diff --git a/bridge/external-disjoints.owl b/bridge/external-disjoints.owl
new file mode 100644
index 0000000000..1ae9d87cc5
--- /dev/null
+++ b/bridge/external-disjoints.owl
@@ -0,0 +1,3794 @@
+
+
+
+ Chris Mungall
+ This ontology contains disjointness axioms between Uberon classes and classes from external ontologies (mostly anatomy ontologies). Use of this ontology can help prevent accidental associations between classes which may on the surface seem similar or equivalent (for example, based on the term) but are in fact completely distinct. This ontology can be used on combination with an OWL reasoner. For more details, see the homepage of this ontology - http://purl.obolibrary.org/obo/uberon/docs/Inter-ontology-disjointness-Design-Pattern
+ Uberon external disjoints
+ 1.2
+
+ http://purl.obolibrary.org/obo/uberon/docs/Inter-ontology-disjointness-Design-Pattern
+
+
+
+
+
+
+
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+
+ http://purl.org/dc/elements/1.1/creator
+ dc-creator
+ true
+ dc-creator
+ creator
+
+
+
+
+
+
+
+ http://purl.org/dc/elements/1.1/description
+ dc-description
+ true
+ dc-description
+ description
+
+
+
+
+
+
+
+ http://purl.org/dc/elements/1.1/title
+ dc-title
+ true
+ dc-title
+ title
+
+
+
+
+
+
+
+ database_cross_reference
+
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+
+ has_obo_format_version
+
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+ shorthand
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+
+
+ http://www.w3.org/2000/01/rdf-schema#seeAlso
+ seeAlso
+ true
+ seeAlso
+ see also
+
+
+
+
+
+
+
+ http://xmlns.com/foaf/0.1/homepage
+ foaf-homepage
+ true
+ foaf-homepage
+ homepage
+
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+ Wikipedia:Tympanum_(zoology)
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+ UBERON:0000165
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+ UBERON:0000312
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+ UBERON:0002218
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diff --git a/src/ontology/assert-equivalent-classes-module.owl b/src/ontology/assert-equivalent-classes-module.owl
deleted file mode 100644
index 88415bf14d..0000000000
--- a/src/ontology/assert-equivalent-classes-module.owl
+++ /dev/null
@@ -1,5019 +0,0 @@
-
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- If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
- is a defining property chain axiom
-
-
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-
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-
-
- If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
- is a defining property chain axiom where second argument is reflexive
-
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- 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
- 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- 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
- external
- protein
- quality
- uberon
- part_of
-
-
-
-
- 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)
- Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
- a core relation that holds between a whole and its part
- 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- 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
- chebi_ontology
- external
- protein
- quality
- uberon
- has_part
-
-
-
- false
- has_part
- We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.
- has part
- has part
- has_part
-
-
-
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-
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-
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-
-
-
-
- X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X).
- 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.
- BFO:0000062
- is preceded by
- takes place after
- uberon
- preceded_by
- preceded_by
- preceded by
- preceded by
- preceded_by
-
-
-
-
- is preceded by
- SIO:000249
-
-
-
-
- takes place after
- Allen:precedes
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
- 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.
- BFO:0000063
- uberon
- precedes
- precedes
- precedes
- precedes
-
-
-
-
-
-
-
-
-
- X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
- 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
- in_left_side_of
- https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
-
-
-
-
- X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
- BSPO:PATO_mtg_2009
-
-
-
-
- X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
- BSPO:PATO_mtg_2009
-
-
-
-
-
-
-
-
- X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
- 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
- in_right_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:PATO_mtg_2009
-
-
-
-
- X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
- BSPO:PATO_mtg_2009
-
-
-
-
-
-
-
-
- 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
- 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
- in_lateral_side_of
- https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
-
-
-
-
- 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
- UBERON:cjm
-
-
-
-
- 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.
-
-
-
-
-
-
-
-
-
-
-
- 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.
- characteristic of
-
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-
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-
- Inverse of characteristic_of
- RO:0000053
- uberon
- bearer_of
- bearer_of
- has characteristic
-
-
-
-
-
-
-
-
-
-
- a relation between a continuant and a process, in which the continuant is somehow involved in the process
- RO:0000056
- uberon
- participates_in
- participates_in
- participates in
-
-
-
-
-
-
-
-
-
-
-
-
-
- a relation between a process and a continuant, in which the continuant is somehow involved in the process
- has participant
-
-
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-
-
- a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
- function of
-
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-
- a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
- quality of
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-
-
- a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
- role of
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-
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-
- a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
- has function
-
-
-
-
-
-
-
-
-
- a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
- RO:0000086
- protein
- uberon
- has_quality
- false
- has_quality
- has quality
-
-
-
-
-
-
-
-
-
-
- a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
- RO:0000087
- has_role
- has role
-
-
-
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-
- a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
- has disposition
-
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- inverse of has disposition
- disposition of
-
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- A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
- has regulatory component activity
-
-
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-
-
-
-
-
-
- A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
- has negative regulatory component activity
-
-
-
-
-
-
-
-
-
- A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
- has positive regulatory component activity
-
-
-
-
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-
-
- has component activity
-
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-
-
-
- w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
- has component process
-
-
-
-
-
-
-
-
-
- directly regulated by
-
-
-
-
-
-
-
-
-
- Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
- directly negatively regulated by
-
-
-
-
- Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
- GOC:dos
-
-
-
-
-
-
-
-
-
- Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
- directly positively regulated by
-
-
-
-
- Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
- GOC:dos
-
-
-
-
-
-
-
-
-
- A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
- has effector activity
-
-
-
-
- A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
- GOC:dos
-
-
-
-
-
-
-
-
-
- RO:0002086
- ends_after
- ends after
-
-
-
-
-
-
-
-
-
- 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
-
-
-
-
-
- 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].
- SIO:000251
-
-
-
-
- is immediately preceded by
- SIO:000251
-
-
-
-
-
-
-
-
- immediately precedes
-
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-
-
-
-
-
-
- x overlaps y if and only if there exists some z such that x has part z and z part of y
- BFO_0000051 some (BFO_0000050 some ?Y)
- RO:0002131
- uberon
- overlaps
- overlaps
- overlaps
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
-
-
-
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-
-
- x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
- RO:0002162
- uberon
- in_taxon
- in_taxon
- in taxon
-
-
-
-
-
-
-
-
- w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
- RO:0002180
- protein
- uberon
- has_component
- false
- has_component
- has component
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- process(P1) regulates process(P2) iff:Â P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
- RO:0002211
- regulates
- regulates
-
-
-
-
-
-
-
-
-
-
- Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
- RO:0002212
- negatively_regulates
- negatively regulates
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
- RO:0002213
- positively_regulates
- positively regulates
-
-
-
-
-
-
-
-
-
-
-
- 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.
- Chris Mungall
- has function realized in
-
-
- For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
- RO:0002215
- protein
- uberon
- capable_of
-
- false
- capable_of
- 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.
- RO:0002216
- uberon
- capable_of_part_of
- capable_of_part_of
- capable of part of
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
-
-
-
- RO:0002222
- temporally_related_to
- 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 at the beginning of p.
- has output
-
-
-
-
-
-
-
-
-
-
-
-
- c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
- acts upstream of
-
-
-
-
-
-
-
-
-
-
-
-
- c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
- acts upstream of or within
-
-
-
-
-
-
-
-
-
- causally upstream of, positive effect
-
-
-
-
-
-
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-
-
- causally upstream of, negative effect
-
-
-
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-
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-
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-
-
-
-
- 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
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
-
- A relationship that holds via some environmental process
- evolutionarily related to
-
-
-
-
-
-
-
- A mereological relationship or a topological relationship
- RO:0002323
- mereotopologically_related_to
- mereotopologically related to
-
-
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-
-
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-
-
-
-
-
-
-
-
-
-
-
- enables
-
-
-
-
-
-
-
- A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
- RO:0002328
- uberon
- functionally_related_to
- functionally_related_to
- functionally related to
-
-
-
-
-
-
-
-
-
-
-
-
- this relation holds between c and p when c is part of some c', and c' is capable of p.
- RO:0002329
- uberon
- part_of_structure_that_is_capable_of
- part_of_structure_that_is_capable_of
- part of structure that is capable of
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
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-
-
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-
-
- c involved_in p if and only if c enables some process p', and p' is part of p
- involved in
-
-
-
-
-
-
-
-
-
- inverse of enables
- enabled by
-
-
-
-
-
-
-
-
-
-
-
- inverse of regulates
- regulated by
-
-
-
-
-
-
-
-
- inverse of negatively regulates
- negatively regulated by
-
-
-
-
-
-
-
-
- inverse of positively regulates
- positively regulated by
-
-
-
-
-
-
-
-
-
- inverse of has input
- RO:0002352
- uberon
- input_of
- input_of
- input of
-
-
-
-
-
-
-
-
-
- inverse of has output
- RO:0002353
- protein
- uberon
- output_of
- false
- output_of
- output of
-
-
-
-
-
-
-
-
-
-
- inverse of upstream of
- causally downstream of
-
-
-
-
-
-
-
-
-
-
- immediately causally downstream of
-
-
-
-
-
-
-
- This relation groups causal relations between material entities and causal relations between processes
- RO:0002410
- causally_related_to
- causally related to
-
-
-
-
-
-
-
-
-
-
- p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
- RO:0002411
- causally_upstream_of
- causally upstream of
-
-
-
-
-
-
-
-
-
- p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
- immediately causally upstream of
-
-
-
-
-
-
-
-
-
-
- p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
- RO:0002418
- causally_upstream_of_or_within
- causally upstream of or within
-
-
-
-
-
-
-
-
-
- inverse of causally upstream of or within
- causally downstream of or within
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- c involved in regulation of p if c is involved in some p' and p' regulates some p
- involved in regulation of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- c involved in regulation of p if c is involved in some p' and p' positively regulates some p
- involved in positive regulation of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
- involved in negative regulation of
-
-
-
-
-
-
-
-
-
-
- c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
- involved in or involved in regulation of
-
-
-
-
-
-
-
-
-
-
- A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
- interacts with
-
-
-
-
-
-
-
-
-
- An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
- molecularly interacts with
-
-
-
-
-
-
-
-
- phosphorylates
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
-
-A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
- directly regulates activity of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
-For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
- directly negatively regulates activity of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
-For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
- directly positively regulates activity of
-
-
-
-
-
-
-
-
-
- A relationship between a material entity and a process where the material entity has some causal role that influences the process
- RO:0002500
- causal_agent_in_process
- causal agent in 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
- RO:0002501
- causal_relation_between_processes
- causal relation between processes
-
-
-
-
-
-
-
- depends on
-
-
-
-
-
-
-
-
-
-
- causal relation between entities
-
-
-
-
-
-
-
-
-
- causally influenced by
-
-
-
-
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-
-
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-
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-
-
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-
-
-
-
-
-
- The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
- causally influences
-
-
-
-
-
-
-
-
-
- Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
- directly regulates
-
-
-
-
-
-
-
-
-
-
-
-
-
- s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
- has part structure that is capable of
-
-
-
-
-
-
-
-
-
-
- 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.
- RO:0002595
- causal_relation_between_material_entity_and_a_process
- causal relation between material entity and a process
-
-
-
-
-
-
-
-
-
-
-
-
- Holds between c and p if and only if c is capable of some activity a, and a regulates p.
- capable of regulating
-
-
-
-
-
-
-
-
-
-
-
-
- Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
- capable of negatively regulating
-
-
-
-
-
-
-
-
-
-
-
-
- Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
- capable of positively regulating
-
-
-
-
-
-
-
-
- Inverse of 'causal agent in process'
- process has causal agent
-
-
-
-
-
-
-
-
-
- Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
- directly positively regulates
-
-
-
-
-
-
-
-
-
- Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
- directly negatively regulates
-
-
-
-
-
-
-
-
-
-
-
-
- Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
- enables subfunction
-
-
-
-
-
-
-
-
-
-
-
-
- acts upstream of or within, positive effect
-
-
-
-
-
-
-
-
-
-
-
-
- acts upstream of or within, negative effect
-
-
-
-
-
-
-
-
-
-
-
-
-
- c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
- acts upstream of, positive effect
-
-
-
-
-
-
-
-
-
-
-
-
-
- c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
- acts upstream of, negative effect
-
-
-
-
-
-
-
-
- causally upstream of or within, negative effect
-
-
-
-
-
-
-
-
- causally upstream of or within, positive effect
-
-
-
-
-
-
-
-
-
-
- The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
- regulates activity of
-
-
-
-
-
-
-
- protein
- has_gene_template
- false
- has_gene_template
-
-
-
-
-
-
-
-
-
-
-
-
- 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
- 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
-
-
-
-
-
-
-
-
-
- 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]
-
-
-
-
-
-
-
-
-
- process
-
-
-
-
-
-
-
-
-
- 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
- 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]
-
-
-
-
-
-
-
-
-
- bfo
- BFO:0000019
- quality
- quality
-
-
-
-
-
-
-
-
- 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]
-
-
-
-
-
-
-
-
-
- bfo
- BFO:0000030
- object
- object
-
-
-
-
-
-
-
-
- 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]
-
-
-
-
-
-
-
-
-
- bfo
- BFO:0000040
- material entity
- material entity
-
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- electron
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- polypeptide
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- protein polypeptide chain
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- peptide
-
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- acyl group
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- carbamoyl group
-
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-
- Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
- chebi_ontology
- CHEBI:23367
- molecular entity
-
-
-
-
- Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
- fake:2
-
-
-
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-
- A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
- chebi_ontology
- CHEBI:24431
- chemical entity
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-
- biological role
-
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- group
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- nitrogen atom
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- nonmetal atom
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- oxygen atom
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- oxygen molecular entity
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- univalent carboacyl group
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- carbon atom
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- amide
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- fundamental particle
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- Any substituent group or skeleton containing carbon.
- chebi_ontology
- CHEBI:33247
- organic group
-
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- atom
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- atomic nucleus
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- nucleon
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- primary amide
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- nutrient
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- heteroorganic entity
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- pnictogen
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- pnictogen molecular entity
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- chalcogen
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- chalcogen molecular entity
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- carbon group element atom
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- main group element atom
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- p-block element atom
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- main group molecular entity
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- carbon group molecular entity
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- p-block molecular entity
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- biomacromolecule
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- information biomacromolecule
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- proteinogenic amino-acid residue
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- When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
- amino acid residue
- protein residue
- chebi_ontology
- CHEBI:33708
- amino-acid residue
-
-
-
-
- When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
- Dummy:dummy
-
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- protein residue
- PRO:DAN
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- alpha-amino-acid residue
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- macromolecule
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- macronutrient
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- organonitrogen compound
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- protein
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- true
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- lepton
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- baryon
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- fermion
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- subatomic particle
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- composite particle
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- hadron
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-
-
-
- nuclear particle
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- polyatomic entity
-
-
-
-
-
-
-
-
-
- organochalcogen compound
-
-
-
-
-
-
-
-
-
- organooxygen compound
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- carboxamide
-
-
-
-
-
-
-
-
- carboacyl group
-
-
-
-
-
-
-
-
- A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
- chebi_ontology
- CHEBI:50047
- organic amino compound
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- organic molecular entity
-
-
-
-
-
-
-
- role
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- nitrogen molecular entity
-
-
-
-
-
-
-
-
- physiological role
-
-
-
-
-
-
-
-
- food component
-
-
-
-
-
-
-
-
- molecular_function
-
-
-
-
-
-
-
-
- The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
- protein anabolism
- biological_process
- GO:0006412
- translation
-
-
-
-
- The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
- GOC:go_curators
-
-
-
-
-
-
-
-
- A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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.
- biological process
- biological_process
- GO:0008150
- Note that, in addition to forming the root of the biological process ontology, this term is recommended for use 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.
- biological_process
-
-
-
-
- A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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.
- GOC:pdt
-
-
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-
-
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-
- root
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- Viruses
-
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- Teleostomi
-
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- Euteleostomi
-
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-
- cellular organisms
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- Dipnotetrapodomorpha
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- Boreoeutheria
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- Bacteria
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-
-
- Archaea
-
-
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-
-
-
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-
-
- ncbi_taxonomy
- euk-
- NCBITaxon:2759
- Eukaryota
-
-
-
-
- euk-
- PRO:DAN
-
-
-
-
-
-
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-
-
- Euarchontoglires
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- Tetrapoda
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-
- Amniota
-
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-
-
- Theria <mammals>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- ncbi_taxonomy
- Fungi/Metazoa group
- NCBITaxon:33154
- Opisthokonta
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- ncbi_taxonomy
- metazoan-
- NCBITaxon:33208
- Metazoa
-
-
-
-
- metazoan-
- PRO:DAN
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Bilateria
-
-
-
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-
- Deuterostomia
-
-
-
-
-
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-
-
-
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-
-
-
-
- mammal
- ncbi_taxonomy
- mammal-
- NCBITaxon:40674
- Mammalia
-
-
-
-
- mammal
-
-
-
-
-
- mammal-
- PRO:DAN
-
-
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- Eumetazoa
-
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- Chordata
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-
- Vertebrata <vertebrates>
-
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-
-
- Gnathostomata <vertebrates>
-
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-
- Sarcopterygii
-
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-
- Craniata <chordates>
-
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- Eutheria
-
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-
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-
- obi
- OBI:0100026
- Category=external.
- organism
- organism
-
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-
-
-
-
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-
-
-
- An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
- natural protein
- native protein
- protein
- PR:000000001
- The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
- protein
-
-
-
-
-
- true
-
-
-
-
- An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
- PRO:DAN
- PRO:WCB
-
-
-
-
- natural protein
- PRO:DAN
-
-
-
-
- native protein
- IEDB:BP
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
- peptide
- polypeptide
- protein
- PR:000018263
- Category=external.
- amino acid chain
-
-
-
-
- An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
- PRO:DAN
- PRO:JSG
-
-
-
-
- peptide
- PRO:DAN
-
-
-
-
- polypeptide
- PRO:DAN
-
-
-
-
-
-
-
- An extent of biological sequence.
- located_sequence_feature
- sequence feature
- sequence
- located sequence feature
- SO:0000110
- sequence_feature
-
-
-
-
- An extent of biological sequence.
- SO:ke
-
-
-
-
-
-
-
-
- A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
- sequence
- SO:0000704
- gene
-
-
-
-
- A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
- SO:immuno_workshop
-
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-
-
-
-
- true
- MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
- infer input from direct reg
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
- GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
-e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
- enabling an MF enables its parts
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
- true
- GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
- involved in BP
-
-
-
-
-
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-
-
-
- This can't be added as a property chain because it causes a circularity violation for 'part of'.
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
- This can't be added as a property chain because it causes a circularity violation for 'part of'.
-
-
-
-
-
-
-
-
-
-
-
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-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- This can't be added as a property chain because it causes a circularity violation for 'part of'.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
- inferring direct reg edge from input to regulatory subfunction
-
-
-
-
-
-
-
-
-
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-
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-
-
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-
-
-
- inferring direct neg reg edge from input to regulatory subfunction
-
-
-
-
-
-
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-
-
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-
-
-
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-
-
- inferring direct positive reg edge from input to regulatory subfunction
-
-
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-
-
- effector input is compound function input
-
-
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-
- Input of effector is input of its parent MF
-
-
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-
- if effector directly regulates X, its parent MF directly regulates X
-
-
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-
-
- if effector directly positively regulates X, its parent MF directly positively regulates X
-
-
-
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-
- if effector directly negatively regulates X, its parent MF directly negatively regulates X
-
-
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-
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-
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-
-
- 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
-
-
-
-
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-
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-
-
-
- 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
-
-
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-
-
diff --git a/src/scripts/make-bridge-ontologies-from-xrefs.pl b/src/scripts/make-bridge-ontologies-from-xrefs.pl
index 89c2c529c1..c81c10f790 100755
--- a/src/scripts/make-bridge-ontologies-from-xrefs.pl
+++ b/src/scripts/make-bridge-ontologies-from-xrefs.pl
@@ -110,11 +110,11 @@
my $prefix = "http://purl.obolibrary.org/obo/".lc($s);
print $fh "[Typedef]\n";
- print $fh "id: $prefix#part_of\n";
- print $fh "equivalent_to: BFO:0000050\n\n";
+ print $fh "id: part_of\n";
+ print $fh "xref: BFO:0000050\n\n";
print $fh "[Typedef]\n";
- print $fh "id: $prefix#develops_from\n";
- print $fh "equivalent_to: RO:0002225\n\n";
+ print $fh "id: develops_from\n";
+ print $fh "xref: RO:0002225\n\n";
open(F,"ftr.obo");
while() {
diff --git a/src/sparql/illegal-annotation-property-violation.sparql b/src/sparql/illegal-annotation-property-violation.sparql
index 946ef98d19..229ac02133 100644
--- a/src/sparql/illegal-annotation-property-violation.sparql
+++ b/src/sparql/illegal-annotation-property-violation.sparql
@@ -51,7 +51,7 @@ SELECT DISTINCT ?annotation WHERE {
,
,
,
- ,
+ ,
,
,
,