An ontology of miscellaneous terms for data annotation in VFB.
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
a core relation that holds between a part and its whole
part of
a core relation that holds between a whole and its part
has part
realized in
realizes
has_exemplar
The inverse property of is_specified_input_of
has_specified_input
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.
is_specified_input_of
The inverse property of is_specified_output_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_specified_output_of
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.
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.
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
Inverse of characteristic_of
has characteristic
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has participant
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
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
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has role
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.
in register with
x overlaps y if and only if there exists some z such that x has part z and z part of y
overlaps
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.
has component
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
expressed in
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.
expresses
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
characteristic of part of
A mereological relationship or a topological relationship
mereotopologically related to
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.
genomically related to
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
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*.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
is carrier of
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 hemidriver
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 driver
entity
continuant
occurrent
independent continuant
process
realizable entity
specifically dependent continuant
role
generically dependent continuant
material entity
immaterial entity
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.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
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.
Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell.
An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.
cell part
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.
An anatomical structure that has no cells or cell parts as a part.
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.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
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.
gross anatomical part
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
An anatomical structure that has more than one cell as a part.
An individual member of a clade of cellular organisms.
Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
An anatomical structure consisting of one or more cells.
cellular anatomical structure
With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell
Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.
The mereological sum of all cells in a single organism in which expression of some specified gene occurs.
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.
Anatomical structure that has multiple cells as parts.
Anatomical entity which is part_of Drosophila melanogaster.
A process that realizes a plan which is the concretization of a plan specification.
planned process
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 role
A planned process with the objective of collecting a specimen.
A objective specification to obtain a material entity for potential use as an input during an investigation.
A material entity that has two or more specimens as its parts.
collection of specimens
A material entity that has the specimen role.
specimen
A multicellular structure that is part of an expression pattern.
expression pattern fragment
A single channel image that is used as a template for image registration.
template image
intersectional expression pattern