The Pain Ontology contains terms for representing pain as defined by the International Association For the Study of Pain (IASP), meaning that pain is both an unpleasant physical sensation and unpleasant emotional experience. It includes terms and axioms to represent the multidimensional aspect of pain, such as temporality (e.g., acute, chronic), qualitative (e.g., sharp, throbbing), extent (e.g., local, widespread), biological mechanism (e.g., nociceptive, neuropathic), and specific anatomical locations (e.g., back, knee).
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588
A URL for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand assertion to
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
has ID digit count
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Person:Alan Ruttenberg
has ID range allocated
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID range allocated to
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
Add as annotation triples in the granting ontology
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
GO ontology
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
logical characteristic of object property
'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing).
A provenance property that denotes a synonym to be the preferred one for a specific community.
CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
A synonym type for describing abbreviations or initialisms
A synonym type for describing ambiguous synonyms
A synonym type for describing dubious synonyms
EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
A synonym type for describing layperson or colloquial synonyms
CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
A synonym type for describing pluralization synonyms
CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
A synonym type for describing UK spelling variants
A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
A synonym type for names that have been used as primary labels in the past.
The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
A synonym type for the legal entity name
CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
A synonym type for describing Latin term synonyms.
NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`.
Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf.
A serial number such as "12324X"; a stop sign; a written proper name such as "OBI
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
has related synonym
Concomitant continuous pain (CCP) in trigeminal neuralgia is often experienced as burning or throbbing.
A relation between a nervous system process and a cognitive process in which the nervous system process is gives rise to an experiential mental process.
experienced as
Brain freeze is a brief, intense pain experienced in the forehead.
A relation between a physical sensation and an anatomical entity or site where an anatomical entity is usually located in which the sensation is subjectively experienced as occurring in the anatomical entity or site.
experienced in
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
part_of
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
has_part
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
is preceded by
preceded_by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
bearer_of
is bearer of
has characteristic
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
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
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
x overlaps y if and only if there exists some z such that x has part z and z part of y
x overlaps y iff they have some part in common.
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
"(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []
overlaps
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
has output
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
characteristic of part of
A mereological relationship or a topological relationship
mereotopologically related to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
functionally related to
enabled by
input of
output of
causally downstream of
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
causally related to
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
inverse of causally upstream of or within
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
Pain that is experienced as a rhythmic, pulsating, or beating sensation in which the pain's intensity waxes and wanes in periodic bursts. Throbbing pain is typically synchronized with the cardiac cycle.
Chronic pain that significantly impacts a person's ability to function.
A behavioral response that includes overt action, cognitive response, verbal response, or physiological reaction in response to a situation or event, or internal process which evokes positive feelings, negative feelings, or surprise (i.e., emotional experiences).
emotion process
A cognitive process during which an organism is aware of something either internal or external to itself.
phenomenal cognitive experience
A phenomenal cognitive experience evaluated as pleasant or unpleasant.
emotional experience (feeling)
A phenomenal cognitive experience produced by the parts of the nervous sysem involved in awareness of the external world (i.e., external stimulus) or changes to internal organs. A sensory experience does not necessarily entail the existence phenomenon experiences (e.g., hallucinations).
sensory experience
Pain that is experienced in the temporomandibular joint.
Chronic pain that is persistently occuring in the background.
Pain that is experienced in the skin, muscles, joints, and bones.
obsolete temperature pain testing procedure
obsolete heat pain testing procedure
obsolete cold pain testing procedure
obsolete temporal summation pain testing procedure
obsolete temporal summation of heat pain testing procedure
obsolete temporal summation of cold pain testing procedure
obsolete pressure pain testing procedure
obsolete punctate pain testing procedure
obsolete temporal summation of punctate pain testing procedure
obsolete temporal summation of temperature pain testing procedure
obsolete pain sensitivity
obsolete pain questionnaire
obsolete In Vivo Coping Questionnaire
obsolete Pain Vigilance and Awareness Questionnaire
obsolete pain scale score
obsolete Kohn Reactivity Scale
obsolete Graded Chronic Pain Scale
obsolete Likert Scale
obsolete Western Ontario and McMaster Universities Osteoarthritis Index
obsolete widespread condition questionnaire
An unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage.
Six key notes and etymology: - Pain is always a personal experience that is influenced to varying degrees by biological, psychological, and social factors. - Pain and nociception are different phenomena. Pain cannot be inferred solely from activity in sensory neurons. - Through their life experiences, individuals learn the concept of pain. - A person’s report of an experience as pain should be respected. - Although pain usually serves an adaptive role, it may have adverse effects on function and social and psychological well-being. - Verbal description is only one of several behaviors to express pain; inability to communicate does not negate the possibility that a human or a nonhuman animal experiences pain.
The "emotional" part of pain captures the affective (i.e., unpleasant) dimension of experiencing pain.
pain
- The Revised IASP definition of pain: concepts, challenges, and compromises. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7680716/ - Merskey H, Albe-Fessard DG, Bonica JJ, et al: Pain terms: A list with definitions and notes on usage. Recommended by the IASP Subcommittee on Taxonomy. Pain 1979; 6:249-252. http://www.iasp-pain.org/source/eforums.
Pain without known cause or of spontaneous origin.
Acute transient pain that is severe and has an intensity that flares over baseline.
Pain that persists for three months or longer.
In many cases, the pain is initially caused by tissue damage or disease. The continuation of the pain is often the result of pathological changes in the central nervous system.
chronic pain
Pain that arises from actual or threatened damage to non-neural tissue and is due to the activation of nociceptors.
nociceptive pain
The term is used to describe pain occurring with a normally functioning somatosensory nervous system to contrast with the abnormal function seen in neuropathic or nociplasitic pain.
A process quality that is the characteristic of a sensory experience.
sensation quality
Pain that arises from altered nociception despite no clear evidence of actual or threatened tissue damage causing the activation of peripheral nociceptors or evidence for disease or lesion of the somatosensory system causing the pain.
nociplastic pain
Pain caused by a lesion or disease of the somatosensory nervous system.
neuropathic pain
Neuropathic pain is a clinical description (and not a diagnosis) which requires a demonstrable lesion or a disease that satisfies established neurological diagnostic criteria. The term lesion is commonly used when diagnostic investigations (e.g. imaging, neurophysiology, biopsies, lab tests) reveal an abnormality or when there was obvious trauma.
Somatosensory refers to information about the body per se including visceral organs, rather than information about the external world (e.g., vision, hearing, or olfaction). The presence of symptoms or signs (e.g., touch-evoked pain) alone does not justify the use of the term neuropathic. Some disease entities, such as trigeminal neuralgia, are currently defined by their clinical presentation rather than by objective diagnostic testing. Other diagnoses such as postherpetic neuralgia are normally based upon the history. It is common when investigating neuropathic pain that diagnostic testing may yield inconclusive or even inconsistent data. In such instances, clinical judgment is required to reduce the totality of findings in a patient into one putative diagnosis or concise group of diagnoses.
damaged neural tissue
Pain caused by a lesion or disease of the central somatosensory nervous system.
central nervous system neuropathic pain
A sensation quality that characterizes a sensation as being persistent, deep, or nagging rather than a sharp or stabbing.
dull sensation quality
Pain that is experienced throughout the body rather than in a specific area.
Pain caused by a lesion or disease of the peripheral somatosensory nervous system.
peripheral nervous system neuropathic pain
Pain that happens suddenly, starts out sharp or intense, and serves as a warning sign of disease or threat to the body.
Acute pain is caused by injury, surgery, illness, trauma, or painful medical procedures and generally lasts from a few minutes to less than six months. Acute pain usually disappears whenever the underlying cause is treated or healed.
acute pain
Pain that is experienced in an area different from the area stimulated.
referred pain
Pain that is experienced in an area where a limb no longer exists.
phantom limb pain
Pain that is confined or restricted to a particular anatomical area (or zone) of the body.
localized pain
knee pain resulting from knee osteoarthritis.
knee osteoarthritis pain
A rhythmic, pulsating, or beating sensation quality in which the intensity waxes and wanes in periodic bursts.
throbbing sensation quality
A intense, searing, or hot sensation quality.
burning sensation quality
Pain that is experienced in the lower back.
Pain that is experienced in the area proximal to an amputation site.
stump pain
A sensation quality that characterizes a sensation as being intensely cold, typically accompanied by qualities of stillness, heaviness, numbness, and in extreme cases a paradoxical burning or painful character.
freezing sensation quality
A sudden, intense, and sharp sensation quality.
shooting sensation quality
A piercing, stabbling, cutting, or prickling sensation quality.
sharp sensation quality
intense sensation quality
A diffuse, sustained, low-to-moderate intensity, dull, deep, pressure-like sensation quality that lacks sharp localization.
aching sensation quality
An intense, sudden, and sharp sensation, often described as a knife-like or shooting, sensation quality that pierces a specific area.
stabbing sensation quality
Pain experienced as an intense, sudden, and sharp sensation, often described as a knife-like or shooting pain that pierces a specific body area.
stabbing pain
Pain that is experienced as piercing, stabbling, cutting, or prickling.
sharp pain
Pain that is experienced as a deep ache, pressure, or heaviness rather than a sharp, stabbing sensation.
dull pain
Pain that is experienced as an intense, searing, or hot sensation.
burning pain
Pain that is experienced as a burning or aching sensation and is the result of cold stimuli.
freezing pain
Pain that is experienced as a sudden, intense, and sharp sensation that moves or radiates through the body, often from one point to another.
shooting pain
Pain that is experienced in a limb, such as an arm or leg.
limb pain
finger pain
Pain that is experienced in a lower limb.
lower limb pain
Pain that is experienced in the main axis of the body.
axial pain
back pain
neck pain
Pain that is experienced in an upper limb.
upper limb pain
hand pain
elbow pain
Pain that is experienced in the shoulder.
shoulder pain
foot pain
toe pain
head pain
Pain that is experienced in the orofacial region, which includes the mouth and face.
orofacial pain
Pain that is experienced in the internal organs.
visceral pain
Chronic pain that is diffuse and experienced in body regions and in at least 3 or more body quadrants (as defined by upper-lower/left-right side of the body) and axial skeleton (neck, back, chest, and abdomen).
Chronic widespread pain (CWP) is associated with significant emotional distress (anxiety, anger/frustration or depressed mood) or functional disability (interference in daily life activities and reduced participation in social roles). CWP is multifactorial: biological, psychological and social factors contribute to the pain syndrome. The diagnosis is appropriate when the pain is not directly attributable to a nociceptive process in these regions and there are features consistent with nociplastic pain and identified psychological and social contributors.
chronic widespread pain
Additional criteria to consider: - Include quantrants/regions of body in the definition. - E.g., >= 3 quadrants & axial - >= 4 body regions - Use the notion of functional region instead of regions divided by joints. define as chronic & multi-localized.
Pain that is experienced in the upper back.
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.
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]
process
disposition
realizable entity
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
material entity
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571
A cell that is capable of detection of a stimulus involved in sensory perception.
The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings.
Editor note: request detection of stimulus involved in sensory perception of pain; add develops_from relationship
A cell whose function is determined by the generation or the reception of an electric signal.
A cell whose function is determined by its response to an electric signal.
A cell that initiates an electrical signal and passes that signal to another cell.
A neuron which conveys sensory information centrally from the periphery.
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
A cell that is part of the nervous system.
characteristic
A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so.
A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
The acquisition and processing of information and/or the storage and retrieval of this information over time.
Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus.
The series of events in which an external stimulus is received by a cell and converted into a molecular signal.
The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal.
The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
The series of events in which a temperature stimulus (hot or cold) is received and converted into a molecular signal.
The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission.
An action potential that occurs in a neuron.
The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. A painful stimulus is any physical or chemical event that has the potential to cause tissue damage (actual or perceived) and activates the nociceptive system.
The series of events required for an organism to receive a fast pain stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. Fast pain is often subjectively described as a sharp or stabbing pain; in humans, the signals from a fast pain stimulus are perceived and relayed along myelinated A-delta fibers to the central nervous system, reaching their target in about 0.1 seconds.
The series of events required for an organism to receive a slow pain stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. Slow pain is often subjectively described as an aching or throbbing pain; in humans, the signals from a slow pain stimulus are perceived and relayed along unmyelinated C fibers to the central nervous system, reaching their target in about 1 second. Slow pain is often associated with tissue destruction.
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
multicellular organismal response to stress
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
A simple form of learning whereby the repeated presence of a stimulus leads to a change in the probability or strength of the response to that stimulus. There is no association of one type of stimulus with another, rather it is a generalized response to the environment.
An increased in a behavioral response to a repeated stimulus. For example, a shock to the tail of the marine snail Aplysia, to which the snail responds by withdrawing its gill, will result in increased gill withdrawal the next time the skin is touched.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
Any process that results in a change in the behavior of an organism as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
An organ system process carried out by any of the organs or tissues of the neurological system.
The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
Any neural process required for an organism to sense and interpret the dimensions of a sensory experience: modality, location, intensity and affect.
Any process in which an emotional response is associated with a particular sensory stimulation.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal.
sensory perception, sensory transduction of stimulus
detection of stimulus involved in sensory perception
The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception.
sensory detection of chemical stimulus during sensory perception
sensory perception, sensory detection of chemical stimulus
sensory perception, sensory transduction of chemical stimulus
sensory transduction of chemical stimulus
sensory transduction of chemical stimulus during sensory perception
detection of chemical stimulus involved in sensory perception
The series of events in which a temperature stimulus is received and converted into a molecular signal as part of sensory perception.
sensory detection of temperature stimulus
sensory detection of temperature stimulus during sensory perception
sensory detection of thermal stimulus during sensory perception
sensory perception, sensory detection of temperature stimulus
sensory perception, sensory detection of thermal stimulus
sensory perception, sensory transduction of temperature stimulus
sensory perception, sensory transduction of thermal stimulus
sensory transduction of temperature stimulus
sensory transduction of temperature stimulus during sensory perception
sensory transduction of thermal stimulus during sensory perception
sensory detection of heat stimulus during sensory perception
sensory perception, sensory detection of heat stimulus
sensory perception, sensory transduction of heat stimulus
sensory transduction of heat stimulus during sensory perception
detection of temperature stimulus involved in sensory perception
The series of events involved in the perception of pain in which a temperature stimulus is received and converted into a molecular signal.
perception of pain, detection of temperature stimulus
perception of pain, sensory detection of temperature stimulus
perception of pain, sensory transduction of temperature stimulus
sensory detection of temperature stimulus during perception of pain
sensory detection of thermal stimulus during sensory perception of pain
sensory perception of pain, sensory detection of thermal stimulus
sensory perception of pain, sensory transduction of thermal stimulus
sensory transduction of temperature stimulus during perception of pain
sensory transduction of thermal stimulus during sensory perception of pain
detection of temperature stimulus involved in sensory perception of pain
The series of events involved in the perception of pain in which a mechanical stimulus is received and converted into a molecular signal.
perception of pain, detection of mechanical stimulus
perception of pain, sensory detection of mechanical stimulus
perception of pain, sensory transduction of mechanical stimulus
sensory detection of mechanical stimulus during perception of pain
sensory transduction of mechanical stimulus during perception of pain
detection of mechanical stimulus involved in sensory perception of pain
OBSOLETE. The series of events that contribute to the perception of pain in which an electrical stimulus is received and converted into a molecular signal.
perception of pain, detection of electrical stimulus
perception of pain, sensory detection of electrical stimulus
perception of pain, sensory transduction of electrical stimulus
detection of electrical stimulus during sensory perception of pain
sensory detection of electrical stimulus during perception of pain
sensory transduction of electrical stimulus during perception of pain
This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
obsolete detection of electrical stimulus involved in sensory perception of pain
The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal.
perception of pain, detection of chemical stimulus
perception of pain, sensory detection of chemical stimulus
perception of pain, sensory transduction of chemical stimulus
sensory detection of chemical stimulus during perception of pain
sensory transduction of chemical stimulus during perception of pain
detection of chemical stimulus involved in sensory perception of pain
The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception.
sensory detection of mechanical stimulus
sensory detection of mechanical stimulus during sensory perception
sensory perception, sensory detection of mechanical stimulus
sensory perception, sensory transduction of mechanical stimulus
sensory transduction of mechanical stimulus
sensory transduction of mechanical stimulus during sensory perception
detection of mechanical stimulus involved in sensory perception
The series of events by which a mechanical stimulus is received and converted into a molecular signal.
The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
OBSOLETE. The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal.
obsolete detection of stimulus involved in sensory perception of pain
Any process that modulates a measurable attribute of any biological process, quality or function.
Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course.
A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location.
A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled.
A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired.
See comments of relational quality of a physical entity.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
A spatial pattern inhering in a bearer by virtue of the bearer's being spread out or scattered about or divided up.
A spatial pattern inhering in a bearer by virtue of the bearer's being confined or restricted to multiple locations.
A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration.
Extremely acute and aggressive onset of a pathological process.
A quality of duration having progressive course of indefinite duration with active, acute-like elements.
A physical quality of a process that is its spatial distribution. For example, bone mineralization follows stereotypical spatial distribution patterns during development, which may be altered in some phenotypes.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
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
A multicellular structure that is a part of an organ.
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
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.
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
The portion of the hindlimb that contains both the stylopod and zeugopod.
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For
we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot
ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
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.
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
The area that extends from the median ocellus to the oral foramen[HAO].
The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)
The part of the forelimb extending from the shoulder to the autopod[cjm].
The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific].
Naming conventions for pod terms under discussion within phenoscape group
A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod.
pedal digit (phalangeal portion) plus soft tissue
A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle).
(...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG]
In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)
A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton.
Note in ZFA 'mandible' is a syn for the ventral mandibular arch, which is a portion of the 1st pharyngeal arch; however the term 'mandibular symphysis' refers to the dentary
'mandible' also refers to either the upper OR lower part of the beak in birds
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA].
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
Distal portion of the hind limb, including tarsal region, metatarsal region and digits.
manual digit (phalangeal portion) plus soft tissue
The bone which normally forms the lateral upper jaw in osteichthyans, including tetrapods.
Dermal bone that forms part of the upper jaw, located antero-ventral to the premaxilla. The maxilla is a paired bone.[TAO]
Paired, intramembranous bone located on the lateral sides of the skull, posterior to the premaxillae.[AAO]
relationship loss: overlaps autopalatine-maxillary joint (TAO:0001942)[TAO]
relationship loss: overlaps premaxillary-maxillary joint (TAO:0002260)[TAO]
In some teleosts, the maxilla is located postero-ventral to the supramaxilla. Commonly, the articular process of the maxilla articulates with the autopalatine and ethmoidal region antero-medially. The maxilla is usually the largest bone in the upper jaw assemblage.[TAO]
Distal segment of the fore limb, including carpal region, metacarpal region and digits.
Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot.
Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.
Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]
[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans).
Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]
digit (phalangeal portion) plus soft tissue
DOI:10.1038/nature07339 Boisvert CA, Mark-Kurik E and Ahlberg PE, The pectoral fin of Panderichthys and the origin of digits. Nature (2008)
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
A bone that is part of a head [Automatically generated definition].
Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
A bone that is part of a facial skeleton [Automatically generated definition].
A synovial joint of the jaw that connects the mandible to the temporal bone.
There are two TMJs, one on either side, working in unison. The unique feature of the TMJs is the articular disc. The disc is composed of fibrocartilagenous tissue (like the firm and flexible elastic cartilage of the ear) which is positioned between the two bones that form the joint. The TMJs are one of the only synovial joints in the human body with an articular disc, another being the sternoclavicular joint. The disc divides each joint into two. The lower joint compartment formed by the mandible and the articular disc is involved in rotational movement -- this is the initial movement of the jaw when the mouth opens. The upper joint compartment formed by the articular disk and the temporal bone is involved in translational movement -- this is the secondary gliding motion of the jaw as it is opened widely. The part of the mandible which mates to the under-surface of the disc is the condyle and the part of the temporal bone which mates to the upper surface of the disk is the glenoid (or mandibular) fossa[WP].
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
An anatomical structure that develops (entirely or partially) from the ectoderm.
The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified].
Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO]
Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO]
The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG]
relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO]
Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG]
In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular.
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248
Dermis-derived entity that is made of skeletal tissue.
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]
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular.
Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.
A proximal-distal subdivision of the digestive tract.
Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA].
overlaps with region sometimes called 'loin'
A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis.
encompasses digits and prepollex. requires review
A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions).
That part of the spine comprising the thoracic vertebrae.
Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]
A collection of all skeletal elements in some subdivision of the vertebral column.
Bone element that arises as a result of intramembranous ossification.
Bone element that arises as a result of intramembranous ossification.[VSAO]
Intramembranous bone that forms deep in the organism.[TAO]
A bone that is part of a craniocervical region.
A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD].
Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]
A limb segment that is part of a hindlimb.
A limb segment that is part of a forelimb.
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
Intramembranous bone that forms superficially in the organism.[TAO]
other AOs are not yet in sync with this classification
An anatomical structure that has more than one cell as a part.
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
An appendage segment that is part of a limb/fin.
A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
subdivision of organism along appendicular axis
Subdivision of skull that consists of the facial bones.
The skull can be divided into two: the neurocranium and the facial skeleton.
Synovial joint that articulates bones of upper and lower jaw.
Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long
Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species).
A bone element that is part of a jaw region.
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Any structure that is placed on one side of the left-right axis of a bilaterian.
An multicellular anatomical structure that has subparts of multiple organs as a part.