VFB Extension Ontology
type: Ontology
description: An ontology of miscellaneous terms for data annotation in VFB.
has_license: https://creativecommons.org/licenses/by/4.0/</terms:license>
date: 29:10:2024 10:21
comment: VFB extension ontology
version info: 2024-10-29

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
IAO_0000115: 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.

source_data_link
type: AnnotationProperty

has_license
type: AnnotationProperty

has_reference
type: AnnotationProperty

has_source
type: AnnotationProperty

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000115: a core relation that holds between a part and its whole
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000115: a core relation that holds between a whole and its part
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process

realizes
type: ObjectProperty
domain: process
range: realizable entity

has_exemplar
type: ObjectProperty

has_specified_input
type: ObjectProperty
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
IAO_0000115: The inverse property of is_specified_input_of

is_specified_input_of
type: ObjectProperty
sub property of: participates in
range: planned process
IAO_0000115: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.

has_specified_output
type: ObjectProperty
sub property of: has participant
inverse of: is_specified_output_of
domain: planned process
IAO_0000115: The inverse property of is_specified_output_of

is_specified_output_of
type: ObjectProperty
sub property of: participates in
range: planned process
IAO_0000115: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: IAO_0000005
IAO_0000115: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.

objective_achieved_by
type: ObjectProperty
domain: IAO_0000005
range: planned process
IAO_0000115: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
IAO_0000115: 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.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
IAO_0000115: Inverse of characteristic_of

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
IAO_0000115: a relation between a continuant and a process, in which the continuant is somehow involved in the process

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: characteristic of
IAO_0000115: a relation between a process and a continuant, in which the continuant is somehow involved in the process
has_source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
IAO_0000115: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
IAO_0000115: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000115: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
IAO_0000115: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence

in register with
type: ObjectProperty
sub property of: mereotopologically related to
domain: image
range: image
IAO_0000115: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-12-07T12:58:06Z

Axiom
annotated source: in register with
annotated property: IAO_0000115
annotated target: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
has db xref: https://orcid.org/0000-0002-7073-9172

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000115: x overlaps y if and only if there exists some z such that x has part z and z part of y
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

has component
type: ObjectProperty
sub property of: has part
IAO_0000115: 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.
in subset: ro-eco

expressed in
type: ObjectProperty
sub property of: genomically related to
inverse of: expresses
domain: continuant
domain: Class
  union of: generically dependent continuant
  union of: material entity
range: UBERON_0000465
property chain axiom: part of
IAO_0000115: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process

expresses
type: ObjectProperty
sub property of: genomically related to
IAO_0000115: y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
IAO_0000115: 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.

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

mereotopologically related to
type: ObjectProperty
IAO_0000115: A mereological relationship or a topological relationship

genomically related to
type: ObjectProperty
domain: continuant
range: continuant
IAO_0000115: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
IAO_0000115: is member of is a mereological relation between a item and a collection.

has member
type: ObjectProperty
sub property of: has part
IAO_0000115: has member is a mereological relation between a collection and an item.

depends on
type: ObjectProperty

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: generically dependent continuant
range: independent continuant
property chain axiom: characteristic of
property chain axiom: is concretized as
IAO_0000115: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.

is carrier of
type: ObjectProperty
domain: independent continuant
range: generically dependent continuant
property chain axiom: concretizes
property chain axiom: has characteristic
IAO_0000115: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*

exemplar_of
type: ObjectProperty
sub property of: member of

has_channel
type: ObjectProperty

has_background_channel
type: ObjectProperty
sub property of: has_channel

has_signal_channel
type: ObjectProperty
sub property of: has_channel

has hemidriver
type: ObjectProperty
domain: intersectional expression pattern
IAO_0000115: A relationship between an interesctional expression pattern and one of the hemidrivers that contributes to driving its expression. For example, the split-GAL4 system drives expression using transgenes encoding a pair of interacting proteins, one with a GAL4 DNA binding domain and one with an transcription activation domain. In cells that co-express these two transgenes, interaction between the two proteins reconsitutes a transcription factor, driving expression from transgenes under the control o f UAS enhancer/promoter elements.
created by: dos
creation date: 2018-09-26T07:48:55Z

Axiom
annotated source: has hemidriver
annotated property: IAO_0000115
annotated target: A relationship between an interesctional expression pattern and one of the hemidrivers that contributes to driving its expression. For example, the split-GAL4 system drives expression using transgenes encoding a pair of interacting proteins, one with a GAL4 DNA binding domain and one with an transcription activation domain. In cells that co-express these two transgenes, interaction between the two proteins reconsitutes a transcription factor, driving expression from transgenes under the control o f UAS enhancer/promoter elements.
has db xref: PMID:17088209

has driver
type: ObjectProperty
sub property of: expresses
domain: expression pattern
IAO_0000115: A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements.
created by: dos
creation date: 2018-09-26T07:49:10Z

Axiom
annotated source: has driver
annotated property: IAO_0000115
annotated target: A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements.
has db xref: PMID:8223268
has db xref: Wikipedia:GAL4/UAS_system

depicts
type: ObjectProperty

entity
type: Class

continuant
type: Class
subclass of: entity
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent

occurrent
type: Class
subclass of: entity
disjoint with: Restriction
  on property: part of
  some values from: continuant

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant

process
type: Class
subclass of: occurrent

realizable entity
type: Class
subclass of: specifically dependent continuant

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant

role
type: Class
subclass of: realizable entity

generically dependent continuant
type: Class
subclass of: continuant

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial entity

immaterial entity
type: Class
subclass of: independent continuant
disjoint with: Restriction
  on property: has part
  some values from: material entity

anatomical entity
type: Class
subclass of: biological entity
IAO_0000115: A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.

Axiom
annotated source: anatomical entity
annotated property: IAO_0000115
annotated target: A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
has db xref: CAROC:Brownsville2014

connected anatomical structure
type: Class
equivalent class: Class
  intersection of: material anatomical entity
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002266
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0010000
subclass of: material anatomical entity
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0002266
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0010000
IAO_0000115: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
in subset: core

organism substance
type: Class
subclass of: gross anatomical part
IAO_0000115: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome.

material anatomical entity
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0000125
subclass of: anatomical entity
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0000125
disjoint with: immaterial anatomical entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial anatomical entity
IAO_0000115: An anatomical entity that has mass.
in subset: core

immaterial anatomical entity
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Class
    complement of: Restriction
      on property: has characteristic
      some values from: PATO_0000125
subclass of: immaterial entity
subclass of: anatomical entity
disjoint with: Restriction
  on property: has part
  some values from: material anatomical entity
IAO_0000115: Anatomical entity that has no mass.
in subset: core

multicellular organism
type: Class
subclass of: cellular organism
IAO_0000115: Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell.

cell
type: Class
subclass of: connected anatomical structure
subclass of: cellular anatomical structure
disjoint with: cell part
disjoint with: acellular anatomical structure
disjoint with: extraembryonic structure
disjoint with: multi-cell-part structure
disjoint with: multicellular anatomical structure
IAO_0000115: An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
has db xref: CL:0000000
has db xref: GO:0005623

cell part
type: Class
subclass of: connected anatomical structure
subclass of: Restriction
  on property: part of
  some values from: cell
disjoint with: acellular anatomical structure
disjoint with: extraembryonic structure
disjoint with: multi-cell-part structure
disjoint with: multicellular anatomical structure
IAO_0000115: Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.

organism subdivision
type: Class
subclass of: multicellular anatomical structure
IAO_0000115: 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.
in subset: core

acellular anatomical structure
type: Class
equivalent class: Class
  intersection of: connected anatomical structure
  intersection of: Restriction
    on property: has component
    qualified cardinality: 0
    on class: cell
  intersection of: Restriction
    on property: has component
    qualified cardinality: 0
    on class: cell part
subclass of: connected anatomical structure
subclass of: gross anatomical part
disjoint with: extraembryonic structure
disjoint with: multi-cell-part structure
disjoint with: multicellular anatomical structure
IAO_0000115: An anatomical structure that has no cells or cell parts as a part.

extraembryonic structure
type: Class
subclass of: connected anatomical structure
subclass of: gross anatomical part
disjoint with: multi-cell-part structure
disjoint with: multicellular anatomical structure
IAO_0000115: A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
in subset: plus

multi-cell-part structure
type: Class
subclass of: gross anatomical part
subclass of: Class
  intersection of: connected anatomical structure
  intersection of: Restriction
    on property: has part
    all values from: Class
      complement of: cell
  intersection of: Restriction
    on property: has component
    min qualified cardinality: 2
    on class: cell part
disjoint with: multicellular anatomical structure
IAO_0000115: A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
in subset: core

gross anatomical part
type: Class
equivalent class: Class
  union of: organism substance
  union of: organism subdivision
  union of: acellular anatomical structure
  union of: extraembryonic structure
  union of: multi-cell-part structure
  union of: multicellular anatomical structure
subclass of: material anatomical entity
subclass of: Restriction
  on property: part of
  some values from: multicellular organism
IAO_0000115: Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
in subset: plus

organism
type: Class
subclass of: material entity
IAO_0000115: Material anatomical entity that is a member of an individual species or is a viral or viroid particle.

multicellular anatomical structure
type: Class
subclass of: connected anatomical structure
subclass of: gross anatomical part
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001993
IAO_0000115: An anatomical structure that has more than one cell as a part.
in subset: core

cellular organism
type: Class
subclass of: connected anatomical structure
subclass of: organism
IAO_0000115: An individual member of a clade of cellular organisms.

disconnected anatomical group
type: Class
equivalent class: Class
  intersection of: material anatomical entity
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0010001
  intersection of: Restriction
    on property: has component
    min qualified cardinality: 2
    on class: connected anatomical structure
subclass of: material anatomical entity
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0010001
subclass of: Restriction
  on property: has component
  some values from: connected anatomical structure
IAO_0000115: Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
in subset: core

cellular anatomical structure
type: Class
equivalent class: Class
subclass of: material anatomical entity
IAO_0000115: An anatomical structure consisting of one or more cells.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2018-09-28T14:20:19Z

Axiom
annotated source: cellular anatomical structure
annotated property: equivalentClass
annotated target: Class
IAO_0000115: With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell

biological entity
type: Class
subclass of: independent continuant
IAO_0000115: Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.

expression pattern
type: Class
subclass of: cellular anatomical structure
subclass of: Restriction
  on property: has part
  some values from: cell
IAO_0000115: The mereological sum of all cells in a single organism in which expression of some specified gene occurs.

anatomical structure
type: Class
subclass of: material anatomical entity
IAO_0000115: Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.
has db xref: CARO:0000003
has db xref: UBERON:0000061
in subset: cur
in subset: larval OF

Axiom
annotated source: anatomical structure
annotated property: IAO_0000115
annotated target: Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.
has db xref: https://orcid.org/0000-0001-9114-8737
has db xref: https://orcid.org/0000-0002-7073-9172

material anatomical entity
type: Class
subclass of: anatomical entity
has db xref: CARO:0000006
has db xref: UBERON:0000465
in subset: cur
in subset: larval OF

multicellular structure
type: Class
subclass of: anatomical structure
IAO_0000115: Anatomical structure that has multiple cells as parts.
has db xref: UBERON:0010000

Axiom
annotated source: multicellular structure
annotated property: IAO_0000115
annotated target: Anatomical structure that has multiple cells as parts.
has db xref: https://orcid.org/0000-0002-7073-9172

anatomical entity
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: part of
    some values from: NCBITaxon 7227
subclass of: anatomical entity
subclass of: Restriction
  on property: part of
  some values from: NCBITaxon 7227
IAO_0000115: Anatomical entity which is part_of Drosophila melanogaster.
has db xref: UBERON:0001062
in subset: EmbDevSlim
in subset: cur
in subset: larval OF

Axiom
annotated source: anatomical entity
annotated property: IAO_0000115
annotated target: Anatomical entity which is part_of Drosophila melanogaster.
has db xref: https://orcid.org/0000-0001-9114-8737

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: IAO_0000104
subclass of: process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: IAO_0000104
IAO_0000115: A process that realizes a plan which is the concretization of a plan specification.

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
IAO_0000115: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
IAO_0000115: A planned process with the objective of collecting a specimen.

specimen collection objective
type: Class
subclass of: IAO_0000005
IAO_0000115: A objective specification to obtain a material entity for potential use as an input during an investigation.

collection of specimens
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has member
    all values from: specimen
subclass of: material entity
IAO_0000115: A material entity that has two or more specimens as its parts.

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
subclass of: Restriction
  on property: has role
  some values from: specimen role
IAO_0000115: A material entity that has the specimen role.

cell cluster
type: Class
subclass of: independent continuant

expression pattern fragment
type: Class
equivalent class: Class
  intersection of: multicellular structure
  intersection of: Restriction
    on property: part of
    some values from: expression pattern
subclass of: multicellular structure
subclass of: Restriction
  on property: part of
  some values from: expression pattern
created by: dos
creation date: 2018-03-04T10:55:59Z
comment: A multicellular structure that is part of an expression pattern.

multi channel image
type: Class
subclass of: image

template image
type: Class
subclass of: channel
created by: dos
creation date: 2018-05-15T15:53:38Z
comment: A single channel image that is used as a template for image registration.

intersectional expression pattern
type: Class
subclass of: anatomical entity
created by: dos
creation date: 2018-09-26T07:54:17Z

channel
type: Class
subclass of: image