is_concretization_of
is_concretized_as
A relation between an entitty and the disposition it realizes
A relation between an entity and a function
hasGrain
A relation between an entity and the quality that inheres in it
The relation between an entity and a role
containedIn
isSpecifiedBy
isInformationAbout
is represented as
isSerializationOf
A spatial relation between two continuants such that one spatially contains the other with no overlap, and one is not a part of the other.
The word 'Boston' denotes the city of Boston by virtue of it being concretized as words on various signs around the city.
g denotes c when a generically dependent continuant g is concretized by a specifically dependent continuant s which inheres in independent continuant c.
A transitive, symmetric, temporal relation in which one continuant is the derivative of another non-identical continuant.
A transitive, temporal relation in which one continuant derives from another non-identical continuant.
glucose-6-phosphate derivesFrom glucose in glucose metabolism
A transitive, temporal relation in which one continuant derives into another non-identical continuant.
A relation between a process and an active continuant.
A relation between an entity and the disposition it realizes.
A reflexive mereological relational such that the entities are not distinct.
A proper part relation in which there is no overlap of the edge of spatial regions.
has part is a reflexive (for all p, p has part p), transitive (for all p, p1, p2 if p part_of p1 and p1 part_of p2, then p part_of p2) and anti-symmetric (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical) relation.
Due to nonstructural restrictions in OWL2, no cardinality restriction may be added to this property due to involvement in property chains. One should use hasProperPart to quantify over. hasPart is effectively reflexive due to the reflexivity of hasImproperPart
person has part arm, workshop has part coffee break
A relation between a process and its a continuant participant.
1. no cardinality restriction may be added to this property due to involvement in role chains. One should use hasAgent/realizes to specify knowledge and to quantify over.
A mereological relation such that when x has proper part y, then x and y are distinct, and the spatial region occupied by y is wholly contained by with that of x.
A relation between an entity and a source of information.
A proper part relation in which there is overlap on the edge of a spatial region.
A relation between a measurement value and the unit that it was measured with.
A non-transitive temporal relation in which one continuant immediately derives from a non-identical continuant such that there are no (known) intermediate continuants between them.
a molecule of alpha-D-glucose-6-phosphate immediately_derives_from D-glucose in glucose metabolism.
A non-transitive temporal relation in which one continuant immediately derives into a non-identical continuant such that there are no intermediate steps between them.
glucose immediatelyDerivesInto glucose-6-phosphate in glucose metabolism
A non-transitive temporal relation in which one process is immediately preceded by another process, such that there is no interval of time between the two processes.
A non-transitive temporal relation in which one process is immediately precedes another process, such that there is no interval of time between the two processes.
i is about c where i is an information content entity or an information carrier and c is an independent continuant.
Two continuants are adjacent to each other if the edges of their spatial regions are in direct contact.
A spatial relation such that when x is after y, then x is positioned numerically greater than y on some spatial coordinate scale.
A relation in which a continuant actively participates in the process.
A relation between an independent continuant and dependent continuant.
A spatial relation such that when x is before y, then x is positioned numerically less than y on some spatial coordinate scale.
A relation between a dependent continuant and an entity.
The ink on the signpost forming the word 'Boston' is a concretization of the word Boston that (generically) denotes the city of Boston.
s is a concretization of g, where s is a specifically dependent continuant and g is a generically dependent continuant.
The word 'Boston' is concretized by the specific pattern of ink on the various signs around the city of Boston.
g is concretized by s, where g is a generically dependent continuant and s is a specifically dependent continuant.
Two objects are connected to each other if their spatial regions are indirectly connected via a sequence of direct connections.
A spatial relation between two continuants such that one is contained in the other, but for which there is no overlap and one is not a part of the other.
c is denoted by g when a generically dependent continuant g is concretized by a specifically dependent continuant s which inheres in independent continuant c.
Two continuants are disconnected when their spatial regions are not adjacent, do not intersect or overlap.
A relation between a disposition and the entity that realizes it.
A relation between a function and the entity that realizes it.
A spatial relation such that when x is immediately after y, then x is positioned adjacent to and numerically greater than y on some spatial coordinate scale.
A spatial relation such that when x is immediately before y, then x is positioned adjacent to and numerically less than y on some spatial coordinate scale.
A reflexive mereological relation such that the entities are not distinct.
A relation between two entities such that one is located in terms of spatial and/or temporal regions.
A relation between two entities such that one is the location of another.
RCC8:non-tangential proper part of (inv)
A transitive relation such that one is a part of itself or another, with disconnected, overlapping or non-overlapping spatial regions.
1. no cardinality restriction may be added to this property due to involvement in property chains. One should use isProperPartOf to quantify over. 2. isPartOf is effectively reflexive due to the reflexivity of isImproperPartOf
arm is part of person; coffee break is part of workshop
A relation in which a continuant participates in some way in the process.
1. no cardinality restriction may be added to this property due to involvement in role chains. One should use isAgentOf/isRealizedIn to specify knowledge and to quantify over.
An irreflexive and anti-symmetric parthood relation such that the entities are distinct.
A relation between a quality and some entity.
A relation between a realizable entity (role, etc) and a process.
A relation between a source of information and an entity.
is related to is a top level symmetric relation.
b is represented by a when a serves as a sign or symbol of b.
A relation between a role and the entity that realizes it.
A relation between a region of space and an oject that occupies that space.
A spatial relation in which two objects are spatially equivalent when their spatial regions exactly overlap.
A relation between an entity and a spatial region.
person isSpatiallyLocatedIn in that three dimensional spatial region
A relation between spatial regions or continuants with respect to the spatial regions they occupy.
carole is the subject of the book "Carole's life"
c is the subject of i where i is an information content entity or an information carrier and c is an independent continuant.
A relation between two temporal entities such that a temporal region is the location of a temporal entity.
A relation between an occurant and a temporal region.
you are reading this phrase over some time interval
A relation between entities at different times.
A relation between a unit and the value of a measurement.
A spatial relationship in which two objects partially overlaps when their spatial regions intersect.
A transitive, temporal relation in which one process is preceded by (has occured later than) another process.
A transitive, temporal relation in which one process precedes (has occured earlier than) another process.
A relation between a process and a realizable entity.
The symbol '1994' as it appears on a graph about car sales in the 1990's, represents the year 1994 (an instance of a temporal interval). The 3D geometric mesh generated by a software program represents the surface of a protein.
a represents b when a serves as a sign or symbol of b.
A data property that marks the beginning of a temporal entity.
A data property that marks the end of a temporal entity.
A datatype relation between a coordinate and its coordinate value on the x-axis.
A datatype relation between a coordinate and its coordinate value on the Y-axis.
A datatype relation between a coordinate and its coordinate value on the Z-axis.
canonical nucleotide residue [chebi:50297]
canonical deoxyribonucleotide residue [chebi:50298]
canonical ribonucleotide residue [chebi:50299]
The spatial arrangement of the atoms in a molecule or molecular part affording distinction between stereoisomers which can be interconverted by rotations about formally single bonds.
PERSON: Colin Batchelor, based on the Leontis-Westhof classification.
A conformation that inheres in an RNA base pair. It may be cis- or trans- depending on the orientations of the ribose rings relative to the edge-edge interaction of the nucleobases.
A base pair conformation where the ribose rings are on the same side of a plane drawn through the middle of the edge-edge hydrogen bonds.
A base pair conformation where the ribose rings are on opposite sides of a plane drawn through the middle of the edge-edge hydrogen bonds.
A conformation that inheres in an nucleoside based on the rotation of the nucleobase about the glycosidic torsion angle χ with the furanose.
A syn nucleoside conformation is a nucleoside conformation characterized by the nucleobase being oriented towards the ribose due to rotation about the glycosidic torsion angle χ. From χ = 0°, where the plane of the base is aligned with the O4’-C1’ bond in a direction towards the O4’ atom, the syn conformation covers the remaining rotations of ±90°: χ = [-90°, 90°].
A anti nucleoside conformation is a nucleoside conformation characterized by the nucleobase being oriented away from the ribose due to rotation about the glycosidic torsion angle χ. From χ = 180°, where the plane of the base is aligned with the O4’-C1’ bond in a direction away from the O4’ atom, the anti conformation covers a rotations of ±90°: χ = [-180°, 90°].
An envelope conformation is a furan ring conformation in which only one of the five fruan atoms (C1’, C2’, C3’, C4’ or O4’) is out of the plane formed by the four others.
An envelope conformation is a furan ring conformation in which two atoms are in opposite sides of the plane formed by the remaining three.
A furan ring conformation is a conformation that inheres in a furan ring and is characterized by the values of torsion angles: θ0-4.
C2'-endo pucker (2E conformation) is an envelope conformation in which the C2' atom is above the plane formed by the other 4 atoms.
C3'-endo pucker (An 3E conformation) is an envelope conformation in which the C3' atom is above the plane formed by the other 4 atoms.
C4'-exo pucker (E4 conformation) is an envelope conformation in which the C4' atom is below the plane formed by the other 4 atoms.
C3'-endo - C4' exo pucker (3E4 conformation) is a twist conformation in which the C3' atom is above the plane and the C4' atom is below the plane.
C3'-endo - C2' exo pucker (3E2 conformation) is a twist conformation in which the C3' atom is above the plane and the C2' atom is below the plane.
A base stack orientation is a conformation that inheres in a base stack by virtue of the orientation of the nucleobases relative to i) the alignment of base normals and ii) their sequence adjacency.
An base stack straight orientation is a base stack orientation in which the normals of both bases are aligned in the same direction.
A base stack reverse orientation is a base stack orientation in which the normals of both bases are aligned in the opposite directions.
A base stack base-normal orientation is a base stack orientation that depends on the relative orientation of the base normals.
A base stack above orientation is a base stack orientation in which the second base (B) is in the same direction as the normal to the first base (A).
A base stack below orientation is a base stack orientation in which the normal of the second base (B) is directed towards the first base (A).
A base stack sequence adjacency is a base stack orientation that depends on whether the stacked nucleobases are part of nucleotides that are sequence adjacent or not.
A base stack adjacent orientation is a base stack orientation in which the stacked nucleobases are part of nucleotides that are sequence adjacent.
A base stack non-adjacent orientation is a base stack orientation in which the stacked nucleobases are part of nucleotides that are not sequence adjacent.
base stack non-adjacent base orientation
data item
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
Data items include counts of things, analyte concentrations, and statistical summaries.
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
data
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
PERSON: Alan Ruttenberg
data set
2/2/2009 Is this what we need. There are also data sets like all measurement taken in a time course experiement on one patient. What is the result of one FACS experiment?
A data set is an information content entity that is an aggregate of other data items that have something in common and are considered to form a unit and are packaged together for some purpose, for example depositing into a repository.
person:Chris Stoeckert
measurement datum
2/2/2009 is_specified_output of some assay?
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by an instrument.
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A settings datum is a datum that denotes some configuration of an instrument.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
A cartesian spatial coordinate datum is a represenation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
one dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
two dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
three dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
A scalar measurement datum that is the result of measurement of length quality
structure model
nucleotide base pair
AA base pair
AT base pair
AU base pair
CA base pair
CC base pair
CU base pair
glycosyl bond base pair orientation
GA base pair
GC base pair
GG base pair
GU base pair
TT base pair
UU base pair
chemical
molecule
A molecule whose formula can be reduced into (CH20)n, for n >= 3
carbohydrate
nucleic acid or component
phosphate component
monosaccharide
pentose
A pentose with an aldehyde functional group in position 1.
aldopentose
A pentose with an ketone functional group in position 2.
ketopentose
furanose
deoxyribose
ribose
Structural parts of nucleotides, generally attached to the 1' carbon of the cognate ribose
nucleobase
nucleic acid
nucleoside residue
Purine or pyrimidine base that is attached to a ribose or deoxyribose, (Nucleoside) and is also attached to at least one phosphate group
nucleotide
phosphate
heterocyclic aromatic compound consisting of a pyrimidine ring fused to an imidazole ring
purine nucleobase
Six member heterocyclic aromatic compound containing two nitrogen atoms at positions 1 and 3
pyrimidine nucleobase
adenine
guanine
xanthine
cytosine
thymine
uracil
A spatial interaction between nucleotides that depends on the direction of their normals.
normal vector base pair orientation
A nucleotide that has a deoxyribose as its sugar
deoxyribonucleotide
A nucleotide that has a ribose as its sugar
ribonucleotide
adenosine monophosphate
adenosine triphosphate
cytidine monophosphate
cytidine triphosphate
guanosine monophosphate
guanosine triphosphate
uridine monophosphate
uridine triphosphate
thymidine monophosphate
deoxyadenosine monophosphate
deoxycytosine monophosphate
deoxyguanosine monophosphate
thymidine triphosphate
deoxyguanosine triphosphate
deoxycytosine triphosphate
deoxyadenosine triphosphate
nucleotide monophosphate
nucleotide diphosphate
nucleotide triphosphate
A nucleoside that has a deoxyribose as its sugar
deoxyribonucleoside residue
A nucleoside that has a ribose as its sugar
ribonucleoside residue
purine nucleoside residue
pyrimidine nucleoside residue
inosine residue
adenosine residue
guanosine residue
cytidine residue
deoxythymidine residue
atom orientation in plane role
uridine residue
deoxyribonucleic acid
double stranded nucleic acid
nucleotide interaction role
ribonucleic acid
single stranded nucleic acid
polynucleotide
molecular structure specification
atom orientation in plane
double stranded DNA
double stranded RNA
single stranded RNA
single stranded DNA
nucleotide edge
Edge composed by the following atoms: Adenine (Nitrogen 6) or Guanine (Oxygen 6), R (Nitrogen 7), Uracil (Oxygen 4) or Cytosine (Nitrogen 4), Y (Carbon 5), R (Carbon 8) Where R = Purines and Y = Pyrimidines
hoogsteen edge
Edge composed by the following atoms: Adenine (Carbon 2) or Guanine (Nitrogen 2), R (Nitrogen 3), Y (Oxygen 2), Furanose (Oxygen 2) Where R = Purines and Y = Pyrimidines
sugar edge
Edge composed by the following atoms: Adenine (Nitrogen 6) or Guanine (Oxygen 6), R (Nitrogen 1), Adenine (Carbon 2) or Guanine (Nitrogen 2), Uracil (Oxygen 4) or Cytosine (Nitrogen 4), Y (Nitrogen 3), Y (Oxygen 2) Where R = Purines and Y = Pyrimidines
watson edge
A part of the nucleotide ribose or base, capable of forming hydrogen bonds.
nucleotide sub edge
bifurcated sub edge
Face composed by the following atom: R (Carbon 8) Where R = Purines
c8 sub edge
hoogsteen sub edge
Face composed by the following atoms: R(Nitrogen 7) , Y (Carbon 5) Where Y = Pyrimidines and R = Purines
hoogsteen hoogsteen sub edge
Face composed by the following atoms: Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4)
hoogsteen watson sub edge
Face composed by the following atom: Furanose O2'
o2 prime sub edge
Face composed by the following atoms: R (Nitrogen 3) Where R = Purines
sugar sugar sub edge
Face composed by the following atoms: Guanine (Nitrogen 2), Y (Oxygen 2) Where Y = Pyrimidines
sugar watson sub edge
watson hoogsteen sub edge
watson sugar sub edge
Face composed by the following atoms: R (Nitrogen 1), Y (Nitrogen 3) Where Y = Pyrimidines and R = Purines
watson watson sub edge
bifurcated hoogsteen sub edge
Face composed by the following atoms: Adenine (Carbon 2) or Guanine (Nitrogen 2), Y (Oxygen 2) Where Y = Pyrimidines
bifurcated sugar sub edge
watson sub edge
sugar sub edge
When considering a horizontal plane on the furanose, and the C5' atom is on the left side, the atoms located over the plane are said to be endo to the C5'
endo
When considering a horizontal plane on the furanose, and teh C5' atom is on the left side, the atoms located under the plane are said to be exo to the C5'
exo
c1 prime endo
c2 prime endo
c3 prime endo
c4 prime endo
molecular structure file
collection of molecules
atom
Downward stacking occurs between bases A and B when the normal of B faces the underside of A, whose normal faces away from B.
downward stacking
Inward stacking occurs between bases A and B when their normals face each other.
inward stacking
Outward stacking occurs between bases A and B when their normals face away from each other.
outward stacking
Upward stacking occurs between bases A and B when the normal of base A faces the underside of base B, whose normal faces away from A.
upward stacking
edge base pair
hoogsteen-hoogsteen base pair
hoogsteen-sugar base pair
sugar-sugar base pair
watson-hoogsteen base pair
watson-sugar base pair
watson-watson base pair
sub-edge interaction
A base pair where the normals are antiparallel.
antiparallel base pair
A base pair where the normals are parallel.
parallel base pair
o4 prime endo
c1 prime exo
c2 prime exo
c3 prime exo
c4 prime exo
o4 prime exo
endo role
exo role
c1 prime endo role
c2 prime endo role
c3 prime endo role
c4 prime endo role
o4 prime endo role
c1 prime exo role
c2 prime exo role
c3 prime exo role
c4 prime exo role
nucleotide stacking role
face away role
facing towards role
A conceptual entity is a generically dependent continuant that is abstract, conceptual or mathematical.
A connected spatial temporal region is a spatial temporal region that is maximally connected in both space and in time.
a molecule, the mass of a molecule, the role of a transcription factor, a transcription factor, a collection of molecules in the cell, a binding site, a region of a cell.
A continuant is an entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and whose parts are only continuants.
the mass of a molecule, the role of a transcription factor
A dependent continuant is a continuant which is borne by an independent continuant.
the part of the cell that is involved in cell adhesion
A fiat object part is a material entity that is part of an object but is not *wholly* demarcated by any physical discontinuities.
A function is realizable entity in which the capacity to execute some end directed activity under a specific circumstance is intrinsic to its composition.
The PDF file being displayed on my screen which is also is stored in memory or in the hard drive. The triangle formed by the peaks of those three mountains.
A generically dependent continuant is a dependent continuant that is borne by one or more independent continuants.
An independent continuant is a continuant that is the bearer of qualities and realizable entities.
a molecule, a transcription factor, a collection of molecules in the cell, a binding site, a region of a cell.
The introduction of a scientific article; a sequence that is the concretization of the quality of primary structure; a geometric mesh that represents a molecular surface; the angle from the sun during the the bee waggle dance gives information about the direction to housing or sustenance.
An information content entity is a generically dependent continuant that is an abstraction of, a representation for, or information about some entity.
An instantaneous process is a process that occurs as a boundary to other processes, and whose beggining and end are exactly the same.
A material entity is an independent continuant that is spatially extended and whose identity is independent of that of other entities and can be maintained through time.
An object is a material entity that is spatially extended, maximally self-connected and self-contained.
An object aggregate is a material entity that is the mereological sum of separate objects and may possess non-connected boundaries.
a collection of molecules, a collection of rocks
the surface of the earth, the surface of a molecule
An object boundary (aka surface) is a fiat object part that exists exactly at the point where the object is separated from other entities.
An occurrent is an entity happens, unfolds or develops through time and whose parts are also occurrents.
cell division, cell death, a set of asynchronous cell divisions.
molecular interaction, cell division, cell death
A process is an occurrent that is a maximally connected in spacetime and has bona fide beginnings and endings corresponding to real discontinuities in time.
A process aggregate is an occurent that is a meriological sum of processes and possesses non-connected temporal boundaries.
the mass of a molecule, the color of a fluorophore
A quality is an specifically dependent continuant that is intrinsically associated with an independent continuant, but whose observed/measured value may change with time.
the disposition to be clumsy, the function of email to deliver messages, the role of a catalyst to increase the rate of reaction.
A realizable entity is a specifically dependent continuant that is solely realized during a process. Realizable entities include dispositions, functions and roles.
A disposition is a realizable entity that reflects a tendency under certain circumstances to cause a specific process or transformation in the object in which it inheres.
A role is a realizable entity that reflects the behavior of an independent continuant in a specific circumstance involving two or more independent continuants.
A scattered spatial temporal region is a spatial temporal region that is not contiguous in either space or time.
The space occupied by the individual substrate molecules in a test tube during several experiments.
A site is an independent continuant defined by a characteristic spatial shape in relation to some arrangement of other continuants and a medium in which it is enclosed in whole or in part. Sites are entities that can be occupied by other continuants.
a binding site, the mitochondrial matrix
a point is the boundary of a 1D object, a line is the boundary of a 2D object, a surface is the boundary of a 3D object.
A spatial boundary is a spatial region that is tangential proper part of a larger spatial region.
A spatial region is a spatial temporal region that is restricted to space.
The spatial location occupied by a cell.
A region of space characterized by its spatial dimension.
cell division occurred in the laboratory over a period of 48 hours.
A spatial temporal region is an entity composed of spatial regions that are parts of space and temporal regions that are parts of time and is the spatial location of continuants and is the temporal location of occurrents.
the mass of a molecule, the color of a fluorophore, the disposition to be clumsy, the function of email to deliver messages, the role of a catalyst to increase the rate of reaction.
A specifically dependent continuant is a continuant that inheres in a specific and unchanging independent continuant.
A temporal boundary is a temporal region that forms at the instantaneous edge of a point in time.
A temporal interval is a a temporal region that is finitely delimited by having a start and end time.
the time it takes for a cell to replicate.
A temporal region is a spatial temporal region that is restricted to time.
The temporal region occupied by cell division.
the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space.