A geographic position is the coordinate of an entity against some geographic coordinate system.
geographic position
A start date is a time instant pertaining to the date of the beginning of a process.
start date
An end date is a time instant pertaining to date of the end of a process.
end date
A spatial quantity is a quantity obtained from measuring the spatial extent of an entity
physical dimensional quantity
spatial quantity
A quantity that extends in single dimension.
1D extent quantity
depth is the dimensional extent into a plane of a 3D projection of the object.
depth
height is the one dimensional extent along the vertical projection of a 3D object from a base plane of reference.
height
length is the longer dimensional extent along a 2D projection of the object.
length
width is the shorter dimensional extent perpendicular to a 2D projection of the object.
width
thickness is the shortest dimensional extent of a 3D projection of an object.
thickness
A quantity that extends in two dimensions.
2D extent quantity
area is a quantity that pertains to the extent of a two-dimensional surface or shape, or planar lamina, in the plane.
area
A perimeter is a length of the outline that surrounds a two-dimensional shape.
length of perimeter
circumference is the length of the outline of a circle or ellipse. it is defined as c = 2*pi*r, where r is the radius.
circumference
A quantity that extends in three dimensions.
3D extent quantity
volume is the quantity of three-dimensional space enclosed by some closed boundary.
volume
A quantity is an informational entity that gives the magnitude of a property.
quantity
A measurement of a spatial location relative to a frame of reference or other objects.
position
orientation is an angle between the bearer and an axis, or the angle between the bearer and another object.
orientation
A measurement value is a quantitative description that reflects the magnitude of some attribute.
measurement value
A coordinate is a measurement of position in n-dimensional space.
coordinate
A Cartesian coordinate is the signed distance of a point to some referent line.
cartesian coordinate
A polar coordinate is a position characterized by a distance from a fixed point and an angle from a fixed direction.
polar coordinate
A unit of measurement is a definite magnitude of a physical quantity, defined and adopted by convention and/or by law, that is used as a standard for measurement of the same physical quantity.
unit of measurement
A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms.
math+
mathematical entity
An algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function.
algorithm
A magazine is a periodical that typically contains essays, stories, poems, etc., by many writers, and often photographs and drawings, frequently specializing in a particular subject or area, as hobbies, news, or sports.
http://purl.org/ontology/bibo/Magazine
magazine
A workflow is an algorithm that is is a depiction of a sequence of operations to achieve one or more objectives.
workflow
A pattern is a generalized representation of some repeatable concrete or informational item.
pattern
A sequence motif is a pattern of nucleotides in a DNA sequence or amino acids in a protein.
sequence motif
A class is a collection of sets which can be unambiguously defined by a property that all its members share.
class
A parameter is variable whose value changes the characteristics of a system or a function.
parameter
A list is any enumeration of a set of items.
list
A book series is a collection of books that have been sequentially published.
book series
A journal is a a peer-reviewed periodical in which scholarship relating to a particular academic discipline is published.
http://purl.org/ontology/bibo/Journal
journal
A periodical is a publication that appears on a regular schedule.
http://purl.org/ontology/bibo/Periodical
periodical
A newspaper is a periodical publication containing news regarding current events, informative articles, diverse features, editorials, and advertising.
http://purl.org/ontology/bibo/Newspaper
newspaper
A page range denotes the start and end page in some document.
page range
A page total is a textual entity that is about the number of pages in some informational entity.
page total
Implication is a logical operator that holds between a set T of propositions and a proposition B, when every model (or interpretation or valuation) of T is also a model of B.
implies (->)
A logical operator is a unary or binary relation to construct logical expressions.
logical operator
AND is a logical operator that has the value true if both of its operands are true, otherwise a value of false.
conjunction (and)
A dimensionless quantity is a quantity that has no associated unit.
dimensionless quantity
A dimensional quantity is a quantity that has an associated unit.
dimensional quantity
mass is the quality of the amount of substance.
mass
OR is a logical operator that results in true whenever one or more of its operands are true.
disjunction (or)
NOT is a logical operator in that has the value true if its operand is false.
negation (not)
XOR, also called exclusive disjunction or (symbolized XOR, EOR, EXOR, or ⊕), is a type of logical disjunction on two operands that results in a value of true if exactly one of the operands has a value of true.
exclusive disjunction (xor)
A set is a collection of entities, for which there may be zero members.
set
A collection of documents is a non-zero set of documents.
http://purl.org/ontology/bibo/Collection
collection of documents
A website is a collection of documents published on the World Wide Web.
website
process number is a number associated with a process that denotes its ordinal position in a set of processes.
process number
An edition number is count of a literary work edited and published, as by a certain editor or in a certain manner including being printed during some interval of time.
edition number
volume number is a count of a sequence of periodicals.
volume number
Longitude is a geographic position that refers to the angle east or west of a reference meridian between the two geographical poles to another meridian that passes through an arbitrary point.
longitude
Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane
latitude
A 3D cartesian coordinate is a coordinate that is composed of an x, y and z coordinate.
3D cartesian coordinate
A number is a mathematical object used to count, label, and measure.
number
A variable is a value that may change within the scope of a given problem or set of operations.
variable
An equation is a mathematical statement that asserts the equality of two expressions.
equation
time measurement is a measurement value of the duration of some interval of time or a particular instant of time (against some frame of reference).
Time intervals are specified as date/datetime ranges.
the duration of my life; the duration of a surgical procedure, the moment of death
time measurement
An x cartesian coordinate is the coordinate of an object onto the x-axis of a cartesian coordinate system.
x cartesian coordinate
An y cartesian coordinate is the coordinate of an object onto the y-axis of a cartesian coordinate system.
y cartesian coordinate
A z cartesian coordinate is the coordinate of an object onto the z-axis of a cartesian coordinate system.
z cartesian coordinate
A time internval is a contiguous temporal region having some duration.
time interval
A time instant is a temporal region which occurs instantaneously, e.g. having no duration.
at this moment; the moment at which a finger is detached in an industrial accident; the moment at which a child is born; the moment of death
time instant
A year is a period of time taken by a planet to make one revolution around the sun.
year
A month is a period of time that divides the year.
month
A day is a period of 24 hours.
day
A century is a period of one hundred years.
century
A millenium is a period of 1000 years
millenium
An hour is a period of 60 minutes.
hour
A minute is a period of 60 seconds.
minute
A second (symbol: s) is the base unit of time in the International System of Units (SI) and is the second division of the hour by sixty, the first division by 60 being the minute.
second
Altitude is a distance above sea level.
altitude
The center of mass (aka barycenter) is the weighted average location of all the mass in a body or group of bodies.
center of mass
A data series is a data set composed of related values displayed in a statistical graph.
Example: The two series that correspond to "Seasonally adjusted" and "Trend" are composed of the seasonally adjusted value of permits in each month and values from a trend derived from some mathematical tranformation across those values, respectively, in Graph 1 of http://tinyurl.com/opwnvm
data series
A collection of points is a geometric entity that contains a non-zero set of geometric points.
collection of points
A diffusion equation describes density fluctuations in a material undergoing diffusion.
diffusion equation
A movement equation describes the displacement of an object in space over time.
movement equation
An ordinary differential equation (ODE) is a differential equation in which the unknown function (also known as the dependent variable) is a function of a single independent variable.
ordinary differential equation
A partial differential equation (PDE) is a differential equation in which the unknown function is a function of multiple independent variables and the equation involves its partial derivatives.
partial differential equation
A differential equation is a mathematical equation for an unknown function of one or several variables that relates the values of the function itself and its derivatives of various orders.
differential equation
A ordinal position is a number that designates the position of an entity from the first entity in an ordered sequence of entities.
offset
ordinal position
A collection is a set for which there exists at least one member, although any member need not to exist at any point in the collection's existence.
collection
An empty set is a set for which there are exactly 0 members.
empty set
A probability measure is quantity of how likely it is that some event will occur.
probability measure
A start time is a time instant pertaining to the time at which a process begins.
start time
An end time is a time instant pertaining to the time at which a process ends.
end time
A p-value or probability value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true
p-value
probability value
A postal code is a geographic coordinate composed of a series of letters and/or digits appended to a postal address for the purpose of sorting mail.
postal code
The uncertainty value (margin of error) of a measurement is a range of values likely to enclose the true value.
uncertainty value
A standard deviation (represented by the symbol σ) is the quantity of variation from the average (mean, or expected value).
standard deviation
A page number is the count of a page in a sequence of pages.
page number
A linear position is the position of some object against a linear positioning system.
linear position
A sequence element position is the position of an element of a linear sequence.
sequence element position
A sequence start position is the start position for a sequence of characters.
sequence start position
A sequence end position is the position of the last character in a sequence of characters relative to some linear frame of reference.
sequence end position
The number of elements of a finite set of objects.
count
An assocation is a relationship between two or more entities derived by some informational analysis.
association
A statistical association is any relationship between two measured quantities that renders them statistically dependent.
statistical association
An independent variable is a variable that may take on different values independent of other elements in a system.
independent variable
A dependent variable is one whose value changes as a consequence of changes in other values in the system.
dependent variable
A correlation is a statistical relationship involving dependence between two random variables or datasets.
correlation
A start position is the proximal position of an object relative to an origin in a linear system.
start position
An interval is a set of real numbers that includes all numbers between any two numbers in the set.
interval
A default parameter is a parameter which has a default value.
default parameter
An end position is the distal position of an object relative to an origin in a linear system.
stop position
end position
A gene-disease association is an association between a gene and a disease.
gene-disease association
A chemical-disease association is an association between a chemical and a disease.
chemical-disease association
age is the length of time that a person has lived or a thing has existed.
age
A ratio is a relationship between two numbers of the same kind expressed arithmetically as a dimensionless quotient of the two which explicitly indicates how many times the first number contains the second.
ratio
A dose is the quantity of a chemical substance administered to a biological system.
dose
effective dose is the amount of a substance required to produce an effect on a predefined percentage of a population.
effective dose
An expected value (or e-value) is the weighted average of all possible values that a random variable can take on.
expected value
The ordinal position of a character in a sequence of characters.
character offset
character position
The position of the first character in a word as an offset from the first character of the text in which it is found.
word start position
word end position is the position of the last character in a word as an offset from the first character of the text in which it is found.
word end position
A control variable that is believed to alter the dependent or independent variables, but may not actually be the focus of the experiment. So that variable will be kept constant or monitored to try to minimise its effect on the experiment.
controlled variable
extraneous variable
control variable
text span start position is the position (offset) of the first character of a text span in relation the text it is from.
text span start position
text span end position is the position (offset) of the last character of a text span in relation the text it is from.
text span end position
A t-statistic is a ratio of the departure of an estimated parameter from its notional value and its standard error.
t-statistic
A gene expression value is a measured value obtained from a gene expression experiment.
gene expression value
A differential gene expression ratio is the ratio of gene expression values from a test sample compared to a control sample.
differential gene expression ratio
A t-statistic based increased differential gene expression is a differential gene expression ratio in which the t-statistic is greater than zero.
t-statistic based increased differential gene expression
A t-statistic based decreased differential gene expression is a differential gene expression ratio in which the t-statistic is less than zero.
t-statistic based decreased differential gene expression
A date of database submission refers to the moment in time in which some information was submitted/received to a database system.
date of database submission
concentration is the quantity of a constituent within a heterogeneous substance.
concentration
pH is a measure of the activity of the (solvated) hydrogen ion.
pH is defined as the decimal logarithm of the reciprocal of the hydrogen ion activity, aH+, in a solution.
pH
A central tendency measure is a central value or a typical value for a probability distribution.
centrality measure
A mean is the central tendency of a collection of numbers taken as the sum of the numbers divided by the size of the collection.
arithmeritic mean
average
mean
A median is the numerical value separating the higher half of a sample, a population, or a probability distribution, from the lower half.
median
A mode is the value that appears most often in a set of data.
mode
A sum is the result of adding a set of values together.
sum
A minimal value is smallest value of an attribute for the entities in the defined set.
min
minimal value
A maximal value is largest value of an attribute for the entities in the defined set.
max
maximal value
A count of the instances of a class or members in a collection.
member count
A union is a list of all of the values of an attribute for the entities in the defined set.
union
An intersection is a list of only the values of an attribute for the entities in the defined set where all entities have that value.
intersection
ordered list
A sequence is an ordered list of entities. Like a set, it contains members (also called elements, or terms).
For example, (M, A, R, Y) is a sequence of letters that differs from (A, R, M, Y), as the ordering matters, and (1, 1, 2, 3, 5, 8), which contains the number 1 at two different positions, is a valid sequence.
sequence
A gene-variant disease association in which a mutation in the gene/protein results in the development or maintenance of the disease.
gene-disease association linked with causal mutation
A gene disease association in which the gene is a therapeutic marker for the disease.
gene-disease association arising from a therapeutic role of the gene/protein
therapeutic gene-disease association
A gene-disease association in which the gene/protein is involved in the etiology or maintenance of the disease.
gene-disease biomarker association
A gene-disease association in which a sequence variation (a mutation, a SNP) is associated with the disease.
gene variant-disease association
gene-disease association linked with genetic variation
A gene-disease association in which the disease phenotype is associated with an altered expression of the gene.
gene-disease association linked with altered gene expression
A gene-disease association in which the disease phenotype is associated with post-translational modifications in the protein product.
methylation or phosphorylation of protein product
gene-disease association linked with post-translational modification
number of objects produced is a count of objects that were produced in some process.
number of objects produced
number of objects consumed is a count of objects that were consumed in some process.
number of objects consumed
A difference in number of objects produced is a count of the number of objects produced with respect to a second variable (space, time, etc)
difference in number of objects produced
An increase in the number of objects produced is the positive value of a difference in number of objects produced.
increase in number of objects produced
An decrease in the number of objects produced is the negative value of a difference in number of objects produced.
decrease in number of objects produced
A database cross-reference is an association between one data item and another.
dbxref
database cross-reference
An exact cross-reference is a database cross-reference in which one entity is equivalent to the other based on all the entitie's attributes (minus the source).
exact cross-reference
A slope or gradient of a line describes its steepness, incline, or grade. A higher slope value indicates a steeper incline. Slope is normally described by the ratio of the "rise" divided by the "run" between two points on a line.
slope
A structural motif is a pattern in a structure formed by a spatial arrangement of objects (e.g. atoms).
structural motif
A catalog is a systemic collection of items of the same type.
registry
catalog
Likelihood is the hypothetical probability that an event that has already occurred would yield a specific outcome.
likelihood
Log likelihood is the natural logarithm of the likelihood function
log likelihood
A standard score is the (signed) number of standard deviations an observation or datum is above the mean.
z-value, z-score, normal score, standardadized variable.
standard score
an interval is a set of real numbers with the property that any number that lies between thwo numbers in the set is also included in the set.
The set of all numbers x satisfying 0<=x<=1 is an interval which contains 0 and 1, as well as numbers between them.
interval
an open interval is an interval that does not include its endpoints.
(0,1) is an open interval that is greater than 0 and less than 1.
open interval
A closed interval is an interval that includes its endpoints, and is denoted with square brackets.
[0,1] is a closed interval that is greater than or equal to 0 and less than or equal to 1.
closed interval
a chemical-pathway association is an association between a chemical and a pathway.
drug-pathway association
chemical-pathway association
a left open interval is an interval in which there is no element that is smaller than all other elements.
left open interval
a right open interval is an interval in which there is no element that is greater than all other elements.
right open interval
a right closed interval is an interval in which there is a real number that is larger than all of its elements.
right closed interval
a left closed interval is an interval in which there is a real number that is smaller than all its elements.
left closed interval
a chemical-gene assocation is an assocation between a chemical and a gene.
chemical-gene assocation
set item is an item in a set.
set item
a collection item is an item in a collection.
collection item
a list item is an item in a list.
list item
an ordered list item is an item in an ordered list.
ordered list item
the date at which an information content entity was made public.
date of issue
an ordered list of authors.
author list
an ordered list is a list in which items are sequentially ordered.
ordered list
A protein expression value is a quantity obtained from a protein expression experiment.
protein expression value
copy number variation refers to the number of deletions/duplications of a DNA region as compared to some reference state.
CNV
copy number variation
epimer association
A gene-disease association in which a gene mutation is known to modify the clinical presentation of the disease.
gene-disease association linked with modifying mutation
A gene-disease association in which a germline mutation in the gene predisposes to the development of the disease, and it is necessary but not sufficient for the manifestation of the disease.
gene-disease association linked with susceptibility mutation
A gene-variant disease association in which a germline mutation in the gene/protein results in the development or maintenance of the disease, and it may be passed on to offspring.
gene-disease association linked with germline causal mutation
A gene-variant disease association in which a somatic mutation in the gene/protein results in the development or maintenance of the disease, and it may not be passed on to offspring.
gene-disease association linked with somatic causal mutation
A gene-variant disease association in which a somatic mutation in the gene modifies the clinical presentation of the disease, and it may not be passed on to offspring.
gene-disease association linked with somatic modifying mutation
A gene-variant disease association in which a germline mutation in the gene modifies the clinical presentation of the disease, and it may be passed on to offspring.
gene-disease association linked with germline modifying mutation
A gene-disease association in which the fusion between two different genes (promotor and/or other coding DNA regions) is associated with the disease.
fusion gene-disease association
A gene-disease association in which the gene is included in a chromosomal rearrangement associated with a particular manifestation of the disease.
gene-disease association linked with chromosomal rearrangement
a gene-disease association that is linked with some genomic alteration
gene-disease association linked with genomic alterations
DisGeNET Disease specificity is a measure of disease coverage. It is calculated from the negative base 2 log of the ratio of number of diseases associated to the total number of diseases.
The measure is described here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#specificity
DisGeNET disease specificity
The DisGeNET pleiotropy index is a measure of specificity as it pertains to classes of disease. The disease pleotropy index is computed from the ratio of the number of disease classes associated with an entity over the total number of disease classes multplied by 100.
The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pleiotropy
DisGeNET Pleiotropy Index
A week is a period of 7 consecutive days.
week
Specific gravity is the ratio of the density of a substance to the density of a reference substance; equivalently, it is the ratio of the mass of a substance to the mass of a reference substance for the same given volume.
specific gravity
The amount of change accumulated per unit time.
rate of change
Frequency is the number of occurrences of a repeating event per unit time
frequency
Speed is the rate of change of an object's position.
speed
The rate of change of an object's position and the direction of that change
velocity
a protein family is a collection of proteins that share a common evolutionary origin, reflected by their related function and similarity in composition or structure.
protein family
a unigene cluster is a collection of transcripts (ESTs and mRNAs) that map to a particular genomic region.
cluster of transcripts
unigene cluster
generation number is a count of the number of biological reproduction events elapsed from some starting reference point.
generation number
A sequence alignment is the character-based alignment of sequences using some method.
sequence alignment
A multiple sequence alignment is a sequence alignment involving more than two sequences.
multiple sequence alignment
A pairwise sequence alignment is the alignment of exactly 2 sequences.
pairwise sequence alignment
A sequence profile is provides the preference for a character at each position of an abstracted sequence.
sequence profile
A collection of 3D molecular structure models is just that.
collection of 3d molecular structure models
sio-subset-math.owl