Crawford Revie
Eva Blomqvist
Karl Hammar
Matthias Filter
Patrick Lambrix
Taras Günther
Fernanda Dórea
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.
Health Surveillance Ontology (HSO)
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.
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.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
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.
SSD_catalogue
"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""."
SSD_termCode
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".
SSD_termExtendedName
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".
SSD_termScopeNote
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.
One-Health Consensus Reference Annotation Checklist (OH-CRAC)
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.
CRAC 1.1 Motivation / cause
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.
CRAC 1.2. Requirement analysis
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.
CRAC 1.3. Surveillance objective and constraints
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.
CRAC 2.1. Framework design
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)
CRAC 2.2. Variable specifications
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)
CRAC 2.3. Surveillance methods/strategy
CRAC 2.4. Sampling plan
"This sub-section specifies the population(s) that were sampled.
"
CRAC 2.4.1. Sampled population
This sub-section describes the design process followed for the sampling plan generation and the sampling criteria.
CRAC 2.4.2. Sampling schema
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).
CRAC 2.4.3. Sample collection
This sub-section details the processing of the samples prior to the analytical processing.
CRAC 2.4.4. Sample preparation
This sub-section reports on the analytical procedures applied to the different sets of samples.
CRAC 2.4.5. Analytical procedures
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.
CRAC 2.5. Data processing/analysis
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.
CRAC 3.1. Practical aspects on sample selection
"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"
CRAC 3.2. Practical support activities
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.
CRAC 3.3. Practical aspects on field and lab work
"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."
CRAC 3.4. Practical aspects on information handling
"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."
CRAC 4.1. Data integration
"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)"
CRAC 4.2. Data classification / encoding
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).
CRAC 4.3. Data validation
"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.
"
CRAC 4.4. Data cleansing and correction
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.
CRAC 4.5. New variable/unit derivation
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).
CRAC 4.6. Weighing of records
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.
CRAC 4.7. Data aggregation
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.
CRAC 5.1. Surveillance output generation
"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."
CRAC 5.2. Surveillance output validation
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.
CRAC 5.3. Surveillance output statistical analysis
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.
CRAC 5.4. Surveillance disclosure control
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
European Food Safety Agency Standard Sample Description Framework - EFSA SSD
surveillance output
discussion
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.
additional information
editor preferred term
example of usage
definition
definition
editor note
term editor
alternative term
definition source
curator note
imported from
elucidation
has associated axiom(nl)
has associated axiom(fol)
has axiom label
A metadata relation between a class and its taxonomic rank (eg species, family)
ncbi_taxonomy
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_rank
has_alternative_id
has broad synonym
has_broad_synonym
database_cross_reference
has exact synonym
has_exact_synonym
has narrow synonym
has_narrow_synonym
has_obo_namespace
has_related_synonym
has synonym
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
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.
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
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'.
part_of
BFO:0000050
uberon
part_of
part_of
part of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
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.
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
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'.
has_part
BFO:0000051
uberon
has_part
has_part
has part
has part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[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])
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
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
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])
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
realizes
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
BFO:0000062
is preceded by
takes place after
uberon
preceded_by
preceded_by
preceded_by
BFO:0000063
uberon
precedes
precedes
precedes
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
cjm
2009-07-31T02:15:46Z
BSPO:0000096
uberon
anterior_to
anterior_to
anterior_to
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).
BSPO:0000097
uberon
distal_to
distal_to
distal_to
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).
BSPO:0000098
uberon
dorsal_to
dorsal_to
dorsal_to
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.
BSPO:0000099
caudal_to
uberon
posterior_to
posterior_to
posterior_to
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).
BSPO:0000102
uberon
ventral_to
ventral_to
ventral_to
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:0000107
uberon
deep_to
deep_to
deep_to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:0000108
uberon
superficial_to
superficial_to
superficial_to
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
BSPO:0000120
uberon
in_left_side_of
in_left_side_of
in_left_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:0000121
uberon
in_right_side_of
in_right_side_of
in_right_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:0000123
uberon
in_anterior_side_of
in_anterior_side_of
in_anterior_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:0000124
uberon
in_proximal_side_of
in_proximal_side_of
in_proximal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:0000125
uberon
in_distal_side_of
in_distal_side_of
in_distal_side_of
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
BSPO:0000126
uberon
in_lateral_side_of
in_lateral_side_of
in_lateral_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
BSPO:0001106
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost_part_of
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
BSPO:0001108
uberon
distalmost_part_of
distalmost_part_of
distalmost_part_of
isSubSpeciesOf
isSerotypeOf
has datum
has specimen datum
has matrix type
sampled from
sampled from anatomical entity
sampled from organism
has specimen from organism type
follows surveillance protocol
excuted in surveillance activity
has legal basis
is legal basis of
has surveillance objective
has surveillance purpose
has surveillance actions
has sampling design
has reporting protocol
has sample collection protocol
has diagnostic protocol
has surveillance context
target population
target geographical area
target country
target host species
target host sector
Mixed outbreaks
target pathogen
causative agent
susceptible species
Specification of the type of sampling strategy planned within a surveillance protocol, and ultimately executed in a surveillance activity.
applies sampling strategy
has sampling unit
has sampler type
sampling stage
sampled specimen
employs assay
property assigning specific datum to diagnostic tests which allows identification of their type
has diagnostic test type
assignment of data available as information content to assays
has assay datum
reporting country
origin country
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
this property allows a dataset to be explictly linked to any entities within it which can be referred to with an unique ID.
contains information about
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
Links an entityt to a specific dataset that contains information about it.
documented in dataset
this property specifies specifically whic country is responsible for the documentation about a specific surveillance activity
reporting country
available in language
place of exposure
place of origin of the problem
hazard status context
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
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.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
has material basis in
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.
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
OBI
OBI
Philly 2011 workshop
is_supported_by_data
has_specified_input
has_specified_input
see is_input_of example_of_usage
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.
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
is_specified_input_of
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
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_input_of
has_specified_output
has_specified_output
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
is_specified_output_of
is_specified_output_of
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_output_of
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
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.
BP, AR, PPPB branch
PPPB branch derived
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
achieves_planned_objective
objective_achieved_by
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.
OBI
OBI
objective_achieved_by
inheres in
this fragility inheres in this vase
this red color inheres in this apple
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
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
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
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.
bearer_of
is bearer of
bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
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).
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).
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.
is concretized as
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).
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).
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.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
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.
function_of
is function of
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
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.
is role of
role_of
role of
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
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.
has_role
has role
disposition of
derives from
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
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
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
RO:0001015
uberon
location_of
location_of
location_of
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
RO:0001025
uberon
RO:0001025
located_in
located_in
located in
located_in
RO:0002002
uberon
has_boundary
has_boundary
has boundary
RO:0002007
uberon
bounding_layer_of
bounding_layer_of
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.
bounding layer of
Relation between occurrents, shares start and end boundaries.
RO:0002082
coincides_with
is_equal_to
uberon
simultaneous_with
simultaneous_with
simultaneous_with
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
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].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
immediately_preceded_by
immediately_preceded_by
immediately_preceded_by
RO:0002150
uberon
continuous_with
continuous_with
continuous_with
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.
RO:0002170
uberon
connected_to
connected_to
Connection does not imply overlaps.
connected to
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.
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)
RO:0002176
uberon
connects
connects
connects
relation between an artery and the structure is supplies with blood.
RO:0002178
arterial supply of
uberon
supplies
supplies
source: FMA
supplies
RO:0002202
uberon
develops_from
develops_from
develops_from
RO:0002203
uberon
develops_into
develops_into
develops_into
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded_by
x adjacent_to y iff: x and y share a boundary
RO:0002220
uberon
adjacent_to
adjacent_to
adjacent_to
inverse of surrounded_by
RO:0002221
uberon
surrounds
surrounds
surrounds
Relation between occurrents, shares a start boundary with.
RO:0002223
uberon
starts
starts
starts
RO:0002224
uberon
starts_with
starts_with
starts with
Relation between occurrents, shares an end boundary with.
RO:0002229
finishes
uberon
ends
ends
ends
RO:0002230
uberon
ends_with
ends_with
ends with
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
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.
RO:0002256
uberon
developmentally_induced_by
developmentally_induced_by
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally_induced_by
RO:0002258
uberon
developmentally_preceded_by
developmentally_preceded_by
developmentally preceded by
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally_replaces
RO:0002351
uberon
has_member
has_member
has member
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
RO:0002433
uberon
contributes_to_morphology_of
contributes_to_morphology_of
contributes to morphology of
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
RO:0002473
uberon
composed_primarily_of
composed_primarily_of
composed primarily of
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
RO:0002488
begins_to_exist_during
uberon
existence_starts_during
existence_starts_during
existence starts during
Relation between continuant and occurrent, such that c comes into existence at the start of p.
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
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.
RO:0002492
ceases_to_exist_during
uberon
existence_ends_during
existence_ends_during
existence ends during
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
RO:0002493
uberon
existence_ends_with
existence_ends_with
existence ends with
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
existence starts during or after
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
existence ends during or before
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
RO:0002551
uberon
has sekeletal support
has supporting framework
has_skeleton
has_skeleton
has skeleton
RO:0002572
uberon
luminal_space_of
luminal_space_of
luminal space of
RO:0002576
uberon
skeleton_of
skeleton_of
skeleton of
RO:0003000
uberon
produces
produces
produces
RO:0003001
uberon
produced_by
produced_by
produced_by
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
x is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
uberon
existence_starts_and_ends_during
existence starts and ends during
uberon
extends_fibers_into
extends_fibers_into
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.
uberon
filtered_through
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
filtered through
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.
uberon
in_central_side_of
in_central_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
uberon
protects
protects
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.
uberon
proximally_connected_to
proximally connected to
uberon
subdivision_of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision of
uberon
transitively_connected_to
transitively_connected to
.
uberon
transitively_proximally_connected_to
transitively proximally connected to
surveillance activity history item
surveillance activity start date
surveillance activity end date
Number of units tested
Number of PSU tested
Number of SSU tested
Number of units positive
Number of PSU positive
Number of SSU positive
Number of units negative
Number of PSU negative
Number of SSU negative
Number of specimen tested
Number of specimen negative
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 sample size
The number of herds to be sampled in a survey targetting livestock animals, which are kept in herds.
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 PSU
The number of animals to be sampled within each herd.
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.
calculated number of SSU
Number of specimen positive
0.0
100.0
Percentage of units positive
0.0
100.0
Percentage of PSU positive
0.0
100.0
Percentage of SSU positive
0.0
100.0
percentage of specimen positive
a collection of properties used to assign numeric results to a surveillance activity
surveillance activity aggregated results
surveillance activity year
year started
Number of cases
Number of domestic cases
Number of imported cases
the weight of a specific collected specimen. use sub-properties to specify weight units
specimen weight
the weight of a specific collected specimen, in grams
sampling weight in grams
the weight of a specific collected specimen, in mililitres
sampling weight in millilitre
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.
https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section3.html
Case fatality rate
Hospitalized cases
Notification rate
Notification rate in domestic cases
Number of deaths
case definition
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
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
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
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
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
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.
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
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
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])
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])
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
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
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])
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])
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
Occurrent
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
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.
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.
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
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.
per discussion with Barry Smith
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
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])
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(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]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
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])
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(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]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
s-region
SpatialRegion
BFO 2 Reference: Spatial regions do not participate in processes.
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.
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])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
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.
per discussion with Barry Smith
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])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
t-region
TemporalRegion
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
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])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
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
per discussion with Barry Smith
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])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
2d-s-region
TwoDimensionalSpatialRegion
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
st-region
SpatiotemporalRegion
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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])
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)
(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]
process
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])
(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]
disposition
Disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
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.
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])
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])
(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]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
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])
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])
(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]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
realizable
RealizableEntity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
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])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(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]
(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]
realizable entity
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])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(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]
(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]
0d-s-region
ZeroDimensionalSpatialRegion
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
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])
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])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(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]
quality
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])
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])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(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]
sdc
SpecificallyDependentContinuant
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
of one-sided specifically dependent continuants: the mass of this tomato
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.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
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])
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.
(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]
specifically dependent continuant
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])
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.
per discussion with Barry Smith
(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]
role
Role
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.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
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])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
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])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
fiat-object-part
FiatObjectPart
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
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
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])
(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]
fiat object part
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])
(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]
1d-s-region
OneDimensionalSpatialRegion
an edge of a cube-shaped portion of space.
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])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
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])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
object-aggregate
ObjectAggregate
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
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)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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).
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.
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])
(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]
object aggregate
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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.
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])
(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]
3d-s-region
ThreeDimensionalSpatialRegion
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
site
Site
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
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])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
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.
site
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])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
object
Object
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
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.
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).
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
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
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])
object
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])
gdc
GenericallyDependentContinuant
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.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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.
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])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
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])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
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.
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
p-boundary
ProcessBoundary
the boundary between the 2nd and 3rd year of your life.
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])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
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])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
1d-t-region
OneDimensionalTemporalRegion
the temporal region during which a process occurs.
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).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
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
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.
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.
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])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(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]
(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]
material entity
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])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(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]
(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]
cf-boundary
ContinuantFiatBoundary
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])
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.
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
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.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(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]
continuant fiat boundary
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])
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.
(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]
immaterial
ImmaterialEntity
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
immaterial entity
1d-cf-boundary
OneDimensionalContinuantFiatBoundary
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
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])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
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])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
process-profile
ProcessProfile
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
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.
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.
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])
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])
(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]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
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])
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])
(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]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
r-quality
RelationalQuality
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.
a marriage bond, an instance of love, an obligation between one person and another.
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])
(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]
relational quality
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])
(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]
2d-cf-boundary
TwoDimensionalContinuantFiatBoundary
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])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
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])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
0d-cf-boundary
ZeroDimensionalContinuantFiatBoundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
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.
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])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
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.
requested by Melanie Courtot
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])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
0d-t-region
ZeroDimensionalTemporalRegion
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
history
History
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])
history
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])
An independent material continuant that is self-connected and retains its identity over time.
portion of material
specimen extraction matrix
Those components of a sample that are not measured by an experiment.
"This observable is important where process of capturing sample can affect dna extraction."
matrix
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.
disease_ontology
DOID:0050338
primary bacterial infectious disease
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.
url:http://en.wikipedia.org/wiki/Infectious_disease
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.
ICD10CM:A02.0
ICD9CM:003.0
Salmonella infection
disease_ontology
DOID:0060859
salmonellosis
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.
url:https://www.cdc.gov/salmonella/general/index.html
url:https://www.foodsafety.gov/poisoning/causes/bacteriaviruses/salmonella
A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
ICD10CM:A49.9
MESH:D001424
NCI:C2890
SNOMEDCT_US_2020_03_01:87628006
UMLS_CUI:C0004623
disease_ontology
DOID:104
bacterial infectious disease
A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
url:http://en.wikipedia.org/wiki/Pathogenic_bacteria
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.
DOID:13621
MESH:D002169
SNOMEDCT_US_2020_03_01:86500004
UMLS_CUI:C0006818
Campylobacteriosis
disease_ontology
DOID:13622
campylobacteriosis
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.
url:http://en.wikipedia.org/wiki/Campylobacteriosis
url:http://www.health.state.ny.us/diseases/communicable/campylobacteriosis/fact_sheet.htm
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.
DOID:4094
DOID:5269
ICD10CM:K52.9
MESH:D005759
NCI:C34632
SNOMEDCT_US_2020_03_01:154278002
UMLS_CUI:C0017160
cholera morbus
infectious colitis, enteritis and gastroenteritis
disease_ontology
DOID:2326
gastroenteritis
MESH:D005759
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.
url:http://www.merck.com/mmhe/sec09/ch122/ch122a.html
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.
MESH:D004194
NCI:C2991
SNOMEDCT_US_2020_03_01:64572001
UMLS_CUI:C0012634
disease_ontology
DOID:4
disease
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.
url:http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
A disease that manifests in a defined anatomical structure.
DOID:1
DOID:2
DOID:5
DOID:71
DOID:72
DOID:8
disease_ontology
DOID:7
disease of anatomical entity
A disease that manifests in a defined anatomical structure.
url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic
A disease of anatomical entity that is located_in the gastrointestinal tract.
DOID:27
DOID:944
ICD10CM:K92.9
ICD9CM:520-579.99
MESH:D004066
SNOMEDCT_US_2020_03_01:53619000
UMLS_CUI:C0012242
GIT disease
Gastroenteropathy
alimentary system disease
digestive system disorder
gastrointestinal disease
gastrointestinal disorder
disease_ontology
DOID:77
gastrointestinal system disease
A disease of anatomical entity that is located_in the gastrointestinal tract.
url:http://en.wikipedia.org/wiki/Human_gastrointestinal_tract
FTT:1242
FTT:1252
FTT:15
FTT:16
FTT:18
FTT:19
FTT:21
FTT:22
FTT:23
FTT:24
FTT:25
FTT:26
FTT:27
FTT:28
FTT:29
FTT:37
SWEETRealm:AdministrativeRegion
TGN:80001
TGN:81099
TGN:81123
https://en.wikipedia.org/wiki/Administrative_region
administrative area
administrative region
state / province / territory / region
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A primary administrative division of a country, such as a state in the United States.
A primary administrative division of a country, such as a state in the United States.
FTT:414
FTT:569
Geonames:A.ADM1
TGN:81100
first-order administrative region
first-order administrative region
A political association with effective dominion over a geographic area.
FTT:424
FTT:566
FTT:567
FTT:571
SWEETRealm:Country
SWEETRealm:State
TGN:80006
TGN:81010
TGN:81011
TGN:81102
https://en.wikipedia.org/wiki/Nation
http://purl.obolibrary.org/obo/NCIT_C25464
nation
independent nation
independent political entity
independent sovereign nation
national geopolitical entity
Place or area with clustered or scattered buildings and a permanent human population.
place
FTT:1097
FTT:33
Geonames:P.PPL
Geonames:P.PPLS
TGN:22201
TGN:83002
https://en.wikipedia.org/wiki/Populated_place
inhabited place
populated place
populated places
settlement
populated place
A geographical region whose affairs and population are administered by an authority.
FTT:1093
Geonames:A.PCL
TGN:80002
political entity
Incorporated populated place.
urban area
EcoLexicon:city
FTT:430
FTT:483
FTT:484
FTT:485
SWEETRealm:City
TGN:83020
TGN:83040
TGN:83043
https://en.wikipedia.org/wiki/City
http://purl.obolibrary.org/obo/NCIT_C80234
city
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.
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.
envoPolar
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.
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.
environmental zone
A settlement with a high density of buildings and inhabitants.
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.
dense settlement
A reference to a place on the Earth, by its name or by its geographical location.
GAZ:00000467
geographic region {alternative name}
geographic location
region
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A subnational region is a type of subnational entity similar to a nation's state, province, or territory.
Damion Dooley
subnational region
This is a catch-all category for listing specimen related terms
Damion Dooley
specimen datum
http://purl.obolibrary.org/obo/GENEPIO_0002105
http://purl.obolibrary.org/obo/OBI_0001616
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.
Damion Dooley
designated area on Earth
a planned process which systematically, continuously or repeatedly measures, collected, collates, analyses, interprets and disseminates health and welfare related data from defined populations.
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).
Surveillance Activity
a role given to a specific herd of domesticated animals, specifying that they are raised in an agricultural setting with a specific purpose.
livestock farming system
Classification of livstock farming systems based on the type of commodity produced. Sub-classes are not mutually exclusive.
product oriented farming type
MTX
A0C7P
Animals farmed for egg production purposes
egg production
MTX
A0C7G
Animals farmed for meat production purposes
meat production
MTX
A0C7N
Animals farmed for milk production purposes
milk production
milk production
MTX
A0C7G
Animals farmed for breeding purposes
reproducer
supra-national geopolitical entity
NUTS region
language
A directive information that qualifies/classifies specimens.
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).
matrix type
whole organism
a specimen collected from an organism.
inferred categorization of specimens based on the informaiton provided in matrix type and/or regarding the anatomical entity targetted
matrix from organism
fluid specimen
organ/tissue specimen
swab specimen
excreta specimen
A directive information that describes the context for data collection in support to a specificsurveillance objective.
https://github.com/SVA-SE/AHSURED/wiki
surveillance context
A directive information used to describe the type of agent who carries out the data collection in a surveillance activity
surveillance sampler type
SAMPLR
surveillance executor type
A directive information that describes how population units will be chosen for sample/data collection in a surveillance activity.
https://github.com/SVA-SE/AHSURED/wiki/Description-of-surveillance-items-in-the-checklist
https://www.fp7-risksur.eu/terminology/glossary
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 strategy
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.
https://stats.oecd.org/glossary/index.htm
sampling unit
Information about an assay which can be used to find of qualify/classify assays.
assay datum
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.
A test category used to group diagnostic tests based on generla characteristics, such as the target for detection (antigen or antibody).
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.
diagnostic test type
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.
A specimen datum used, in conjunction with information about the target sampled anatomical location, in order to specify _how_ the anatomical entity was sampled
specimen from organism type
whole organism specimen
fluid specimen
organ/tissue specimen
excreta specimen
swab specimen
s specimen categorization which described the type of entity from which the specimen was collected
inferred categorization of specimens based on the matrix type informaiton provided regarding their source
specimen by origin
animal specimen
food specimen
environmental specimen
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.
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.
surveillance protocol
A directive information that details the legislative body that supports a specific surveillance activity, or the specific obligations prescried in these legislation.
All the laws or regulations of a country or region which are related to the obligations or permissions associated with a specific surveillance activity.
legislative specification
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
OIE (2014a). Guide to terrestrial animal health surveillance. Paris, France, OIE.
https://www.fp7-risksur.eu/terminology/glossary
surveillance objective
A directive information that describes why surveillance is necessary and what it will accomplish.
https://github.com/SVA-SE/AHSURED/wiki/
https://www.fp7-risksur.eu/terminology/glossary
surveillance purpose
A surveillance objective to search for any animals affected, clinically or not, by the hazard under surveillance.
https://github.com/SVA-SE/AHSURED/wiki
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.
case detection
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.
https://github.com/SVA-SE/AHSURED/wiki
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.
demonstration of disease freedom
A surveillance objective to detect any hazard cases as soon as possible.
https://github.com/SVA-SE/AHSURED/wiki
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.
early detection
A surveillance objective focusedon gathering data to estimate the true or apparent prevalence of a hazard in a given population.
https://github.com/SVA-SE/AHSURED/wiki
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.
prevalence estimation
https://github.com/SVA-SE/AHSURED/wiki
verify health intervention success purpose
verify success
https://github.com/SVA-SE/AHSURED/wiki
maintaining hazard freedom purpose
maintain freedom
https://github.com/SVA-SE/AHSURED/wiki
detect hazard introduction purpose
detect introduction
https://github.com/SVA-SE/AHSURED/wiki
outbreak control purpose
control outbreak
https://github.com/SVA-SE/AHSURED/wiki
informing health intervention purpose
inform intervention
https://github.com/SVA-SE/AHSURED/wiki
detect changes in hazard occurrence purpose
detect changes
https://github.com/SVA-SE/AHSURED/wiki
hazard control purpose
control
https://github.com/SVA-SE/AHSURED/wiki
hazard erradication purpose
eradicate
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.
A sampling scheme design to meet a specific surveillance objective and/or purpose of a surveillance activity.
sampling design protocol
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.
reporting protocol
A protocol detailing how specimens will be collected as part of the data gathering phase of a surveillance activity.
sample collection protocol
This does not include the definition of how many samples will collected, but specifically how they will be collected - where, by whom, etc.
specimen collection protocol
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.
A protocol to be used within a surveillance activity to classify epidemiological units according to a specific outcome.
diagnostic protocol
An action specification for specific actions to be taken as part of a health surveillance activity.
surveillance methods specification
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.
https://github.com/SVA-SE/AHSURED/wiki
Continuous data collection
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.
https://github.com/SVA-SE/AHSURED/wiki
https://www.fp7-risksur.eu/terminology/glossary
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.
Sentinel surveillance
A surveillance context which explores traditional information networks by using participatory rural appraisal methods.
https://github.com/SVA-SE/AHSURED/wiki
https://www.fp7-risksur.eu/terminology/glossary
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.
Participatory surveillance
A surveillance context in which data are generated through the identification of cases based on agreed-upon definitions.
https://github.com/SVA-SE/AHSURED/wiki
https://www.fp7-risksur.eu/terminology/glossary
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
Indicator−based surveillance
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.
https://github.com/SVA-SE/AHSURED/wiki
https://www.fp7-risksur.eu/terminology/glossary#group-S
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.
Syndromic surveillance
https://github.com/SVA-SE/AHSURED/wiki
census sampling
https://github.com/SVA-SE/AHSURED/wiki
convenience sampling
A sampling strategy in which population units are selected such that each possible unit has a fixed and known or equal probability of selection.
"Random Sample" (p.238) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated.
https://github.com/SVA-SE/AHSURED/wiki
simple random sampling
simple random
https://github.com/SVA-SE/AHSURED/wiki
systematic random sampling
systematic random
https://github.com/SVA-SE/AHSURED/wiki
risk-based sampling
https://github.com/SVA-SE/AHSURED/wiki
purposeful sampling
https://github.com/SVA-SE/AHSURED/wiki
objective sampling
A surveillance context in which activities are specifically triggered by the detection of an outbreak
outbreak investigation
a type of outbreak investigation that focus specifically on foodborne agents/vehicles
food-borne outbreak investigation
a surveillance activity with the specific surveillance context of investigating a foodborne outbreak
FBO investigation
A sampling strategy in which population units are chosen for investigation into a disease cluster or outbreak.
a specific type of surveillance activity which has as surveillance context an outbreak investigation
Cluster/Outbreak investigation
A directive information that described specific detailsgathered during an outbreak investigation.
outbreak investigation datum
Food vehicle of outbreak
Food vehicle
Nature of evidence in an outbreak
Nature of evidence
Outbreak contributory factors
Contributory factors
Extent of outbreak
A directive information that described the manadatory actions that follow on specific agents upon suspicion or confirmation of specific hazards under surveillance.
reporting obligations
A directive information used to identify diseases which, by law, must be reported to public health authorities upon diagnosis.
notifiable upon diagnosis
A directive information used to identify diseases which, by law, must be reported to public health authorities upon suspicion
notifiable upon suspicion
a quality that specifies the known status of a hazard occurrence in a given geograhial region.
status of hazard presence in a geographical region
historically absent
absent (eradicated)
Single cases without a specific temporal pattern, but also without geographical pattern or other associations and where import to location is related to travel.
sporadic travel-related cases
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
endemic
unknown status
stratified random sampling
A surveillance sampling strategy in which an aspired outcome is explicity stated.
"Target" (p.279) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated.
targeted sampling
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.
Baseline surveillance
A surveillance sampling strategy in which an aspired outcome is explicity stated.
Targeted surveillance
A targeted surveillance strategy in which the aim is early detection of variants of concern (VoC) in individuals.
Screening for Variants of Concern (VoC)
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.
Longitudinal surveillance
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.
Re-infection surveillance
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.
Vaccine escape surveillance
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.
Travel-associated surveillance
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.
Domestic travel surveillance
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.
Interstate/ interprovincial travel surveillance
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.
Intra-state/ intra-provincial travel surveillance
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.
International travel surveillance
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 or ground transport
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 air travel
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 of international border crossing by ground transport
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 from international worker testing
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.
Multi-jurisdictional outbreak investigation
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.
Intra-jurisdictional outbreak investigation
genetic epidemiology surveillance datum
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
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.
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."
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.
Answers the question, why did you do this experiment?
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
Alan Ruttenberg
OBI Plan and Planned Process branch
action specification
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
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.
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.
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.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
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
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
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).
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.
PERSON: Chris Stoeckert
OBI_0000142
information content entity
1
1
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
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
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
directive information entity
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
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.
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
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.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000042
group:OBI
data set
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
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.
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.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
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
plan specification
measurement datum
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,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
OBI_0000305
group:OBI
measurement datum
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
PERSON: Lawrence Hunter
document
A scalar measurement datum that is the result of measuring a temporal interval
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
time measurement datum
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
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
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
time stamped measurement datum
NCBITaxon:580032
NCBITaxon:580034
GC_ID:11
PMID:19767353
ncbi_taxonomy
Campylobacter volucris
GC_ID:11
Campylobacter sputorum bv. faecalis
ncbi_taxonomy
Campylobacter sputorum biovar fecalis
Campylobacter sputorum bv. fecalis
Campylobacter sputorum biovar faecalis
Escherichia coli O157
Escherichia coli O157
Escherichia coli O111
Escherichia coli O111
Escherichia coli O103
Escherichia coli O103
Escherichia coli O113:H21
Escherichia coli O113:H21
Escherichia coli O45:H2
Escherichia coli O45:H2
Salmonella enterica subsp. enterica serovar Newport
Salmonella enterica subsp. enterica serovar Newport
Escherichia coli O18
Escherichia coli O18
GC_ID:11
ncbi_taxonomy
'Campylobacter faecalis'
Campylobacter faecalis
Proteobacteria
purple bacteria
purple bacteria and relatives
purple non-sulfur bacteria
purple photosynthetic bacteria
purple photosynthetic bacteria and relatives
Proteobacteria
Escherichia coli O103:H11
Escherichia coli O103:H11
NCBITaxon:1244530
NCBITaxon:1442825
NCBITaxon:1442826
NCBITaxon:1442827
GC_ID:11
PMID:25574036
ncbi_taxonomy
Campylobacter iguaniorum
Escherichia coli 151_06
Escherichia coli 151_06
GC_ID:11
ncbi_taxonomy
Campylobacter jejuni X
GC_ID:1
PMID:11743200
PMID:11791233
ncbi_taxonomy
Boreotheria
Boreoeutheria
NCBITaxon:1448858
NCBITaxon:1448859
GC_ID:11
PMID:24744327
PMID:24876239
ncbi_taxonomy
Campylobacter sp. CIT045
Campylobacter sp. CIT056
Campylobacter sp. CIT058
Campylobacter corcagiensis
Salmonella enterica subsp. enterica serovar Hadar
Salmonella enterica subsp. enterica serovar Hadar
Salmonella enterica subsp. enterica serovar Enteritidis
Salmonella enterica subsp. enterica serovar Enteritidis
GC_ID:11
PMID:24336365
PMID:24899653
ncbi_taxonomy
Campylobacter fetus subsp. testudinum
NCBITaxon:1660068
NCBITaxon:1660069
NCBITaxon:1886620
NCBITaxon:1886621
NCBITaxon:1886668
NCBITaxon:1886669
NCBITaxon:1886671
GC_ID:11
PMID:28629508
ncbi_taxonomy
Campylobacter pinnipediorum subsp. pinnipediorum
NCBITaxon:1780361
NCBITaxon:1780363
GC_ID:11
PMID:27266587
ncbi_taxonomy
Campylobacter geochelonis
GC_ID:11
PMID:27498969
ncbi_taxonomy
Campylobacter hepaticus
GC_ID:11
PMID:28126040
ncbi_taxonomy
Campylobacter ornithocola
NCBITaxon:1660070
NCBITaxon:1660071
GC_ID:11
PMID:28629508
ncbi_taxonomy
Campylobacter pinnipediorum subsp. caledonicus
Salmonella enterica subsp. enterica serovar Stanley
Salmonella enterica subsp. enterica serovar Stanley
Campylobacter
GC_ID:11
PMID:11542086
PMID:12361288
PMID:16627635
PMID:1704793
PMID:19801389
PMID:29034857
ncbi_taxonomy
Ampylobacter
Campylobacter
NCBITaxon:2172530
NCBITaxon:2340791
NCBITaxon:28078
GC_ID:11
PMID:11321120
PMID:11411703
PMID:7857809
PMID:8590689
PMID:9336905
ncbi_taxonomy
Campylobacter hyoilei
Vibrio coli
Campylobacter coli
GC_ID:11
PMID:11321120
PMID:1354478
ncbi_taxonomy
Spirillum fetus
Vibrio fetus
Campylobacter fetus
GC_ID:11
PMID:28629508
ncbi_taxonomy
Campylobacter pinnipediorum
NCBITaxon:2172531
NCBITaxon:2182326
NCBITaxon:2201165
NCBITaxon:2211407
NCBITaxon:2211408
NCBITaxon:2211409
NCBITaxon:2293848
NCBITaxon:2293849
NCBITaxon:2293850
NCBITaxon:2303571
NCBITaxon:2305452
NCBITaxon:2305453
NCBITaxon:2305454
NCBITaxon:2305455
NCBITaxon:2305456
NCBITaxon:2305457
NCBITaxon:2305458
NCBITaxon:2305459
NCBITaxon:2340789
NCBITaxon:2478524
GC_ID:11
PMID:11321120
ncbi_taxonomy
Ampylobacter jejuni
Campylobacter fetus subsp. jejuni
Vibrio hepaticus
Vibrio jejuni
Campylobacter jejuni
GC_ID:11
PMID:10425776
PMID:3998100
PMID:7547297
ncbi_taxonomy
Campylobacter hyointestinalis
GC_ID:11
PMID:28729281
ncbi_taxonomy
Campylobacter concisus
Bacteria
eubacteria
Bacteria
GC_ID:11
PMID:1704793
PMID:1854636
ncbi_taxonomy
Wolinella curva
Campylobacter curvus
GC_ID:11
PMID:19406805
PMID:2223613
ncbi_taxonomy
Campylobacter laridis
Campylobacter lari
GC_ID:11
PMID:11321120
PMID:4614347
ncbi_taxonomy
Campylobacter sputorum mucosalis
Campylobacter sputorum subsp. mucosalis
Campylobacter mucosalis
GC_ID:11
PMID:1704793
PMID:1854636
ncbi_taxonomy
Wolinella recta
Campylobacter rectus
GC_ID:11
PMID:7694633
ncbi_taxonomy
Campylobacter showae
NCBITaxon:2044588
GC_ID:11
PMID:29624164
ncbi_taxonomy
Campylobacter blaseri
GC_ID:11
ncbi_taxonomy
Campylobacter sp.
GC_ID:11
PMID:11321120
PMID:9542089
ncbi_taxonomy
Vibrio sputorum
Campylobacter sputorum
GC_ID:11
ncbi_taxonomy
Campylobacter jejuni-like bacterium
Escherichia coli O128:H2
Escherichia coli O128:H2
Escherichia coli O26:H11
Escherichia coli O26:H11
GC_ID:11
ncbi_taxonomy
unclassified Campylobacter
GC_ID:11
PMID:15545485
ncbi_taxonomy
Campylobacter insulaenigrae
GC_ID:1
PMID:23020233
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
Eukaryota
GC_ID:11
ncbi_taxonomy
Campylobacter mucosalis-like sp.
Campylobacter mucosalis-like bacterium
GC_ID:11
ncbi_taxonomy
CNW group
catalase-negative or weak group of campylobacteria
Campylobacter upsaliensis
GC_ID:11
PMID:1479353
ncbi_taxonomy
Campylobacter helveticus
Salmonella enterica
Salmonella enterica
GC_ID:11
Campylobacter lawrenci
ncbi_taxonomy
'Campylobacter lawrenceae '
Campylobacter lawrenceae
GC_ID:11
PMID:11321120
PMID:12508904
Campylobacter fetus fetus
ncbi_taxonomy
Vibrio fetus subsp. intestinalis
Campylobacter fetus subsp. fetus
GC_ID:11
PMID:11321120
Campylobacter fetus subsp. venereus
Campylobacter fetus venerealis
Vibrio foetus venerealis
ncbi_taxonomy
Vibrio fetus subsp. venerealis
Campylobacter fetus subsp. venerealis
GC_ID:11
PMID:11321120
Campylobacter jejuni doylei
ncbi_taxonomy
Campylobacter jejuni subsp. doylei
GC_ID:11
PMID:11321120
Campylobacter jejuni jejuni
ncbi_taxonomy
Campylobacter jejuni subsp. jejuni
GC_ID:11
Campylobacter sputorum bubulus
ncbi_taxonomy
Campylobacter bubulus
Vibrio bubulus
Campylobacter sputorum subsp. bubulus
GC_ID:11
PMID:11321120
PMID:9542089
Campylobacter sputorum bv. sputorum
Campylobacter sputorum sputorum
ncbi_taxonomy
Campylobacter sputorum subsp. sputorum
Campylobacter sputorum biovar sputorum
GC_ID:1
amniotes
ncbi_taxonomy
Amniota
Salmonella enterica subsp. enterica serovar Javiana
Salmonella enterica subsp. enterica serovar Javiana
NCBITaxon:525139
NCBITaxon:525140
NCBITaxon:525141
NCBITaxon:525142
NCBITaxon:525143
NCBITaxon:525144
NCBITaxon:525145
GC_ID:11
PMID:19542108
ncbi_taxonomy
Campylobacter cuniculorum
Escherichia coli O103:H2
Escherichia coli O103:H2
Escherichia coli O142:H6
Escherichia coli O142:H6
Escherichia coli O26:NM
Escherichia coli O26:NM
Escherichia coli O26
Escherichia coli O26
NCBITaxon:2703845
GC_ID:11
PMID:17978232
ncbi_taxonomy
Campylobacter canadensis
Salmonella enterica subsp. enterica serovar Virchow
Salmonella enterica subsp. enterica serovar Virchow
GC_ID:11
PMID:19406805
ncbi_taxonomy
Campylobacter lari subsp. concheus
GC_ID:11
PMID:19406805
ncbi_taxonomy
Campylobacter peloridis
GC_ID:11
PMID:19661523
ncbi_taxonomy
Campylobacter subantarcticus
NCBITaxon:522483
GC_ID:11
PMID:19620353
ncbi_taxonomy
Campylobacter avium
Enterobacteriaceae
Enterobacteriaceae
Salmonella bongori
Salmonella bongori
Escherichia coli
E. coli
Escherichia/Shigella coli
Escherichia coli
Salmonella
Salmonella
Salmonella enterica subsp. enterica
Salmonella enterica subsp. enterica
GC_ID:11
Campylobacter sputorum bv. paraureolyticus
ncbi_taxonomy
Campylobacter sputorum biovar paraureolyticus
Salmonella enterica subsp. enterica serovar Infantis
Salmonella enterica subsp. enterica serovar Infantis
Salmonella enterica subsp. enterica serovar Heidelberg
Salmonella enterica subsp. enterica serovar Heidelberg
GC_ID:11
PMID:19406805
ncbi_taxonomy
Campylobacter lari subsp. lari
NCBITaxon:535089
NCBITaxon:654364
NCBITaxon:654365
GC_ID:11
PMID:21278267
ncbi_taxonomy
Campylobacter troglodytis
GC_ID:11
PMID:10758898
ncbi_taxonomy
Campylobacter lanienae
GC_ID:11
PMID:11321111
PMID:7857801
PMID:8123559
PMID:9720027
ncbi_taxonomy
Candidatus Campylobacter hominis
Campylobacter hominis
GC_ID:11
PMID:1854636
PMID:26383656
PMID:7857794
ncbi_taxonomy
Bacteroides gracilis
Campylobacter gracilis
GC_ID:11
PMID:1854636
PMID:19801389
PMID:7857794
ncbi_taxonomy
Bacteroides corrodens
Bacteroides ureolyticus
Campylobacter ureolyticus
GC_ID:1
bantam
chicken
chickens
ncbi_taxonomy
Gallus domesticus
Gallus gallus domesticus
Gallus gallus
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Typhimurium
GC_ID:11
PMID:10425776
PMID:7547297
ncbi_taxonomy
Campylobacter hyointestinalis subsp. hyointestinalis
GC_ID:11
PMID:10425776
PMID:7547297
ncbi_taxonomy
Campylobacter hyointestinalis subsp. lawsonii
GC_ID:1
whales, hippos, ruminants, pigs, camels etc.
ncbi_taxonomy
even-toed ungulates
Cetartiodactyla
GC_ID:1
human
man
ncbi_taxonomy
Home sapiens
Homo sampiens
Homo sapeins
Homo sapian
Homo sapians
Homo sapien
Homo sapience
Homo sapiense
Homo sapients
Homo sapines
Homo spaiens
Homo spiens
Humo sapiens
Homo sapiens
GC_ID:1
pig
pigs
swine
wild boar
ncbi_taxonomy
Sus scrofus
Sus scrofa
GC_ID:11
ncbi_taxonomy
Campylobacter cf. lanienae UB 992
GC_ID:11
ncbi_taxonomy
Campylobacter cf. lanienae UB 994
NCBITaxon:272461
GC_ID:1
bovine
cattle
cow
dairy cow
domestic cattle
domestic cow
ncbi_taxonomy
Bos Tauurus
Bos bovis
Bos primigenius taurus
Bos taurus
Escherichia coli O103:H25
Escherichia coli O103:H25
Escherichia coli O121:H19
Escherichia coli O121:H19
Escherichia coli O145:NM
Escherichia coli O145:NM
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.
COUNTRY
Country
Country
http://purl.obolibrary.org/obo/GEO_000000396
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A region, district or division of a country; a tract; a portion a state, especially one remote from the capital.
Province
Province
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A political unit, such as a city, town, or village, incorporated for local self-government.
Municipality
Municipality
http://semanticscience.org/resource/SIO_000665
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A constituent administrative district of a nation.
State
Territory
State
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A geographical area under the jurisdiction of a sovereign state and marked off for administrative or other purposes.
Territory
Territory
planned process
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'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.)
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.
Bjoern Peters
branch derived
6/11/9: Edited at workshop. Used to include: is initiated by an agent
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)
planned process
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Bjoern Peters
OBI branch derived
Could add specific objective specification
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
study
investigation
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
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.
PlanAndPlannedProcess Branch
measuring
scientific observation
OBI branch derived
study assay
any method
assay
specimen role
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.
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
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.
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.
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.
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.
GROUP: Role Branch
OBI
specimen role
organization
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.
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.
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
GROUP: OBI
organization
plan
The plan of researcher X to perform an experiment according to a protocol.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
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.
AR, BP, JM, MC, PRS
branch derived
plan
protocol
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.
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.
PlanAndPlannedProcess Branch
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
study protocol
protocol
interpreting data
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.
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
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
Bjoern Peters
drawing a conclusion based on data
planning
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.
a process of creating or modifying a plan specification
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'.
Bjoern Peters
Bjoern Peters
Plans and Planned Processes Branch
planning
study design execution
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
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.
branch derived
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.
study design execution
specimen collection process
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
A planned process with the objective of collecting a specimen.
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.
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.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker:
http://sourceforge.net/p/obi/obi-terms/716/
Bjoern Peters
specimen collection
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
6/9/09: used at workshop
specimen collection process
specimen collection objective
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
Bjoern Peters
Bjoern Peters
specimen collection objective
hospital
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]
A medical organization at which sick or injured people are given clinical care
Person:Alan Ruttenberg
Person:Helen Parkinson
http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n
modified from the wording of the wordnet definition
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
hospital
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".
An information content entity that is inferred from data.
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.
Group:2013 Philly Workshop group
Group:2013 Philly Workshop group
conclusion based on data
surveillance process
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.
Chris Stoeckert
Shane Babcock, OBI
https://github.com/obi-ontology/obi/issues/1181
IDO, VEuPathDB
surveillance process
organism
animal
fungus
plant
virus
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.
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')
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.
GROUP: OBI Biomaterial Branch
WEB: http://en.wikipedia.org/wiki/Organism
organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
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.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
specimen
study design
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.
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: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
PERSON: Chris Stoeckert
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
study design
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].
The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]
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]
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]
AAO:0010407
BTO:0000434
CALOHA:TS-1241
EMAPA:35328
EV:0100093
FMA:16017
MA:0002415
NCIT:C32546
TAO:0001249
UMLS:C0553695
VHOG:0000048
XAO:0000137
ZFA:0001249
exocrine pancreas
pars exocrina pancreatis
uberon
exocrine component of pancreas
exocrine part of pancreas
UBERON:0000017
exocrine pancreas
An organ that is capable of transducing sensory stimulus to the nervous system.
AEO:0000094
BSA:0000121
BTO:0000202
CALOHA:TS-2043
EHDAA2:0001824
EHDAA:500
EMAPA:35955
FBbt:00005155
GAID:63
HAO:0000930
MA:0000017
MESH:D012679
NCIT:C33224
UMLS:C0935626
VHOG:0001407
WBbt:0006929
organ of sense organ system
organ of sensory organ system
organ of sensory system
sense organ system organ
sensory organ
sensory organ system organ
sensory system organ
sensillum
uberon
Sinnesorgan
sensor
UBERON:0000020
sense organ
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.
Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]
BTO:0000784
CALOHA:TS-0579
EFO:0000872
EMAPA:35523
EV:0100050
FMA:5034
GAID:947
MA:0000139
MAT:0000442
MESH:D008198
NCIT:C12745
NCIT:C33027
OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA
TAO_RETIRED:0005318
UMLS:C0024204
VHOG:0001273
ZFA_RETIRED:0005318
galen:Lymphnode
uberon
lymph gland
nodus lymphaticus
UBERON:0000029
lymph node
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
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]
AAO:0010396
BTO:0000706
CALOHA:TS-1306
EFO:0000840
EMAPA:19252
EV:0100077
FMA:7201
GAID:306
MA:0000333
MESH:A03.492.411.495
MIAA:0000046
NCIT:C12379
OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA
UMLS:C0021851
VHOG:0000054
XAO:0000131
galen:LargeIntestine
uberon
intestinum crassum
UBERON:0000059
large intestine
cjm
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
ISBN10:0073040584
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]
2012-09-17
VHOG:0000054
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566
UMLS:C0021851
ncithesaurus:Large_Intestine
intestinum crassum
BTO:0000706
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
biological structure
connected biological structure
uberon
UBERON:0000061
anatomical structure
Anatomical structure that performs a specific function or group of functions [WP].
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.
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
CARO:0020004
EFO:0000634
EMAPA:35949
ENVO:01000162
FMA:67498
MA:0003001
NCIT:C13018
OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
UMLS:C0178784
WBbt:0003760
uberon
anatomical unit
body organ
element
UBERON:0000062
organ
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
AAO:0011124
EFO:0000635
FMA:82472
cardinal organ part
uberon
regional part of organ
UBERON:0000064
organ part
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.
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]
zona pellucida - vitelline membrane
BTO:0003135
EHDAA2:0002220
EHDAA:31
EHDAA:62
EMAPA:16035
FMA:18674
GAID:410
MA:0001715
MESH:D015044
NCIT:C33896
TAO:0001111
UMLS:C0043519
VHOG:0000720
ZFA:0001111
uberon
oolemma
pellucid zone
striated membrane
vitelline envelope
vitelline membrane
zona radiata
zona striata
UBERON:0000086
zona pellucida
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]
cjm
2009-07-30T05:19:13Z
membrane
FMA:7145
membrane of organ
uberon
UBERON:0000094
membrane organ
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.
This class is probably too inclusive
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
intestinal
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.
AAO:0000246
ANISEED:1235303
BSA:0000093
BTO:0000648
CALOHA:TS-0490
EFO:0000834
EMAPA:32874
EV:0100071
FMA:7199
GAID:295
MA:0000328
MA:0001524
MESH:A03.492.411
MIAA:0000043
NCIT:C12736
TAO:0001338
UMLS:C0021853
VHOG:0000056
WBbt:0005772
XAO:0000129
ZFA:0001338
galen:Intestine
bowel
uberon
intestinal tract
UBERON:0000160
intestine
cjm
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.
GOC:GO
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
2012-06-20
AAO:0000246
AAO
AAO:EJS
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000056
VHOG
UMLS:C0021853
ncithesaurus:Intestine
1
1
1
1
The pair of anatomical structures comprised of a left lung and right lung.
FMA:68877
OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
lungs
lungs pair
pulmones
set of lungs
uberon
UBERON:0000170
pair of lungs
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.
EMAPA:17607
SPD:0000428
TGMA:0001247
apparatus respiratorius organ
breathing organ
organ of apparatus respiratorius
organ of respiratory system
respiratory organ
respiratory system organ
uberon
gas exchange organ
UBERON:0000171
respiration organ
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
UBERON:0000324
UBERON:0007550
AEO:0000184
BTO:0000491
EHDAA2_RETIRED:0003184
ENVO:02000022
FMA:9674
galen:Excretion
excreted substance
portion of excreted substance
waste substance
uberon
excretion
UBERON:0000174
excreta
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
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]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
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]
AAO:0000046
BTO:0000089
CALOHA:TS-0079
EFO:0000296
EHDAA2:0000176
EHDAA:418
EMAPA:16332
ENVO:02000027
EV:0100047
FMA:9670
GAID:965
MA:0000059
MESH:D001769
MIAA:0000315
NCIT:C12434
OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA
TAO:0000007
UMLS:C0005767
VHOG:0000224
XAO:0000124
ZFA:0000007
galen:Blood
portion of blood
vertebrate blood
uberon
whole blood
UBERON:0000178
blood
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
cjm
2009-04-08T04:38:19Z
CARO:0000081
uberon
blood or blood analog
circulating fluid
UBERON:0000179
haemolymphatic fluid
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.
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.
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].
BTO:0000449
CALOHA:TS-0360
EFO:0001323
FBbt:00005333
FMA:63919
GAID:552
MESH:D005333
NCIT:C13235
OpenCyc:Mx4rvZfC2ZwpEbGdrcN5Y29ycA
UMLS:C0015965
fetus
uberon
embryo late growth stage
embryo late stage
UBERON:0000323
late embryo
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.
BTO:0000503
EMAPA:27181
FMA:14919
uberon
UBERON:0000325
gastric gland
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
BTO:0001837
EMAPA:37950
FMA:62889
uberon
UBERON:0000409
serous gland
A gland in which the principal secretory cells are mucus secreting cells.
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]
AAO:0010601
BTO:0001979
EMAPA:37913
FMA:62888
glandula mucosa
uberon
muciparous gland
mucous secreting gland
mucus gland
mucus-secreting gland
UBERON:0000414
mucous gland
A portion of organism substance that is produced by exocrine glands.
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
UBERON:0006540
secretion
AEO:0001005
BTO:0002977
BTO:0002979
EMAPA:36535
FMA:9675
MA:0002504
MESH:D012634
NCIT:C34062
UMLS:C1516992
galen:Secretion
bodily secretion
exocrine gland fluid/secretion
secreted substance
uberon
exocrine gland fluid
exocrine gland fluid or secretion
exocrine gland secretion
external secretion
UBERON:0000456
secretion of exocrine gland
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.
AAO:0010839
AEO:0000004
BILA:0000004
CALOHA:TS-2101
CARO:0000004
EHDAA2:0003004
EMAPA:35178
FBbt:00007019
FMA:9669
HAO:0000004
MA:0002450
NCIT:C13236
SPD:0000008
TAO:0001487
TGMA:0001824
VHOG:0001726
XAO:0004001
ZFA:0001487
galen:BodySubstance
body fluid or substance
body substance
organism substance
portion of body substance
portion of organism substance
uberon
UBERON:0000463
organism substance
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
system
AAO:0000007
AEO:0000011
BILA:0000011
BSA:0000049
CALOHA:TS-2088
CARO:0000011
EHDAA2:0003011
EHDAA:392
EMAPA:16103
EV:0100000
FBbt:00004856
FMA:7149
HAO:0000011
MA:0000003
NCIT:C12919
OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
TAO:0001439
TGMA:0001831
UMLS:C0460002
VHOG:0001725
WBbt:0005746
WBbt:0005763
XAO:0003002
ZFA:0001439
galen:AnatomicalSystem
body system
connected anatomical system
organ system
uberon
anatomical systems
UBERON:0000467
anatomical system
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
organismal
organism
AAO:0010026
AEO:0000191
BILA:0000012
BSA:0000038
BTO:0000042
CARO:0000012
EFO:0002906
EHDAA2:0003103
EHDAA2:0003191
EHDAA:1
EMAPA:25765
EV:0100016
FBbt:00000001
FMA:256135
HAO:0000012
NCIT:C13041
TADS:0000001
TAO:0001094
TGMA:0001832
VHOG:0000671
WBbt:0007833
XAO:0003004
ZFA:0001094
galen:Organism
ncithesaurus:Whole_Organism
multi-cellular organism
animal
uberon
Koerper
body
whole body
whole organism
UBERON:0000468
multicellular organism
The organs and associated structures associated with bearing offspring in a female animal.
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]
BTO:0000083
CALOHA:TS-1303
EFO:0000969
EHDAA2:0000506
EHDAA:8116
EMAPA:17959
EV:0100110
FBbt:00004864
FMA:45663
GAID:364
HAO:0000324
MA:0000381
MESH:D005836
MIAA:0000028
NCIT:C12402
OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA
TGMA:0000635
UMLS:C0700038
VHOG:0000726
WBbt:0006748
WikipediaCategory:Female_reproductive_system
XAO:0000156
female organism genitalia
female organism reproductive system
genitalia of female organism
reproductive system of female organism
uberon
female genital system
female genital tract
female genitalia
female genitals
female reproductive tract
gynaecological tissue
systema genitale femininum
UBERON:0000474
female reproductive system
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
AAO:0010268
AEO:0000040
BILA:0000040
CARO:0000040
EHDAA2:0003040
FBbt:00007013
FMA:63863
HAO:0000040
TAO:0000382
TGMA:0001841
XAO:0003162
ZFA:0000382
uberon
acellular anatomical structures
UBERON:0000476
acellular anatomical structure
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.
changed label and definition to reflect CARO2
AAO:0000607
AAO:0010054
AEO:0000043
BILA:0000043
CALOHA:TS-2090
CARO:0000043
EHDAA2:0003043
EMAPA:35868
FBbt:00007003
FMA:9637
HAO:0000043
MA:0003002
MESH:D014024
NCIT:C12801
TAO:0001477
TGMA:0001844
UMLS:C0040300
VHOG:0001757
WBbt:0005729
XAO:0003040
ZFA:0001477
galen:Tissue
portion of tissue
tissue portion
simple tissue
uberon
UBERON:0000479
tissue
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.
AAO:0010048
AEO:0000055
BILA:0000055
CARO:0000055
EHDAA2:0003055
FBbt:00007010
HAO:0000055
TAO:0001488
TGMA:0001847
VHOG:0001762
XAO:0003037
ZFA:0001488
uberon
multi-tissue structures
UBERON:0000481
multi-tissue structure
Compound organ that contains one or more macroscopic anatomical spaces.
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
AAO:0010016
AEO:0000072
BILA:0000072
CARO:0000072
EHDAA2:0003072
FMA:55671
HAO:0000072
TAO:0001490
TGMA:0001857
VHOG:0001730
XAO:0003165
ZFA:0001490
cavitated organ
uberon
cavitated compound organs
UBERON:0000489
cavitated compound organ
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.
mucoid
mucous
CALOHA:TS-2144
ENVO:02000040
FMA:66938
GAID:1164
MESH:D009093
NCIT:C13259
OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA
UMLS:C0026727
galen:Mucus
uberon
UBERON:0000912
mucus
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.
ENVO:02000042
FMA:9673
NCIT:C120839
intercellular fluid
tissue fluid
uberon
UBERON:0000913
interstitial fluid
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.
embryonic
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
AAO:0011035
AEO:0000169
BILA:0000056
BSA:0000039
BTO:0000379
CALOHA:TS-0229
EFO:0001367
EHDAA2:0000002
EHDAA2_RETIRED:0003236
EHDAA:38
EMAPA:16039
FBbt:00000052
FMA:69068
GAID:963
MAT:0000226
MESH:D004622
MIAA:0000019
NCIT:C28147
OGEM:000001
OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA
UMLS:C0013935
VHOG:0001766
XAO:0000113
ZFA:0000103
embryonic organism
uberon
developing organism
developmental tissue
UBERON:0000922
embryo
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.
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
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]
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
AAO:0000579
ANISEED:1235297
BTO:0001307
CALOHA:TS-0980
EFO:0000837
EHDAA2:0001915
EHDAA:2993
EMAPA:17021
EV:0100070
FMA:7148
GAID:293
MA:0000353
MAT:0000051
MESH:A03.492.766
MIAA:0000051
NCIT:C12391
OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA
TAO:0002121
UMLS:C0038351
VHOG:0000408
XAO:0000128
galen:Stomach
stomach chamber
uberon
anterior intestine
gaster
mesenteron
ventriculus
UBERON:0000945
stomach
cjm
cjm
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.
ISBN10:0073040584
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
2012-06-20
AAO:0000579
AAO
AAO:EJS
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]
2012-09-17
VHOG:0000408
VHOG
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)
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
WP:Stomach#In_other_animals
UMLS:C0038351
ncithesaurus:Stomach
gaster
BTO:0001307
ventriculus
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
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]
endocrine
AAO:0010279
CALOHA:TS-1301
EFO:0002969
EHDAA2:0002224
EMAPA:35306
EV:0100128
FBbt:00005068
FMA:9668
GAID:439
MA:0000012
MESH:D004703
NCIT:C12705
TAO:0001158
UMLS:C0014136
VHOG:0000098
XAO:0000158
ZFA:0001158
endocrine glandular system
endocrine system
systema endocrinum
uberon
UBERON:0000949
endocrine system
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].
requires review for applicability to invertebrate structures, e.g. synganglion
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
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)
(...) 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]
AAO:0010478
ABA:Brain
BAMS:Br
BAMS:Brain
BILA:0000135
BTO:0000142
CALOHA:TS-0095
DHBA:10155
EFO:0000302
EHDAA2:0000183
EHDAA:2641
EHDAA:6485
EMAPA:16894
EV:0100164
FBbt:00005095
FMA:50801
GAID:571
HBA:4005
MA:0000168
MAT:0000098
MBA:8
MBA:997
MESH:D001921
MIAA:0000098
NCIT:C12439
OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
PBA:3999
TAO:0000008
UMLS:C0006104
UMLS:C1269537
VHOG:0000157
XAO:0000010
ZFA:0000008
galen:Brain
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21
uberon
encephalon
suprasegmental levels of nervous system
suprasegmental structures
synganglion
the brain
UBERON:0000955
brain
Anatomical system that has as its parts the organs concerned with reproduction.
consider splitting genitalia from reproductive system
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
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]
AAO:0010258
BILA:0000103
BTO:0000081
CALOHA:TS-1318
EFO:0000809
EHDAA2:0001603
EHDAA:5923
EMAPA:17381
EV:0100100
FBbt:00004857
FMA:7160
GAID:363
HAO:0000374
HAO:0000895
MA:0000326
MIAA:0000305
NCIT:C12841
OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA
TAO:0000632
UMLS:C1261210
VHOG:0000182
WBbt:0005747
XAO:0000142
ZFA:0000632
uberon
Geschlechtsorgan
animal reproductive system
genital system
genital tract
genitalia
organa genitalia
reproductive tissue
reproductive tract
systemata genitalia
UBERON:0000990
reproductive system
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
AAO:0000541
BTO:0000203
CALOHA:TS-1319
EFO:0000804
EHDAA2:0001604
EHDAA:2203
EMAPA:16727
EV:0100036
FMA:7158
GAID:78
MA:0000327
MAT:0000030
MESH:D012137
MIAA:0000030
NCIT:C12779
OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA
TAO:0000272
UMLS:C0035237
VHOG:0000202
XAO:0000117
ZFA:0000272
apparatus respiratorius
respiratory system
uberon
Atmungssystem
apparatus respiratorius
systema respiratorium
UBERON:0001004
respiratory system
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
digestive
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
AAO:0000129
BILA:0000082
BTO:0000058
CALOHA:TS-1293
EFO:0000793
EV:0100056
FBbt:00005055
FMA:7152
GAID:278
MA:0002431
MAT:0000018
MESH:D004064
MIAA:0000018
TADS:0000170
TAO:0000339
WBbt:0005748
XAO:0000125
ZFA:0000339
galen:DigestiveSystem
ncithesaurus:Digestive_System
uberon
alimentary system
alimentary tract
gastrointestinal system
gut
UBERON:0001007
digestive system
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..
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
An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
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]
In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
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
AAO:0010257
BILA:0000015
BTO:0001244
BTO:0003092
CALOHA:TS-1323
EFO:0000803
EHDAA2:0001601
EHDAA:5901
EMAPA:17366
EV:0100095
FBbt:00005056
FMA:7159
GAID:391
MA:0000325
MAT:0000027
MESH:D014551
MIAA:0000027
NCIT:C12413
TADS:0000162
TAO:0000163
UMLS:C1508753
VHOG:0000723
WBbt:0005736
XAO:0000143
ZFA:0000163
galen:UrinaryTract
excretory system
renal system
systema urinaria
systema urinarium
urinary system
urinary tract
uberon
renal or urinary system
renal/urinary system
UBERON:0001008
renal system
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].
the cardiovascular system and the lymphatic system are parts of the circulatory system
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]
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]
AAO:0000959
CALOHA:TS-2103
FBbt:00005057
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
VHOG:0001248
uberon
systema cardiovasculare
UBERON:0001009
circulatory system
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].
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]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
nervous
neural
AAO:0000324
BILA:0000079
BTO:0001484
CALOHA:TS-1313
EFO:0000802
EHDAA2:0001246
EHDAA:826
EMAPA:16469
EV:0100162
FBbt:00005093
FMA:7157
GAID:466
MA:0000016
MAT:0000026
MESH:D009420
MIAA:0000026
NCIT:C12755
OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA
TAO:0000396
UMLS:C0027763
VHOG:0000402
WBbt:0005735
XAO:0000177
ZFA:0000396
neurological system
nerve net
uberon
systema nervosum
UBERON:0001016
nervous system
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
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]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
AAO:0000555
BAMS:SEN
BILA:0000099
EFO:0000805
EHDAA2:0003094
EMAPA:16192
FBbt:00007692
FMA:75259
MA:0002442
MAT:0000031
MIAA:0000031
TAO:0000282
VHOG:0001674
XAO:0003194
ZFA:0000282
organa sensuum
sense organ subsystem
sense organs
sense organs set
sensory subsystem
sensory systems
uberon
organa sensuum
sensory organ system
set of sense organs
UBERON:0001032
sensory system
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).
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]
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]
esophageal
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)
AAO:0000145
ANISEED:1235301
BTO:0000959
CALOHA:TS-0700
EFO:0000835
EHDAA2:0001285
EHDAA:2937
EMAPA:16833
EV:0100069
FMA:7131
GAID:291
MA:0000352
MAT:0000048
MESH:A03.365
MIAA:0000048
NCIT:C12389
OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA
TAO:0000204
UMLS:C0014876
VHOG:0000450
XAO:0000127
ZFA:0000204
galen:Esophagus
gullet
oesophagus
uberon
UBERON:0001043
esophagus
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).
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]
2012-06-20
AAO:0000145
AAO
AAO:EJS
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]
2012-09-17
VHOG:0000450
VHOG
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)
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)
MA
UMLS:C0014876
ncithesaurus:Esophagus
the terminal portion of the intestinal tube, terminating with the anus
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]
rectal
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
AAO:0010401
BTO:0001158
CALOHA:TS-1180
EFO:0000848
EHDAA2:0001592
EHDAA:5836
EMAPA:17896
EV:0100081
FMA:14544
GAID:311
MA:0000336
MAT:0000050
MESH:A03.492.411.495.767
MIAA:0000050
NCIT:C12390
OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA
UMLS:C0034896
VHOG:0001751
XAO:0000238
galen:Rectum
terminal portion of intestine
uberon
intestinum rectum
rectal sac
terminal portion of large intestine
UBERON:0001052
rectum
4
cjm
MA
ISBN10:0073040584
the terminal portion of the intestinal tube, terminating with the anus
ISBN:0-683-40008-8
MP:0000492
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]
2012-09-17
VHOG:0001751
VHOG
UMLS:C0034896
ncithesaurus:Rectum
intestinum rectum
BTO:0001158
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.
AAO:0010841
AEO:0000000
BILA:0000000
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
It provides nutrients and lubrication for articular cartilage
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
BTO:0001339
CALOHA:TS-0996
ENVO:02000039
FMA:12277
GAID:265
MA:0002544
MESH:D013582
NCIT:C33718
TAO:0005154
UMLS:C0039097
ZFA:0005154
galen:SynovialFluid
joint fluid
uberon
UBERON:0001090
synovial fluid
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.
caecal
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.
BTO:0000166
CALOHA:TS-0122
EFO:0000850
EHDAA2:0000206
EHDAA:3913
EMAPA:35197
EV:0100397
FMA:14541
GAID:307
MA:0000334
MESH:A03.492.411.495.209
MIAA:0000288
NCIT:C12381
OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA
UMLS:C0007531
VHOG:0001559
galen:Cecum
caecum
cecum
intestinum crassum caecum
caeca
ceca
uberon
blind intestine
blindgut
intestinum caecum
intestinum crassum cecum
UBERON:0001153
Kardong: in some herbivorous lizards, a cecum is present between small and large intestines
caecum
EHDAA2
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.
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.
WP
UMLS:C0007531
ncithesaurus:Cecum
caecum
VHOG:0001559
cecum
FMA:14541
caeca
NCBITaxon:8782
ceca
NCBITaxon:8782
blind intestine
BTO:0000166
blindgut
BTO:0000166
intestinum caecum
BTO:0000166
intestinum crassum cecum
BTO:0000166
Last portion of the large intestine before it becomes the rectum.
TODO - abstract this such that it legitimately covers all vertebrates
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
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]
colonic
In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
it extracts water and salt from solid wastes before they are eliminated from the body[WP]
AAO:0010400
BTO:0000269
CALOHA:TS-0158
EFO:0000361
EMAPA:18939
EV:0100079
FMA:14543
GAID:309
MA:0000335
MAP:0000001
MAT:0000526
MESH:A03.492.411.495.356
NCIT:C12382
OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA
TAO:0000706
UMLS:C0009368
VHOG:0000648
XAO:0000243
ZFA:0000706
galen:Colon
large bowel
posterior intestine
uberon
hindgut
UBERON:0001155
colon
3
cjm
FMA
Last portion of the large intestine before it becomes the rectum.
ZFIN:curator
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
2012-06-20
AAO:0010400
AAO
UBERON:0001155
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
2012-08-14
TAO:0000706
TAO
ZFIN:curator
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]
2012-09-17
VHOG:0000648
VHOG
ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
UMLS:C0009368
ncithesaurus:Colon
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.
Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]
AAO:0011020
EMAPA:35172
FMA:14665
UMLS:C0005423
XAO:0000455
uberon
biliary tract
UBERON:0001173
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]
biliary tree
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
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]
pancreatic
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)
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
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
AAO:0010112
BTO:0000988
CALOHA:TS-0736
EFO:0000855
EHDAA2:0001367
EHDAA:6893
EMAPA:17503
EV:0100092
FMA:7198
GAID:334
MA:0000120
MAT:0000075
MESH:D010179
MIAA:0000075
NCIT:C12393
OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA
TAO:0000140
UMLS:C0030274
VHOG:0000050
XAO:0000136
ZFA:0000140
galen:Pancreas
uberon
UBERON:0001264
pancreas
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
check ncita
EMAPA:37621
FMA:34836
GAID:263
MA:0001519
MESH:D017746
NCIT:C32259
NCIT:C84388
UMLS:C0206207
galen:JointCapsule
capsula articularis
fibrous capsule of joint
joint capsule
joint fibrous capsule
uberon
capsulae articulares
UBERON:0001484
articular capsule
A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males.
Originally this was classified as a female reproductive structure, as it was in the MP in 2011
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]
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]
mammary
A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts
The male Dayak fruit bat has lactating mammary glands
The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges.
The BTO class represents the combination of nipple plus lobe
The FMA class represents an individule lobe. The nipple is not a part
The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts
BTO:0000817
CALOHA:TS-0595
EFO:0000854
EMAPA:17759
EV:0100125
FMA:286452
MA:0000145
MAT:0000073
MESH:D008321
MIAA:0000073
NCIT:C12367
OpenCyc:Mx4rvVjVq5wpEbGdrcN5Y29ycA
UMLS:C0929301
VHOG:0000398
glandula mammaria
lactiferous gland
lobe of breast
milk patch
uberon
Brustdruese
dug
glandula mammaria
lobe of mammary gland
mamma
mammae
UBERON:0001911
mammary gland
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
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.
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]
ncit:Milk refers specifically to cow milk
BTO:0000868
CALOHA:TS-0636
EMAPA:36540
ENVO:02000031
EV:0100126
FMA:62100
GAID:1230
MA:0002552
MAT:0000056
MESH:A13.622
MIAA:0000056
NCIT:C13401
OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA
UMLS:C1511310
VHOG:0001263
galen:Milk
mammary gland milk
uberon
UBERON:0001913
milk
The liquid component of blood, in which erythrocytes are suspended.
plasma
portion of plasma
BTO:0000131
CALOHA:TS-0800
EFO:0001905
EMAPA:35690
FMA:62970
GAID:1178
MA:0002501
MAT:0000052
MESH:D010949
MIAA:0000052
NCIT:C13356
OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
UMLS:C0032105
blood plasm
portion of blood plasma
uberon
UBERON:0001969
blood plasma
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.
In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.
aids the process of digestion of lipids in the small intestine
bile salts function to emulsify dietary fats and facilitate their intestinal absorption
elimination of cholesterol
major excretory route for potentially harmful exogenous lipophilic substances
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
protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine
BTO:0000121
CALOHA:TS-1172
ENVO:02000023
FMA:62971
GAID:1157
MA:0002513
MESH:D001646
NCIT:C13192
UMLS:C0005388
ZFA:0005857
galen:Bile
uberon
fel
gall
UBERON:0001970
bile
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.
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]
placental
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
BTO:0001078
CALOHA:TS-0799
EFO:0001407
EMAPA:35689
EV:0100119
FMA:63934
GAID:379
MA:0000386
MAT:0000279
MESH:A16.759
MIAA:0000279
NCIT:C13272
OpenCyc:Mx4rvv4zZ5wpEbGdrcN5Y29ycA
UMLS:C0032043
VHOG:0001266
allantoic placenta
eutherian placenta
uberon
UBERON:0001987
Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities.
placenta
Portion of semisolid bodily waste discharged through the anus[MW,modified]
Excretion in semisolid state processed by the intestine.[FMA]
fecal
excreta
BTO:0000440
CALOHA:TS-2345
ENVO:00002003
FMA:64183
GAID:1199
MA:0002509
MAT:0000053
MESH:D005243
MIAA:0000053
NCIT:C13234
OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA
UMLS:C0015733
galen:Feces
faeces
fecal material
fecal matter
matières fécales@fr
merde@fr
partie de la merde@fr
piece of shit
porción de mierda@es
portion of excrement
portion of faeces
portion of fecal material
portion of fecal matter
portion of feces
portionem cacas
stool
teil der fäkalien@de
cow dung
cow pat
dung
fewmet
frass
guano
portion of dung
portion of guano
portion of scat
scat
spraint
uberon
droppings
excrement
ordure
spoor
UBERON:0001988
feces
Respiration organ that develops as an oupocketing of the esophagus.
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
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]
pulmonary
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
AAO:0000275
AAO:0010567
BTO:0000763
CALOHA:TS-0568
EFO:0000934
EHDAA2:0001042
EHDAA:1554
EHDAA:2205
EMAPA:16728
EV:0100042
FMA:7195
GAID:345
MA:0000415
MAT:0000135
MESH:D008168
MIAA:0000135
NCIT:C12468
OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
UMLS:C0024109
VHOG:0000310
XAO:0000119
galen:Lung
pulmo
uberon
UBERON:0002048
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]
lung
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
in FMA embryo is_a embryonic structure
AAO:0000138
BILA:0000034
BTO:0000174
CALOHA:TS-2110
EFO:0000461
FBbt:00004208
FMA:69067
GAID:407
MESH:D004628
NCIT:C13229
RETIRED_EHDAA2:0003169
TAO:0001105
UMLS:C0013948
VSAO:0000178
XAO:0003042
ZFA:0001105
developing embryonic structure
embryonic anatomical structure
uberon
developing structure
embryonale Struktur
embryonic structures
UBERON:0002050
embryonic structure
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.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
AAO:0010386
BTO:0001491
EHDAA:512
EMAPA:16245
FMA:7085
MA:0000019
MESH:D014781
NCIT:C28287
RETIRED_EHDAA2:0002201
UMLS:C0042779
XAO:0003034
visceral organ
visceral organ system
uberon
Organsystem@de
splanchnic tissue
viscera
visceral tissue
UBERON:0002075
viscus
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
MA uses the term skin to refer to what is called here: zone of skin
BTO:0001253
CALOHA:TS-0934
EFO:0000962
EHDAA2:0001844
EMAPA:17525
FMA:7163
MESH:D012867
MFMO:0000099
NCIT:C12470
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
UMLS:C1123023
XAO:0000023
galen:Skin
entire skin
skin organ
uberon
entire integument
integument
integumental organ
pelt
skin
UBERON:0002097
skin of body
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
The sensory system used for balance and hearing.[AAO]
AAO:0000631
EMAPA:36002
EMAPA:37985
FMA:78500
TAO:0001138
XAO:0003195
ZFA:0001138
auditory organ system
vestibuloauditory system
uberon
auditory system
auditory/vestibular system
vestibuloauditory system
UBERON:0002105
vestibulo-auditory system
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].
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
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]
hepatic
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).
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.
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].
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.
AAO:0010111
BTO:0000759
CALOHA:TS-0564
EFO:0000887
EHDAA2:0000997
EHDAA:2197
EMAPA:16846
EV:0100089
FMA:7197
GAID:288
MA:0000358
MAT:0000097
MESH:D008099
MIAA:0000097
NCIT:C12392
OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA
TAO:0000123
UMLS:C0023884
VHOG:0000257
XAO:0000133
ZFA:0000123
galen:Liver
uberon
iecur
jecur
UBERON:0002107
liver
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].
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]
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]
AAO:0010397
BTO:0000651
CALOHA:TS-0942
EFO:0000841
EMAPA:32834
EV:0100072
FMA:7200
GAID:313
MA:0000337
MAT:0000047
MESH:A03.492.411.620
MIAA:0000047
NCIT:C12386
OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA
TAO:0001323
UMLS:C0021852
VHOG:0000055
XAO:0000130
ZFA:0001323
galen:SmallIntestine
small bowel
small intestine
uberon
anterior intestine
intestinum tenue
mid intestine
UBERON:0002108
small intestine
2
cjm
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].
ISBN10:0073040584
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]
2012-08-14
TAO:0001323
TAO
ZFIN:curator
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]
2012-09-17
VHOG:0000055
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566
UMLS:C0021852
ncithesaurus:Small_Intestine
intestinum tenue
intestinum tenue
BTO:0000651
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).
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]
duodenal
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.
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.
AAO:0010402
BTO:0000365
CALOHA:TS-0214
EFO:0000851
EMAPA:18852
EV:0100073
FMA:7206
GAID:284
MA:0000338
MAT:0000044
MESH:A03.492.411.620.270
MIAA:0000044
NCIT:C12263
OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA
UMLS:C0013303
VHOG:0000052
XAO:0000236
galen:Duodenum
uberon
proximal intestine
upper intestine
UBERON:0002114
duodenum
3
cjm
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).
ISBN:0815318960
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]
2012-09-17
VHOG:0000052
VHOG
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.
NCBITaxon:32443
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.
NCBITaxon:9606
UMLS:C0013303
ncithesaurus:Duodenum
proximal intestine
BTO:0000365
upper intestine
BTO:0000365
the portion of the small intestine that extends from the duodenum to the ileum
TODO consider ZFA:0001323 mid intestine, see also small intestine
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]
jejunal
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]
BTO:0000657
CALOHA:TS-0496
EFO:0001333
EMAPA:18666
EV:0100074
FMA:7207
GAID:318
MA:0000340
MAT:0000045
MESH:A03.492.411.620.625
MIAA:0000045
NCIT:C12388
OpenCyc:Mx4rwATkPJwpEbGdrcN5Y29ycA
UMLS:C0022378
VHOG:0000053
galen:Jejunum
uberon
intestinum jejunum
mid-intestine
middle intestine
UBERON:0002115
jejunum
3
cjm
the portion of the small intestine that extends from the duodenum to the ileum
MGI:monikat
MP:0004002
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]
2012-09-17
VHOG:0000053
VHOG
UMLS:C0022378
ncithesaurus:Jejunum
intestinum jejunum
BTO:0000657
mid-intestine
middle intestine
BTO:0000657
the portion of the small intestine that extends from the jejunum to the colon
TODO consider ZFA:0000706 posterior intestine, see also colon
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]
ileal
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]
AAO:0010403
BTO:0000620
CALOHA:TS-0472
EFO:0001334
EMAPA:32764
EV:0100075
FMA:7208
GAID:315
MA:0000339
MAT:0000282
MESH:A03.492.411.620.484
MIAA:0000282
NCIT:C12387
OpenCyc:Mx4rvdcLHZwpEbGdrcN5Y29ycA
UMLS:C0020885
VHOG:0000647
XAO:0000237
galen:Ileum
uberon
distal intestine
intestinum ileum
lower intestine
posterior intestine
UBERON:0002116
ileum
3
cjm
the portion of the small intestine that extends from the jejunum to the colon
ISBN:0-683-40008-8
MGI:csmith
MP:0002581
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]
2012-09-17
VHOG:0000647
VHOG
ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
UMLS:C0020885
ncithesaurus:Ileum
distal intestine
BTO:0000620
intestinum ileum
BTO:0000620
lower intestine
BTO:0000620
posterior intestine
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
EHDAA2:0001730
EHDAA:4969
EMAPA:17661
FMA:7309
MA:0000426
NCIT:C33483
OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA
UMLS:C0225706
VHOG:0000301
uberon
UBERON:0002167
right lung
Lung which consists of the left upper lobe and left lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
EHDAA2:0000943
EHDAA:4947
EMAPA:17653
FMA:7310
MA:0000425
NCIT:C32967
OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA
UMLS:C0225730
VHOG:0000618
uberon
UBERON:0002168
left lung
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
CALOHA:TS-2018
EHDAA2:0004615
EMAPA:18765
FMA:74562
MA:0000013
hematolymphoid system
lymphomyeloid complex
uberon
haemolymphoid system
UBERON:0002193
hemolymphoid system
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
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]
musculoskeletal
AAO:0010546
CALOHA:TS-1311
EMAPA:32714
EV:0100139
FMA:7482
GAID:98
MA:0002418
MESH:D009141
NCIT:C12754
OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g
UMLS:C0026860
VHOG:0001275
VSAO:0000031
XAO:0000168
musculo-skeletal system
uberon
UBERON:0002204
musculoskeletal system
An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
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
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
AAO:0010180
BTO:0001772
FBbt:00005158
FMA:77659
VHOG:0000287
XAO:0000273
olfactory organ
olfactory sense organ
olfactory sensory organ
main olfactory organ
primary olfactory organ
uberon
olfactory neuroepithelium
organ olfactus
organum olfactorium
UBERON:0002268
olfactory organ
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].
CALOHA:TS-2057
EHDAA2:0002225
EMAPA:35329
FMA:85539
MA:0002411
NCIT:C12957
UMLS:C1516995
WikipediaCategory:Exocrine_system
exocrine glandular system
uberon
UBERON:0002330
exocrine system
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
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
AEO:0000097
BTO:0000765
CALOHA:TS-2012
EHDAA2:0003097
EMAPA:35327
FMA:9596
GAID:34
MA:0002564
MESH:D005088
NCIT:C12712
UMLS:C0015282
ducted gland
glandula exocrina
uberon
UBERON:0002365
exocrine gland
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
AEO:0000098
BTO:0001488
CALOHA:TS-1300
EHDAA2:0003098
EMAPA:35999
FMA:9602
GAID:335
MA:0002563
MESH:D004702
NCIT:C12704
OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA
UMLS:C0014133
ductless gland
glandula endocrina
uberon
ductless gland
glandulae endocrinae
UBERON:0002368
endocrine gland
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
hematopoietic
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
AAO:0011002
BTO:0000570
CALOHA:TS-0449
EFO:0000798
EMAPA:35402
EV:0100045
FMA:9667
GAID:1008
MA:0002434
MAT:0000022
MESH:D006413
MIAA:0000022
NCIT:C12909
TAO:0005023
UMLS:C0018957
VHOG:0001624
XAO:0000122
ZFA:0005023
haematological system
haemopoietic system
organa haemopoietica
uberon
Blutbildungssystem
haematopoietic system
hematological system
hematolymphoid system
hemopoietic system
UBERON:0002390
hematopoietic system
Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
BTO:0000855
CALOHA:TS-0580
EFO:0000871
ENVO:02000041
EV:0100049
FMA:9671
GAID:1186
MA:0002520
MAT:0000055
MESH:A12.207.630
MIAA:0000055
NCIT:C13252
OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA
UMLS:C0024202
VHOG:0001590
ZFA:0005658
galen:Lymph
uberon
lympha
UBERON:0002391
lymph
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.
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]
AAO:0011003
BILA:0000104
BTO:0005810
FMA:9825
GAID:328
MA:0002711
MESH:D007107
NCIT:C12735
OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA
TAO:0001159
UMLS:C0020962
VHOG:0001247
XAO:0003152
ZFA:0001159
uberon
UBERON:0002405
immune system
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.
(...) 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]
UBERON:0007029
AEO:0000154
BILA:0000118
CALOHA:TS-1299
CARO:0002001
EFO:0000807
EHDAA2:0000836
EHDAA2_RETIRED:0003154
EHDAA:6520
EMAPA:17524
EV:0100151
FBbt:00004969
FMA:72979
HAO:0000421
MA:0000014
MAT:0000033
MESH:D034582
MIAA:0000033
NCIT:C12907
TADS:0000108
UMLS:C0037267
VHOG:0000403
XAO:0000176
galen:Surface
integumentary system
uberon
body surface
dermal system
external covering of organism
integumentum commune
organism surface
surface
UBERON:0002416
integumental system
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].
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]
Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]
lymphoid
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]
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]
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.
UBERON:0002096
EHDAA2:0001043
EHDAA:8677
EMAPA:37664
FMA:74594
GAID:931
MA:0002435
MAT:0000197
MIAA:0000197
NCIT:C12746
OpenCyc:Mx4rwQAKT5wpEbGdrcN5Y29ycA
TAO:0000385
UMLS:C0024235
VHOG:0000842
XAO:0003199
ZFA:0000385
lymphatic system
uberon
lymphatic circulatory system
lymphatic drainage system
systema lymphoideum
UBERON:0002465
lymphoid system
an organ that functions as a secretory or excretory organ
glandular
UBERON:MIAA_0000021
AAO:0000212
AEO:0000096
BTO:0000522
EFO:0000797
EHDAA2:0003096
EHDAA:2161
EHDAA:4475
EHDAA:6522
EMAPA:18425
FBbt:00100317
FMA:7146
FMA:86294
HAO:0000375
MA:0003038
MAT:0000021
MIAA:0000021
NCIT:C13319
OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
UMLS:C1285092
WikipediaCategory:Glands
galen:Gland
glandular organ
uberon
Druese
glandula
UBERON:0002530
gland
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.
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
AAO:0010015
AEO:0000024
BILA:0000024
CARO:0000024
EHDAA2:0003024
HAO:0000024
TADS:0000598
TAO:0000496
TGMA:0001837
VHOG:0001723
XAO:0003041
ZFA:0000496
uberon
organ
UBERON:0003103
compound organ
An organ involved in reproduction
GO uses genitalia for the singular organ
EMAPA:17381
EMAPA:37731
MA:0001752
MESH:D005835
NCIT:C25177
OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA
TGMA:0000591
UMLS:C0017420
WBbt:0008422
genital organ
reproductive system organ
sex organ
uberon
genitalia
UBERON:0003133
reproductive organ
A gland that is part of a foregut [Automatically generated definition].
EHDAA2:0000567
EHDAA:950
EMAPA:16557
VHOG:0000650
foregut gland
uberon
UBERON:0003294
gland of foregut
A gland that is part of a integumental system [Automatically generated definition].
EHDAA2:0000837
EHDAA:6522
EMAPA:17758
MA:0000144
VHOG:0000654
integumental gland
integumental system gland
integumentary gland
uberon
UBERON:0003297
gland of integumental system
A gland that is part of a digestive tract [Automatically generated definition].
EMAPA:18815
MA:0003202
digestive tract gland
gland of digestive tract
gland of lower gastrointestinal tract
gut gland
lower gastrointestinal tract gland
uberon
UBERON:0003408
gland of digestive tract
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
AEO:0000080
EHDAA2:0003080
FMA:242873
foramen
foramina
uberon
opening
ostia
ostium
UBERON:0004111
anatomical conduit
An anatomical structure that develops (entirely or partially) from the endoderm.
Grouping term for query purposes
uberon
UBERON:0004119
endoderm-derived structure
An anatomical structure that develops (entirely or partially) from the mesoderm.
Grouping term for query purposes
FBbt:00025998
mesodermal derivative
uberon
UBERON:0004120
mesoderm-derived structure
An anatomical structure that develops (entirely or partially) from the ectoderm.
Grouping term for query purposes
FBbt:00025990
ectodermal deriviative
uberon
UBERON:0004121
ectoderm-derived structure
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]
relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
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]
genitourinary
urogenital
AAO:0000624
BILA:0000122
BTO:0003091
EFO:0003864
EHDAA:1013
EMAPA:16367
EV:0100094
FMA:280610
GAID:362
MESH:D014566
NCIT:C12810
OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g
UMLS:C0042066
VHOG:0000286
XAO:0000140
galen:GenitoUrinarySystem
urogenital system
uberon
GU tract
UG tract
Urogenitalsystem
genito-urinary system
genitourinary tract
urogenital tract
UBERON:0004122
genitourinary system
The external genitalia are the outer sex organs, such as the penis or vulva in mammals
FMA:45643
external genitalia
uberon
external reproductive organ
external sex organ
UBERON:0004176
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
external genitalia
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
skeletal
AEO:0000168
EHDAA2:0001843
EHDAA:5047
EMAPA:17213
FMA:23875
GAID:177
MA:0003006
MAT:0000032
MESH:D012863
MIAA:0000032
OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA
VSAO:0000026
XAO:0004053
galen:Skeleton
set of all bones
set of bones of body
uberon
UBERON:0004288
skeleton
https://github.com/obophenotype/uberon/wiki/The-skeletal-system
Sum of all sensory systems in an organism.
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
FMA:78499
sense organ system
uberon
UBERON:0004456
entire sense organ system
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
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]
AAO:0011001
BILA:0000016
BTO:0000088
CALOHA:TS-1297
EFO:0000791
EHDAA2:0000216
EHDAA:394
EMAPA:16104
EMAPA:16370
EV:0100017
FMA:7161
GAID:467
MA:0000010
MAT:0000016
MESH:D002319
MIAA:0000016
NCIT:C12686
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
TAO:0000010
UMLS:C0007226
VHOG:0000302
WikipediaCategory:Cardiovascular_system
XAO:0000100
XAO:0001010
ZFA:0000010
uberon
CV system
Herz und Gefaesssystem
UBERON:0004535
cardiovascular system
The part of the cardiovascular system consisting of all arteries.
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]
BTO:0004690
EHDAA2:0000143
EHDAA:396
EMAPA:16201
EMAPA:16371
MA:0002719
VHOG:0000273
uberon
UBERON:0004572
arterial system
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.
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]
BTO:0004692
EHDAA2:0002171
EHDAA:486
EMAPA:16240
MA:0002720
NCIT:C33858
UMLS:C1267406
VHOG:0000277
vein system
uberon
UBERON:0004582
venous system
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
AAO:0011129
TAO:0001890
VSAO:0000128
XAO:0004012
ZFA:0005494
galen:SkeletalStructure
uberon
UBERON:0004765
skeletal element
Anatomical system that consists of all the joints of the body.
EMAPA:35150
FMA:23878
MA:0003007
VSAO:0000181
joint system
set of all joints of body
uberon
set of all joints
set of joints of body
UBERON:0004770
articular system
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
FBbt:00100315
FMA:71131
uberon
alimentary system subdivision
intestinal tract
segment of intestinal tract
subdivision of alimentary system
UBERON:0004921
subdivision of digestive tract
A proximal-distal subdivision of the digestive tract.
alimentary system subdivision
FMA:71131
subdivision of alimentary system
FMA:71131
An organ that is part of a immune system [Automatically generated definition].
immune system organ
uberon
UBERON:0005057
immune organ
Any anatomical structure that is part of the reproductive system.
reproductive system element
reproductive system structure
uberon
UBERON:0005156
reproductive structure
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
MA:0000522
abdomen organ
uberon
UBERON:0005172
abdomen element
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.
EMAPA:37062
MA:0000529
abdominal segment organ
uberon
UBERON:0005173
abdominal segment element
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
EMAPA:37274
MA:0001901
back organ
dorsal region organ
uberon
UBERON:0005174
dorsal region element
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.
EMAPA:37270
MA:0000516
trunk organ
uberon
UBERON:0005177
trunk region element
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
EMAPA:37273
MA:0000557
thoracic cavity organ
uberon
UBERON:0005178
thoracic cavity element
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
EMAPA:37271
MA:0000563
uberon
upper body organ
UBERON:0005181
thoracic segment organ
The part of the digestive system that excludes the hepatobiliary system.
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
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
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.
BTO:0000058
CALOHA:TS-0407
EHDAA2:0000110
EHDAA:514
EMAPA:16246
EV:0100056
FMA:71132
GAID:294
MA:0000323
MESH:A03.492
NCIT:C12378
UMLS:C0012240
VHOG:0000412
galen:GastrointestinalTract
uberon
GI tract
alimentary system
alimentary tract
gastro-intestinal system
gastroenterological system
gastrointestinal (GI) tract
gastrointestinal system
gastrointestinal tract
UBERON:0005409
alimentary part of gastrointestinal system
AEO:0000125
CALOHA:TS-2122
EHDAA2:0003125
FBbt:00007006
FMA:292313
MIAA:0000019
uberon
developing structure
developmental structure
developmental tissue
UBERON:0005423
developing anatomical structure
A acellular anatomical structure that is the bounding layer of a anatomical structure.
FMA:63871
uberon
UBERON:0005764
acellular membrane
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.
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.
AAO:0010596
FMA:63872
GAID:915
NCIT:C13191
UMLS:C0004799
basement membrane of connective tissue
membrana basalis
uberon
basement membrane
UBERON:0005769
basement membrane of epithelium
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
fluid
EMAPA:37441
FMA:280556
GAID:266
MESH:D001826
galen:BodyFluid
body fluid
uberon
UBERON:0006314
bodily fluid
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.
EMAPA:36538
MA:0002505
uberon
lactiferous gland fluid
lactiferous gland secretion
mammary gland fluid
mammary gland secreted fluid
mammary gland secretion
secretion of mammary gland
UBERON:0006539
mammary gland fluid/secretion
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
branchial
pharyngeal
FBbt:00005380
MAT:0000049
MIAA:0000049
uberon
anterior part of foregut
pharyngeal tube
UBERON:0006562
pharynx
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
GO:0060465
Any gland that is part of the digestive system.
AAO:0000130
BTO:0000345
uberon
digestive gland
UBERON:0006925
digestive system gland
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
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
FBbt:00003154
SPD:0000130
TADS:0000147
dorsal tube
heart
uberon
adult heart
UBERON:0007100
Gene notes: Bmp, Nkx, Gata
primary circulatory organ
The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum.
retriculo-rumen
uberon
UBERON:0007364
reticulorumen
The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum.
The hard-shelled reproductive body produced by a bird and especially by the common domestic chicken; also: its contents used as food.
BSA:0000081
BTO:0000369
uberon
egg
UBERON:0007379
shelled egg
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
transudative
characteristically low in protein and cellular content (unless there has been secondary concentration)
FMA:12276
GAID:1195
MESH:D005122
ncithesaurus:Transudate
uberon
plasma ultrafiltrate
UBERON:0007779
transudate
Any fluid produced by a serous gland.
serous fluid
serosal fluid
serous gland fluid
uberon
UBERON:0007794
secretion of serous gland
Anatomical system that consists of all blood and lymph vessels.
consider merging with vasculature
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
BTO:0001085
CALOHA:TS-2053
EHDAA2:0004520
EMAPA:35905
MA:0002718
NCIT:C33854
UMLS:C0489903
uberon
Gefaesssystem@de
UBERON:0007798
vascular system
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].
check relationship to pylorus vs antrum
EMAPA:27211
FMA:14922
NCIT:C33431
UMLS:C0227239
glandula pylorica
pyloric antrum gland
pyloric gland
pyloric mucuous gland
uberon
UBERON:0008861
pyloric gastric gland
EHDAA2:0001371
uberon
pancreatis dorsalis
UBERON:0009708
dorsal pancreas
EHDAA2:0001393
uberon
pancreatis ventralis
UBERON:0009709
ventral pancreas
Branch or outpocketing of the digestive tract.
FBbt:00100316
uberon
diverticulum of gut
intestinal pouch
UBERON:0009854
digestive tract diverticulum
Branch or outpocketing of the digestive tract.
diverticulum of gut
FBbt:00100316
galen:Diverticulum
pouch
uberon
diverticulum
UBERON:0009856
sac
An anatomical structure that has more than one cell as a part.
CARO:0010000
FBbt:00100313
multicellular structure
uberon
UBERON:0010000
multicellular anatomical structure
An organ of the digestive tract that is capable of retaining and storing food
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
BSA:0000123
TADS:0000172
TGMA:0001041
uberon
UBERON:0010039
food storage organ
the FMA class specifically refers to ureter
FMA:63212
MESH:D024022
NCIT:C32339
NIF_Subcellular:sao7547390221
uberon
UBERON:0011860
collection of collagen fibrils
A blood that is part of a vein.
FMA:83067
blood in vein
portion of venous blood
venous blood
uberon
UBERON:0013756
venous blood
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
EMAPA:37843
digestive organ
digestive system organ
uberon
UBERON:0013765
digestive system element
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
uberon
UBERON:0015212
lateral structure
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.
heart
SPD:0000130
cardiac pump
heart or heart like organ
circulatory vessel
uberon
cardiac structure
UBERON:0015228
circulatory organ
EMAPA:37597
MA:0002449
heart/pericardium
uberon
UBERON:0015410
heart plus pericardium
A viscus that is part of a abdomen.
FMA:32413
FMA:67355
abdominal viscera
abdominal viscera set
set of abdominal viscera
uberon
UBERON:0017672
abdominal viscera
An exocrine gland that is part of a integumental system.
integumental exocrine gland
integumental system exocrine gland
uberon
UBERON:0019319
exocrine gland of integumental system
Any substance in the body or expelled from the body that is in a gaseous state.
FMA:84580
gas in anatomical space
portion of gas in anatomical space
uberon
UBERON:0034873
bodily gas
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
FMA:84581
respiratory air
respiratory system air
uberon
UBERON:0034874
air in respiratory system
An multicellular anatomical structure that has subparts of multiple organs as a part.
CARO:0020001
uberon
anatomical cluster
UBERON:0034921
multi organ part structure
A cluster of cells, largely surrounded by a morphological boundary.
CARO:0020002
FMA:62807
uberon
UBERON:0034922
cell cluster
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
uberon
UBERON:0034925
anatomical collection
Any portion of gas located in a part of the respiratory system.
respiratory gas
respiratory system gas
uberon
UBERON:0034947
gas in respiratory system
awaiting ontology review/placement
Variant of Concern
Variant of Interest
Variant Under Monitoring
a geopolitical region is a geographic region recognized by social or legal convention.
geopolitical region
A township is a rural or sub-urban settlement.
township
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。
A collection of data, published or curated by a single source, and available for access or download in one or more represenations.
Kolekce dat poskytovaná či řízená jedním zdrojem, která je k dispozici pro přístup či stažení v jednom či více formátech.
Raccolta di dati, pubblicati o curati da un'unica fonte, disponibili per l'accesso o il download in uno o più formati.
Una colección de datos, publicados o conservados por una única fuente, y disponibles para ser accedidos o descargados en uno o más formatos.
Une collection de données, publiée ou élaborée par une seule source, et disponible pour accès ou téléchargement dans un ou plusieurs formats.
Μία συλλογή από δεδομένα, δημοσιευμένη ή επιμελημένη από μία και μόνο πηγή, διαθέσιμη δε προς πρόσβαση ή μεταφόρτωση σε μία ή περισσότερες μορφές.
قائمة بيانات منشورة أو مجموعة من قبل مصدر ما و متاح الوصول إليها أو تحميلها
Conjunto de datos
Dataset
Dataset
Datová sada
Jeu de données
Σύνολο Δεδομένων
قائمة بيانات
データセット
2018-02 - odstraněno tvrzení o podtřídě dctype:Dataset, jelikož rozsah dcat:Dataset zahrnuje několik dalších typů ze slovníku dctype.
2018-02 - se eliminó el axioma de subclase con dctype:Dataset porque el alcance de dcat:Dataset incluye muchos otros tipos del vocabulario dctype.
2018-02 - sottoclasse di dctype:Dataset rimosso perché l'ambito di dcat:Dataset include diversi altri tipi dal vocabolario dctype.
2018-02 - subclass of dctype:Dataset removed because scope of dcat:Dataset includes several other types from the dctype vocabulary.
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。
A collection of data, published or curated by a single source, and available for access or download in one or more represenations.
Kolekce dat poskytovaná či řízená jedním zdrojem, která je k dispozici pro přístup či stažení v jednom či více formátech.
Raccolta di dati, pubblicati o curati da un'unica fonte, disponibili per l'accesso o il download in uno o più formati.
Una colección de datos, publicados o conservados por una única fuente, y disponibles para ser accedidos o descargados en uno o más formatos.
Une collection de données, publiée ou élaborée par une seule source, et disponible pour accès ou téléchargement dans un ou plusieurs formats.
Μία συλλογή από δεδομένα, δημοσιευμένη ή επιμελημένη από μία και μόνο πηγή, διαθέσιμη δε προς πρόσβαση ή μεταφόρτωση σε μία ή περισσότερες μορφές.
قائمة بيانات منشورة أو مجموعة من قبل مصدر ما و متاح الوصول إليها أو تحميلها
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.
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'.
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.
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.
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".
This class describes the conceptual dataset. One or more representations might be available, with differing schematic layouts and formats or serializations.
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.
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.
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。
COUNTRY
CY
Cyprus
Republic of Cyprus
Cyprus
COUNTRY
AU
Australia
Commonwealth of Australia
Australia
COUNTRY
NZ
New Zealand
New Zealand
New Zealand
COUNTRY
TR
Turkey
Republic of Turkey
Turkey
COUNTRY
SD
Sudan
Republic of the Sudan
Sudan
COUNTRY
TN
Tunisia
Republic of Tunisia
Tunisia
COUNTRY
DZ
Algeria
People’s Democratic Republic of Algeria
Algeria
COUNTRY
MA
Morocco
Kingdom of Morocco
Morocco
COUNTRY
LY
Libya
Libya
Libya
COUNTRY
ET
Ethiopia
Federal Democratic Republic of Ethiopia
Ethiopia
COUNTRY
ER
Eritrea
State of Eritrea
Eritrea
COUNTRY
DJ
Djibouti
Republic of Djibouti
Djibouti
COUNTRY
MR
Mauritania
Islamic Republic of Mauritania
Mauritania
COUNTRY
ML
Mali
Republic of Mali
Mali
COUNTRY
NE
Niger
Republic of Niger
Niger
COUNTRY
TD
Chad
Republic of Chad
Chad
COUNTRY
ES
Spain
Kingdom of Spain
Spain
COUNTRY
IS
Iceland
Iceland
Iceland
COUNTRY
BJ
Benin
Republic of Benin
Benin
COUNTRY
BF
Burkina Faso
Burkina Faso
Burkina Faso
COUNTRY
CI
Côte d’Ivoire
Republic of Côte d’Ivoire
Cote d'Ivoire
COUNTRY
GM
The Gambia
Republic of The Gambia
Gambia
COUNTRY
GH
Ghana
Republic of Ghana
Ghana
COUNTRY
GN
Guinea
Republic of Guinea
Guinea
COUNTRY
GW
Guinea-Bissau
Republic of Guinea-Bissau
Guinea-Bissau
COUNTRY
LR
Liberia
Republic of Liberia
Liberia
COUNTRY
NG
Nigeria
Federal Republic of Nigeria
Nigeria
COUNTRY
SN
Senegal
Republic of Senegal
Senegal
COUNTRY
SL
Sierra Leone
Republic of Sierra Leone
Sierra Leone
COUNTRY
TG
Togo
Togolese Republic
Togo
COUNTRY
CG
Congo
Republic of the Congo
Democratic Republic of the Congo
COUNTRY
RW
Rwanda
Republic of Rwanda
Rwanda
COUNTRY
CD
Democratic Republic of the Congo
Democratic Republic of the Congo
Republic of Congo
COUNTRY
BI
Burundi
Republic of Burundi
Burundi
COUNTRY
GQ
Equatorial Guinea
Republic of Equatorial Guinea
Equatorial Guinea
COUNTRY
GA
Gabon
Gabonese Republic
Gabon
COUNTRY
CM
Cameroon
Republic of Cameroon
Cameroon
COUNTRY
ZA
South Africa
Republic of South Africa
Republic of South Africa
COUNTRY
AO
Angola
Republic of Angola
Angola
COUNTRY
NA
Namibia
Republic of Namibia
Namibia
COUNTRY
BW
Botswana
Republic of Botswana
Botswana
COUNTRY
LS
Lesotho
Kingdom of Lesotho
Lesotho
COUNTRY
SZ
Swaziland
Kingdom of Swaziland
Swaziland
COUNTRY
MZ
Mozambique
Republic of Mozambique
Mozambique
COUNTRY
KE
Kenya
Republic of Kenya
Kenya
COUNTRY
UG
Uganda
Republic of Uganda
Uganda
COUNTRY
TZ
Tanzania
United Republic of Tanzania
Tanzania
COUNTRY
SO
Somalia
Federal Republic of Somalia
Somalia
COUNTRY
MW
Malawi
Republic of Malawi
Malawi
COUNTRY
ZW
Zimbabwe
Republic of Zimbabwe
Zimbabwe
COUNTRY
ZM
Zambia
Republic of Zambia
Zambia
COUNTRY
CV
Cape Verde
Republic of Cape Verde
Cape Verde
COUNTRY
BB
Barbados
Barbados
Barbados
COUNTRY
JO
Jordan
Hashemite Kingdom of Jordan
Jordan
COUNTRY
SY
Syria
Syrian Arab Republic
Syria
COUNTRY
IL
Israel
State of Israel
Israel
COUNTRY
LB
Lebanon
Lebanese Republic
Lebanon
COUNTRY
BO
Bolivia
Plurinational State of Bolivia
Bolivia
COUNTRY
GY
Guyana
Cooperative Republic of Guyana
Guyana
COUNTRY
SR
Suriname
Republic of Suriname
Suriname
COUNTRY
CA
Canada
Canada
Canada
COUNTRY
GB
United Kingdom
United Kingdom of Great Britain and Northern Ireland
United Kingdom
Scotland
Wales
England
COUNTRY
DE
Germany
Federal Republic of Germany
begin_date: 1990-10-03.
Germany
COUNTRY
IT
Italy
Italian Republic
Italy
COUNTRY
NO
Norway
Kingdom of Norway
Norway
COUNTRY
HR
Croatia
Republic of Croatia
Croatia
COUNTRY
RU
Russia
Russian Federation
begin_date: 1991-12.
Russia
COUNTRY
UA
Ukraine
Ukraine
Ukraine
COUNTRY
SE
Sweden
Kingdom of Sweden
Sweden
COUNTRY
BS
Bahamas
Commonwealth of the Bahamas
The Bahamas
COUNTRY
JP
Japan
Japan
Japan
COUNTRY
KP
North Korea
Democratic People’s Republic of Korea
North Korea
COUNTRY
CL
Chile
Republic of Chile
Chile
COUNTRY
BR
Brazil
Federative Republic of Brazil
Brazil
India
COUNTRY
CN
China
People’s Republic of China
China
COUNTRY
MX
Mexico
United Mexican States
Mexico
COUNTRY
PA
Panama
Republic of Panama
Panama
COUNTRY
HN
Honduras
Republic of Honduras
Honduras
COUNTRY
CR
Costa Rica
Republic of Costa Rica
Costa Rica
COUNTRY
EC
Ecuador
Republic of Ecuador
Ecuador
COUNTRY
AR
Argentina
Argentine Republic
Argentina
COUNTRY
CO
Colombia
Republic of Colombia
Colombia
COUNTRY
UY
Uruguay
Eastern Republic of Uruguay
Uruguay
COUNTRY
VE
Venezuela
Bolivarian Republic of Venezuela
Venezuela
COUNTRY
PE
Peru
Republic of Peru
Peru
COUNTRY
PY
Paraguay
Republic of Paraguay
Paraguay
COUNTRY
BZ
Belize
Belize
Belize
COUNTRY
SV
El Salvador
Republic of El Salvador
El Salvador
COUNTRY
GT
Guatemala
Republic of Guatemala
Guatemala
COUNTRY
FI
Finland
Republic of Finland
Finland
COUNTRY
BE
Belgium
Kingdom of Belgium
Belgium
COUNTRY
PL
Poland
Republic of Poland
Poland
COUNTRY
FR
France
French Republic
France
COUNTRY
CH
Switzerland
Swiss Confederation
Switzerland
COUNTRY
AT
Austria
Republic of Austria
Austria
COUNTRY
IE
Ireland
Ireland
Ireland
COUNTRY
PT
Portugal
Portuguese Republic
Portugal
COUNTRY
GR
Greece
Hellenic Republic
Greece
COUNTRY
LU
Luxembourg
Grand Duchy of Luxembourg
Luxembourg
COUNTRY
AD
Andorra
Principality of Andorra
Andorra
COUNTRY
BG
Bulgaria
Republic of Bulgaria
Bulgaria
COUNTRY
RO
Romania
Romania
Romania
COUNTRY
HU
Hungary
Hungary
Hungary
COUNTRY
AL
Albania
Republic of Albania
Albania
COUNTRY
CZ
Czech Republic
Czech Republic
Czech Republic
COUNTRY
SI
Slovenia
Republic of Slovenia
Slovenia
COUNTRY
SK
Slovakia
Slovak Republic
Slovakia
COUNTRY
RS
Serbia
Republic of Serbia
Serbia
COUNTRY
LV
Latvia
Republic of Latvia
ISO3166-2 codes for 2009 revision of admin. units seem not to have been assigned.
Latvia
COUNTRY
EE
Estonia
Republic of Estonia
Estonia
COUNTRY
LT
Lithuania
Republic of Lithuania
Lithuania
COUNTRY
NI
Nicaragua
Republic of Nicaragua
Nicaragua
COUNTRY
SM
San Marino
Republic of San Marino
San Marino
COUNTRY
VA
the Holy See/ Vatican City State
the Holy See/ Vatican City State
Vatican City
COUNTRY
ID
Indonesia
Republic of Indonesia
Indonesia
COUNTRY
TH
Thailand
Kingdom of Thailand
Thailand
COUNTRY
BD
Bangladesh
People’s Republic of Bangladesh
Bangladesh
COUNTRY
VN
Vietnam
Socialist Republic of Vietnam
Viet Nam
COUNTRY
CU
Cuba
Republic of Cuba
Cuba
COUNTRY
TT
Trinidad and Tobago
Republic of Trinidad and Tobago
Trinidad and Tobago
COUNTRY
JM
Jamaica
Jamaica
Jamaica
COUNTRY
MC
Monaco
Principality of Monaco
Monaco
COUNTRY
LI
Liechtenstein
Principality of Liechtenstein
Liechtenstein
COUNTRY
MD
Moldova
Republic of Moldova
Moldova
COUNTRY
BN
Brunei
Brunei Darussalam
Brunei Darussalam
COUNTRY
MY
Malaysia
Malaysia
Malaysia
COUNTRY
BT
Bhutan
Kingdom of Bhutan
Bhutan
COUNTRY
PG
Papua New Guinea
Independent State of Papua New Guinea
Papua New Guinea
COUNTRY
SG
Singapore
Republic of Singapore
Singapore
COUNTRY
LK
Sri Lanka
Democratic Socialist Republic of Sri Lanka
Sri Lanka
COUNTRY
TL
Timor-Leste
Democratic Republic of Timor-Leste
Timor
COUNTRY
EG
Egypt
Arab Republic of Egypt
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).
Egypt
COUNTRY
DO
Dominican Republic
Dominican Republic
Dominican Republic
COUNTRY
HT
Haiti
Republic of Haiti
Haiti
COUNTRY
AM
Armenia
Republic of Armenia
Armenia
COUNTRY
NP
Nepal
Federal Democratic Republic of Nepal
Nepal
COUNTRY
IR
Iran
Islamic Republic of Iran
Iran
COUNTRY
IQ
Iraq
Republic of Iraq
Iraq
COUNTRY
PH
Philippines
Republic of the Philippines
The Philippines
COUNTRY
AZ
Azerbaijan
Republic of Azerbaijan
Azerbaijan
COUNTRY
GE
Georgia
Georgia
begin_date: 1936-12-05. end_date: 1990-10-20.
Georgia
COUNTRY
UZ
Uzbekistan
Republic of Uzbekistan
begin_date: 1991-12-31.
Uzbekistan
COUNTRY
KZ
Kazakhstan
Republic of Kazakhstan
Geographically the western regions of Kazakhstan may be in Europe.
Kazakhstan
COUNTRY
TM
Turkmenistan
Turkmenistan
Turkmenistan
COUNTRY
PK
Pakistan
Islamic Republic of Pakistan
Pakistan
COUNTRY
SA
Saudi Arabia
Kingdom of Saudi Arabia
Saudi Arabia
COUNTRY
BH
Bahrain
Kingdom of Bahrain
Bahrain
COUNTRY
AE
United Arab Emirates
United Arab Emirates
United Arab Emirates
COUNTRY
OM
Oman
Sultanate of Oman
Oman
COUNTRY
YE
Yemen
Republic of Yemen
Yemen
COUNTRY
KW
Kuwait
State of Kuwait
Kuwait
COUNTRY
QA
Qatar
State of Qatar
Qatar
COUNTRY
TW
Taiwan
Taiwan
Republic of China
COUNTRY
KM
Comoros
Union of the Comoros
Comoros
COUNTRY
AF
Afghanistan
Islamic Republic of Afghanistan
Afghanistan
COUNTRY
AG
Antigua and Barbuda
Antigua and Barbuda
Antigua and Barbuda
COUNTRY
BY
Belarus
Republic of Belarus
begin_date: 1990-07-27.
Belarus
COUNTRY
BA
Bosnia and Herzegovina
Bosnia and Herzegovina
Bosnia and Herzegovina
COUNTRY
KH
Cambodia
Kingdom of Cambodia
Cambodia
COUNTRY
LA
Laos
Lao People’s Democratic Republic
Laos
COUNTRY
DM
Dominica
Commonwealth of Dominica
Dominica
COUNTRY
FJ
Fiji
Republic of Fiji
Fiji
Kyrgyzstan
COUNTRY
KG
Kyrgyzstan
Kyrgyz Republic
Kiribati
COUNTRY
MK
Former Yugoslav Republic of Macedonia, the
Former Yugoslav Republic of Macedonia, the. This code is in accordance with ISO 3166-2, code taken from name in Macedonian: Makedonija.
Macedonia
COUNTRY
ME
Montenegro
Montenegro
Montenegro
COUNTRY
MM
Myanmar/Burma
Myanmar/Burma
Myanmar
COUNTRY
NR
Nauru
Republic of Nauru
Nauru
COUNTRY
NU
Niue
Niue
Niue Fekai
COUNTRY
PW
Palau
Republic of Palau
Palau
COUNTRY
KN
Saint Kitts and Nevis
Federation of Saint Kitts and Nevis
Saint Kitts-Nevis
COUNTRY
LC
Saint Lucia
Saint Lucia
Saint Lucia
COUNTRY
AS
American Samoa
American Samoa: territory of the USA.
Samoa
COUNTRY
TJ
Tajikistan
Republic of Tajikistan
Tajikistan
COUNTRY
TO
Tonga
Kingdom of Tonga
Tonga
COUNTRY
VU
Vanuatu
Republic of Vanuatu
Vanuatu
COUNTRY
ST
São Tomé and Príncipe
Democratic Republic of São Tomé and Príncipe
Sao Tome and Principe
COUNTRY
MN
Mongolia
Mongolia
Mongolia
COUNTRY
TV
Tuvalu
Tuvalu
Tuvalu
Kosovo
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.
[Former] Yugoslavia
COUNTRY
SS
South Sudan
Republic of South Sudan
South Sudan
COUNTRY
TK
Tokelau
Tokelau: territory of New Zealand.
Tokelau
COUNTRY
VC
Saint Vincent and the Grenadines
Saint Vincent and the Grenadines
Saint Vincent and the Grenadines
COUNTRY
GD
Grenada
Grenada
Grenada
MTX
A0C78
Gallus gallus broiler
Gallus gallus animals raised for meat production purposes. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Broiler
broiler chickens
MTX
A0C9L
Dairy cows
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
dairy cattle
MTX
A0C9Q
Meat production cattle
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
beef cattle
Person:Alan Ruttenberg
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])
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])
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])
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])