross_reference: Reproductive system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1261210
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/278875001
database_cross_reference: AAO:0010258
database_cross_reference: BILA:0000103
database_cross_reference: BTO:0000081
database_cross_reference: CALOHA:TS-1318
database_cross_reference: EFO:0000809
database_cross_reference: EHDAA2:0001603
database_cross_reference: EHDAA:5923
database_cross_reference: EMAPA:17381
database_cross_reference: EV:0100100
database_cross_reference: FBbt:00004857
database_cross_reference: FMA:7160
database_cross_reference: GAID:363
database_cross_reference: HAO:0000374
database_cross_reference: HAO:0000895
database_cross_reference: MA:0000326
database_cross_reference: MIAA:0000305
database_cross_reference: NCIT:C12841
database_cross_reference: OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000632
database_cross_reference: UMLS:C1261210
database_cross_reference: VHOG:0000182
database_cross_reference: WBbt:0005747
database_cross_reference: XAO:0000142
database_cross_reference: ZFA:0000632
has_obo_namespace: uberon
has_related_synonym: Geschlechtsorgan
has_related_synonym: animal reproductive system
has_related_synonym: genital system
has_related_synonym: genital tract
has_related_synonym: genitalia
has_related_synonym: organa genitalia
has_related_synonym: reproductive tissue
has_related_synonym: reproductive tract
has_related_synonym: systemata genitalia
id: UBERON:0000990
in subset: efo slim
in subset: functional classification
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

respiratory system
type: Class
subclass of: anatomical system
definition: Functional system which consists of structures involved in respiration.
imported from: uberon.owl
UBPROP_0000001: The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
UBPROP_0000003: There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
database_cross_reference: Respiratory system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0035237
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/278197002
database_cross_reference: AAO:0000541
database_cross_reference: BTO:0000203
database_cross_reference: CALOHA:TS-1319
database_cross_reference: EFO:0000804
database_cross_reference: EHDAA2:0001604
database_cross_reference: EHDAA:2203
database_cross_reference: EMAPA:16727
database_cross_reference: EV:0100036
database_cross_reference: FMA:7158
database_cross_reference: GAID:78
database_cross_reference: MA:0000327
database_cross_reference: MAT:0000030
database_cross_reference: MESH:D012137
database_cross_reference: MIAA:0000030
database_cross_reference: NCIT:C12779
database_cross_reference: OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000272
database_cross_reference: UMLS:C0035237
database_cross_reference: VHOG:0000202
database_cross_reference: XAO:0000117
database_cross_reference: ZFA:0000272
has exact synonym: apparatus respiratorius
has exact synonym: respiratory system
has_obo_namespace: uberon
has_related_synonym: Atmungssystem
has_related_synonym: apparatus respiratorius
has_related_synonym: systema respiratorium
id: UBERON:0001004
in subset: efo slim
in subset: functional classification
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

digestive system
type: Class
subclass of: anatomical system
definition: Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
imported from: uberon.owl
UBPROP_0000001: An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
UBPROP_0000007: digestive
UBPROP_0000012: many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
database_cross_reference: Digestive system
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/278859004
database_cross_reference: AAO:0000129
database_cross_reference: BILA:0000082
database_cross_reference: BTO:0000058
database_cross_reference: CALOHA:TS-1293
database_cross_reference: EFO:0000793
database_cross_reference: EV:0100056
database_cross_reference: FBbt:00005055
database_cross_reference: FMA:7152
database_cross_reference: GAID:278
database_cross_reference: MA:0002431
database_cross_reference: MAT:0000018
database_cross_reference: MESH:D004064
database_cross_reference: MIAA:0000018
database_cross_reference: TADS:0000170
database_cross_reference: TAO:0000339
database_cross_reference: WBbt:0005748
database_cross_reference: XAO:0000125
database_cross_reference: ZFA:0000339
database_cross_reference: galen:DigestiveSystem
database_cross_reference: ncithesaurus:Digestive_System
has_obo_namespace: uberon
has_related_synonym: alimentary system
has_related_synonym: alimentary tract
has_related_synonym: gastrointestinal system
has_related_synonym: gut
id: UBERON:0001007
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

renal system
type: Class
subclass of: anatomical system
definition: The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products..
editor note: In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
imported from: uberon.owl
UBPROP_0000001: An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
UBPROP_0000003: Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
UBPROP_0000008: In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
UBPROP_0000008: This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
database_cross_reference: Excretory system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1508753
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362204003
database_cross_reference: AAO:0010257
database_cross_reference: BILA:0000015
database_cross_reference: BTO:0001244
database_cross_reference: BTO:0003092
database_cross_reference: CALOHA:TS-1323
database_cross_reference: EFO:0000803
database_cross_reference: EHDAA2:0001601
database_cross_reference: EHDAA:5901
database_cross_reference: EMAPA:17366
database_cross_reference: EV:0100095
database_cross_reference: FBbt:00005056
database_cross_reference: FMA:7159
database_cross_reference: GAID:391
database_cross_reference: MA:0000325
database_cross_reference: MAT:0000027
database_cross_reference: MESH:D014551
database_cross_reference: MIAA:0000027
database_cross_reference: NCIT:C12413
database_cross_reference: TADS:0000162
database_cross_reference: TAO:0000163
database_cross_reference: UMLS:C1508753
database_cross_reference: VHOG:0000723
database_cross_reference: WBbt:0005736
database_cross_reference: XAO:0000143
database_cross_reference: ZFA:0000163
database_cross_reference: galen:UrinaryTract
has exact synonym: excretory system
has exact synonym: renal system
has exact synonym: systema urinaria
has exact synonym: systema urinarium
has exact synonym: urinary system
has exact synonym: urinary tract
has_obo_namespace: uberon
has_related_synonym: renal or urinary system
has_related_synonym: renal/urinary system
id: UBERON:0001008
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

circulatory system
type: Class
subclass of: anatomical system
definition: organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
curator note: the cardiovascular system and the lymphatic system are parts of the circulatory system
imported from: uberon.owl
RO_0002174: NCBITaxon 6231
UBPROP_0000001: Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
UBPROP_0000003: We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
database_cross_reference: Circulatory system
database_cross_reference: AAO:0000959
database_cross_reference: CALOHA:TS-2103
database_cross_reference: FBbt:00005057
database_cross_reference: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
database_cross_reference: VHOG:0001248
has_obo_namespace: uberon
has_related_synonym: systema cardiovasculare
id: UBERON:0001009
in subset: uberon slim

nervous system
type: Class
subclass of: anatomical system
definition: The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
imported from: uberon.owl
UBPROP_0000001: A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
UBPROP_0000001: Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
UBPROP_0000003: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
UBPROP_0000007: nervous
UBPROP_0000007: neural
database_cross_reference: http://braininfo.rprc.washington.edu/centraldirectory.aspx
database_cross_reference: Nervous system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0027763
database_cross_reference: birnlex 844
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/278196006
database_cross_reference: AAO:0000324
database_cross_reference: BILA:0000079
database_cross_reference: BTO:0001484
database_cross_reference: CALOHA:TS-1313
database_cross_reference: EFO:0000802
database_cross_reference: EHDAA2:0001246
database_cross_reference: EHDAA:826
database_cross_reference: EMAPA:16469
database_cross_reference: EV:0100162
database_cross_reference: FBbt:00005093
database_cross_reference: FMA:7157
database_cross_reference: GAID:466
database_cross_reference: MA:0000016
database_cross_reference: MAT:0000026
database_cross_reference: MESH:D009420
database_cross_reference: MIAA:0000026
database_cross_reference: NCIT:C12755
database_cross_reference: OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000396
database_cross_reference: UMLS:C0027763
database_cross_reference: VHOG:0000402
database_cross_reference: WBbt:0005735
database_cross_reference: XAO:0000177
database_cross_reference: ZFA:0000396
has exact synonym: neurological system
has narrow synonym: nerve net
has_obo_namespace: uberon
has_related_synonym: systema nervosum
id: UBERON:0001016
in subset: cumbo
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

sensory system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: entire sense organ system
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part of
    some values from: nervous system
definition: Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
imported from: uberon.owl
UBPROP_0000003: An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
UBPROP_0000012: note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
database_cross_reference: Sensory system
database_cross_reference: nlx anat 090816
database_cross_reference: AAO:0000555
database_cross_reference: BAMS:SEN
database_cross_reference: BILA:0000099
database_cross_reference: EFO:0000805
database_cross_reference: EHDAA2:0003094
database_cross_reference: EMAPA:16192
database_cross_reference: FBbt:00007692
database_cross_reference: FMA:75259
database_cross_reference: MA:0002442
database_cross_reference: MAT:0000031
database_cross_reference: MIAA:0000031
database_cross_reference: TAO:0000282
database_cross_reference: VHOG:0001674
database_cross_reference: XAO:0003194
database_cross_reference: ZFA:0000282
has exact synonym: organa sensuum
has exact synonym: sense organ subsystem
has exact synonym: sense organs
has exact synonym: sense organs set
has exact synonym: sensory subsystem
has exact synonym: sensory systems
has_obo_namespace: uberon
has_related_synonym: organa sensuum
has_related_synonym: sensory organ system
has_related_synonym: set of sense organs
id: UBERON:0001032
in subset: efo slim
in subset: uberon slim
in subset: vertebrate core

esophagus
type: Class
subclass of: subdivision of digestive tract
subclass of: thoracic cavity element
subclass of: digestive system element
definition: Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
UBPROP_0000001: Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
UBPROP_0000003: The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
UBPROP_0000007: esophageal
UBPROP_0000012: esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
database_cross_reference: Esophagus
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0014876
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181245004
database_cross_reference: AAO:0000145
database_cross_reference: ANISEED:1235301
database_cross_reference: BTO:0000959
database_cross_reference: CALOHA:TS-0700
database_cross_reference: EFO:0000835
database_cross_reference: EHDAA2:0001285
database_cross_reference: EHDAA:2937
database_cross_reference: EMAPA:16833
database_cross_reference: EV:0100069
database_cross_reference: FMA:7131
database_cross_reference: GAID:291
database_cross_reference: MA:0000352
database_cross_reference: MAT:0000048
database_cross_reference: MESH:A03.365
database_cross_reference: MIAA:0000048
database_cross_reference: NCIT:C12389
database_cross_reference: OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000204
database_cross_reference: UMLS:C0014876
database_cross_reference: VHOG:0000450
database_cross_reference: XAO:0000127
database_cross_reference: ZFA:0000204
database_cross_reference: galen:Esophagus
has exact synonym: gullet
has exact synonym: oesophagus
has_obo_namespace: uberon
id: UBERON:0001043
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: esophagus
annotated property: definition
annotated target: Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
database_cross_reference: Esophagus
database_cross_reference: oesophagus

Axiom
annotated source: esophagus
annotated property: UBPROP_0000001
annotated target: Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000145
ontology: AAO
source: AAO:EJS

Axiom
annotated source: esophagus
annotated property: UBPROP_0000003
annotated target: The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000450
ontology: VHOG
source: bgee.unil.ch
source: DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)

Axiom
annotated source: esophagus
annotated property: UBPROP_0000012
annotated target: esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
external ontology: MA

Axiom
annotated source: esophagus
annotated property: database_cross_reference
annotated target: UMLS:C0014876
source: ncithesaurus:Esophagus

rectum
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: part of
  some values from: large intestine
subclass of: Restriction
  on property: distalmost_part_of
  some values from: large intestine
subclass of: Restriction
  on property: contributes to morphology of
  some values from: large intestine
definition: the terminal portion of the intestinal tube, terminating with the anus
UBPROP_0000001: The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBPROP_0000007: rectal
UBPROP_0000008: In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
database_cross_reference: Rectum
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0034896
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181261002
database_cross_reference: AAO:0010401
database_cross_reference: BTO:0001158
database_cross_reference: CALOHA:TS-1180
database_cross_reference: EFO:0000848
database_cross_reference: EHDAA2:0001592
database_cross_reference: EHDAA:5836
database_cross_reference: EMAPA:17896
database_cross_reference: EV:0100081
database_cross_reference: FMA:14544
database_cross_reference: GAID:311
database_cross_reference: MA:0000336
database_cross_reference: MAT:0000050
database_cross_reference: MESH:A03.492.411.495.767
database_cross_reference: MIAA:0000050
database_cross_reference: NCIT:C12390
database_cross_reference: OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0034896
database_cross_reference: VHOG:0001751
database_cross_reference: XAO:0000238
database_cross_reference: galen:Rectum
has exact synonym: terminal portion of intestine
has_obo_namespace: uberon
has_related_synonym: intestinum rectum
has_related_synonym: rectal sac
has_related_synonym: terminal portion of large intestine
id: UBERON:0001052
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: rectum
annotated property: subClassOf
annotated target: subdivision of digestive tract
order: 4
source: cjm

Axiom
annotated source: rectum
annotated property: subClassOf
annotated target: Restriction
  on property: part of
  some values from: large intestine
source: MA

Axiom
annotated source: rectum
annotated property: subClassOf
annotated target: Restriction
  on property: distalmost_part_of
  some values from: large intestine
source: ISBN10:0073040584

Axiom
annotated source: rectum
annotated property: definition
annotated target: the terminal portion of the intestinal tube, terminating with the anus
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: ISBN:0-683-40008-8
database_cross_reference: MP:0000492

Axiom
annotated source: rectum
annotated property: UBPROP_0000001
annotated target: The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001751
ontology: VHOG
source: bgee.unil.ch

Axiom
annotated source: rectum
annotated property: database_cross_reference
annotated target: UMLS:C0034896
source: ncithesaurus:Rectum

Axiom
annotated source: rectum
annotated property: has_related_synonym
annotated target: intestinum rectum
database_cross_reference: BTO:0001158

anatomical entity
type: Class
subclass of: material entity
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
imported from: uberon.owl
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1515976
database_cross_reference: birnlex 6
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BILA:0000000
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FBbt:10000000
database_cross_reference: FBbt_root:00000000
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
has_obo_namespace: uberon
id: UBERON:0001062
in subset: upper level

synovial fluid
type: Class
subclass of: transudate
subclass of: secretion of serous gland
definition: Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
imported from: uberon.owl
UBPROP_0000001: Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
UBPROP_0000009: It provides nutrients and lubrication for articular cartilage
UBPROP_0000010: The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
database_cross_reference: Synovial fluid
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0039097
database_cross_reference: BTO:0001339
database_cross_reference: CALOHA:TS-0996
database_cross_reference: ENVO:02000039
database_cross_reference: FMA:12277
database_cross_reference: GAID:265
database_cross_reference: MA:0002544
database_cross_reference: MESH:D013582
database_cross_reference: NCIT:C33718
database_cross_reference: TAO:0005154
database_cross_reference: UMLS:C0039097
database_cross_reference: ZFA:0005154
database_cross_reference: galen:SynovialFluid
has exact synonym: joint fluid
has_obo_namespace: uberon
id: UBERON:0001090
in subset: uberon slim
in subset: vertebrate core

caecum
type: Class
subclass of: digestive tract diverticulum
subclass of: Restriction
  on property: part of
  some values from: colon
definition: A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
UBPROP_0000007: caecal
UBPROP_0000008: A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
database_cross_reference: Cecum
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0007531
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181256004
database_cross_reference: BTO:0000166
database_cross_reference: CALOHA:TS-0122
database_cross_reference: EFO:0000850
database_cross_reference: EHDAA2:0000206
database_cross_reference: EHDAA:3913
database_cross_reference: EMAPA:35197
database_cross_reference: EV:0100397
database_cross_reference: FMA:14541
database_cross_reference: GAID:307
database_cross_reference: MA:0000334
database_cross_reference: MESH:A03.492.411.495.209
database_cross_reference: MIAA:0000288
database_cross_reference: NCIT:C12381
database_cross_reference: OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0007531
database_cross_reference: VHOG:0001559
database_cross_reference: galen:Cecum
has exact synonym: caecum
has exact synonym: cecum
has exact synonym: intestinum crassum caecum
has narrow synonym: caeca
has narrow synonym: ceca
has_obo_namespace: uberon
has_related_synonym: blind intestine
has_related_synonym: blindgut
has_related_synonym: intestinum caecum
has_related_synonym: intestinum crassum cecum
id: UBERON:0001153
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
comment: Kardong: in some herbivorous lizards, a cecum is present between small and large intestines

Axiom
annotated source: caecum
annotated property: subClassOf
annotated target: Restriction
  on property: part of
  some values from: colon
source: EHDAA2

Axiom
annotated source: caecum
annotated property: definition
annotated target: A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
database_cross_reference: Cecum

Axiom
annotated source: caecum
annotated property: UBPROP_0000008
annotated target: A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
source: WP

Axiom
annotated source: caecum
annotated property: database_cross_reference
annotated target: UMLS:C0007531
source: ncithesaurus:Cecum

Axiom
annotated source: caecum
annotated property: has exact synonym
annotated target: caecum
database_cross_reference: VHOG:0001559

Axiom
annotated source: caecum
annotated property: has exact synonym
annotated target: cecum
database_cross_reference: FMA:14541

Axiom
annotated source: caecum
annotated property: has narrow synonym
annotated target: caeca
database_cross_reference: NCBITaxon:8782
has synonym type: PLURAL

Axiom
annotated source: caecum
annotated property: has narrow synonym
annotated target: ceca
database_cross_reference: NCBITaxon:8782
has synonym type: PLURAL

Axiom
annotated source: caecum
annotated property: has_related_synonym
annotated target: blind intestine
database_cross_reference: BTO:0000166

Axiom
annotated source: caecum
annotated property: has_related_synonym
annotated target: blindgut
database_cross_reference: BTO:0000166

Axiom
annotated source: caecum
annotated property: has_related_synonym
annotated target: intestinum caecum
database_cross_reference: BTO:0000166

Axiom
annotated source: caecum
annotated property: has_related_synonym
annotated target: intestinum crassum cecum
database_cross_reference: BTO:0000166

colon
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: part of
  some values from: large intestine
subclass of: Restriction
  on property: contributes to morphology of
  some values from: large intestine
definition: Last portion of the large intestine before it becomes the rectum.
editor note: TODO - abstract this such that it legitimately covers all vertebrates
UBPROP_0000001: The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
UBPROP_0000001: The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
UBPROP_0000003: Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
UBPROP_0000007: colonic
UBPROP_0000008: In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
UBPROP_0000008: In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
UBPROP_0000009: it extracts water and salt from solid wastes before they are eliminated from the body[WP]
database_cross_reference: Colon (anatomy)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0009368
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/302508007
database_cross_reference: AAO:0010400
database_cross_reference: BTO:0000269
database_cross_reference: CALOHA:TS-0158
database_cross_reference: EFO:0000361
database_cross_reference: EMAPA:18939
database_cross_reference: EV:0100079
database_cross_reference: FMA:14543
database_cross_reference: GAID:309
database_cross_reference: MA:0000335
database_cross_reference: MAP:0000001
database_cross_reference: MAT:0000526
database_cross_reference: MESH:A03.492.411.495.356
database_cross_reference: NCIT:C12382
database_cross_reference: OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000706
database_cross_reference: UMLS:C0009368
database_cross_reference: VHOG:0000648
database_cross_reference: XAO:0000243
database_cross_reference: ZFA:0000706
database_cross_reference: galen:Colon
has exact synonym: large bowel
has narrow synonym: posterior intestine
has_obo_namespace: uberon
has_related_synonym: hindgut
id: UBERON:0001155
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: colon
annotated property: subClassOf
annotated target: subdivision of digestive tract
order: 3
source: cjm

Axiom
annotated source: colon
annotated property: subClassOf
annotated target: Restriction
  on property: part of
  some values from: large intestine
source: FMA

Axiom
annotated source: colon
annotated property: definition
annotated target: Last portion of the large intestine before it becomes the rectum.
database_cross_reference: Colon (anatomy)
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: ZFIN:curator

Axiom
annotated source: colon
annotated property: UBPROP_0000001
annotated target: The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010400
ontology: AAO
source: UBERON:0001155

Axiom
annotated source: colon
annotated property: UBPROP_0000001
annotated target: The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000706
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: colon
annotated property: UBPROP_0000003
annotated target: Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000648
ontology: VHOG
source: bgee.unil.ch
source: ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11

Axiom
annotated source: colon
annotated property: database_cross_reference
annotated target: UMLS:C0009368
source: ncithesaurus:Colon

biliary tree
type: Class
subclass of: endoderm-derived structure
subclass of: digestive system element
definition: A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder.
imported from: uberon.owl
UBPROP_0000001: Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]
database_cross_reference: Biliary tract
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0005423
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181267003
database_cross_reference: AAO:0011020
database_cross_reference: EMAPA:35172
database_cross_reference: FMA:14665
database_cross_reference: UMLS:C0005423
database_cross_reference: XAO:0000455
has_obo_namespace: uberon
has_related_synonym: biliary tract
id: UBERON:0001173
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
comment: The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP]

pancreas
type: Class
subclass of: viscus
definition: An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
imported from: uberon.owl
UBPROP_0000001: Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
UBPROP_0000003: In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
UBPROP_0000007: pancreatic
UBPROP_0000008: As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
UBPROP_0000008: The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
UBPROP_0000009: The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans
database_cross_reference: Pancreas
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0030274
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181277001
database_cross_reference: AAO:0010112
database_cross_reference: BTO:0000988
database_cross_reference: CALOHA:TS-0736
database_cross_reference: EFO:0000855
database_cross_reference: EHDAA2:0001367
database_cross_reference: EHDAA:6893
database_cross_reference: EMAPA:17503
database_cross_reference: EV:0100092
database_cross_reference: FMA:7198
database_cross_reference: GAID:334
database_cross_reference: MA:0000120
database_cross_reference: MAT:0000075
database_cross_reference: MESH:D010179
database_cross_reference: MIAA:0000075
database_cross_reference: NCIT:C12393
database_cross_reference: OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000140
database_cross_reference: UMLS:C0030274
database_cross_reference: VHOG:0000050
database_cross_reference: XAO:0000136
database_cross_reference: ZFA:0000140
database_cross_reference: galen:Pancreas
has_obo_namespace: uberon
id: UBERON:0001264
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

articular capsule
type: Class
subclass of: membrane organ
definition: An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
imported from: uberon.owl
UBPROP_0000012: check ncita
database_cross_reference: Articular capsule
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0206207
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/182238002
database_cross_reference: EMAPA:37621
database_cross_reference: FMA:34836
database_cross_reference: GAID:263
database_cross_reference: MA:0001519
database_cross_reference: MESH:D017746
database_cross_reference: NCIT:C32259
database_cross_reference: NCIT:C84388
database_cross_reference: UMLS:C0206207
database_cross_reference: galen:JointCapsule
has exact synonym: capsula articularis
has exact synonym: fibrous capsule of joint
has exact synonym: joint capsule
has exact synonym: joint fibrous capsule
has_obo_namespace: uberon
has_related_synonym: capsulae articulares
id: UBERON:0001484
in subset: organ slim
in subset: uberon slim

mammary gland
type: Class
subclass of: ectoderm-derived structure
subclass of: exocrine gland of integumental system
subclass of: Restriction
  on property: produces
  some values from: milk
definition: A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males.
editor note: Originally this was classified as a female reproductive structure, as it was in the MP in 2011
imported from: uberon.owl
UBPROP_0000001: Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG]
UBPROP_0000003: The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]
UBPROP_0000007: mammary
UBPROP_0000008: A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts
UBPROP_0000008: The male Dayak fruit bat has lactating mammary glands
UBPROP_0000008: The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges.
UBPROP_0000012: The BTO class represents the combination of nipple plus lobe
UBPROP_0000012: The FMA class represents an individule lobe. The nipple is not a part
UBPROP_0000012: The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts
database_cross_reference: Mammary gland
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0929301
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/361720005
database_cross_reference: BTO:0000817
database_cross_reference: CALOHA:TS-0595
database_cross_reference: EFO:0000854
database_cross_reference: EMAPA:17759
database_cross_reference: EV:0100125
database_cross_reference: FMA:286452
database_cross_reference: MA:0000145
database_cross_reference: MAT:0000073
database_cross_reference: MESH:D008321
database_cross_reference: MIAA:0000073
database_cross_reference: NCIT:C12367
database_cross_reference: OpenCyc:Mx4rvVjVq5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0929301
database_cross_reference: VHOG:0000398
has exact synonym: glandula mammaria
has exact synonym: lactiferous gland
has narrow synonym: lobe of breast
has narrow synonym: milk patch
has_obo_namespace: uberon
has_related_synonym: Brustdruese
has_related_synonym: dug
has_related_synonym: glandula mammaria
has_related_synonym: lobe of mammary gland
has_related_synonym: mamma
has_related_synonym: mammae
id: UBERON:0001911
in subset: efo slim
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

milk
type: Class
subclass of: bodily fluid
subclass of: mammary gland fluid/secretion
definition: An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
editor note: to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular.
imported from: uberon.owl
UBPROP_0000003: The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]
UBPROP_0000012: ncit:Milk refers specifically to cow milk
database_cross_reference: Breast milk
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1511310
database_cross_reference: BTO:0000868
database_cross_reference: CALOHA:TS-0636
database_cross_reference: EMAPA:36540
database_cross_reference: ENVO:02000031
database_cross_reference: EV:0100126
database_cross_reference: FMA:62100
database_cross_reference: GAID:1230
database_cross_reference: MA:0002552
database_cross_reference: MAT:0000056
database_cross_reference: MESH:A13.622
database_cross_reference: MIAA:0000056
database_cross_reference: NCIT:C13401
database_cross_reference: OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C1511310
database_cross_reference: VHOG:0001263
database_cross_reference: galen:Milk
has exact synonym: mammary gland milk
has_obo_namespace: uberon
id: UBERON:0001913
in subset: pheno slim
in subset: uberon slim

blood plasma
type: Class
subclass of: haemolymphatic fluid
subclass of: Restriction
  on property: part of
  some values from: blood
definition: The liquid component of blood, in which erythrocytes are suspended.
imported from: uberon.owl
has broad synonym: plasma
has broad synonym: portion of plasma
database_cross_reference: Blood plasma
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0032105
database_cross_reference: BTO:0000131
database_cross_reference: CALOHA:TS-0800
database_cross_reference: EFO:0001905
database_cross_reference: EMAPA:35690
database_cross_reference: FMA:62970
database_cross_reference: GAID:1178
database_cross_reference: MA:0002501
database_cross_reference: MAT:0000052
database_cross_reference: MESH:D010949
database_cross_reference: MIAA:0000052
database_cross_reference: NCIT:C13356
database_cross_reference: OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
database_cross_reference: UMLS:C0032105
has exact synonym: blood plasm
has exact synonym: portion of blood plasma
has_obo_namespace: uberon
id: UBERON:0001969
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

bile
type: Class
equivalent class: Class
  intersection of: secretion of exocrine gland
  intersection of: Restriction
    on property: produced_by
    some values from: liver
subclass of: secretion of exocrine gland
subclass of: bodily fluid
subclass of: Restriction
  on property: produced_by
  some values from: liver
definition: vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
imported from: uberon.owl
UBPROP_0000008: In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.
UBPROP_0000009: aids the process of digestion of lipids in the small intestine
UBPROP_0000009: bile salts function to emulsify dietary fats and facilitate their intestinal absorption
UBPROP_0000009: elimination of cholesterol
UBPROP_0000009: major excretory route for potentially harmful exogenous lipophilic substances
UBPROP_0000009: many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates
UBPROP_0000009: protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine
database_cross_reference: Bile
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0005388
database_cross_reference: BTO:0000121
database_cross_reference: CALOHA:TS-1172
database_cross_reference: ENVO:02000023
database_cross_reference: FMA:62971
database_cross_reference: GAID:1157
database_cross_reference: MA:0002513
database_cross_reference: MESH:D001646
database_cross_reference: NCIT:C13192
database_cross_reference: UMLS:C0005388
database_cross_reference: ZFA:0005857
database_cross_reference: galen:Bile
has_obo_namespace: uberon
has_related_synonym: fel
has_related_synonym: gall
id: UBERON:0001970
in subset: pheno slim
in subset: uberon slim

placenta
type: Class
subclass of: organ
subclass of: mesoderm-derived structure
subclass of: reproductive structure
subclass of: Restriction
  on property: part of
  some values from: female reproductive system
definition: organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
imported from: uberon.owl
UBPROP_0000003: Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]
UBPROP_0000007: placental
UBPROP_0000008: Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN10:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: http://dx.doi.org/10.1002/jmor.11011
database_cross_reference: Placenta
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0032043
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181455002
database_cross_reference: BTO:0001078
database_cross_reference: CALOHA:TS-0799
database_cross_reference: EFO:0001407
database_cross_reference: EMAPA:35689
database_cross_reference: EV:0100119
database_cross_reference: FMA:63934
database_cross_reference: GAID:379
database_cross_reference: MA:0000386
database_cross_reference: MAT:0000279
database_cross_reference: MESH:A16.759
database_cross_reference: MIAA:0000279
database_cross_reference: NCIT:C13272
database_cross_reference: OpenCyc:Mx4rvv4zZ5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0032043
database_cross_reference: VHOG:0001266
has exact synonym: allantoic placenta
has exact synonym: eutherian placenta
has_obo_namespace: uberon
id: UBERON:0001987
in subset: efo slim
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
comment: Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities.

feces
type: Class
subclass of: excreta
definition: Portion of semisolid bodily waste discharged through the anus[MW,modified]
imported from: uberon.owl
UBPROP_0000001: Excretion in semisolid state processed by the intestine.[FMA]
UBPROP_0000007: fecal
has broad synonym: excreta
database_cross_reference: Feces
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0015733
database_cross_reference: BTO:0000440
database_cross_reference: CALOHA:TS-2345
database_cross_reference: ENVO:00002003
database_cross_reference: FMA:64183
database_cross_reference: GAID:1199
database_cross_reference: MA:0002509
database_cross_reference: MAT:0000053
database_cross_reference: MESH:D005243
database_cross_reference: MIAA:0000053
database_cross_reference: NCIT:C13234
database_cross_reference: OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0015733
database_cross_reference: galen:Feces
has exact synonym: faeces
has exact synonym: fecal material
has exact synonym: fecal matter
has exact synonym: matières fécales@fr
has exact synonym: merde@fr
has exact synonym: partie de la merde@fr
has exact synonym: piece of shit
has exact synonym: porción de mierda@es
has exact synonym: portion of excrement
has exact synonym: portion of faeces
has exact synonym: portion of fecal material
has exact synonym: portion of fecal matter
has exact synonym: portion of feces
has exact synonym: portionem cacas
has exact synonym: stool
has exact synonym: teil der fäkalien@de
has narrow synonym: cow dung
has narrow synonym: cow pat
has narrow synonym: dung
has narrow synonym: fewmet
has narrow synonym: frass
has narrow synonym: guano
has narrow synonym: portion of dung
has narrow synonym: portion of guano
has narrow synonym: portion of scat
has narrow synonym: scat
has narrow synonym: spraint
has_obo_namespace: uberon
has_related_synonym: droppings
has_related_synonym: excrement
has_related_synonym: ordure
has_related_synonym: spoor
id: UBERON:0001988
in subset: pheno slim
in subset: uberon slim

lung
type: Class
subclass of: respiration organ
subclass of: endoderm-derived structure
subclass of: thoracic cavity element
subclass of: lateral structure
subclass of: Restriction
  on property: part of
  some values from: pair of lungs
subclass of: Restriction
  on property: in_lateral_side_of
  some values from: pair of lungs
subclass of: Restriction
  on property: contributes to morphology of
  some values from: respiratory system
definition: Respiration organ that develops as an oupocketing of the esophagus.
imported from: uberon.owl
UBPROP_0000001: Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
UBPROP_0000003: Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
UBPROP_0000007: pulmonary
UBPROP_0000008: respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
database_cross_reference: Lung
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0024109
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181216001
database_cross_reference: AAO:0000275
database_cross_reference: AAO:0010567
database_cross_reference: BTO:0000763
database_cross_reference: CALOHA:TS-0568
database_cross_reference: EFO:0000934
database_cross_reference: EHDAA2:0001042
database_cross_reference: EHDAA:1554
database_cross_reference: EHDAA:2205
database_cross_reference: EMAPA:16728
database_cross_reference: EV:0100042
database_cross_reference: FMA:7195
database_cross_reference: GAID:345
database_cross_reference: MA:0000415
database_cross_reference: MAT:0000135
database_cross_reference: MESH:D008168
database_cross_reference: MIAA:0000135
database_cross_reference: NCIT:C12468
database_cross_reference: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0024109
database_cross_reference: VHOG:0000310
database_cross_reference: XAO:0000119
database_cross_reference: galen:Lung
has exact synonym: pulmo
has_obo_namespace: uberon
id: UBERON:0002048
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
comment: Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]

embryonic structure
type: Class
equivalent class: Class
  intersection of: developing anatomical structure
  intersection of: Restriction
    on property: part of
    some values from: embryo
subclass of: developing anatomical structure
subclass of: Restriction
  on property: part of
  some values from: embryo
definition: Anatomical structure that is part of an embryo.
imported from: uberon.owl
UBPROP_0000001: Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
UBPROP_0000001: Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
UBPROP_0000001: Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
UBPROP_0000012: in FMA embryo is_a embryonic structure
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0013948
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/667009
database_cross_reference: AAO:0000138
database_cross_reference: BILA:0000034
database_cross_reference: BTO:0000174
database_cross_reference: CALOHA:TS-2110
database_cross_reference: EFO:0000461
database_cross_reference: FBbt:00004208
database_cross_reference: FMA:69067
database_cross_reference: GAID:407
database_cross_reference: MESH:D004628
database_cross_reference: NCIT:C13229
database_cross_reference: RETIRED_EHDAA2:0003169
database_cross_reference: TAO:0001105
database_cross_reference: UMLS:C0013948
database_cross_reference: VSAO:0000178
database_cross_reference: XAO:0003042
database_cross_reference: ZFA:0001105
has exact synonym: developing embryonic structure
has exact synonym: embryonic anatomical structure
has_obo_namespace: uberon
has_related_synonym: developing structure
has_related_synonym: embryonale Struktur
has_related_synonym: embryonic structures
id: UBERON:0002050
in subset: efo slim
in subset: inconsistent with fma
in subset: vertebrate core

viscus
type: Class
subclass of: trunk region element
definition: An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
imported from: uberon.owl
UBPROP_0000001: An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
UBPROP_0000012: general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
database_cross_reference: Viscus
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0042779
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/118760003
database_cross_reference: AAO:0010386
database_cross_reference: BTO:0001491
database_cross_reference: EHDAA:512
database_cross_reference: EMAPA:16245
database_cross_reference: FMA:7085
database_cross_reference: MA:0000019
database_cross_reference: MESH:D014781
database_cross_reference: NCIT:C28287
database_cross_reference: RETIRED_EHDAA2:0002201
database_cross_reference: UMLS:C0042779
database_cross_reference: XAO:0003034
has exact synonym: visceral organ
has exact synonym: visceral organ system
has_obo_namespace: uberon
has_related_synonym: Organsystem@de
has_related_synonym: splanchnic tissue
has_related_synonym: viscera
has_related_synonym: visceral tissue
id: UBERON:0002075
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: upper level

skin of body
type: Class
subclass of: organ
subclass of: ectoderm-derived structure
definition: The organ covering the body that consists of the dermis and epidermis.
curator note: consider 'integumentary system' for invertebrates
imported from: uberon.owl
UBPROP_0000012: MA uses the term skin to refer to what is called here: zone of skin
database_cross_reference: Skin
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1123023
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181469002
database_cross_reference: BTO:0001253
database_cross_reference: CALOHA:TS-0934
database_cross_reference: EFO:0000962
database_cross_reference: EHDAA2:0001844
database_cross_reference: EMAPA:17525
database_cross_reference: FMA:7163
database_cross_reference: MESH:D012867
database_cross_reference: MFMO:0000099
database_cross_reference: NCIT:C12470
database_cross_reference: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C1123023
database_cross_reference: XAO:0000023
database_cross_reference: galen:Skin
has exact synonym: entire skin
has exact synonym: skin organ
has_obo_namespace: uberon
has_related_synonym: entire integument
has_related_synonym: integument
has_related_synonym: integumental organ
has_related_synonym: pelt
has_related_synonym: skin
id: UBERON:0002097
in subset: efo slim
in subset: major organ
in subset: pheno slim
in subset: uberon slim

vestibulo-auditory system
type: Class
subclass of: sensory system
definition: Sensory system responsible for the perception of spatial orientation and auditory stimuli.
imported from: uberon.owl
UBPROP_0000001: The sensory system used for balance and hearing.[AAO]
database_cross_reference: AAO:0000631
database_cross_reference: EMAPA:36002
database_cross_reference: EMAPA:37985
database_cross_reference: FMA:78500
database_cross_reference: TAO:0001138
database_cross_reference: XAO:0003195
database_cross_reference: ZFA:0001138
has exact synonym: auditory organ system
has exact synonym: vestibuloauditory system
has_obo_namespace: uberon
has_related_synonym: auditory system
has_related_synonym: auditory/vestibular system
has_related_synonym: vestibuloauditory system
id: UBERON:0002105
in subset: functional classification
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

liver
type: Class
subclass of: exocrine gland
subclass of: endoderm-derived structure
subclass of: abdomen element
subclass of: digestive system gland
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part of
    some values from: immune system
subclass of: Restriction
  on property: produces
  some values from: bile
definition: An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
imported from: uberon.owl
UBPROP_0000001: Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
UBPROP_0000002: relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
UBPROP_0000003: All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
UBPROP_0000007: hepatic
UBPROP_0000008: An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
UBPROP_0000008: The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
UBPROP_0000009: secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
UBPROP_0000012: Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
database_cross_reference: Liver
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0023884
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181268008
database_cross_reference: AAO:0010111
database_cross_reference: BTO:0000759
database_cross_reference: CALOHA:TS-0564
database_cross_reference: EFO:0000887
database_cross_reference: EHDAA2:0000997
database_cross_reference: EHDAA:2197
database_cross_reference: EMAPA:16846
database_cross_reference: EV:0100089
database_cross_reference: FMA:7197
database_cross_reference: GAID:288
database_cross_reference: MA:0000358
database_cross_reference: MAT:0000097
database_cross_reference: MESH:D008099
database_cross_reference: MIAA:0000097
database_cross_reference: NCIT:C12392
database_cross_reference: OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000123
database_cross_reference: UMLS:C0023884
database_cross_reference: VHOG:0000257
database_cross_reference: XAO:0000133
database_cross_reference: ZFA:0000123
database_cross_reference: galen:Liver
has_obo_namespace: uberon
has_related_synonym: iecur
has_related_synonym: jecur
id: UBERON:0002107
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

small intestine
type: Class
subclass of: subdivision of digestive tract
subclass of: digestive system element
subclass of: Restriction
  on property: part of
  some values from: intestine
subclass of: Restriction
  on property: contributes to morphology of
  some values from: intestine
definition: Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
UBPROP_0000001: The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
UBPROP_0000003: Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
database_cross_reference: Small intestine
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0021852
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181250005
database_cross_reference: AAO:0010397
database_cross_reference: BTO:0000651
database_cross_reference: CALOHA:TS-0942
database_cross_reference: EFO:0000841
database_cross_reference: EMAPA:32834
database_cross_reference: EV:0100072
database_cross_reference: FMA:7200
database_cross_reference: GAID:313
database_cross_reference: MA:0000337
database_cross_reference: MAT:0000047
database_cross_reference: MESH:A03.492.411.620
database_cross_reference: MIAA:0000047
database_cross_reference: NCIT:C12386
database_cross_reference: OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0001323
database_cross_reference: UMLS:C0021852
database_cross_reference: VHOG:0000055
database_cross_reference: XAO:0000130
database_cross_reference: ZFA:0001323
database_cross_reference: galen:SmallIntestine
has exact synonym: small bowel
has exact synonym: small intestine
has_obo_namespace: uberon
has_related_synonym: anterior intestine
has_related_synonym: intestinum tenue
has_related_synonym: mid intestine
id: UBERON:0002108
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: small intestine
annotated property: subClassOf
annotated target: subdivision of digestive tract
order: 2
source: cjm

Axiom
annotated source: small intestine
annotated property: definition
annotated target: Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
database_cross_reference: Small intestine
database_cross_reference: ISBN10:0073040584

Axiom
annotated source: small intestine
annotated property: UBPROP_0000001
annotated target: The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001323
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: small intestine
annotated property: UBPROP_0000003
annotated target: Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000055
ontology: VHOG
source: bgee.unil.ch
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566

Axiom
annotated source: small intestine
annotated property: database_cross_reference
annotated target: UMLS:C0021852
source: ncithesaurus:Small_Intestine

Axiom
annotated source: small intestine
annotated property: has_related_synonym
annotated target: intestinum tenue
database_cross_reference: Small intestine
has synonym type: LATIN

Axiom
annotated source: small intestine
annotated property: has_related_synonym
annotated target: intestinum tenue
database_cross_reference: BTO:0000651

duodenum
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: part of
  some values from: small intestine
subclass of: Restriction
  on property: proximalmost_part_of
  some values from: small intestine
subclass of: Restriction
  on property: contributes to morphology of
  some values from: small intestine
definition: The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
UBPROP_0000001: The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBPROP_0000007: duodenal
UBPROP_0000008: In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.
UBPROP_0000008: In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.
database_cross_reference: Duodenum
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0013303
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181247007
database_cross_reference: AAO:0010402
database_cross_reference: BTO:0000365
database_cross_reference: CALOHA:TS-0214
database_cross_reference: EFO:0000851
database_cross_reference: EMAPA:18852
database_cross_reference: EV:0100073
database_cross_reference: FMA:7206
database_cross_reference: GAID:284
database_cross_reference: MA:0000338
database_cross_reference: MAT:0000044
database_cross_reference: MESH:A03.492.411.620.270
database_cross_reference: MIAA:0000044
database_cross_reference: NCIT:C12263
database_cross_reference: OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0013303
database_cross_reference: VHOG:0000052
database_cross_reference: XAO:0000236
database_cross_reference: galen:Duodenum
has_obo_namespace: uberon
has_related_synonym: proximal intestine
has_related_synonym: upper intestine
id: UBERON:0002114
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: duodenum
annotated property: subClassOf
annotated target: subdivision of digestive tract
order: 3
source: cjm

Axiom
annotated source: duodenum
annotated property: definition
annotated target: The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
database_cross_reference: Duodenum
database_cross_reference: ISBN:0815318960

Axiom
annotated source: duodenum
annotated property: UBPROP_0000001
annotated target: The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000052
ontology: VHOG
source: bgee.unil.ch

Axiom
annotated source: duodenum
annotated property: UBPROP_0000008
annotated target: In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.
has scope: NCBITaxon:32443
source: Duodenum

Axiom
annotated source: duodenum
annotated property: UBPROP_0000008
annotated target: In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.
has scope: NCBITaxon:9606
source: Duodenum

Axiom
annotated source: duodenum
annotated property: database_cross_reference
annotated target: UMLS:C0013303
source: ncithesaurus:Duodenum

Axiom
annotated source: duodenum
annotated property: has_related_synonym
annotated target: proximal intestine
database_cross_reference: BTO:0000365

Axiom
annotated source: duodenum
annotated property: has_related_synonym
annotated target: upper intestine
database_cross_reference: BTO:0000365

jejunum
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: part of
  some values from: small intestine
subclass of: Restriction
  on property: contributes to morphology of
  some values from: small intestine
definition: the portion of the small intestine that extends from the duodenum to the ileum
editor note: TODO consider ZFA:0001323 mid intestine, see also small intestine
UBPROP_0000001: The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBPROP_0000007: jejunal
UBPROP_0000008: The jejunum is the middle section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms middle intestine or mid-gut may be used instead of jejunum.[Wikipedia:Jejunum]
database_cross_reference: Jejunum
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0022378
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181248002
database_cross_reference: BTO:0000657
database_cross_reference: CALOHA:TS-0496
database_cross_reference: EFO:0001333
database_cross_reference: EMAPA:18666
database_cross_reference: EV:0100074
database_cross_reference: FMA:7207
database_cross_reference: GAID:318
database_cross_reference: MA:0000340
database_cross_reference: MAT:0000045
database_cross_reference: MESH:A03.492.411.620.625
database_cross_reference: MIAA:0000045
database_cross_reference: NCIT:C12388
database_cross_reference: OpenCyc:Mx4rwATkPJwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0022378
database_cross_reference: VHOG:0000053
database_cross_reference: galen:Jejunum
has_obo_namespace: uberon
has_related_synonym: intestinum jejunum
has_related_synonym: mid-intestine
has_related_synonym: middle intestine
id: UBERON:0002115
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: jejunum
annotated property: subClassOf
annotated target: subdivision of digestive tract
order: 3
source: cjm

Axiom
annotated source: jejunum
annotated property: definition
annotated target: the portion of the small intestine that extends from the duodenum to the ileum
database_cross_reference: MGI:monikat
database_cross_reference: MP:0004002

Axiom
annotated source: jejunum
annotated property: UBPROP_0000001
annotated target: The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000053
ontology: VHOG
source: bgee.unil.ch

Axiom
annotated source: jejunum
annotated property: database_cross_reference
annotated target: UMLS:C0022378
source: ncithesaurus:Jejunum

Axiom
annotated source: jejunum
annotated property: has_related_synonym
annotated target: intestinum jejunum
database_cross_reference: BTO:0000657

Axiom
annotated source: jejunum
annotated property: has_related_synonym
annotated target: mid-intestine
database_cross_reference: Jejunum

Axiom
annotated source: jejunum
annotated property: has_related_synonym
annotated target: middle intestine
database_cross_reference: BTO:0000657

ileum
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: part of
  some values from: small intestine
subclass of: Restriction
  on property: contributes to morphology of
  some values from: small intestine
definition: the portion of the small intestine that extends from the jejunum to the colon
editor note: TODO consider ZFA:0000706 posterior intestine, see also colon
UBPROP_0000003: Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
UBPROP_0000007: ileal
UBPROP_0000008: The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.[Wikipedia:Ileum]
database_cross_reference: Ileum
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0020885
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181249005
database_cross_reference: AAO:0010403
database_cross_reference: BTO:0000620
database_cross_reference: CALOHA:TS-0472
database_cross_reference: EFO:0001334
database_cross_reference: EMAPA:32764
database_cross_reference: EV:0100075
database_cross_reference: FMA:7208
database_cross_reference: GAID:315
database_cross_reference: MA:0000339
database_cross_reference: MAT:0000282
database_cross_reference: MESH:A03.492.411.620.484
database_cross_reference: MIAA:0000282
database_cross_reference: NCIT:C12387
database_cross_reference: OpenCyc:Mx4rvdcLHZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0020885
database_cross_reference: VHOG:0000647
database_cross_reference: XAO:0000237
database_cross_reference: galen:Ileum
has_obo_namespace: uberon
has_related_synonym: distal intestine
has_related_synonym: intestinum ileum
has_related_synonym: lower intestine
has_related_synonym: posterior intestine
id: UBERON:0002116
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

Axiom
annotated source: ileum
annotated property: subClassOf
annotated target: subdivision of digestive tract
order: 3
source: cjm

Axiom
annotated source: ileum
annotated property: definition
annotated target: the portion of the small intestine that extends from the jejunum to the colon
database_cross_reference: ISBN:0-683-40008-8
database_cross_reference: MGI:csmith
database_cross_reference: MP:0002581

Axiom
annotated source: ileum
annotated property: UBPROP_0000003
annotated target: Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000647
ontology: VHOG
source: bgee.unil.ch
source: ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11

Axiom
annotated source: ileum
annotated property: database_cross_reference
annotated target: UMLS:C0020885
source: ncithesaurus:Ileum

Axiom
annotated source: ileum
annotated property: has_related_synonym
annotated target: distal intestine
database_cross_reference: BTO:0000620

Axiom
annotated source: ileum
annotated property: has_related_synonym
annotated target: intestinum ileum
database_cross_reference: BTO:0000620

Axiom
annotated source: ileum
annotated property: has_related_synonym
annotated target: lower intestine
database_cross_reference: BTO:0000620

Axiom
annotated source: ileum
annotated property: has_related_synonym
annotated target: posterior intestine
database_cross_reference: Ileum

right lung
type: Class
equivalent class: Class
  intersection of: lung
  intersection of: Restriction
    on property: in_right_side_of
    some values from: pair of lungs
subclass of: lung
subclass of: Restriction
  on property: in_right_side_of
  some values from: pair of lungs
definition: Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
imported from: uberon.owl
UBPROP_0000003: Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
UBPROP_0000006: https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
database_cross_reference: Right lung
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0225706
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/361967000
database_cross_reference: EHDAA2:0001730
database_cross_reference: EHDAA:4969
database_cross_reference: EMAPA:17661
database_cross_reference: FMA:7309
database_cross_reference: MA:0000426
database_cross_reference: NCIT:C33483
database_cross_reference: UMLS:C0225706
database_cross_reference: VHOG:0000301
has_obo_namespace: uberon
id: UBERON:0002167
in subset: pheno slim
in subset: uberon slim

left lung
type: Class
equivalent class: Class
  intersection of: lung
  intersection of: Restriction
    on property: in_left_side_of
    some values from: pair of lungs
subclass of: lung
subclass of: Restriction
  on property: in_left_side_of
  some values from: pair of lungs
definition: Lung which consists of the left upper lobe and left lower lobe.[FMA]
imported from: uberon.owl
UBPROP_0000003: Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
UBPROP_0000006: https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
database_cross_reference: Left lung
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0225730
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/361982005
database_cross_reference: EHDAA2:0000943
database_cross_reference: EHDAA:4947
database_cross_reference: EMAPA:17653
database_cross_reference: FMA:7310
database_cross_reference: MA:0000425
database_cross_reference: NCIT:C32967
database_cross_reference: UMLS:C0225730
database_cross_reference: VHOG:0000618
has_obo_namespace: uberon
id: UBERON:0002168
in subset: pheno slim
in subset: uberon slim

hemolymphoid system
type: Class
subclass of: anatomical system
definition: Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
imported from: uberon.owl
database_cross_reference: CALOHA:TS-2018
database_cross_reference: EHDAA2:0004615
database_cross_reference: EMAPA:18765
database_cross_reference: FMA:74562
database_cross_reference: MA:0000013
has exact synonym: hematolymphoid system
has exact synonym: lymphomyeloid complex
has_obo_namespace: uberon
has_related_synonym: haemolymphoid system
id: UBERON:0002193

musculoskeletal system
type: Class
subclass of: anatomical system
definition: Anatomical system that consists of the muscular and skeletal systems.
imported from: uberon.owl
UBPROP_0000001: Anatomical system that provides locomotion and physical support to the organism.[AAO]
UBPROP_0000003: There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
UBPROP_0000007: musculoskeletal
contributor: cmungall
database_cross_reference: Musculoskeletal system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0026860
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/278858007
database_cross_reference: AAO:0010546
database_cross_reference: CALOHA:TS-1311
database_cross_reference: EMAPA:32714
database_cross_reference: EV:0100139
database_cross_reference: FMA:7482
database_cross_reference: GAID:98
database_cross_reference: MA:0002418
database_cross_reference: MESH:D009141
database_cross_reference: NCIT:C12754
database_cross_reference: OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g
database_cross_reference: UMLS:C0026860
database_cross_reference: VHOG:0001275
database_cross_reference: VSAO:0000031
database_cross_reference: XAO:0000168
has exact synonym: musculo-skeletal system
has_obo_namespace: uberon
id: UBERON:0002204
in subset: uberon slim

olfactory organ
type: Class
subclass of: sense organ
definition: An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
editor note: An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
imported from: uberon.owl
UBPROP_0000012: fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
database_cross_reference: AAO:0010180
database_cross_reference: BTO:0001772
database_cross_reference: FBbt:00005158
database_cross_reference: FMA:77659
database_cross_reference: VHOG:0000287
database_cross_reference: XAO:0000273
has exact synonym: olfactory organ
has exact synonym: olfactory sense organ
has exact synonym: olfactory sensory organ
has narrow synonym: main olfactory organ
has narrow synonym: primary olfactory organ
has_obo_namespace: uberon
has_related_synonym: olfactory neuroepithelium
has_related_synonym: organ olfactus
has_related_synonym: organum olfactorium
id: UBERON:0002268
in subset: functional classification

exocrine system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: composed primarily of
  some values from: exocrine gland
definition: Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
imported from: uberon.owl
database_cross_reference: Exocrine gland
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1516995
database_cross_reference: CALOHA:TS-2057
database_cross_reference: EHDAA2:0002225
database_cross_reference: EMAPA:35329
database_cross_reference: FMA:85539
database_cross_reference: MA:0002411
database_cross_reference: NCIT:C12957
database_cross_reference: UMLS:C1516995
database_cross_reference: WikipediaCategory:Exocrine_system
has exact synonym: exocrine glandular system
has_obo_namespace: uberon
id: UBERON:0002330
in subset: pheno slim
in subset: uberon slim

exocrine gland
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part of
    some values from: exocrine system
subclass of: gland
subclass of: Restriction
  on property: part of
  some values from: exocrine system
definition: A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
editor note: Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
imported from: uberon.owl
database_cross_reference: Exocrine gland
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0015282
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/115976003
database_cross_reference: AEO:0000097
database_cross_reference: BTO:0000765
database_cross_reference: CALOHA:TS-2012
database_cross_reference: EHDAA2:0003097
database_cross_reference: EMAPA:35327
database_cross_reference: FMA:9596
database_cross_reference: GAID:34
database_cross_reference: MA:0002564
database_cross_reference: MESH:D005088
database_cross_reference: NCIT:C12712
database_cross_reference: UMLS:C0015282
has exact synonym: ducted gland
has exact synonym: glandula exocrina
has_obo_namespace: uberon
id: UBERON:0002365
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

endocrine gland
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part of
    some values from: endocrine system
subclass of: gland
subclass of: Restriction
  on property: part of
  some values from: endocrine system
definition: Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
imported from: uberon.owl
database_cross_reference: Endocrine gland
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0014133
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/40818001
database_cross_reference: AEO:0000098
database_cross_reference: BTO:0001488
database_cross_reference: CALOHA:TS-1300
database_cross_reference: EHDAA2:0003098
database_cross_reference: EMAPA:35999
database_cross_reference: FMA:9602
database_cross_reference: GAID:335
database_cross_reference: MA:0002563
database_cross_reference: MESH:D004702
database_cross_reference: NCIT:C12704
database_cross_reference: OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0014133
has exact synonym: ductless gland
has exact synonym: glandula endocrina
has_obo_namespace: uberon
has_related_synonym: ductless gland
has_related_synonym: glandulae endocrinae
id: UBERON:0002368
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

hematopoietic system
type: Class
subclass of: anatomical system
subclass of: mesoderm-derived structure
subclass of: Restriction
  on property: part of
  some values from: hemolymphoid system
definition: Anatomical system that is involved in the production of hematopoietic cells.
imported from: uberon.owl
UBPROP_0000001: Anatomical system that consists of the blood and blood forming tissues.[AAO]
UBPROP_0000003: Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
UBPROP_0000007: hematopoietic
UBPROP_0000008: In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
database_cross_reference: Haematopoiesis
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0018957
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362587009
database_cross_reference: AAO:0011002
database_cross_reference: BTO:0000570
database_cross_reference: CALOHA:TS-0449
database_cross_reference: EFO:0000798
database_cross_reference: EMAPA:35402
database_cross_reference: EV:0100045
database_cross_reference: FMA:9667
database_cross_reference: GAID:1008
database_cross_reference: MA:0002434
database_cross_reference: MAT:0000022
database_cross_reference: MESH:D006413
database_cross_reference: MIAA:0000022
database_cross_reference: NCIT:C12909
database_cross_reference: TAO:0005023
database_cross_reference: UMLS:C0018957
database_cross_reference: VHOG:0001624
database_cross_reference: XAO:0000122
database_cross_reference: ZFA:0005023
has exact synonym: haematological system
has exact synonym: haemopoietic system
has exact synonym: organa haemopoietica
has_obo_namespace: uberon
has_related_synonym: Blutbildungssystem
has_related_synonym: haematopoietic system
has_related_synonym: hematological system
has_related_synonym: hematolymphoid system
has_related_synonym: hemopoietic system
id: UBERON:0002390
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

lymph
type: Class
subclass of: haemolymphatic fluid
subclass of: Restriction
  on property: develops_from
  some values from: interstitial fluid
subclass of: Restriction
  on property: transformation of
  some values from: interstitial fluid
definition: Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
imported from: uberon.owl
database_cross_reference: Lymph
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0024202
database_cross_reference: BTO:0000855
database_cross_reference: CALOHA:TS-0580
database_cross_reference: EFO:0000871
database_cross_reference: ENVO:02000041
database_cross_reference: EV:0100049
database_cross_reference: FMA:9671
database_cross_reference: GAID:1186
database_cross_reference: MA:0002520
database_cross_reference: MAT:0000055
database_cross_reference: MESH:A12.207.630
database_cross_reference: MIAA:0000055
database_cross_reference: NCIT:C13252
database_cross_reference: OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0024202
database_cross_reference: VHOG:0001590
database_cross_reference: ZFA:0005658
database_cross_reference: galen:Lymph
has_obo_namespace: uberon
has_related_synonym: lympha
id: UBERON:0002391
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

immune system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: protects
  some values from: multicellular organism
definition: Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
imported from: uberon.owl
UBPROP_0000003: The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
database_cross_reference: Immune system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0020962
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362590003
database_cross_reference: AAO:0011003
database_cross_reference: BILA:0000104
database_cross_reference: BTO:0005810
database_cross_reference: FMA:9825
database_cross_reference: GAID:328
database_cross_reference: MA:0002711
database_cross_reference: MESH:D007107
database_cross_reference: NCIT:C12735
database_cross_reference: OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA
database_cross_reference: TAO:0001159
database_cross_reference: UMLS:C0020962
database_cross_reference: VHOG:0001247
database_cross_reference: XAO:0003152
database_cross_reference: ZFA:0001159
has_obo_namespace: uberon
id: UBERON:0002405
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

integumental system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: bounding layer of
  some values from: multicellular organism
definition: Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
imported from: uberon.owl
UBPROP_0000003: (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
contributor: cmungall
contributor: tfhayamizu
has_alternative_id: UBERON:0007029
database_cross_reference: Integumentary system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0037267
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/361692004
database_cross_reference: AEO:0000154
database_cross_reference: BILA:0000118
database_cross_reference: CALOHA:TS-1299
database_cross_reference: CARO:0002001
database_cross_reference: EFO:0000807
database_cross_reference: EHDAA2:0000836
database_cross_reference: EHDAA2_RETIRED:0003154
database_cross_reference: EHDAA:6520
database_cross_reference: EMAPA:17524
database_cross_reference: EV:0100151
database_cross_reference: FBbt:00004969
database_cross_reference: FMA:72979
database_cross_reference: HAO:0000421
database_cross_reference: MA:0000014
database_cross_reference: MAT:0000033
database_cross_reference: MESH:D034582
database_cross_reference: MIAA:0000033
database_cross_reference: NCIT:C12907
database_cross_reference: TADS:0000108
database_cross_reference: UMLS:C0037267
database_cross_reference: VHOG:0000403
database_cross_reference: XAO:0000176
database_cross_reference: galen:Surface
has exact synonym: integumentary system
has_obo_namespace: uberon
has_related_synonym: body surface
has_related_synonym: dermal system
has_related_synonym: external covering of organism
has_related_synonym: integumentum commune
has_related_synonym: organism surface
has_related_synonym: surface
id: UBERON:0002416
in subset: efo slim
in subset: grouping class
in subset: pheno slim

lymphoid system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: hemolymphoid system
subclass of: Restriction
  on property: part of
  some values from: immune system
definition: The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].
imported from: uberon.owl
UBPROP_0000001: Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]
UBPROP_0000003: Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]
UBPROP_0000007: lymphoid
UBPROP_0000008: The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013]
UBPROP_0000008: The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013]
UBPROP_0000012: We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments.
has_alternative_id: UBERON:0002096
database_cross_reference: Lymphoid system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0024235
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362589007
database_cross_reference: EHDAA2:0001043
database_cross_reference: EHDAA:8677
database_cross_reference: EMAPA:37664
database_cross_reference: FMA:74594
database_cross_reference: GAID:931
database_cross_reference: MA:0002435
database_cross_reference: MAT:0000197
database_cross_reference: MIAA:0000197
database_cross_reference: NCIT:C12746
database_cross_reference: OpenCyc:Mx4rwQAKT5wpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000385
database_cross_reference: UMLS:C0024235
database_cross_reference: VHOG:0000842
database_cross_reference: XAO:0003199
database_cross_reference: ZFA:0000385
has narrow synonym: lymphatic system
has_obo_namespace: uberon
has_related_synonym: lymphatic circulatory system
has_related_synonym: lymphatic drainage system
has_related_synonym: systema lymphoideum
id: UBERON:0002465
in subset: uberon slim
in subset: vertebrate core

gland
type: Class
subclass of: organ
subclass of: Restriction
  on property: produces
  some values from: organism substance
definition: an organ that functions as a secretory or excretory organ
imported from: uberon.owl
UBPROP_0000007: glandular
has_alternative_id: UBERON:MIAA_0000021
database_cross_reference: Gland
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1285092
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/134358001
database_cross_reference: AAO:0000212
database_cross_reference: AEO:0000096
database_cross_reference: BTO:0000522
database_cross_reference: EFO:0000797
database_cross_reference: EHDAA2:0003096
database_cross_reference: EHDAA:2161
database_cross_reference: EHDAA:4475
database_cross_reference: EHDAA:6522
database_cross_reference: EMAPA:18425
database_cross_reference: FBbt:00100317
database_cross_reference: FMA:7146
database_cross_reference: FMA:86294
database_cross_reference: HAO:0000375
database_cross_reference: MA:0003038
database_cross_reference: MAT:0000021
database_cross_reference: MIAA:0000021
database_cross_reference: NCIT:C13319
database_cross_reference: OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C1285092
database_cross_reference: WikipediaCategory:Glands
database_cross_reference: galen:Gland
has exact synonym: glandular organ
has_obo_namespace: uberon
has_related_synonym: Druese
has_related_synonym: glandula
id: UBERON:0002530
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

compound organ
type: Class
subclass of: organ
definition: Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
curator note: this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
imported from: uberon.owl
database_cross_reference: AAO:0010015
database_cross_reference: AEO:0000024
database_cross_reference: BILA:0000024
database_cross_reference: CARO:0000024
database_cross_reference: EHDAA2:0003024
database_cross_reference: HAO:0000024
database_cross_reference: TADS:0000598
database_cross_reference: TAO:0000496
database_cross_reference: TGMA:0001837
database_cross_reference: VHOG:0001723
database_cross_reference: XAO:0003041
database_cross_reference: ZFA:0000496
has_obo_namespace: uberon
has_related_synonym: organ
id: UBERON:0003103
in subset: organ slim
in subset: upper level

reproductive organ
type: Class
subclass of: organ
subclass of: reproductive structure
definition: An organ involved in reproduction
imported from: uberon.owl
UBPROP_0000012: GO uses genitalia for the singular organ
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0017420
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/128181006
database_cross_reference: EMAPA:17381
database_cross_reference: EMAPA:37731
database_cross_reference: MA:0001752
database_cross_reference: MESH:D005835
database_cross_reference: NCIT:C25177
database_cross_reference: OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA
database_cross_reference: TGMA:0000591
database_cross_reference: UMLS:C0017420
database_cross_reference: WBbt:0008422
has exact synonym: genital organ
has exact synonym: reproductive system organ
has exact synonym: sex organ
has_obo_namespace: uberon
has_related_synonym: genitalia
id: UBERON:0003133
in subset: functional classification
in subset: organ slim
in subset: pheno slim

gland of foregut
type: Class
subclass of: gland of digestive tract
definition: A gland that is part of a foregut [Automatically generated definition].
imported from: uberon.owl
database_cross_reference: EHDAA2:0000567
database_cross_reference: EHDAA:950
database_cross_reference: EMAPA:16557
database_cross_reference: VHOG:0000650
has exact synonym: foregut gland
has_obo_namespace: uberon
id: UBERON:0003294

gland of integumental system
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part of
    some values from: integumental system
subclass of: gland
subclass of: Restriction
  on property: part of
  some values from: integumental system
definition: A gland that is part of a integumental system [Automatically generated definition].
imported from: uberon.owl
database_cross_reference: EHDAA2:0000837
database_cross_reference: EHDAA:6522
database_cross_reference: EMAPA:17758
database_cross_reference: MA:0000144
database_cross_reference: VHOG:0000654
has exact synonym: integumental gland
has exact synonym: integumental system gland
has exact synonym: integumentary gland
has_obo_namespace: uberon
id: UBERON:0003297

gland of digestive tract
type: Class
subclass of: gland
subclass of: digestive system element
definition: A gland that is part of a digestive tract [Automatically generated definition].
imported from: uberon.owl
database_cross_reference: EMAPA:18815
database_cross_reference: MA:0003202
has exact synonym: digestive tract gland
has exact synonym: gland of digestive tract
has exact synonym: gland of lower gastrointestinal tract
has exact synonym: gut gland
has exact synonym: lower gastrointestinal tract gland
has_obo_namespace: uberon
id: UBERON:0003408

anatomical conduit
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: conduit for
  some values from: anatomical structure
definition: Any tube, opening or passage that connects two distinct anatomical spaces.
imported from: uberon.owl
UBPROP_0000012: FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
database_cross_reference: Foramen
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/346902003
database_cross_reference: AEO:0000080
database_cross_reference: EHDAA2:0003080
database_cross_reference: FMA:242873
has narrow synonym: foramen
has narrow synonym: foramina
has_obo_namespace: uberon
has_related_synonym: opening
has_related_synonym: ostia
has_related_synonym: ostium
id: UBERON:0004111

endoderm-derived structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that develops (entirely or partially) from the endoderm.
curator note: Grouping term for query purposes
imported from: uberon.owl
has_obo_namespace: uberon
id: UBERON:0004119
in subset: grouping class

mesoderm-derived structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that develops (entirely or partially) from the mesoderm.
curator note: Grouping term for query purposes
imported from: uberon.owl
database_cross_reference: FBbt:00025998
has exact synonym: mesodermal derivative
has_obo_namespace: uberon
id: UBERON:0004120
in subset: grouping class

ectoderm-derived structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that develops (entirely or partially) from the ectoderm.
curator note: Grouping term for query purposes
imported from: uberon.owl
database_cross_reference: FBbt:00025990
has exact synonym: ectodermal deriviative
has_obo_namespace: uberon
id: UBERON:0004121
in subset: grouping class

genitourinary system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: has part
    some values from: reproductive system
  intersection of: Restriction
    on property: has part
    some values from: renal system
subclass of: anatomical system
subclass of: Restriction
  on property: has part
  some values from: reproductive system
subclass of: Restriction
  on property: has part
  some values from: renal system
definition: Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
imported from: uberon.owl
UBPROP_0000001: Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]
UBPROP_0000002: relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
UBPROP_0000003: Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]
UBPROP_0000007: genitourinary
UBPROP_0000007: urogenital
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0042066
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/278861008
database_cross_reference: AAO:0000624
database_cross_reference: BILA:0000122
database_cross_reference: BTO:0003091
database_cross_reference: EFO:0003864
database_cross_reference: EHDAA:1013
database_cross_reference: EMAPA:16367
database_cross_reference: EV:0100094
database_cross_reference: FMA:280610
database_cross_reference: GAID:362
database_cross_reference: MESH:D014566
database_cross_reference: NCIT:C12810
database_cross_reference: OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g
database_cross_reference: UMLS:C0042066
database_cross_reference: VHOG:0000286
database_cross_reference: XAO:0000140
database_cross_reference: galen:GenitoUrinarySystem
has exact synonym: urogenital system
has_obo_namespace: uberon
has_related_synonym: GU tract
has_related_synonym: UG tract
has_related_synonym: Urogenitalsystem
has_related_synonym: genito-urinary system
has_related_synonym: genitourinary tract
has_related_synonym: urogenital tract
id: UBERON:0004122
in subset: efo slim
in subset: pheno slim

external genitalia
type: Class
subclass of: reproductive organ
definition: The external genitalia are the outer sex organs, such as the penis or vulva in mammals
imported from: uberon.owl
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362207005
database_cross_reference: FMA:45643
has exact synonym: external genitalia
has_obo_namespace: uberon
has_related_synonym: external reproductive organ
has_related_synonym: external sex organ
id: UBERON:0004176
in subset: organ slim
in subset: pheno slim
comment: TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547

skeleton
type: Class
subclass of: anatomical collection
subclass of: Restriction
  on property: has member
  some values from: skeletal element
definition: Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
imported from: uberon.owl
UBPROP_0000001: Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
UBPROP_0000007: skeletal
database_cross_reference: Skeleton
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/361378004
database_cross_reference: AEO:0000168
database_cross_reference: EHDAA2:0001843
database_cross_reference: EHDAA:5047
database_cross_reference: EMAPA:17213
database_cross_reference: FMA:23875
database_cross_reference: GAID:177
database_cross_reference: MA:0003006
database_cross_reference: MAT:0000032
database_cross_reference: MESH:D012863
database_cross_reference: MIAA:0000032
database_cross_reference: OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA
database_cross_reference: VSAO:0000026
database_cross_reference: XAO:0004053
database_cross_reference: galen:Skeleton
has exact synonym: set of all bones
has exact synonym: set of bones of body
has_obo_namespace: uberon
id: UBERON:0004288
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

entire sense organ system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part of
    some values from: nervous system
definition: Sum of all sensory systems in an organism.
imported from: uberon.owl
UBPROP_0000012: note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
database_cross_reference: FMA:78499
has exact synonym: sense organ system
has_obo_namespace: uberon
id: UBERON:0004456
in subset: uberon slim

cardiovascular system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: circulatory system
definition: Anatomical system that has as its parts the heart and blood vessels.
curator note: we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
imported from: uberon.owl
UBPROP_0000003: The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0007226
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/278198007
database_cross_reference: AAO:0011001
database_cross_reference: BILA:0000016
database_cross_reference: BTO:0000088
database_cross_reference: CALOHA:TS-1297
database_cross_reference: EFO:0000791
database_cross_reference: EHDAA2:0000216
database_cross_reference: EHDAA:394
database_cross_reference: EMAPA:16104
database_cross_reference: EMAPA:16370
database_cross_reference: EV:0100017
database_cross_reference: FMA:7161
database_cross_reference: GAID:467
database_cross_reference: MA:0000010
database_cross_reference: MAT:0000016
database_cross_reference: MESH:D002319
database_cross_reference: MIAA:0000016
database_cross_reference: NCIT:C12686
database_cross_reference: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000010
database_cross_reference: UMLS:C0007226
database_cross_reference: VHOG:0000302
database_cross_reference: WikipediaCategory:Cardiovascular_system
database_cross_reference: XAO:0000100
database_cross_reference: XAO:0001010
database_cross_reference: ZFA:0000010
has_obo_namespace: uberon
has_related_synonym: CV system
has_related_synonym: Herz und Gefaesssystem
id: UBERON:0004535
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

arterial system
type: Class
subclass of: vascular system
definition: The part of the cardiovascular system consisting of all arteries.
imported from: uberon.owl
UBPROP_0000003: The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362030008
database_cross_reference: BTO:0004690
database_cross_reference: EHDAA2:0000143
database_cross_reference: EHDAA:396
database_cross_reference: EMAPA:16201
database_cross_reference: EMAPA:16371
database_cross_reference: MA:0002719
database_cross_reference: VHOG:0000273
has_obo_namespace: uberon
id: UBERON:0004572
in subset: pheno slim

venous system
type: Class
subclass of: vascular system
definition: The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
imported from: uberon.owl
UBPROP_0000003: The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1267406
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362060003
database_cross_reference: BTO:0004692
database_cross_reference: EHDAA2:0002171
database_cross_reference: EHDAA:486
database_cross_reference: EMAPA:16240
database_cross_reference: MA:0002720
database_cross_reference: NCIT:C33858
database_cross_reference: UMLS:C1267406
database_cross_reference: VHOG:0000277
has exact synonym: vein system
has_obo_namespace: uberon
id: UBERON:0004582

skeletal element
type: Class
subclass of: organ
definition: Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
imported from: uberon.owl
UBPROP_0000001: Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
UBPROP_0000001: Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
database_cross_reference: AAO:0011129
database_cross_reference: TAO:0001890
database_cross_reference: VSAO:0000128
database_cross_reference: XAO:0004012
database_cross_reference: ZFA:0005494
database_cross_reference: galen:SkeletalStructure
has_obo_namespace: uberon
id: UBERON:0004765
in subset: organ slim
in subset: uberon slim

articular system
type: Class
subclass of: anatomical collection
definition: Anatomical system that consists of all the joints of the body.
imported from: uberon.owl
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/361827000
database_cross_reference: EMAPA:35150
database_cross_reference: FMA:23878
database_cross_reference: MA:0003007
database_cross_reference: VSAO:0000181
has exact synonym: joint system
has exact synonym: set of all joints of body
has_obo_namespace: uberon
has_related_synonym: set of all joints
has_related_synonym: set of joints of body
id: UBERON:0004770

subdivision of digestive tract
type: Class
subclass of: organ part
definition: A proximal-distal subdivision of the digestive tract.
curator note: intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
database_cross_reference: FBbt:00100315
database_cross_reference: FMA:71131
has_obo_namespace: uberon
has_related_synonym: alimentary system subdivision
has_related_synonym: intestinal tract
has_related_synonym: segment of intestinal tract
has_related_synonym: subdivision of alimentary system
id: UBERON:0004921
in subset: non informative

Axiom
annotated source: subdivision of digestive tract
annotated property: definition
annotated target: A proximal-distal subdivision of the digestive tract.
database_cross_reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: subdivision of digestive tract
annotated property: has_related_synonym
annotated target: alimentary system subdivision
database_cross_reference: FMA:71131

Axiom
annotated source: subdivision of digestive tract
annotated property: has_related_synonym
annotated target: subdivision of alimentary system
database_cross_reference: FMA:71131

immune organ
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: part of
    some values from: immune system
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: immune system
definition: An organ that is part of a immune system [Automatically generated definition].
imported from: uberon.owl
has exact synonym: immune system organ
has_obo_namespace: uberon
id: UBERON:0005057
in subset: organ slim
in subset: pheno slim

reproductive structure
type: Class
equivalent class: Class
  intersection of: multicellular anatomical structure
  intersection of: Restriction
    on property: part of
    some values from: reproductive system
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: reproductive system
definition: Any anatomical structure that is part of the reproductive system.
imported from: uberon.owl
has exact synonym: reproductive system element
has exact synonym: reproductive system structure
has_obo_namespace: uberon
id: UBERON:0005156
in subset: grouping class

abdomen element
type: Class
subclass of: abdominal segment element
definition: An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
imported from: uberon.owl
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/272631008
database_cross_reference: MA:0000522
has exact synonym: abdomen organ
has_obo_namespace: uberon
id: UBERON:0005172
in subset: non informative

abdominal segment element
type: Class
subclass of: trunk region element
definition: An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
imported from: uberon.owl
database_cross_reference: EMAPA:37062
database_cross_reference: MA:0000529
has exact synonym: abdominal segment organ
has_obo_namespace: uberon
id: UBERON:0005173
in subset: non informative

dorsal region element
type: Class
subclass of: organ
definition: An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
imported from: uberon.owl
database_cross_reference: EMAPA:37274
database_cross_reference: MA:0001901
has exact synonym: back organ
has exact synonym: dorsal region organ
has_obo_namespace: uberon
id: UBERON:0005174
in subset: non informative

trunk region element
type: Class
subclass of: organ
definition: An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
imported from: uberon.owl
database_cross_reference: EMAPA:37270
database_cross_reference: MA:0000516
has exact synonym: trunk organ
has_obo_namespace: uberon
id: UBERON:0005177
in subset: non informative
in subset: organ slim

thoracic cavity element
type: Class
subclass of: thoracic segment organ
definition: An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
imported from: uberon.owl
database_cross_reference: EMAPA:37273
database_cross_reference: MA:0000557
has exact synonym: thoracic cavity organ
has_obo_namespace: uberon
id: UBERON:0005178
in subset: non informative
in subset: pheno slim

thoracic segment organ
type: Class
subclass of: trunk region element
definition: An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
imported from: uberon.owl
database_cross_reference: EMAPA:37271
database_cross_reference: MA:0000563
has_obo_namespace: uberon
has_related_synonym: upper body organ
id: UBERON:0005181
in subset: non informative

alimentary part of gastrointestinal system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: digestive system
definition: The part of the digestive system that excludes the hepatobiliary system.
editor note: the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
imported from: uberon.owl
UBPROP_0000001: The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
UBPROP_0000003: All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
UBPROP_0000012: that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0012240
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/373871007
database_cross_reference: BTO:0000058
database_cross_reference: CALOHA:TS-0407
database_cross_reference: EHDAA2:0000110
database_cross_reference: EHDAA:514
database_cross_reference: EMAPA:16246
database_cross_reference: EV:0100056
database_cross_reference: FMA:71132
database_cross_reference: GAID:294
database_cross_reference: MA:0000323
database_cross_reference: MESH:A03.492
database_cross_reference: NCIT:C12378
database_cross_reference: UMLS:C0012240
database_cross_reference: VHOG:0000412
database_cross_reference: galen:GastrointestinalTract
has_obo_namespace: uberon
has_related_synonym: GI tract
has_related_synonym: alimentary system
has_related_synonym: alimentary tract
has_related_synonym: gastro-intestinal system
has_related_synonym: gastroenterological system
has_related_synonym: gastrointestinal (GI) tract
has_related_synonym: gastrointestinal system
has_related_synonym: gastrointestinal tract
id: UBERON:0005409
in subset: pheno slim

developing anatomical structure
type: Class
subclass of: material anatomical entity
imported from: uberon.owl
database_cross_reference: AEO:0000125
database_cross_reference: CALOHA:TS-2122
database_cross_reference: EHDAA2:0003125
database_cross_reference: FBbt:00007006
database_cross_reference: FMA:292313
database_cross_reference: MIAA:0000019
has_obo_namespace: uberon
has_related_synonym: developing structure
has_related_synonym: developmental structure
has_related_synonym: developmental tissue
id: UBERON:0005423

acellular membrane
type: Class
equivalent class: Class
  intersection of: acellular anatomical structure
  intersection of: Restriction
    on property: bounding layer of
    some values from: anatomical structure
subclass of: acellular anatomical structure
subclass of: Restriction
  on property: bounding layer of
  some values from: anatomical structure
definition: A acellular anatomical structure that is the bounding layer of a anatomical structure.
imported from: uberon.owl
database_cross_reference: FMA:63871
has_obo_namespace: uberon
id: UBERON:0005764

basement membrane of epithelium
type: Class
subclass of: acellular membrane
definition: An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
curator note: this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
imported from: uberon.owl
RO_0002175: NCBITaxon_80999
database_cross_reference: Basement membrane
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0004799
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/68989006
database_cross_reference: AAO:0010596
database_cross_reference: FMA:63872
database_cross_reference: GAID:915
database_cross_reference: NCIT:C13191
database_cross_reference: UMLS:C0004799
has exact synonym: basement membrane of connective tissue
has exact synonym: membrana basalis
has_obo_namespace: uberon
has_related_synonym: basement membrane
id: UBERON:0005769

bodily fluid
type: Class
subclass of: organism substance
definition: Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
imported from: uberon.owl
has broad synonym: fluid
database_cross_reference: Body fluid
database_cross_reference: birnlex 20
database_cross_reference: EMAPA:37441
database_cross_reference: FMA:280556
database_cross_reference: GAID:266
database_cross_reference: MESH:D001826
database_cross_reference: galen:BodyFluid
has exact synonym: body fluid
has_obo_namespace: uberon
id: UBERON:0006314
in subset: pheno slim

mammary gland fluid/secretion
type: Class
equivalent class: Class
  intersection of: organism substance
  intersection of: Restriction
    on property: produced_by
    some values from: mammary gland
subclass of: secretion of exocrine gland
subclass of: Restriction
  on property: produced_by
  some values from: mammary gland
definition: A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards.
imported from: uberon.owl
database_cross_reference: EMAPA:36538
database_cross_reference: MA:0002505
has_obo_namespace: uberon
has_related_synonym: lactiferous gland fluid
has_related_synonym: lactiferous gland secretion
has_related_synonym: mammary gland fluid
has_related_synonym: mammary gland secreted fluid
has_related_synonym: mammary gland secretion
has_related_synonym: secretion of mammary gland
id: UBERON:0006539

pharynx
type: Class
subclass of: subdivision of digestive tract
definition: The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
curator note: currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
UBPROP_0000007: branchial
UBPROP_0000007: pharyngeal
database_cross_reference: FBbt:00005380
database_cross_reference: MAT:0000049
database_cross_reference: MIAA:0000049
has_obo_namespace: uberon
has_related_synonym: anterior part of foregut
has_related_synonym: pharyngeal tube
id: UBERON:0006562
in subset: grouping class
in subset: uberon slim

Axiom
annotated source: pharynx
annotated property: definition
annotated target: The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
database_cross_reference: GO:0060465

digestive system gland
type: Class
equivalent class: Class
  intersection of: endocrine gland
  intersection of: Restriction
    on property: part of
    some values from: digestive system
subclass of: endocrine gland
subclass of: digestive system element
definition: Any gland that is part of the digestive system.
imported from: uberon.owl
database_cross_reference: AAO:0000130
database_cross_reference: BTO:0000345
has_obo_namespace: uberon
has_related_synonym: digestive gland
id: UBERON:0006925
in subset: organ slim

primary circulatory organ
type: Class
subclass of: circulatory organ
definition: A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
imported from: uberon.owl
UBPROP_0000008: note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
database_cross_reference: FBbt:00003154
database_cross_reference: SPD:0000130
database_cross_reference: TADS:0000147
has narrow synonym: dorsal tube
has narrow synonym: heart
has_obo_namespace: uberon
has_related_synonym: adult heart
id: UBERON:0007100
in subset: grouping class
comment: Gene notes: Bmp, Nkx, Gata

reticulorumen
type: Class
subclass of: subdivision of digestive tract
definition: The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum.
database_cross_reference: Reticulorumen
has exact synonym: retriculo-rumen
has_obo_namespace: uberon
id: UBERON:0007364

Axiom
annotated source: reticulorumen
annotated property: definition
annotated target: The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum.
database_cross_reference: Reticulorumen
database_cross_reference: http://orcid.org/0000-0002-6601-2165

shelled egg
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: develops_from
  some values from: female reproductive system
definition: The hard-shelled reproductive body produced by a bird and especially by the common domestic chicken; also: its contents used as food.
imported from: uberon.owl
database_cross_reference: Egg (biology)
database_cross_reference: BSA:0000081
database_cross_reference: BTO:0000369
has_obo_namespace: uberon
has_related_synonym: egg
id: UBERON:0007379

transudate
type: Class
subclass of: bodily fluid
subclass of: Restriction
  on property: develops_from
  some values from: blood plasma
subclass of: Restriction
  on property: transformation of
  some values from: blood plasma
definition: Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
imported from: uberon.owl
UBPROP_0000007: transudative
UBPROP_0000010: characteristically low in protein and cellular content (unless there has been secondary concentration)
database_cross_reference: FMA:12276
database_cross_reference: GAID:1195
database_cross_reference: MESH:D005122
database_cross_reference: ncithesaurus:Transudate
has_obo_namespace: uberon
has_related_synonym: plasma ultrafiltrate
id: UBERON:0007779

secretion of serous gland
type: Class
equivalent class: Class
  intersection of: bodily fluid
  intersection of: Restriction
    on property: produced_by
    some values from: serous gland
subclass of: secretion of exocrine gland
subclass of: bodily fluid
subclass of: Restriction
  on property: produced_by
  some values from: serous gland
definition: Any fluid produced by a serous gland.
imported from: uberon.owl
has broad synonym: serous fluid
database_cross_reference: Serous fluid
has exact synonym: serosal fluid
has exact synonym: serous gland fluid
has_obo_namespace: uberon
id: UBERON:0007794

vascular system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part of
  some values from: cardiovascular system
definition: Anatomical system that consists of all blood and lymph vessels.
editor note: consider merging with vasculature
imported from: uberon.owl
UBPROP_0000001: The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
UBPROP_0000012: in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0489903
database_cross_reference: BTO:0001085
database_cross_reference: CALOHA:TS-2053
database_cross_reference: EHDAA2:0004520
database_cross_reference: EMAPA:35905
database_cross_reference: MA:0002718
database_cross_reference: NCIT:C33854
database_cross_reference: UMLS:C0489903
has_obo_namespace: uberon
has_related_synonym: Gefaesssystem@de
id: UBERON:0007798
in subset: pheno slim

pyloric gastric gland
type: Class
subclass of: gastric gland
subclass of: mucous gland
definition: The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP].
editor note: check relationship to pylorus vs antrum
imported from: uberon.owl
database_cross_reference: Pyloric gland
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0227239
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/70710007
database_cross_reference: EMAPA:27211
database_cross_reference: FMA:14922
database_cross_reference: NCIT:C33431
database_cross_reference: UMLS:C0227239
has exact synonym: glandula pylorica
has exact synonym: pyloric antrum gland
has exact synonym: pyloric gland
has exact synonym: pyloric mucuous gland
has_obo_namespace: uberon
id: UBERON:0008861
in subset: pheno slim

dorsal pancreas
type: Class
subclass of: exocrine gland
subclass of: endoderm-derived structure
subclass of: trunk region element
subclass of: Restriction
  on property: part of
  some values from: pancreas
imported from: uberon.owl
database_cross_reference: EHDAA2:0001371
has_obo_namespace: uberon
has_related_synonym: pancreatis dorsalis
id: UBERON:0009708
in subset: organ slim

ventral pancreas
type: Class
subclass of: exocrine gland
subclass of: endoderm-derived structure
subclass of: trunk region element
subclass of: Restriction
  on property: part of
  some values from: pancreas
imported from: uberon.owl
database_cross_reference: EHDAA2:0001393
has_obo_namespace: uberon
has_related_synonym: pancreatis ventralis
id: UBERON:0009709
in subset: organ slim

digestive tract diverticulum
type: Class
subclass of: subdivision of digestive tract
subclass of: sac
definition: Branch or outpocketing of the digestive tract.
database_cross_reference: FBbt:00100316
has_obo_namespace: uberon
has_related_synonym: diverticulum of gut
has_related_synonym: intestinal pouch
id: UBERON:0009854

Axiom
annotated source: digestive tract diverticulum
annotated property: definition
annotated target: Branch or outpocketing of the digestive tract.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: digestive tract diverticulum
annotated property: has_related_synonym
annotated target: diverticulum of gut
database_cross_reference: FBbt:00100316

sac
type: Class
subclass of: anatomical structure
imported from: uberon.owl
database_cross_reference: galen:Diverticulum
has exact synonym: pouch
has_obo_namespace: uberon
has_related_synonym: diverticulum
id: UBERON:0009856

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
imported from: uberon.owl
database_cross_reference: CARO:0010000
database_cross_reference: FBbt:00100313
has exact synonym: multicellular structure
has_obo_namespace: uberon
id: UBERON:0010000
in subset: upper level

food storage organ
type: Class
subclass of: digestive system element
subclass of: Restriction
  on property: part of
  some values from: alimentary part of gastrointestinal system
definition: An organ of the digestive tract that is capable of retaining and storing food
curator note: This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
imported from: uberon.owl
database_cross_reference: BSA:0000123
database_cross_reference: TADS:0000172
database_cross_reference: TGMA:0001041
has_obo_namespace: uberon
id: UBERON:0010039
in subset: functional classification
in subset: grouping class

collection of collagen fibrils
type: Class
subclass of: acellular anatomical structure
imported from: uberon.owl
UBPROP_0000012: the FMA class specifically refers to ureter
database_cross_reference: FMA:63212
database_cross_reference: MESH:D024022
database_cross_reference: NCIT:C32339
database_cross_reference: NIF_Subcellular:sao7547390221
has_obo_namespace: uberon
id: UBERON:0011860

venous blood
type: Class
subclass of: blood
definition: A blood that is part of a vein.
imported from: uberon.owl
database_cross_reference: FMA:83067
has exact synonym: blood in vein
has exact synonym: portion of venous blood
has exact synonym: venous blood
has_obo_namespace: uberon
id: UBERON:0013756

digestive system element
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: part of
    some values from: digestive system
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: digestive system
definition: Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
imported from: uberon.owl
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/272627002
database_cross_reference: EMAPA:37843
has exact synonym: digestive organ
has exact synonym: digestive system organ
has_obo_namespace: uberon
id: UBERON:0013765
in subset: grouping class
in subset: pheno slim

lateral structure
type: Class
equivalent class: Class
  intersection of: anatomical structure
  intersection of: Restriction
    on property: in_lateral_side_of
    some values from: material anatomical entity
subclass of: anatomical structure
subclass of: Restriction
  on property: in_lateral_side_of
  some values from: material anatomical entity
definition: Any structure that is placed on one side of the left-right axis of a bilaterian.
curator note: This class is primarily to implement taxon constraints. It may be removed in the future.
imported from: uberon.owl
has_obo_namespace: uberon
id: UBERON:0015212
in subset: grouping class
in subset: non informative

circulatory organ
type: Class
subclass of: compound organ
subclass of: Restriction
  on property: part of
  some values from: circulatory system
definition: A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
imported from: uberon.owl
has broad synonym: heart
database_cross_reference: SPD:0000130
has exact synonym: cardiac pump
has exact synonym: heart or heart like organ
has narrow synonym: circulatory vessel
has_obo_namespace: uberon
has_related_synonym: cardiac structure
id: UBERON:0015228
in subset: grouping class

heart plus pericardium
type: Class
subclass of: thoracic cavity element
subclass of: Restriction
  on property: part of
  some values from: cardiovascular system
imported from: uberon.owl
database_cross_reference: EMAPA:37597
database_cross_reference: MA:0002449
has exact synonym: heart/pericardium
has_obo_namespace: uberon
id: UBERON:0015410

abdominal viscera
type: Class
subclass of: viscus
subclass of: abdomen element
definition: A viscus that is part of a abdomen.
imported from: uberon.owl
database_cross_reference: FMA:32413
database_cross_reference: FMA:67355
has exact synonym: abdominal viscera
has exact synonym: abdominal viscera set
has exact synonym: set of abdominal viscera
has_obo_namespace: uberon
id: UBERON:0017672
in subset: pheno slim

exocrine gland of integumental system
type: Class
equivalent class: Class
  intersection of: exocrine gland
  intersection of: Restriction
    on property: part of
    some values from: integumental system
subclass of: exocrine gland
subclass of: gland of integumental system
definition: An exocrine gland that is part of a integumental system.
imported from: uberon.owl
has exact synonym: integumental exocrine gland
has exact synonym: integumental system exocrine gland
has_obo_namespace: uberon
id: UBERON:0019319

bodily gas
type: Class
subclass of: organism substance
definition: Any substance in the body or expelled from the body that is in a gaseous state.
imported from: uberon.owl
database_cross_reference: FMA:84580
has exact synonym: gas in anatomical space
has exact synonym: portion of gas in anatomical space
has_obo_namespace: uberon
id: UBERON:0034873

air in respiratory system
type: Class
subclass of: gas in respiratory system
definition: Any portion of gas located in a part of the respiratory system that is composed primarily of air.
imported from: uberon.owl
database_cross_reference: FMA:84581
has exact synonym: respiratory air
has exact synonym: respiratory system air
has_obo_namespace: uberon
id: UBERON:0034874

multi organ part structure
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: composed primarily of
  some values from: organ part
definition: An multicellular anatomical structure that has subparts of multiple organs as a part.
imported from: uberon.owl
database_cross_reference: CARO:0020001
has_obo_namespace: uberon
has_related_synonym: anatomical cluster
id: UBERON:0034921

cell cluster
type: Class
subclass of: multicellular anatomical structure
definition: A cluster of cells, largely surrounded by a morphological boundary.
imported from: uberon.owl
database_cross_reference: CARO:0020002
database_cross_reference: FMA:62807
has_obo_namespace: uberon
id: UBERON:0034922

anatomical collection
type: Class
subclass of: material anatomical entity
subclass of: Restriction
  on property: has member
  some values from: anatomical structure
definition: A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
editor note: resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
imported from: uberon.owl
has_obo_namespace: uberon
id: UBERON:0034925

gas in respiratory system
type: Class
equivalent class: Class
  intersection of: bodily gas
  intersection of: Restriction
    on property: located in
    some values from: respiratory system
subclass of: bodily gas
subclass of: Restriction
  on property: located in
  some values from: respiratory system
definition: Any portion of gas located in a part of the respiratory system.
imported from: uberon.owl
has exact synonym: respiratory gas
has exact synonym: respiratory system gas
has_obo_namespace: uberon
id: UBERON:0034947

awaiting ontology review/placement
type: Class

Variant of Concern
type: Class
subclass of: genetic epidemiology surveillance datum

Variant of Interest
type: Class
subclass of: genetic epidemiology surveillance datum

Variant Under Monitoring
type: Class
subclass of: genetic epidemiology surveillance datum

geopolitical region
type: Class
subclass of: designated area on Earth
definition: a geopolitical region is a geographic region recognized by social or legal convention.
imported from: sio.owl

township
type: Class
subclass of: dense settlement
subclass of: Municipality
definition: A township is a rural or sub-urban settlement.
imported from: sio.owl

Dataset
type: Class
subclass of: Resource
comment: 1つのエージェントによって公開またはキュレートされ、1つ以上の形式でアクセスまたはダウンロードできるデータの集合。 @ja
comment: A collection of data, published or curated by a single source, and available for access or download in one or more represenations.
comment: Kolekce dat poskytovaná či řízená jedním zdrojem, která je k dispozici pro přístup či stažení v jednom či více formátech. @cs
comment: Raccolta di dati, pubblicati o curati da un'unica fonte, disponibili per l'accesso o il download in uno o più formati. @it
comment: Una colección de datos, publicados o conservados por una única fuente, y disponibles para ser accedidos o descargados en uno o más formatos. @es
comment: Une collection de données, publiée ou élaborée par une seule source, et disponible pour accès ou téléchargement dans un ou plusieurs formats. @fr
comment: Μία συλλογή από δεδομένα, δημοσιευμένη ή επιμελημένη από μία και μόνο πηγή, διαθέσιμη δε προς πρόσβαση ή μεταφόρτωση σε μία ή περισσότερες μορφές. @el
comment: قائمة بيانات منشورة أو مجموعة من قبل مصدر ما و متاح الوصول إليها أو تحميلها @ar
label: Conjunto de datos @es
label: Datová sada @cs
label: Jeu de données @fr
label: Σύνολο Δεδομένων @el
label: قائمة بيانات @ar
label: データセット @ja
change note: 2018-02 - odstraněno tvrzení o podtřídě dctype:Dataset, jelikož rozsah dcat:Dataset zahrnuje několik dalších typů ze slovníku dctype. @cs
change note: 2018-02 - se eliminó el axioma de subclase con dctype:Dataset porque el alcance de dcat:Dataset incluye muchos otros tipos del vocabulario dctype. @es
change note: 2018-02 - sottoclasse di dctype:Dataset rimosso perché l'ambito di dcat:Dataset include diversi altri tipi dal vocabolario dctype. @it
change note: 2018-02 - subclass of dctype:Dataset removed because scope of dcat:Dataset includes several other types from the dctype vocabulary.
scope note: Cette classe représente le jeu de données publié par le fournisseur de données. Dans les cas où une distinction est nécessaire entre le jeu de donénes et son entrée dans le catalogue, la classe registre de données peut être utilisée pour ce dernier. @fr
scope note: Esta clase representa el conjunto de datos publicados. En los casos donde es necesario distinguir entre el conjunto de datos y su entrada en el catálogo de datos, se debe utilizar la clase 'registro del catálogo'. @es
scope note: Questa classe descrive il dataset dal punto di vista concettuale. Possono essere disponibili una o più rappresentazioni, con diversi layout e formati schematici o serializzazioni. @it
scope note: Questa classe rappresenta il dataset come pubblicato dall’editore. Nel caso in cui sia necessario operare una distinzione fra i metadati originali del dataset e il record dei metadati ad esso associato nel catalogo (ad esempio, per distinguere la data di modifica del dataset da quella del dataset nel catalogo) si può impiegare la classe catalog record. @it
scope note: Tato třída reprezentuje datovou sadu tak, jak je publikována poskytovatelem dat. V případě potřeby rozlišení datové sady a jejího katalogizačního záznamu (jelikož metadata jako datum modifikace se mohou lišit) pro něj může být použita třída "katalogizační záznam". @cs
scope note: This class describes the conceptual dataset. One or more representations might be available, with differing schematic layouts and formats or serializations.
scope note: This class represents the actual dataset as published by the dataset provider. In cases where a distinction between the actual dataset and its entry in the catalog is necessary (because metadata such as modification date and maintainer might differ), the catalog record class can be used for the latter.
scope note: Η κλάση αυτή αναπαριστά το σύνολο δεδομένων αυτό καθ'εαυτό, όπως έχει δημοσιευθεί από τον εκδότη. Σε περιπτώσεις όπου είναι απαραίτητος ο διαχωρισμός μεταξύ του συνόλου δεδομένων και της καταγραφής αυτού στον κατάλογο (γιατί μεταδεδομένα όπως η ημερομηνία αλλαγής και ο συντηρητής μπορεί να διαφέρουν) η κλάση της καταγραφής καταλόγου μπορεί να χρησιμοποιηθεί για το τελευταίο. @el
scope note: このクラスは、データセットの公開者が公開する実際のデータセットを表わします。カタログ内の実際のデータセットとそのエントリーとの区別が必要な場合（修正日と維持者などのメタデータが異なるかもしれないので）は、後者にcatalog recordというクラスを使用できます。 @ja

Cyprus
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CY
HSO_0000004: Cyprus
HSO_0000005: Republic of Cyprus

Australia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AU
HSO_0000004: Australia
HSO_0000005: Commonwealth of Australia

New Zealand
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: NZ
HSO_0000004: New Zealand
HSO_0000005: New Zealand

Turkey
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TR
HSO_0000004: Turkey
HSO_0000005: Republic of Turkey

Sudan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SD
HSO_0000004: Sudan
HSO_0000005: Republic of the Sudan

Tunisia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TN
HSO_0000004: Tunisia
HSO_0000005: Republic of Tunisia

Algeria
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: DZ
HSO_0000004: Algeria
HSO_0000005: People’s Democratic Republic of Algeria

Morocco
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MA
HSO_0000004: Morocco
HSO_0000005: Kingdom of Morocco

Libya
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LY
HSO_0000004: Libya
HSO_0000005: Libya

Ethiopia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ET
HSO_0000004: Ethiopia
HSO_0000005: Federal Democratic Republic of Ethiopia

Eritrea
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ER
HSO_0000004: Eritrea
HSO_0000005: State of Eritrea

Djibouti
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: DJ
HSO_0000004: Djibouti
HSO_0000005: Republic of Djibouti

Mauritania
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MR
HSO_0000004: Mauritania
HSO_0000005: Islamic Republic of Mauritania

Mali
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ML
HSO_0000004: Mali
HSO_0000005: Republic of Mali

Niger
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: NE
HSO_0000004: Niger
HSO_0000005: Republic of Niger

Chad
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TD
HSO_0000004: Chad
HSO_0000005: Republic of Chad

Spain
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ES
HSO_0000004: Spain
HSO_0000005: Kingdom of Spain

Iceland
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: IS
HSO_0000004: Iceland
HSO_0000005: Iceland

Benin
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BJ
HSO_0000004: Benin
HSO_0000005: Republic of Benin

Burkina Faso
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BF
HSO_0000004: Burkina Faso
HSO_0000005: Burkina Faso

Cote d'Ivoire
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CI
HSO_0000004: Côte d’Ivoire
HSO_0000005: Republic of Côte d’Ivoire

Gambia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GM
HSO_0000004: The Gambia
HSO_0000005: Republic of The Gambia

Ghana
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GH
HSO_0000004: Ghana
HSO_0000005: Republic of Ghana

Guinea
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GN
HSO_0000004: Guinea
HSO_0000005: Republic of Guinea

Guinea-Bissau
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GW
HSO_0000004: Guinea-Bissau
HSO_0000005: Republic of Guinea-Bissau

Liberia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LR
HSO_0000004: Liberia
HSO_0000005: Republic of Liberia

Nigeria
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: NG
HSO_0000004: Nigeria
HSO_0000005: Federal Republic of Nigeria

Senegal
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SN
HSO_0000004: Senegal
HSO_0000005: Republic of Senegal

Sierra Leone
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SL
HSO_0000004: Sierra Leone
HSO_0000005: Republic of Sierra Leone

Togo
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TG
HSO_0000004: Togo
HSO_0000005: Togolese Republic

Democratic Republic of the Congo
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CG
HSO_0000004: Congo
HSO_0000005: Republic of the Congo

Rwanda
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: RW
HSO_0000004: Rwanda
HSO_0000005: Republic of Rwanda

Republic of Congo
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CD
HSO_0000004: Democratic Republic of the Congo
HSO_0000005: Democratic Republic of the Congo

Burundi
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BI
HSO_0000004: Burundi
HSO_0000005: Republic of Burundi

Equatorial Guinea
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GQ
HSO_0000004: Equatorial Guinea
HSO_0000005: Republic of Equatorial Guinea

Gabon
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GA
HSO_0000004: Gabon
HSO_0000005: Gabonese Republic

Cameroon
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CM
HSO_0000004: Cameroon
HSO_0000005: Republic of Cameroon

Republic of South Africa
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ZA
HSO_0000004: South Africa
HSO_0000005: Republic of South Africa

Angola
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AO
HSO_0000004: Angola
HSO_0000005: Republic of Angola

Namibia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: NA
HSO_0000004: Namibia
HSO_0000005: Republic of Namibia

Botswana
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BW
HSO_0000004: Botswana
HSO_0000005: Republic of Botswana

Lesotho
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LS
HSO_0000004: Lesotho
HSO_0000005: Kingdom of Lesotho

Swaziland
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SZ
HSO_0000004: Swaziland
HSO_0000005: Kingdom of Swaziland

Mozambique
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MZ
HSO_0000004: Mozambique
HSO_0000005: Republic of Mozambique

Kenya
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: KE
HSO_0000004: Kenya
HSO_0000005: Republic of Kenya

Uganda
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: UG
HSO_0000004: Uganda
HSO_0000005: Republic of Uganda

Tanzania
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TZ
HSO_0000004: Tanzania
HSO_0000005: United Republic of Tanzania

Somalia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SO
HSO_0000004: Somalia
HSO_0000005: Federal Republic of Somalia

Malawi
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MW
HSO_0000004: Malawi
HSO_0000005: Republic of Malawi

Zimbabwe
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ZW
HSO_0000004: Zimbabwe
HSO_0000005: Republic of Zimbabwe

Zambia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ZM
HSO_0000004: Zambia
HSO_0000005: Republic of Zambia

Cape Verde
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CV
HSO_0000004: Cape Verde
HSO_0000005: Republic of Cape Verde

Barbados
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BB
HSO_0000004: Barbados
HSO_0000005: Barbados

Jordan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: JO
HSO_0000004: Jordan
HSO_0000005: Hashemite Kingdom of Jordan

Syria
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SY
HSO_0000004: Syria
HSO_0000005: Syrian Arab Republic

Israel
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: IL
HSO_0000004: Israel
HSO_0000005: State of Israel

Lebanon
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LB
HSO_0000004: Lebanon
HSO_0000005: Lebanese Republic

Bolivia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BO
HSO_0000004: Bolivia
HSO_0000005: Plurinational State of Bolivia

Guyana
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GY
HSO_0000004: Guyana
HSO_0000005: Cooperative Republic of Guyana

Suriname
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SR
HSO_0000004: Suriname
HSO_0000005: Republic of Suriname

Canada
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CA
HSO_0000004: Canada
HSO_0000005: Canada

United Kingdom
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GB
HSO_0000004: United Kingdom
HSO_0000005: United Kingdom of Great Britain and Northern Ireland

Scotland
type: NamedIndividual
type: Country

Wales
type: NamedIndividual
type: Country

England
type: NamedIndividual
type: Country

Germany
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: DE
HSO_0000004: Germany
HSO_0000005: Federal Republic of Germany
comment: begin_date: 1990-10-03.

Italy
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: IT
HSO_0000004: Italy
HSO_0000005: Italian Republic

Norway
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: NO
HSO_0000004: Norway
HSO_0000005: Kingdom of Norway

Croatia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: HR
HSO_0000004: Croatia
HSO_0000005: Republic of Croatia

Russia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: RU
HSO_0000004: Russia
HSO_0000005: Russian Federation
comment: begin_date: 1991-12.

Ukraine
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: UA
HSO_0000004: Ukraine
HSO_0000005: Ukraine

Sweden
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SE
HSO_0000004: Sweden
HSO_0000005: Kingdom of Sweden

The Bahamas
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BS
HSO_0000004: Bahamas
HSO_0000005: Commonwealth of the Bahamas

Japan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: JP
HSO_0000004: Japan
HSO_0000005: Japan

North Korea
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: KP
HSO_0000004: North Korea
HSO_0000005: Democratic People’s Republic of Korea

Chile
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CL
HSO_0000004: Chile
HSO_0000005: Republic of Chile

Brazil
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BR
HSO_0000004: Brazil
HSO_0000005: Federative Republic of Brazil

India
type: NamedIndividual
type: Country

China
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CN
HSO_0000004: China
HSO_0000005: People’s Republic of China

Mexico
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MX
HSO_0000004: Mexico
HSO_0000005: United Mexican States

Panama
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: PA
HSO_0000004: Panama
HSO_0000005: Republic of Panama

Honduras
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: HN
HSO_0000004: Honduras
HSO_0000005: Republic of Honduras

Costa Rica
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CR
HSO_0000004: Costa Rica
HSO_0000005: Republic of Costa Rica

Ecuador
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: EC
HSO_0000004: Ecuador
HSO_0000005: Republic of Ecuador

Argentina
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AR
HSO_0000004: Argentina
HSO_0000005: Argentine Republic

Colombia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CO
HSO_0000004: Colombia
HSO_0000005: Republic of Colombia

Uruguay
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: UY
HSO_0000004: Uruguay
HSO_0000005: Eastern Republic of Uruguay

Venezuela
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: VE
HSO_0000004: Venezuela
HSO_0000005: Bolivarian Republic of Venezuela

Peru
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: PE
HSO_0000004: Peru
HSO_0000005: Republic of Peru

Paraguay
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: PY
HSO_0000004: Paraguay
HSO_0000005: Republic of Paraguay

Belize
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BZ
HSO_0000004: Belize
HSO_0000005: Belize

El Salvador
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SV
HSO_0000004: El Salvador
HSO_0000005: Republic of El Salvador

Guatemala
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GT
HSO_0000004: Guatemala
HSO_0000005: Republic of Guatemala

Finland
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: FI
HSO_0000004: Finland
HSO_0000005: Republic of Finland

Belgium
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BE
HSO_0000004: Belgium
HSO_0000005: Kingdom of Belgium

Poland
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: PL
HSO_0000004: Poland
HSO_0000005: Republic of Poland

France
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: FR
HSO_0000004: France
HSO_0000005: French Republic

Switzerland
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CH
HSO_0000004: Switzerland
HSO_0000005: Swiss Confederation

Austria
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AT
HSO_0000004: Austria
HSO_0000005: Republic of Austria

Ireland
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: IE
HSO_0000004: Ireland
HSO_0000005: Ireland

Portugal
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: PT
HSO_0000004: Portugal
HSO_0000005: Portuguese Republic

Greece
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GR
HSO_0000004: Greece
HSO_0000005: Hellenic Republic

Luxembourg
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LU
HSO_0000004: Luxembourg
HSO_0000005: Grand Duchy of Luxembourg

Andorra
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AD
HSO_0000004: Andorra
HSO_0000005: Principality of Andorra

Bulgaria
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BG
HSO_0000004: Bulgaria
HSO_0000005: Republic of Bulgaria

Romania
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: RO
HSO_0000004: Romania
HSO_0000005: Romania

Hungary
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: HU
HSO_0000004: Hungary
HSO_0000005: Hungary

Albania
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AL
HSO_0000004: Albania
HSO_0000005: Republic of Albania

Czech Republic
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CZ
HSO_0000004: Czech Republic
HSO_0000005: Czech Republic

Slovenia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SI
HSO_0000004: Slovenia
HSO_0000005: Republic of Slovenia

Slovakia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SK
HSO_0000004: Slovakia
HSO_0000005: Slovak Republic

Serbia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: RS
HSO_0000004: Serbia
HSO_0000005: Republic of Serbia

Latvia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LV
HSO_0000004: Latvia
HSO_0000005: Republic of Latvia
comment: ISO3166-2 codes for 2009 revision of admin. units seem not to have been assigned.

Estonia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: EE
HSO_0000004: Estonia
HSO_0000005: Republic of Estonia

Lithuania
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LT
HSO_0000004: Lithuania
HSO_0000005: Republic of Lithuania

Nicaragua
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: NI
HSO_0000004: Nicaragua
HSO_0000005: Republic of Nicaragua

San Marino
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SM
HSO_0000004: San Marino
HSO_0000005: Republic of San Marino

Vatican City
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: VA
HSO_0000004: the Holy See/ Vatican City State
HSO_0000005: the Holy See/ Vatican City State

Indonesia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ID
HSO_0000004: Indonesia
HSO_0000005: Republic of Indonesia

Thailand
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TH
HSO_0000004: Thailand
HSO_0000005: Kingdom of Thailand

Bangladesh
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BD
HSO_0000004: Bangladesh
HSO_0000005: People’s Republic of Bangladesh

Viet Nam
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: VN
HSO_0000004: Vietnam
HSO_0000005: Socialist Republic of Vietnam

Cuba
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: CU
HSO_0000004: Cuba
HSO_0000005: Republic of Cuba

Trinidad and Tobago
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TT
HSO_0000004: Trinidad and Tobago
HSO_0000005: Republic of Trinidad and Tobago

Jamaica
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: JM
HSO_0000004: Jamaica
HSO_0000005: Jamaica

Monaco
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MC
HSO_0000004: Monaco
HSO_0000005: Principality of Monaco

Liechtenstein
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LI
HSO_0000004: Liechtenstein
HSO_0000005: Principality of Liechtenstein

Moldova
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MD
HSO_0000004: Moldova
HSO_0000005: Republic of Moldova

Brunei Darussalam
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BN
HSO_0000004: Brunei
HSO_0000005: Brunei Darussalam

Malaysia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MY
HSO_0000004: Malaysia
HSO_0000005: Malaysia

Bhutan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BT
HSO_0000004: Bhutan
HSO_0000005: Kingdom of Bhutan

Papua New Guinea
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: PG
HSO_0000004: Papua New Guinea
HSO_0000005: Independent State of Papua New Guinea

Singapore
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SG
HSO_0000004: Singapore
HSO_0000005: Republic of Singapore

Sri Lanka
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LK
HSO_0000004: Sri Lanka
HSO_0000005: Democratic Socialist Republic of Sri Lanka

Timor
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TL
HSO_0000004: Timor-Leste
HSO_0000005: Democratic Republic of Timor-Leste

Egypt
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: EG
HSO_0000004: Egypt
HSO_0000005: Arab Republic of Egypt
comment: The 2nd level administrative regions of Egypt are very confusuing and different sources conflicting. Those in gaz.obo are from GeoHive (http://www.xist.org/default1.aspx) and are not fully in agreement with those from the WHO (the file EGY_SALB_table.xls downloaded from http://www.who.int/whosis/database/gis/salb/salb_coding.aspx#DATA).

Dominican Republic
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: DO
HSO_0000004: Dominican Republic
HSO_0000005: Dominican Republic

Haiti
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: HT
HSO_0000004: Haiti
HSO_0000005: Republic of Haiti

Armenia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AM
HSO_0000004: Armenia
HSO_0000005: Republic of Armenia

Nepal
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: NP
HSO_0000004: Nepal
HSO_0000005: Federal Democratic Republic of Nepal

Iran
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: IR
HSO_0000004: Iran
HSO_0000005: Islamic Republic of Iran

Iraq
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: IQ
HSO_0000004: Iraq
HSO_0000005: Republic of Iraq

The Philippines
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: PH
HSO_0000004: Philippines
HSO_0000005: Republic of the Philippines

Azerbaijan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AZ
HSO_0000004: Azerbaijan
HSO_0000005: Republic of Azerbaijan

Georgia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GE
HSO_0000004: Georgia
HSO_0000005: Georgia
comment: begin_date: 1936-12-05. end_date: 1990-10-20.

Uzbekistan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: UZ
HSO_0000004: Uzbekistan
HSO_0000005: Republic of Uzbekistan
comment: begin_date: 1991-12-31.

Kazakhstan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: KZ
HSO_0000004: Kazakhstan
HSO_0000005: Republic of Kazakhstan
comment: Geographically the western regions of Kazakhstan may be in Europe.

Turkmenistan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TM
HSO_0000004: Turkmenistan
HSO_0000005: Turkmenistan

Pakistan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: PK
HSO_0000004: Pakistan
HSO_0000005: Islamic Republic of Pakistan

Saudi Arabia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SA
HSO_0000004: Saudi Arabia
HSO_0000005: Kingdom of Saudi Arabia

Bahrain
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BH
HSO_0000004: Bahrain
HSO_0000005: Kingdom of Bahrain

United Arab Emirates
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AE
HSO_0000004: United Arab Emirates
HSO_0000005: United Arab Emirates

Oman
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: OM
HSO_0000004: Oman
HSO_0000005: Sultanate of Oman

Yemen
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: YE
HSO_0000004: Yemen
HSO_0000005: Republic of Yemen

Kuwait
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: KW
HSO_0000004: Kuwait
HSO_0000005: State of Kuwait

Qatar
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: QA
HSO_0000004: Qatar
HSO_0000005: State of Qatar

Republic of China
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TW
HSO_0000004: Taiwan
HSO_0000005: Taiwan

Comoros
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: KM
HSO_0000004: Comoros
HSO_0000005: Union of the Comoros

Afghanistan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AF
HSO_0000004: Afghanistan
HSO_0000005: Islamic Republic of Afghanistan

Antigua and Barbuda
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AG
HSO_0000004: Antigua and Barbuda
HSO_0000005: Antigua and Barbuda

Belarus
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BY
HSO_0000004: Belarus
HSO_0000005: Republic of Belarus
comment: begin_date: 1990-07-27.

Bosnia and Herzegovina
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: BA
HSO_0000004: Bosnia and Herzegovina
HSO_0000005: Bosnia and Herzegovina

Cambodia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: KH
HSO_0000004: Cambodia
HSO_0000005: Kingdom of Cambodia

Laos
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LA
HSO_0000004: Laos
HSO_0000005: Lao People’s Democratic Republic

Dominica
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: DM
HSO_0000004: Dominica
HSO_0000005: Commonwealth of Dominica

Fiji
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: FJ
HSO_0000004: Fiji
HSO_0000005: Republic of Fiji

Kyrgyzstan
type: NamedIndividual
type: Country

Kiribati
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: KG
HSO_0000004: Kyrgyzstan
HSO_0000005: Kyrgyz Republic

Macedonia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MK
HSO_0000004: Former Yugoslav Republic of Macedonia, the
HSO_0000005: Former Yugoslav Republic of Macedonia, the. This code is in accordance with ISO 3166-2, code taken from name in Macedonian: Makedonija.

Montenegro
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ME
HSO_0000004: Montenegro
HSO_0000005: Montenegro

Myanmar
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MM
HSO_0000004: Myanmar/Burma
HSO_0000005: Myanmar/Burma

Nauru
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: NR
HSO_0000004: Nauru
HSO_0000005: Republic of Nauru

Niue Fekai
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: NU
HSO_0000004: Niue
HSO_0000005: Niue

Palau
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: PW
HSO_0000004: Palau
HSO_0000005: Republic of Palau

Saint Kitts-Nevis
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: KN
HSO_0000004: Saint Kitts and Nevis
HSO_0000005: Federation of Saint Kitts and Nevis

Saint Lucia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: LC
HSO_0000004: Saint Lucia
HSO_0000005: Saint Lucia

Samoa
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: AS
HSO_0000004: American Samoa
HSO_0000005: American Samoa: territory of the USA.

Tajikistan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TJ
HSO_0000004: Tajikistan
HSO_0000005: Republic of Tajikistan

Tonga
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TO
HSO_0000004: Tonga
HSO_0000005: Kingdom of Tonga

Vanuatu
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: VU
HSO_0000004: Vanuatu
HSO_0000005: Republic of Vanuatu

Sao Tome and Principe
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: ST
HSO_0000004: São Tomé and Príncipe
HSO_0000005: Democratic Republic of São Tomé and Príncipe

Mongolia
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: MN
HSO_0000004: Mongolia
HSO_0000005: Mongolia

Tuvalu
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TV
HSO_0000004: Tuvalu
HSO_0000005: Tuvalu

Kosovo
type: NamedIndividual
type: Country

[Former] Yugoslavia
type: NamedIndividual
type: Country
comment: begin_date: 1943-11-29. end_date: 1991-06-25. Previous to 1943: Kingdom of Yugoslavia, begins_in: 1918-12-01; end_date: 1941-04_17.

South Sudan
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: SS
HSO_0000004: South Sudan
HSO_0000005: Republic of South Sudan

Tokelau
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: TK
HSO_0000004: Tokelau
HSO_0000005: Tokelau: territory of New Zealand.

Saint Vincent and the Grenadines
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: VC
HSO_0000004: Saint Vincent and the Grenadines
HSO_0000005: Saint Vincent and the Grenadines

Grenada
type: NamedIndividual
type: Country
HSO_0000002: COUNTRY
HSO_0000003: GD
HSO_0000004: Grenada
HSO_0000005: Grenada

broiler chickens
type: NamedIndividual
type: meat production
HSO_0000002: MTX
HSO_0000003: A0C78
HSO_0000004: Gallus gallus broiler
HSO_0000005: Gallus gallus animals raised for meat production purposes. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Broiler

dairy cattle
type: NamedIndividual
type: milk production
HSO_0000002: MTX
HSO_0000003: A0C9L
HSO_0000004: Dairy cows
HSO_0000005: Cattle having reached the physical maturity, for milk production. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Dairy_cattle

beef cattle
type: NamedIndividual
type: meat production
HSO_0000002: MTX
HSO_0000003: A0C9Q
HSO_0000004: Meat production cattle
HSO_0000005: Cattle having reached the physical maturity, for meat production. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Beef_cattle

bfo-spec-label
definition source: Person:Alan Ruttenberg

BFO_0000134
elucidation: To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
elucidation: To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])

Axiom
annotated source: BFO_0000134
annotated property: elucidation
annotated target: To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/080-003

Axiom
annotated source: BFO_0000134
annotated property: elucidation
annotated target: To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/081-003