A bar is a rectangle that is located in the plot of a statistical graph in which its length is proportional to the values that it represents. bar effective specification action specification An action specification is a specification composed of a sequence of instructions to achieve some objective. 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 corporation A corporation is an organization that is granted a charter recognizing it as a separate legal entity. diagnosis A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms. A blog is a publication accessible at some website and is typically about various experiences. blog A molecular structure file is a file that contains a description of molecular structure. molecular structure file The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm left value axis A left value axis is a value axis that is spatially positioned to the left of the plot area. scientific name A scientific name is a name given through scientific nomenclature. A PDB record identifier is an identifier for a PDB generated record. PDB record identifier thickness thickness is the shortest dimensional extent of a 3D projection of an object. 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 versioned record is a record for which there exists another variant based that was derived via modification of the facts. versioned record A page range denotes the start and end page in some document. page range A start position is the proximal position of an object relative to an origin in a linear system. start position A definition is a description that succintly characterizes an entity. definition A chemical identifier is an identifier for a chemical entity chemical identifier A movie is a series of images that are displayed in rapid succession to give the impression of movement. movie film moving pictures sequence element position A sequence element position is the position of an element of a linear sequence. expected value An expected value (or e-value) is the weighted average of all possible values that a random variable can take on. A hypernym is a term with a broader meaning. hypernym A minor tick mark is a tick mark that indicates the position of a specific numeric value but has no adjacent value label, or is one of a pair of tick marks that delineates the boundary of a categorical value but has no adjacent category label on the categorical axis. minor tick mark address An address is a position that indicates the physical location of some entity using a social convention. A right value axis is a value axis that is spatially positioned to the right of the plot area. right value axis crystal structure A crystal structure is the arrangement of atoms or molecules in a crystalline liquid or solid. An image is an affine projection of a visual entity to a two dimensional surface. image depiction A peer reviewed article is an article that has undergone peer-review and deemed acceptable for publication. peer reviewed article written language is a language that is communicated through a writing system. written language A language label is a label that denotes the language of a textual entity. language label word tree A word tree is a chart that links phrases with contexts through a tree-like branching structure. treemap A treemap is a chart that fully partitions the area into a set of rectangles whose area represents its relative value. A university is an institution of higher education and research which grants academic degrees in a variety of subjects and provides both undergraduate education and postgraduate education. university number of objects produced number of objects produced is a count of objects that were produced in some process. valid argument A valid argument is an argument where the truth of the conclusion is a logical consequence of the premises and (consequently) its corresponding conditional is a necessary truth. Graphs 6,7 in http://tinyurl.com/opwnvm A stacked bar graph is a bar graph in which each rectangular bar is partioned by the categorical value of each series of data. stacked bar graph 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. email address an email address is an identifier to send mail to particular electronic mailbox. orientation orientation is an angle between the bearer and an axis, or the angle between the bearer and another object. endpoint An endpoint is a terminal point that is the last of an ordered pair of points. 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 brief A brief is a written legal document used in various legal adversarial systems that is presented to a court arguing why one party to a particular case should prevail. 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 An objective is a proposition that indicates a planned or anticipated outcome. objective stop position An end position is the distal position of an object relative to an origin in a linear system. end position An OBO ontology is an ontology document as specified by the Open Biological Ontology community. OBO ontology A nucleic acid sequence is a symbolic sequence of nucleic acid residues in a nucleic acid. nucleic acid sequence spherical coordinate system A spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane. publication A publication is a document that has been made available by a publisher. streamgraph A streamgraph is a multi-line stacked graph that yields the appearance of continuous y-values across the x-axis. The value of a plotted geometric objects (e.g. point) can be obtained from the perpendicular projection of the position of the object onto the axis. Axis may also be associated with a textual description of what the values on the axis represents. An axis is a line segment that is part of a statistical graph in which the position along the line corresponds to a numeric or categorical value. axis The left vertical and bottom horizontal lines with tickmarks in Graph 1 http://tinyurl.com/opwnvm metadata metadata is data that provides information about data. question A question is a linguistic expression used to make a request for information. book section quadrilateral A quadrilateral is a polygon with composed of four points and four line segments, in which each point is fully connected to two other points. evidence is the body of facts or information indicating whether a belief or proposition is true or valid. evidence default parameter A default parameter is a parameter which has a default value. dendrogram A dendrogram is a tree diagram used to illustrate the arrangement of the clusters produced by hierarchical clustering. 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. speed Speed is the rate of change of an object's position. web service A web service is a software application that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services. A local minimum stationary point is a point that has a lower value in some axis than adjacent points. local minimum stationary point core ice+ information content entity is an object that requires some background knowledge or procedure to correctly interpret. information content entity The surface area of a is a measure of the total area that the surface of the object occupies. surface area unique identifier A unique identifier is an identifier that uniquely identifies some thing. metabolic pathway A metabolic pathway is a series of biochemical reactions that begins with one or more substrates and ends with one or more products. y cartesian coordinate An y cartesian coordinate is the coordinate of an object onto the y-axis of a cartesian coordinate system. speculation speculation is an opinion based on incomplete evidence. versioned dataset a versioned dataset is a dataset with a particular release date or release number. A slideshow is a visual presentation of information contained within a collection of slides. slideshow 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 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. A variable is a value that may change within the scope of a given problem or set of operations. variable vowel A vowel is a verbal entity of language that is pronounced with an open vocal tract so that there is no build-up of air pressure at any point above the glottis. A symbol is a proposition about what an entity represents. symbol cellular phone number a cellular phone number is a number to connect to a mobile device 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 author section is a document section that lists the contributing authors. author section A mode is the value that appears most often in a set of data. mode scaled value axis A scaled value axis is a value axis in which the value range was subject to a mathematic transformation. RNA sequence ribonucleic acid sequence A ribonucleic acid sequence is a symbolic sequence of ribonucleic acid residues in a ribonucleic acid. inclusion criterion An inclusion criterion is a criterion that must be present to satisfy some objective. apartment number An apartment number is the number assigned to identify an apartment in a building of apartments. 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 consonant A consonant is a verbal entity of language that is articulated with complete or partial closure of the vocal tract. 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. A premise is a proposition of an argument from which the conclusion is drawn. premise drug regulatory authority A drug regulatory authority is a regulatory authority which acts to control what substances may be used to treat individuals. A polygonal face is a polygon bounded by a circuit of polygon edges, and includes the flat (plane) region inside the boundary. polygonal face volume is the quantity of three-dimensional space enclosed by some closed boundary. volume polygon vertex A polygon vertex is a terminal point at which two polygon edges meet and are part of a polygon. chemical structure is the structure of a chemical entity in terms of its molecular geometry and electronic structure. chemical structure A histogram is a graphical representation of data which consists of tabular frequencies, shown as adjacent rectangles, over discrete intervals (bins) , with an area equal to the frequency of the observations in the interval. histogram The colored line segments and the adjacent textual descriptions in Graph 1 of http://tinyurl.com/opwnvm A legend is a part of a figure that associates textual descriptions with symbols pertaining to plotted entities. legend A z cartesian coordinate is the coordinate of an object onto the z-axis of a cartesian coordinate system. z cartesian coordinate A ray is a line which that is bounded by a startpoint and extends outwards infinitely along one dimension. ray A verbal language entity is a language entity that is manifested through sound. verbal language entity semantic web service a semantic web service is a web service that provides a formal, machine understanble description of its functionality. end time An end time is a time instant pertaining to the time at which a process ends. A y-axis is a Cartesian coordinate axis that is spatially oriented perpendicular to the x-axis. vertical axis y-axis software application A software application is software that can be directly executed by some processing unit. last name A last name (surname) is a name added to a given name and is part of a personal name and is often the family name. 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. epimer association Uniform Resource Locator A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource. URL a left open interval is an interval in which there is no element that is smaller than all other elements. left open interval category A category is a class of entities having particular shared characteristics. A maximal value is largest value of an attribute for the entities in the defined set. maximal value max The results section is a document section describing the main findings of the study. results section medical history A medical history is a record of the events of a recipient of medical care. A database is a set of tables. database A deoxyribonucleic acid sequence is a symbolic sequence of deoxyribonucleic acid residues in a deoxyribonucleic acid. DNA sequence deoxyribonucleic acid sequence middle initial a middle initial is an abbreviated middle name. 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 A hypothesis is a proposed explanation for a phenomenon. hypothesis A polar coordinate is a position characterized by a distance from a fixed point and an angle from a fixed direction. polar coordinate node a node or vertex is a point in a graph. vertex pharmacodynamic pathway a pharmacodynamic pathay is a regulatory pathway in which a drug molecule regulates the activity of one or more components organized in a pathway. global maximal stationary point A global maximum stationary point is a data point that corresponds to a measurement value is larger than that of all other plotted datapoints. A logarithmic value axis is a scaled value axis that corresponds to a scaling factor of the logarithm of the value range. logarithmic value axis A positional description is a description of location using some system or frame of reference. positional identifier middle name a middle name is a name assigned to an individual that is not the first or last name. academic department An academic department is a division of a university or school faculty devoted to a particular academic discipline. A primary graph title is a primary title that describes a statistical graph. "Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm primary graph title A revision number is a version of a software in which bugs have been fixed from a prior version. revision number discussion section The discussion section is a document section containing a summary of the findings, a reflection on the significance of findings, comparison with related work, among others. methods section The methods section is a document section containing a description of the methods used in the study. A quantity that extends in two dimensions. 2D extent quantity A conference proceedings is a book composed of papers presented at a conference. conference proceedings A gene expression value is a measured value obtained from a gene expression experiment. gene expression value A document title is a textual entity that summarizes the topic of the document in one sentence. document title A local maximum stationary point is a point that has a higher value in some axis than adjacent points. local maximum stationary point 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 dag directed acyclic graph a directed acyclic graph or DAG is a network digram that contains directed edges in which nodes may have multiple parents, but there are no cycles. A thesis document is the written research component of a post-secondary institution that contains a statement supported by arguments. thesis document 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 A flowchart is a diagram that represents an algorithm or process, showing the steps as boxes of various kinds, and their order by connecting these with arrows. flowchart secondary graph title A secondary graph title is a secondary title that describes a statistical graph. 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 design specification A design specification is a specification that provides precise and explicit information about the requirements for a product design. A term variant is a term that is a variant of another term. term variant statistical graph line A statistical graph line is a line used in a statistical graph to communicate some trend or feature of the embedded data. A term is a word or phrase used to denote one or more entities. term 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. REST web service a REST web service is a web service that provides functionality according to the Representational State Transfer (REST) specification. http://en.wikipedia.org/wiki/REST chemical reaction pathway A chemical reaction pathway specifies a series of chemical reactions towards producing some chemical product. A secondary title is a title of lesser importance that should be used after the first title in describing some entity. secondary title subtitle, alternative title A keyword is a descriptor in which the association of the word with the entity facilitates information retrieval. keyword collection ovopub A collection ovopub is an ovopub that contains and links to one or more assertion subgraphs and/or ovopubs, as well as statements describing its provenance. It is used to share a specific set of items or restrict a search to the resources contained therein. A tag cloud is a visualization of word frequencies. word cloud tag cloud A line-bar graph statistical graph that contains both lines and bars. Graph 8 in http://tinyurl.com/opwnvm line-bar graph 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. study protocol study design A study design is a protocol for the proper execution of a study which normally requires a carefullly crafted research question or hypothesis and at least one variable under observation and observed values for that variable. A sequence is a primary structure descriptor in which each of the letters in the string represents a monomeric unit (residue) in which adjacent letters represent the connectivity between the monomeric units. biopolymer sequence character offset The ordinal position of a character in a sequence of characters. character position surface normal A surface normal is a vector that is perpendicular to a flat surface. identifier An identifier is a label that specifically refers to (identifies) an entity (instance/type). media media are audo/visual/audiovisual modes of communicating information for mass consumption. generation number generation number is a count of the number of biological reproduction events elapsed from some starting reference point. line A line is curve that extends in a single dimension (e.g. straight line; exhibits no curvature), and is composed of at least two fully connected points. A linear position is the position of some object against a linear positioning system. linear position measurement value A measurement value is a quantitative description that reflects the magnitude of some attribute. A book volume is a book that is part of a collection. book volume An abstract section is a document section that provides brief summary of a document that explains the main argument(s), topic(s) or findings. abstract section A map is a a visual representation of an area that depicts the relationship between elements of that space. map affiliation An affiliation is a social relation which indicates the partnership between two or more entities. The category axis that corresponds to months in Graph 1 of http://tinyurl.com/opwnvm A secondary category axis is a category axis that defines a finer granular part (or subset) of the value range of the primary category axis. secondary category axis A top value axis is a value axis that is spatially positioned to the top of the plot area. top value axis A tertiary structure descriptor describes 3D topological patterns in a biopolymer. tertiary structure descriptor [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. A value axis is an axis in which the position along the line is partioned into numeric values. A value axis holds the properties of having a minimum and a maximum value, and is usually associated with tickmarks that indicate intervals along the axis. value axis The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm count The number of elements of a finite set of objects. An idea is a proposition about some object of conceptual thought. idea 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 an edge is a line connecting two graph vertices. edge conclusion A conclusion is a proposition which is reached after considering the evidence, arguments or premises. polyhedral skeleton A polyhedral skeleton is a collection of polygon edges. Language is a language entity which is the result of encoding and decoding information through systematic creation and usage of systems of symbols, each pairing a specific sign with an intended meaning, established through social conventions language cylindrical coordinate system A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis. chart A chart is a figure that displays the relationship among tabular numeric data, functions or some kinds of qualitative structures. A figure is a graphical entity which consists of a visual (n-dimentional) arrangement of information entities. figure diagram 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. A quantity that extends in single dimension. 1D extent quantity An x-axis is a Cartesian coordinate axis that is aligned with the horizon. horizontal axis x-axis In most figures, this axis represents categories, such as months, market segments, or other non-numeric data. The horizontal axis in http://tinyurl.com/opwnvm cell (informational) The minimal unit of a cellular automaton that can change state and has an associated behavior. spatial quantity A spatial quantity is a quantity obtained from measuring the spatial extent of an entity physical dimensional quantity molecular structure molecular structure is the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together. molecular geometry A 1D cartesian point is a point whose position is specified along a single dimension using Cartesian coordinates. 1D cartesian point (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 A start date is a time instant pertaining to the date of the beginning of a process. start date A report is a textual document made that present focused, salient content to a specific audience. report A novel is a fictitious prose narrative of book length, typically representing character and action with some degree of realism. novel medical health record A medical health record is a record of a single patient's medical history. personal name full name A personal name is a name to identify an individual person and usually comprises of a first name and a last name. 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 A Gantt chart is a bar chart that illustrates a project schedule. Gantt chart model A model is a representation of some thing. A polygon is a planar entity that is bounded by a closed path or circuit, composed of a finite connected sequence3 of straight line segments. polygon 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 notation a notation is a series or system of written symbols used to represent numbers, amounts, or elements. A microarray probe set identifier is an identifier for a set of probe pairs selected to represent expressed sequences on an array. microarray probe set identifier A boxplot (box-and-whisker diagram) is a convenient way of graphically depicting groups of numerical data through their five-number summaries: the smallest observation (sample minimum), lower quartile (Q1), median (Q2), upper quartile (Q3), and largest observation (sample maximum). boxplot A collection of points is a geometric entity that contains a non-zero set of geometric points. collection of points legal name A legal name is a name given at birth, or which appears on their birth certificate, marriage certificate, or change of name certificate. A description is language entity in which elements of a language (formal or natural) are used to characterize an entity. description A catalog is a systemic collection of items of the same type. registry catalog A photograph is an image created by light falling on a light-sensitive surface. photograph photo 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 effective dose effective dose is the amount of a substance required to produce an effect on a predefined percentage of a population. selector text span A text span is a subset of contiguous sequence of characters of a textual entity. genetic data is data pertaining to genetics. genetic data legislation A legal document proposing or enacting a law or a group of laws. 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. probability measure A probability measure is quantity of how likely it is that some event will occur. A standard is a socially-agreed upon specification. standard introduction section An introduction section is a document section that generally provides background, motivation and goals of the work. A polygon edge is a line segment joining two polygon vertices. polygon edge An end date is a time instant pertaining to date of the end of a process. end date author list an ordered list of authors. 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. database key A database key is an informational entity whose value is constructed from one or more database columns. A directed line segment is a line segment that is contained by an ordered pair of endpoints (a start point and an endpoint). directed line segment software module A software module is software composed of a collection of software methods. file http://www.w3.org/ns/dcat#Distribution A file is an information-bearing object that contains a physical embodiment of some information using a particular character encoding. A PhD thesis is a thesis prepared as a requirement for a doctoral degree. phd thesis An antonym is a word with opposite or nearly opposite meaning. antonym Graph 4,5 in http://tinyurl.com/opwnvm vertical bar graph A vertical bar graph is a bar graph in which the rectangular bars are vertically oriented in space. A figure part is a part of a figure. figure part A number is a tensor of rank 0. number rank 0 tensor right open interval a right open interval is an interval in which there is no element that is greater than all other elements. uncertainty value The uncertainty value (margin of error) of a measurement is a range of values likely to enclose the true value. database entry database record A database entry is a single, implicitly structured data item in a table. An arrowed line is a directed line segment in which one or both endpoints is tangentially part of a triangle that bisects the line. arrowed line segment z-axis A z-axis is a Cartesian coordinate axis that is spatially oriented normal to the plane formed by the x- and y-axes. vocabulary A vocabulary is a collection of terms. A deductive argument is an argument that asserts that the truth of the conclusion is a logical consequence of the premises. deductive argument book series A book series is a collection of books that have been sequentially published. 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. A paragraph is a self-contained unit of written discourse consisting of one or more sentences. paragraph a rank nonzero tensor is a tensor with a rank greater than zero. rank nonzero tensor answer An answer is a reply to a question. A statement is a proposition that is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. statement NOT is a logical operator in that has the value true if its operand is false. negation (not) document version A document version is a version of a work in some sequence of derivative works. dimensionless quantity A dimensionless quantity is a quantity that has no associated unit. cartesian coordinate A Cartesian coordinate is the signed distance of a point to some referent line. coordinate system A coordinate system is a specification for spatial location that uses a set of numbers, or coordinates, to uniquely determine the position of a point or other geometric element. A hyponym is a term with a narrower meaning. hyponym argument An argument is a set of one or more declarative sentences (or propositions) known as the premises along with another declarative sentence (or proposition) known as the conclusion. real number a real number is a complex number whose imaginary part is zero, e.g. a + 0i. 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. trend line A trend line is a line, line segment or ray that is part of a statistical graph which indicates a statistical or visual direction across categorical or value data. chapter A chapter is a document section of a book or thesis. polygonal chain, polygonal curve, polygonal path, piecewise linear curve A polyline is a connected sequence of line segments. polyline 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 dimensional quantity A dimensional quantity is a quantity that has an associated unit. A logical operator is a unary or binary relation to construct logical expressions. logical operator A set is a collection of entities, for which there may be zero members. set list A list is any enumeration of a set of items. likelihood Likelihood is the hypothetical probability that an event that has already occurred would yield a specific outcome. A comment is a verbal or written remark often related to an added piece of information, or an observation or statement. comment A specification is a description of the essential technical attributes/requirements for an object or procedure, and may be used to determine that the object / procedure meets its requirements/attributes. specification A specification for spatial location is an effective specification towards representation spatial position or spatial data. spatial specification article An article is a publication that is stand-alone section of a larger work. width width is the shorter dimensional extent perpendicular to a 2D projection of the object. Graph 1 in http://tinyurl.com/opwnvm A line graph is a statistical graph in which lines contains the evaluation of functions or individual points connected by line segments. line graph line chart 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. bottom value axis A bottom value axis is a value axis that is spatially positioned to the bottom of the plot area. A molecular identifier is an identifier for a molecular entity. molecular identifier protein-disease association A protein-disease association is an association between a protein and a disease. A biomolecular structure descriptor is structure description for organic compounds. biomolecular structure descriptor A tick mark is a line segment that is spatially positioned perpendicular to the axis of a statistical graph and indicates the position of a specific numeric value (which may be indicated by an adjacent value label) on a value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value (which may be indicated by an adjacent category label) on the categorical axis. tick mark replicate a replicate is an object that is a facsimile, reproduction, or copy of another item. The materials and methods section is a document section containing a description of the materials and methods used in the study. materials and methods section A 3D cartesian point is a point whose position is specified along three dimensions using Cartesian coordinates. 3D cartesian point purpose is the reason for which something is done or created or for which something exists. purpose A linear value axis is a value axis that corresponds to a scaling factor of 1 of the value range. linear value axis A sound argument is a valid argument with true premises. sound argument tree diagram A tree diagram is a hierarchical network diagram in which a root vertex is connected to one or more other vertices through a directed edge, which in turn may be connected to other vertices. verbal language A verbal language is a language that uses sounds to communicate. An edited publication is a publication that has been examined and potentially changed by an editor. edited publication population A population is all the organisms that both belong to the same group or species and live in the same geographical area. decimal scale A decimal scale of measurement is one that only specifies decimal values. A line segment is a line and a part of a curve that is (inclusively) bounded by two terminal points. line segment A namespace is an informational entity that defines a logical container for a set of symbols or identifiers. namespace telephone number a telephone number is an identifier used to connect to a physical device capable of transfering voice or data over a network. website A website is a collection of documents published on the World Wide Web. annotation An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information. A symbolic sequence is a data item that encodes a finite, ordered list of symbols drawn from a specified alphabet, where the identity and position of each symbol are essential to the meaning of the sequence. symbolic sequence A television program is a audiovisual media that is produced and broadcast using a television. television program A concept is term that refers to a generalization of a set of attributes or entities. concept 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 stack graph is a statistical graph which presents multiple series in which the distance between one series and another indicates the relative contribution to the total for any x-value. stack graph A synonym is a word with the same or very similar meanings. synonym A century is a period of one hundred years. century manual A manual is a document that instructs on the usage of a device. A Venn diagram is a chart that illustrates all possible logical relations between a finite collection of sets as overlapping circles. venn diagram number of objects consumed number of objects consumed is a count of objects that were consumed in some process. disease-disease association A disease-disease association is an association between two diseases. An experimental protocol is an action specification with respect to the design and implementation of experiments. In addition to providing a detailed set of procedures and lists of required equipment and instruments, experimental protocols often include information on safety precautions, the calculation of results and reporting standards, including statistical analysis and rules for predefining and documenting excluded data to avoid bias. experimental protocol periodical http://purl.org/ontology/bibo/Periodical A periodical is a publication that appears on a regular schedule. generic name A generic name is the preferred name provided by manufacturer. An ethnic group is a group of people whose members identify with each other through a common heritage, consisting of a common culture, including a shared language or dialect. ethnic group software script A software script is software whose instructions can be executed using a software interpreter. protein-protein association A protein-protein association is an association between two proteins. An increasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is positive. increasing line rectangle A rectangle is a quadrilateral in which one pair of line segments are parallel and the other pair are perpendicular to the first pair. conjunction (and) AND is a logical operator that has the value true if both of its operands are true, otherwise a value of false. The table of contents is a document section that lists all sections (and optionally subsections) in a sequential order along with their page number. table of contents A database row is a row that is part of a database table. database row a fax number is a number to connect to fax device fax number a statement of consequence is a statement concerning the result or effect of an action or condition. statement of consequence block histogram A block histogram contains an x-axis that is divided into bins which correspond to value ranges. Each item in the data set is drawn as a rectangular block, and the blocks are piled into the bins to show how many values in each range. process model A process model is a representation of some process. data item A data item consists of information that has been collected/generated towards some purpose. A drop line is a statistical graph line that vertically or horizontally connects a data series line with a value axis in a statistical graph. drop line PDB file A PDB file is a molecular structure file specified by the Protein DataBank (PDB). matrix chart A matrix chart summarizes a multidimensional data set in a grid. Frequency is the number of occurrences of a repeating event per unit time frequency A reason is a justification that specifies the motive for an action or a determination. reason A correspondence section is a document section that contains the details for contacting the corresponding author. correspondence section prognosis A prognosis is a proposition about the likely course of a disease, the chance of recovery or recurrence. 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. A 3D cartesian coordinate is a coordinate that is composed of an x, y and z coordinate. 3D cartesian coordinate OWL ontology An OWL ontology is an ontology as specified by the W3C OWL specification. An empty set is a set for which there are exactly 0 members. empty set positionally oriented line A positionally oriented line is a line that is positioned against some axis of reference. gene-disease association linked with genomic alterations a gene-disease association that is linked with some genomic alteration A primary database key is a database key that identifies every row of a table. primary database key A version label is a label for a particular form or variation of an earlier or original type. version label A book is a publication composed of a large number of entries. book an ordered list item is an item in an ordered list. ordered list item week A week is a period of 7 consecutive days. altitude Altitude is a distance above sea level. decreasing line An decreasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is negative. A collection of documents is a non-zero set of documents. collection of documents http://purl.org/ontology/bibo/Collection representation A representation is a entity that in some way represents another entity (or attribute thereof). electronic structure is the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals. electronic configuration the electron configuration of the neon atom is 1s2 2s2 2p6. electronic structure A document section is a component of a document. document section x cartesian coordinate An x cartesian coordinate is the coordinate of an object onto the x-axis of a cartesian coordinate system. textual chart A textual chart is a chart containing text. syllable A syllable is a verbal entity of language having one vowel sound, with or without surrounding consonants, forming the whole or a part of a word. ontology an ontology is a formal specification of entities, their attributes and relationships. A percentage is a number that is a ratio expressed as a fraction of 100. It is denoted using the percent sign "%". percentage A regulatory pathway is a series of biochemical reactions that lead to the increase or decrease of activity of participating molecular components. regulatory pathway A network diagram consists of a set of vertices connected by edges. network diagram A plan is a set of intended actions, through which one expects to achieve a goal. plan An assertion ovopub is an ovopub that contains and links to an assertion subgraph with one or more statements that may be true or false, as well as statements describing its provenance. assertion ovopub velocity The rate of change of an object's position and the direction of that change belief A belief is a proposition that is believed to be true. An hour is a period of 60 minutes. hour A web page is a document that is published according to World Wide Web standards. web page 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. database table A database table is a set of named columns with zero or more rows composed of cells that contain column values and is part of a database. work phone number a work phone number is the number to connect to an phone at a place of work. An object model is a representation of an object. object model A perimeter is a length of the outline that surrounds a two-dimensional shape. length of perimeter A booklet is a document that lacks a named publisher or sponsoring institution. booklet A pathway is an effective specification that outlines a set of actions that forms a way to achieve an objective. biological pathway pathway A diffusion equation describes density fluctuations in a material undergoing diffusion. diffusion equation An acknowledgements section is a document section that identifies individuals, groups or organizations for their support in the development of the work. acknowledgements section 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. A pie chart is a circular chart divided into sectors each of whose length is proportional to the quantity it represents. pie chart quote A quote is a excerpt that is attributed to a particular source. justification A justification is a proposition that defends, explains or excuses some argument. A year is a period of time taken by a planet to make one revolution around the sun. year A movement equation describes the displacement of an object in space over time. movement equation excerpt An excerpt is a contiguous or discontiguous portion of a document. 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. A preferred name is the name that is generally used by some organization. preferred name database column A database collumn is a column in a database table. letter A letter is a document that contains a personal communication from one part to another. A class is a collection of sets which can be unambiguously defined by a property that all its members share. class referencing cell A referenceing cell is a cell of a cellular automata that refers to another cell. 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 vertical line is a line that is positionally oriented perpendicular to the horizon. vertical line a home phone number is the number to connect to an phone at a place of residence. home phone number 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 sequence assembly is a symbolic sequence representing an ordered sequence of biological symbols that is produced by a sequence assembly process through the integration of multiple sequence inputs. sequence assembly An ontology document is a document that contains an ontology. ontology document descriptor A descriptor (index term, subject term, subject heading) is a term that captures the essence of the topic of a document. scatterplot scatter chart scatter diagram scatter graph A scatterplot is a statistical graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. A pairwise sequence alignment is the alignment of exactly 2 sequences. pairwise sequence alignment independent variable An independent variable is a variable that may take on different values independent of other elements in a system. 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. A 2D cartesian point is a point whose position is specified along two dimensions using Cartesian coordinates. 2D cartesian point An ovopub is an information content entity that contains and links to one or more resources and/or statements, including those describing its provenance, and is itself a dereferenceable resource. ovopub ovopub+ email Email message is a digital document that is composed of a header and a body and is transmitted using the SMTP protocol. An author contribution section is a document section that describes the contribution of the authors. author contribution section depth is the dimensional extent into a plane of a 3D projection of the object. depth functional specification A functional specification is a specification that describes the characteristics of an object. A namespace label is a short name for a namespace. namespace label 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 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 software method A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. A group of people affiliated by consanguinity, affinity, or co-residence. family 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) criterion A criterion is a specification to describe properties used for evaluation. software entity A software entity is a computational entity that can be interpreted by or directly executed by a processing unit. 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). 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. primary category axis The category axis that corresponds to years in Graph 1 of http://tinyurl.com/opwnvm A primary category axis is a category axis that either defines the sole value range or holds the larger set of categorical values specified by the secondary category axis. The aspect ratio of a geometric shape is the ratio of its sizes in different dimensions. aspect ratio record A record is a document containing a collection of statements about some entity. statistical association A statistical association is any relationship between two measured quantities that renders them statistically dependent. tensor a tensor is a n-dimensional array. mass is the quality of the amount of substance. mass height is the one dimensional extent along the vertical projection of a 3D object from a base plane of reference. height A legal document is a formally executed written document that can be formally attributed to its author, records and formally expresses a legally enforceable act, process, or contractual duty, obligation, or right, and therefore evidences that act, process, or agreement. legal document An algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. algorithm double arrowed line segment A double arrowed line is an arrowed line in which both terminal points are tangentially part of different triangles that bisect the line. A homonym is a word that sounds the same but has different meaning. homonym A binary scale is a measurement scale that specifies a choice between two values. binary scale first name A first name is a name that denotes a specific individual between members of a group of individuals, whose members usually share the same surname. A sign language (also signed language) is a language that involves manual communication and body language to convey meaning. This can involve simultaneously combining hand shapes, orientation and movement of the hands, arms or body, and facial expressions to fluidly express a speaker's thoughts. sign language min minimal value A minimal value is smallest value of an attribute for the entities in the defined set. stationary point A stationary point is a point that is part of a curve in which the derivative at that point is zero, and hence its value is at least a local maximum or minimum. collection of 3d molecular structure models A collection of 3D molecular structure models is just that. A sequence motif is a pattern of nucleotides in a DNA sequence or amino acids in a protein. sequence motif 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. day A day is a period of 24 hours. 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 A curve is a geometric entity that may be located in n-dimensional spatial region whose extension may be n-dimensional, is composed of at least two fully connected points and does not intersect itself. curve a coding sequence is a sequence of nucleotides which encode a RNA or protein product.. coding sequence horizontal line A horizontal line is a line that is positionally oriented with the horizon. 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-ice.owl Graphs 3,4,5 in http://tinyurl.com/opwnvm bar graph A bar graph is a statistical graph with rectangular bars of lengths proportional to that value that they represent. a gene symbol is a short name assigned to a gene. gene symbol an ordered list is a list in which items are sequentially ordered. ordered list sequence start position A sequence start position is the start position for a sequence of characters. InCHI notation sadi a SADI semantic web service is a semantic web service that follows the SADI specification SADI semantic web service http://en.wikipedia.org/wiki/SADI referent cell A referent cell is a cell that is the referent of some function or pointer. scientific data is data obtained from some scientific procedure. scientific data 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 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 3D extent quantity A quantity that extends in three dimensions. A curve segment is a part of a curve that consists of at least three points. curve segment A start point is a terminal point which is the first of an ordered pair of points. start point A dependent variable is one whose value changes as a consequence of changes in other values in the system. dependent variable single arrowed line segment A single arrowed line is directed line in which the endpoint is tangentially part of a triangle that bisects the line. institute institute is a society or organization having a object or common factor, and is normally applied to those with a scientific, educational, or social objective. unique cell A unique cell is a cell that contains a unique value in the cellular automaton. street name A street name is the token given to identify a particular street. informational entity identifier An informational entity identifier is an identifier for an informational entity. A quaternary structure descriptor describes topological patterns in a multi-unit biopolymer complex. quaternary structure A correlation is a statistical relationship involving dependence between two random variables or datasets. correlation minute A minute is a period of 60 seconds. protein expression value A protein expression value is a quantity obtained from a protein expression experiment. molecular structure descriptor molecular structure descriptor is data that describes some aspect of the molecular structure (composition) and is about some chemical entity. CHEMINF:000085 statistical graph A statistical graph is a figure that displays the relationship among numeric data and/or mathematical functions. chart A multiple sequence alignment is a sequence alignment involving more than two sequences. multiple sequence alignment An exclusion criterion is a criterion that must be absent to satistify the objective. exclusion criterion family history family history is the systematic narrative and research of past events relating to a specific family, or specific families. standard deviation A standard deviation (represented by the symbol σ) is the quantity of variation from the average (mean, or expected value). history is a sequence of past events. history chemical-disease association A chemical-disease association is an association between a chemical and a disease. 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. dose A dose is the quantity of a chemical substance administered to a biological system. A percentile (or a centile) is a quantile that divides the given probability distribution, or sample, into 100 equal-sized intervals. percentile academic organization An academic organization is a lawfully recognized organization that confers diplomas, degrees and other forms of recognition of academic achievement. 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. bubble chart A bubble chart contains circles whose area corresponds to a value. 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 foreign database key is a database key that refers to a key in some table. foreign database key A chemical degradation pathway is a pathway involved in the disassembly of a chemical. chemical degradation pathway materials section The materials section is a document section containing a description of the materials used in the study. the date at which an information content entity was made public. date of issue document component A bibliographic attribute is an attribute related to publications. 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. An inductive argument is an argument that asserts that the truth of the conclusion is supported by the premises. inductive argument A nominal scale of measurement only specifies a limited set of categories. nomimal scale polar coordinate system A polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction. integer scale An integer scale of measurement is one that only specifies integer values. A manuscript is a document prior to publication. manuscript A geographic heatmap is a graphical representation of data over a geographic region where individual values are represented as colors. geographic heatmap Density (volumetric mass density) is the quantity of mass per unit volume of a substance. density 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. A sentence is a grammatical unit consisting of one or more words that bear minimal syntactic relation to the words that precede or follow it. sentence A dataset is a data item that is a collection of data items. data set http://www.w3.org/ns/dcat#Dataset dataset A parameter is variable whose value changes the characteristics of a system or a function. parameter 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. 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 A proposition is a sentence expressing something true or false. proposition terminal point A terminal point is a point that defines the finite extension of a line. A word is the smallest free form (an item that may be expressed in isolation with semantic or pragmatic content) in a language. word a pharmacokinetic pathway is a metabolic pathway which describes the metabolism of a drug molecule. pharmacokinetic pathway invalid argument An invalid argument is an argument where the truth of the conclusion is false because it is not a logical consequence of the premises. copy number variation CNV copy number variation refers to the number of deletions/duplications of a DNA region as compared to some reference state. label a label is a term that is associated with some entity A measurement of a spatial location relative to a frame of reference or other objects. position software process identifier A software process identifier is an identifier for a software process in some operating system. major tick mark A major tick mark is a tick mark that indicates the position of a specific numeric value and is adjacent to its value label on the value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value indicated by an adjacent category label on the categorical axis. clause A clause consists of a subject and a predicate. infinite line An infinite line is a line that extends outwards in both directions of a single dimensional and is not bounded by terminal points. A coordinate is a measurement of position in n-dimensional space. coordinate An audio recording is an electrical or mechanical inscription and re-creation of sound waves, such as spoken voice, singing, instrumental music, or sound effects. audio recording A Cartesian coordinate axis is an axis whose behavior follows that of a Cartesian coordinate system. Cartesian coordinate axis heatmap A heatmap is a graphical representation of data where the individual values contained in a matrix are represented as colors. mereological chart A mereological chart is a chart that illustrates the parts in the context of the whole. primary title A primary title is a title that should be first used in describing some entity. sequence variation notation structure structure is the specification that refers to the composition and arrangement of parts of an object. A numeric label is a number used as a label. numeric label social structure A social structure is a social entity which consists of relationships between two or more entities. PDB chain identifier A PDB chain identifier is a alphabetical label to identify a molecule in a structure provided by the Protein DataBank . A formal specification is a mathematical description of software or hardware that may be used to develop an implementation. formal specification opinion An opinion is a belief that is the result of emotion or interpretation of facts. evolutionary lineage is a sequence of species, that form a line of descent, each new species the direct result of speciation from an immediate ancestral species. evolutionary lineage A millenium is a period of 1000 years millennium set item set item is an item in a set. chemical-gene association a chemical-gene association is an association between a chemical and a gene. A collective is a group of entities that share or are motivated by at least one common issue or interest, or work together on a specific project(s) to achieve a common objective. group collective global minimal stationary point A global minimum data point is a data point that corresponds to a measurement value is smaller than that of all other plotted datapoints. SOAP web service http://en.wikipedia.org/wiki/SOAP a SOAP web service is a web service that implements Simple Object Access Protocol (SOAP). A numeric scale of measurement is one that only specifies numeric values. numeric scale rate of change The amount of change accumulated per unit time. user account allows a user to authenticate to system services and be granted authorization to access them. user account A primary structure descriptor describes a biomolecular object in terms of a 1D or 2D topology. primary structure descriptor chemical-chemical association A chemical-chemical association is an association between two chemical entities. 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. 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 minor version number is a version of a software that exhibits minor features or significant fix from a prior version. minor version number vector space a vector space is a set of vectors. A vertext normal is the normalized average of the surface normals of the faces that contain that vertex. vertex normal process number is a number associated with a process that denotes its ordinal position in a set of processes. process number 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. A name is a label used to identify an entity. name 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. social relation A social relation is a social entity that describes a relationship between two or more individuals or groups. arc an arc is a closed segment of a differentiable curve. 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 A specification of an object, manifested by an agent, intended to accomplish goals, in a particular environment, using a set of primitive components, satisfying a set of requirements, subject to constraints. design A table is a figure that consists of an ordered arrangement of columns and rows. table A Master's thesis is a thesis prepared as a requirement for a Master's degree. master's thesis medical report A medical report is a report prepared by a health care practioner about test outcomes or health status of an individual. 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 terminology is a set of terms used for a specified application. terminology quantity A quantity is an informational entity that gives the magnitude of a property. A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. software library 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. A diary is a document which describes day-to-day experiences. diary A start time is a time instant pertaining to the time at which a process begins. start time character A character is a language symbol used to construct words. physical entity identifier A physical entity identifier is an identifier for a physical entity. CHEMINF:000123 A chemical descriptor is a data item that identifies or describes some chemical entity and which conforms to some specification, either for how it is calculated or for how it is measured. chemical descriptor A polyhedral surface is composed of polygonal faces. polyhedral surface triangle A triangle is a polygon composed of three points and three line segments, in which each point is fully connected to another point along through the line segment. A phrase is a group of words functioning as a single unit in the syntax of a sentence. phrase A horizontal bar graph is a bar graph in which the rectangular bars are horizontally oriented in space. horizontal bar graph Graph 3 in http://tinyurl.com/opwnvm A central tendency measure is a central value or a typical value for a probability distribution. centrality measure An plateau line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is zero. plateau line record identifier A record identifier is an identifier for a database entry. secondary structure descriptor A secondary structure descriptor describes local topological patterns in a biopolymer. A control group is a group of individuals that are not subject to an intervention of interest, but rather serve as a baseline to compare the outcomes in the intervention group. control group A time internval is a contiguous temporal region having some duration. time interval concentration is the amount of substance per unit volume of a solution concentration human population A human population refers to a collection of human beings. 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 The HGVS (human genome variation society) notation is a notation to specify a sequence variation in dna, rna, proteins, and other biomolecules. hgvs notation A regulatory authority is an organization responsible for exercising regulatory or supervisory capacity in some area of human activity. regulatory authority A textual entity is language entity that is manifested as a sequence of one or more distinct characters. textual entity A slide is an visual representation meant to communicate some information. slide a collection item is an item in a collection. collection item An intervention group is a group of individuals that are subject to an intervention. intervention group morpheme A morpheme is the smallest semantically meaningful unit in a language. biochemical pathway A biochemical pathway specifies a series of biochemical modifications and transformations towards achieving some biological outcome. drug-pathway association chemical-pathway association a chemical-pathway association is an association between a chemical and a pathway. a notation to describe a chemical entity chemical notation A copyright section is a document section that contains a notice of copyright. copyright section page total A page total is a textual entity that is about the number of pages in some informational entity. A Cartesian coordinate system specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length. cartesian coordinate system major version number A major version number is a version of a software that exhibits a significant change in functionalilty from a prior version. gene-disease association A gene-disease association is an association between a gene and a disease. biological data biological data is scientific data relevant to biology. A column is a vertical sequence of cells in a cellular automata. column A software interpreter is a software application that executes some specified input software. software interpreter Log likelihood is the natural logarithm of the likelihood function log likelihood document A document is a bounded physical or digital representation of a body of information designed with the capacity (and usually intent) to communicate. A month is a period of time that divides the year. month IP address IP number an IP number is an number to connect to a device on the internet. reference A reference is a textual entity that describes a single source used in the preparation or development of the work. bioinformatic data bioinformatic data is data genereated or used for computer-based investigations of biological phenomena. list item a list item is an item in a list. syndrome A syndrome is composed of a set of several clinically recognizable features, signs (observed by someone other than the patient), symptoms (reported by the patient), phenomena or characteristics that often occur together. major.minor[.build[.revision]] A software version label is a version label for a piece of software. software version label gene-gene association A gene-gene association is an association between two genes. 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. polypeptide sequence amino acid sequence A protein sequence is a symbolic sequence of amino acid residues in a protein or class of proteins. protein sequence A computational entity is an information content entity operated on using some computational system. computational entity a vector is a rank 1 tensor that is described by n-dimension of scalars. rank 1 tensor vector A union is a list of all of the values of an attribute for the entities in the defined set. union point A point is a geometric entity that is located in a zero-dimensional spatial region and whose position is defined by its coordinates in some coordinate system. a duplicate is an object that is an exact copy of another item duplicate measurement scale A measurement scale is a functional specification that specifies an allowed range of categories or values. A page number is the count of a page in a sequence of pages. page number A technical report is a publication published by a school or other institution, usually numbered within a series. technical report nlp+ language entity A language entity implements some language specification for the visual interpretation and is part of some document. A row represents a single, implicitly structured data item in a table. row RDFS ontology An RDFS ontology is an ontology that conforms to the syntax and semantics of the Resource Description Framework Schema (RDFS). 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 A citation is a textual entity which denotes a source described in the bibliography or reference section of a document. citation 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 brand name A brand name is a trademarked and marketed name of a product. 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. chemical-protein association A chemical-protein association is an association between a chemical and a protein. title A title is a textual entity that summarily describes some entity. A structural motif is a pattern in a structure formed by a spatial arrangement of objects (e.g. atoms). structural motif note A note is a brief document. A graph title is a title that describes a graph. graph title Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm A sequence alignment is the character-based alignment of sequences using some method. sequence alignment length is the longer dimensional extent along a 2D projection of the object. length phrase net diagram A phrase net diagram illustrates the relationship between different words used in a text. 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. An organization is a collective with a complex articulation of tasks, roles and responsibilities. organization area is a quantity that pertains to the extent of a two-dimensional surface or shape, or planar lamina, in the plane. area A common name is a name that is commonly used. common name A recipe is a set of instructions that describe how to prepare or make something. recipe social entity A social entity pertains to the interaction among individuals and groups. geometric entity A geometric entity is an information content entity that pertains to the structure and topology of a space. geometry+ vector line A vector line is a line which that is bounded by a startpoint and extends outwards along one dimension. category axis The horizontal axis corresponding to months of the year in graph 4 of http://tinyurl.com/opwnvm A category axis is an axis in which the position along the line is partioned into categories. 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 chemical synthesis pathway is a pathway involved in the assembly of a chemical. chemical synthesis pathway genotype A genotype is a functional specification of a biological entity in terms of its genetic composition (or lack thereof). medical data medical data is data of interest to medicine. pattern A pattern is a generalized representation of some repeatable concrete or informational item. 3d structure model A 3D structure model is a representation of the spatial arrangement of one or more chemical entities. equation An equation is a mathematical statement that asserts the equality of two expressions. 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 study group A study group is a group of individuals that are subjects in an observational or intervention study. An honor's thesis is a thesis prepared as a requirement for an honor's undergraduate degree. honor's thesis The square portion of the chart bounded by lines that overlap with the two axes in Graph 1 of http://tinyurl.com/opwnvm A plot is a part of a figure that corresponds to the spatial region between the set of axes. plot A visual language entity is a language entity that is manifested within the spectrum of light and can be pereceived and processed by a visual system. visual language entity 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 bibliography section A bibliography section is a document section that is composed of a list of references used in the development of the work. An issue is a single instance of a periodically published journal, magazine, or newspaper. issue diagnostic opinion A diagnostic opinion is an opinion resulting from a medical diagnostic procedure. A standard operating procedure is a specification approved for use in specific environments. standard operating procedure A t-statistic is a ratio of the departure of an estimated parameter from its notional value and its standard error. t-statistic A patent is an information entity granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. patent A bill is proposed legislation under consideration by a legislature. bill A community is a sizeable social unit that shares common values. community statute A statute is a formal written enactment of a legislative authority that governs a state, city or country. sum A sum is the result of adding a set of values together. association An association is a relationship between two or more entities derived by some informational analysis. left closed interval a left closed interval is an interval in which there is a real number that is smaller than all its elements. geographic image A geographic image is a photograph of some geographical area. age is the length of time that a person has lived or a thing has existed. age A data point is a point that which corresponds to the projection of the values of measurement data against the axes of a statistical graph. data point