epimer association gene-disease association linked with post-translational modification methylation or phosphorylation of protein product A gene-disease association in which the disease phenotype is associated with post-translational modifications in the protein product. probability value 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 A millenium is a period of 1000 years millennium 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. mathematical entity math+ A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms. 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 thickness thickness is the shortest dimensional extent of a 3D projection of an object. A start position is the proximal position of an object relative to an origin in a linear system. start position A percentile (or a centile) is a quantile that divides the given probability distribution, or sample, into 100 equal-sized intervals. percentile sequence element position A sequence element position is the position of an element of a linear sequence. gene-disease association linked with genetic variation A gene-disease association in which a sequence variation (a mutation, a SNP) is associated with the disease. gene variant-disease association en Contributors are those that engage in discussions in the context of SIO (in alphabetical order): sivaram arabandi christopher baker joachim baran jerven bolleman matthew brush alison callahan leonid chepelev kevin cohen melanie courtot geraint duck laura furlong elisa kendall tatsuya kushida luke mccarthy jim mccusker jose miguel cruz-toledo chris mungall robert hoehndorf simon jupp jin-dong kim dana klassen thomas luetteke james malone chris mungall david osumi-sutherland tazro ohta nuria queralt stephen reed alexandre riazanov matthias samwald robert stevens mark wilkinson karin verspoor natalia villanueva-rosales Michel Dumontier http://orcid.org/0000-0003-4727-9435 The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. website: http://semanticscience.org email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology 2010-03-29 free to use,share,modify. modify with attribution [http://creativecommons.org/licenses/by/4.0/]. Semanticscience Integrated Ontology (SIO) http://www.jbiomedsem.com/content/5/1/14 sio http://semanticscience.org/resource/ general class inclusion axioms: 'is part of' some 'physical entity' subClassOf 'is located in' some 'physical entity' role chains: 'has capability' o 'is realized in' -> 'is participant in' http://sio.semanticscience.org 2026-05-01 sio.owl sio-subset-math.owl pattern A pattern is a generalized representation of some repeatable concrete or informational item. 5i is an imaginary number, and its square is -25. An imaginary number is a complex number whose real part is zero e.g. 0 + bi, and is expressed as a multiple of the square root of -1. imaginary number number of objects produced number of objects produced is a count of objects that were produced in some process. orientation orientation is an angle between the bearer and an axis, or the angle between the bearer and another object. control variable extraneous variable controlled variable 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. A geographic position is the coordinate of an entity against some geographic coordinate system. geographic position 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 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 pH 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. process number is a number associated with a process that denotes its ordinal position in a set of processes. process number stop position An end position is the distal position of an object relative to an origin in a linear system. end position An end date is a time instant pertaining to date of the end of a process. end date width width is the shorter dimensional extent perpendicular to a 2D projection of the object. number of objects consumed number of objects consumed is a count of objects that were consumed in some process. [0,1] is a closed interval that is greater than or equal to 0 and less than or equal to 1. closed interval A closed interval is an interval that includes its endpoints, and is denoted with square brackets. collection of 3d molecular structure models A collection of 3D molecular structure models is just that. differential gene expression ratio A differential gene expression ratio is the ratio of gene expression values from a test sample compared to a control sample. A page range denotes the start and end page in some document. page range replicate a replicate is an object that is a facsimile, reproduction, or copy of another item. A sequence alignment is the character-based alignment of sequences using some method. sequence alignment copy number variation CNV copy number variation refers to the number of deletions/duplications of a DNA region as compared to some reference state. default parameter A default parameter is a parameter which has a default value. t-statistic based increased differential gene expression A t-statistic based increased differential gene expression is a differential gene expression ratio in which the t-statistic is greater than zero. quantile A quantile is a quantity that divides the range of a probability distribution into continuous intervals with equal probabilities, or dividing the observations in a sample in the same way. speed Speed is the rate of change of an object's position. y cartesian coordinate An y cartesian coordinate is the coordinate of an object onto the y-axis of a cartesian coordinate system. A multiple sequence alignment is a sequence alignment involving more than two sequences. multiple sequence alignment A variable is a value that may change within the scope of a given problem or set of operations. variable http://purl.org/ontology/bibo/Journal journal A journal is a a peer-reviewed periodical in which scholarship relating to a particular academic discipline is published. 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). the duration of my life; the duration of a surgical procedure, the moment of death time measurement Time intervals are specified as date/datetime ranges. scalar a scalar is a rank 0 tensor and is an element of a field that is used to define a vector space. rank 0 tensor 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 A mode is the value that appears most often in a set of data. mode Log likelihood is the natural logarithm of the likelihood function log likelihood A sequence profile is provides the preference for a character at each position of an abstracted sequence. sequence profile interval An interval is a set of real numbers that includes all numbers between any two numbers in the set. 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 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 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 chemical-chemical association A chemical-chemical association is an association between two chemical entities. matrix rank 2 tensor a matrix is a rank 2 tensor. It is represented as a rectangular array or table of numbers, symbols, or expressions arranged in rows and columns. A workflow is an algorithm that is is a depiction of a sequence of operations to achieve one or more objectives. workflow A standard score is the (signed) number of standard deviations an observation or datum is above the mean. standard score z-value, z-score, normal score, standardadized variable. an ordered list is a list in which items are sequentially ordered. ordered list area is a quantity that pertains to the extent of a two-dimensional surface or shape, or planar lamina, in the plane. area gene-disease association linked with susceptibility 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. height is the one dimensional extent along the vertical projection of a 3D object from a base plane of reference. height volume is the quantity of three-dimensional space enclosed by some closed boundary. volume gene-gene association A gene-gene association is an association between two genes. 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 An algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. algorithm A z cartesian coordinate is the coordinate of an object onto the z-axis of a cartesian coordinate system. z cartesian coordinate A quantity that extends in two dimensions. 2D extent quantity end time An end time is a time instant pertaining to the time at which a process ends. dimensional quantity A dimensional quantity is a quantity that has an associated unit. t-statistic based decreased 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. offset ordinal position A ordinal position is a number that designates the position of an entity from the first entity in an ordered sequence of entities. a left open interval is an interval in which there is no element that is smaller than all other elements. left open interval chemical-disease association A chemical-disease association is an association between a chemical and a disease. A maximal value is largest value of an attribute for the entities in the defined set. maximal value max a collection of replicates is a collection composed of items that are a facsimile, reproduction, or copy of other items in the collection. replicates a collection of replicates A coordinate is a measurement of position in n-dimensional space. coordinate A polar coordinate is a position characterized by a distance from a fixed point and an angle from a fixed direction. polar coordinate gene-disease association linked with genomic alterations a gene-disease association that is linked with some genomic alteration periodical http://purl.org/ontology/bibo/Periodical A periodical is a publication that appears on a regular schedule. A number is a tensor of rank 0. number rank 0 tensor page total A page total is a textual entity that is about the number of pages in some informational entity. A gene expression value is a measured value obtained from a gene expression experiment. gene expression value 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 included in a chromosomal rearrangement associated with a particular manifestation of the disease. gene-disease association linked with chromosomal rearrangement character offset The ordinal position of a character in a sequence of characters. character position 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 a unigene cluster is a collection of transcripts (ESTs and mRNAs) that map to a particular genomic region. unigene cluster cluster of transcripts http://purl.org/ontology/bibo/Newspaper A newspaper is a periodical publication containing news regarding current events, informative articles, diverse features, editorials, and advertising. newspaper A union is a list of all of the values of an attribute for the entities in the defined set. union A sequence motif is a pattern of nucleotides in a DNA sequence or amino acids in a protein. sequence motif measurement value A measurement value is a quantitative description that reflects the magnitude of some attribute. A collection of points is a geometric entity that contains a non-zero set of geometric points. collection of points text span start position text span start position is the position (offset) of the first character of a text span in relation the text it is from. A page number is the count of a page in a sequence of pages. page number protein-disease association A protein-disease association is an association between a protein and a disease. generation number generation number is a count of the number of biological reproduction events elapsed from some starting reference point. A linear position is the position of some object against a linear positioning system. linear position drug-pathway association chemical-pathway association a chemical-pathway association is an association between a chemical and a pathway. count The number of elements of a finite set of objects. dose A dose is the quantity of a chemical substance administered to a biological system. gene-disease association linked with altered gene expression A gene-disease association in which the disease phenotype is associated with an altered expression of the gene. volume number is a count of a sequence of periodicals. volume number A gene-disease association in which the gene/protein is involved in the etiology or maintenance of the disease. gene-disease biomarker association a duplicate is an object that is an exact copy of another item duplicate A median is the numerical value separating the higher half of a sample, a population, or a probability distribution, from the lower half. median day A day is a period of 24 hours. A t-statistic is a ratio of the departure of an estimated parameter from its notional value and its standard error. t-statistic equation An equation is a mathematical statement that asserts the equality of two expressions. A collection of documents is a non-zero set of documents. collection of documents http://purl.org/ontology/bibo/Collection effective dose effective dose is the amount of a substance required to produce an effect on a predefined percentage of a population. A quantity that extends in single dimension. 1D extent quantity A perimeter is a length of the outline that surrounds a two-dimensional shape. length of perimeter A time internval is a contiguous temporal region having some duration. time interval 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 dependent variable is one whose value changes as a consequence of changes in other values in the system. dependent variable list A list is any enumeration of a set of items. 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 spatial quantity A spatial quantity is a quantity obtained from measuring the spatial extent of an entity physical dimensional quantity quantity A quantity is an informational entity that gives the magnitude of a property. A start date is a time instant pertaining to the date of the beginning of a process. start date A parameter is variable whose value changes the characteristics of a system or a function. parameter 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 protein family 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. A month is a period of time that divides the year. month A structural motif is a pattern in a structure formed by a spatial arrangement of objects (e.g. atoms). structural motif gene-disease association linked with somatic modifying 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. A catalog is a systemic collection of items of the same type. registry catalog chemical-gene association a chemical-gene association is an association between a chemical and a gene. implies (->) 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. member count A count of the instances of a class or members in a collection. dbxref database cross-reference A database cross-reference is an association between one data item and another. 3D extent quantity A quantity that extends in three dimensions. a complex number is an element of a number system that extends the real numbers with an imaginary unit i. Every complex number can be expressed in the form a + bi, where a and b are real numbers. complex number Density (volumetric mass density) is the quantity of mass per unit volume of a substance. density uncertainty value The uncertainty value (margin of error) of a measurement is a range of values likely to enclose the true value. author list an ordered list of authors. circumference 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. 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 right open interval a right open interval is an interval in which there is no element that is greater than all other elements. (0,1) is an open interval that is greater than 0 and less than 1. an open interval is an interval that does not include its endpoints. open interval book series A book series is a collection of books that have been sequentially published. week A week is a period of 7 consecutive days. specific gravity 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. NOT is a logical operator in that has the value true if its operand is false. negation (not) dimensionless quantity A dimensionless quantity is a quantity that has no associated unit. an interval is a set of real numbers with the property that any number that lies between two numbers in the set is also included in the set. interval The set of all numbers x satisfying 0<=x<=1 is an interval which contains 0 and 1, as well as numbers between them. velocity The rate of change of an object's position and the direction of that change slope 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. concentration is the amount of substance per unit volume of a solution concentration list item a list item is an item in a list. 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 latitude Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane 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 logical operator is a unary or binary relation to construct logical expressions. logical operator Frequency is the number of occurrences of a repeating event per unit time frequency sum A sum is the result of adding a set of values together. increase 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. association An association is a relationship between two or more entities derived by some informational analysis. real number a real number is a complex number whose imaginary part is zero, e.g. a + 0i. website A website is a collection of documents published on the World Wide Web. A data series is a data set composed of related values displayed in a statistical graph. data series 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 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 central tendency measure is a central value or a typical value for a probability distribution. centrality measure A century is a period of one hundred years. century 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 altitude Altitude is a distance above sea level. disease-disease association A disease-disease association is an association between two diseases. protein-protein association A protein-protein association is an association between two proteins. conjunction (and) AND is a logical operator that has the value true if both of its operands are true, otherwise a value of false. left closed interval a left closed interval is an interval in which there is a real number that is smaller than all its elements. A set is a collection of entities, for which there may be zero members. set A start time is a time instant pertaining to the time at which a process begins. start time An empty set is a set for which there are exactly 0 members. empty set chemical-protein association A chemical-protein association is an association between a chemical and a protein. magazine http://purl.org/ontology/bibo/Magazine 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. an ordered list item is an item in an ordered list. ordered list item x cartesian coordinate An x cartesian coordinate is the coordinate of an object onto the x-axis of a cartesian coordinate system. probability measure A probability measure is quantity of how likely it is that some event will occur. A percentage is a number that is a ratio expressed as a fraction of 100. It is denoted using the percent sign "%". percentage exact 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). the date at which an information content entity was made public. date of issue An hour is a period of 60 minutes. hour vector space a vector space is a set of vectors. a vector is a rank 1 tensor that is described by n-dimension of scalars. rank 1 tensor vector a rank nonzero tensor is a tensor with a rank greater than zero. rank nonzero tensor A diffusion equation describes density fluctuations in a material undergoing diffusion. diffusion equation duplicates a collection of duplicates is a collection composed of items that are an exact copy of other items in the collection. a collection of duplicates disjunction (or) OR is a logical operator that results in true whenever one or more of its operands are true. 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 A 3D cartesian coordinate is a coordinate that is composed of an x, y and z coordinate. 3D cartesian coordinate arithmeritic mean average mean 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. independent variable An independent variable is a variable that may take on different values independent of other elements in a system. A year is a period of time taken by a planet to make one revolution around the sun. year The surface area of a is a measure of the total area that the surface of the object occupies. surface area likelihood Likelihood is the hypothetical probability that an event that has already occurred would yield a specific outcome. 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 text span end position text span end position is the position (offset) of the last character of a text span in relation the text it is from. ordinary differential 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. protein expression value A protein expression value is a quantity obtained from a protein expression experiment. A pairwise sequence alignment is the alignment of exactly 2 sequences. pairwise sequence alignment cartesian coordinate A Cartesian coordinate is the signed distance of a point to some referent line. depth is the dimensional extent into a plane of a 3D projection of the object. depth DisGeNET Pleiotropy Index 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 decrease 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. The aspect ratio of a geometric shape is the ratio of its sizes in different dimensions. aspect ratio statistical association A statistical association is any relationship between two measured quantities that renders them statistically dependent. age is the length of time that a person has lived or a thing has existed. age gene-disease association linked with somatic 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. min minimal value A minimal value is smallest value of an attribute for the entities in the defined set. A time instant is a temporal region which occurs instantaneously, e.g. having no duration. time instant 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 sequence start position A sequence start position is the start position for a sequence of characters. therapeutic gene-disease association gene-disease association arising from a therapeutic role of the gene/protein A gene disease association in which the gene is a therapeutic marker for the disease. minute A minute is a period of 60 seconds. standard deviation A standard deviation (represented by the symbol σ) is the quantity of variation from the average (mean, or expected value). A correlation is a statistical relationship involving dependence between two random variables or datasets. correlation expected value An expected value (or e-value) is the weighted average of all possible values that a random variable can take on. sequence end position A sequence end position is the position of the last character in a sequence of characters relative to some linear frame of reference. A measurement of a spatial location relative to a frame of reference or other objects. position mass is the quality of the amount of substance. mass set item set item is an item in a set. 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 rate of change The amount of change accumulated per unit time. unit of measurement 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. tensor a tensor is a n-dimensional array. A class is a collection of sets which can be unambiguously defined by a property that all its members share. class A movement equation describes the displacement of an object in space over time. movement equation length is the longer dimensional extent along a 2D projection of the object. length a collection item is an item in a collection. collection item gene-disease association linked with modifying mutation A gene-disease association in which a gene mutation is known to modify the clinical presentation of the disease. gene-disease association A gene-disease association is an association between a gene and a disease.