normality is the quality in which the value may differ from normal or average normality SIO_000307 A drug is a chemical substance that contains one or more active ingredients that regulate one or more biological processes. drug SIO_010038 thallium atom CHEBI:49920 SIO_011066 A process that modulates the frequency, rate or extent of process involved in the creation or destruction of a molecule. regulation of molecular quantity SIO_001127 A vertext normal is the normalized average of the surface normals of the faces that contain that vertex. vertex normal SIO_000541 The quality of not having a charge. uncharged SIO_000806 A partial positive charge is a partial charge where the value of the charge is positive. partial negative charge SIO_000808 A quantity is an informational entity that gives the magnitude of a property. quantity SIO_000052 to serve as host is the capability to act in a manner that provides hospitality, serves to harbour an organism in or on itself. to serve as a host SIO_000543 to modulate to regulate is to control or maintain the rate or speed of an object or process. to regulate SIO_000395 A structural motif is a pattern in a structure formed by a spatial arrangement of objects (e.g. atoms). structural motif SIO_001197 A definition is a description that succintly characterizes an entity. definition SIO_000135 to change energetically is the capability to change the energetic aspects of an object. to change energetically SIO_000385 has disposition is the relation between an entity and a disposition that it bears. has disposition SIO_000235 A gene-variant disease association in which a somatic mutation in the gene/protein results in the development or maintenance of the disease, and it may not be passed on to offspring. gene-disease association linked with somatic causal mutation SIO_001345 A copyright section is a document section that contains a notice of copyright. copyright section SIO_000193 A week is a period of 7 consecutive days. week SIO_001354 creation development formulation production synthesis creating is the process in which an entity comes into existence. creating SIO_000588 is agent in is a relation between an entity and a process, where the entity is present throughout the process, no permanent material change occurs, and is a causal participant in the process. sadi is agent in hexokinase is an agent in the conversion of glucose to glucose-6-phosphate SIO_000063 A social structure is a social entity which consists of relationships between two or more entities. social structure SIO_000010 The role of a chemical entity that is modified in a chemical reaction. substrate role SIO_000797 is about is a relation between an information content entity and the entity that its primary subject. is about SIO_000332 A pseudo gene is a region of a nucleic acid that either cannot be transcribed, or its RNA transcript cannot be translated. http://purl.obolibrary.org/obo/SO_0000336 pseudogene SIO_000988 An academic role is a social role that pertains to the academic institution. academic role SIO_000711 to be moved to be translocated is the capability to be physically displaced from one location to another to be translocated SIO_000720 A deoxyribonucleic acid template is a deoxyribonucleic acid that provides the template to synthesize a complementary strand of DNA through transcription. deoxyribonucleic acid template SIO_010092 dubnium atom CHEBI:33349 SIO_011076 editor reviewed is the quality of a textual entity that has been examined and commented on by an editor. editor reviewed SIO_001038 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 SIO_000522 to interact with is a capabililty that involves another object. to interact with SIO_000701 A PhD thesis is a thesis prepared as a requirement for a doctoral degree. phd thesis SIO_000168 A has concretization B iff A is an informational entity and B is the a quality of some material entity. has concretization SIO_000213 ununseptium atom SIO_011088 Behaviour is the set of actions and mannerisms made by systems (biological or otherwise) in response to stimuli or inputs, whether internal or external, conscious or subconscious, overt or covert, and voluntary or involuntary. behaviour+ core behaviour SIO_001195 terror is the extreme feeling of fear. terror SIO_000871 A physical entity identifier is an identifier for a physical entity. physical entity identifier SIO_000730 OBO_REL:preceded_by is preceded by SIO_000249 A chart is a figure that displays the relationship among tabular numeric data, functions or some kinds of qualitative structures. chart SIO_000904 A time internval is a contiguous temporal region having some duration. time interval SIO_000417 salt a chemical salt is a molecular complex composed of an ionic assembly of cations and anions. chemical salt SIO_001422 A submolecule is any part of a molecule. submolecule SIO_010441 2 An organ is a collection of tissues joined in structural unit to serve a common function. organ SIO_010003 1 is directly before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity, and the entities are adjacent to one another. is directly before SIO_000242 a protein family is a collection of proteins that share a common evolutionary origin, reflected by their related function and similarity in composition or structure. protein family SIO_001380 2 to be interacted with is the capability of an object to be target of a physical interaction. to be interacted with SIO_000702 A database is a set of tables. database SIO_000750 An empty set is a set for which there are exactly 0 members. empty set SIO_000617 medicine A pharmaceutical preparation is a chemical substance that is approved for use in the medical diagnosis, cure, treatment, or prevention of disease. pharmaceutical drug SIO_010039 A professor is an individual that is a scholarly teacher. professor SIO_000404 to be a member of is the capability to be considered a part of a collection. to be a member of SIO_000777 A generic name is the preferred name provided by manufacturer. generic name SIO_000077 study protocol 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. study design SIO_001041 A monomer is a submolecule that is proper part of some polymer, and is a building block for such polymer. monomer SIO_000146 A document version is a version of a work in some sequence of derivative works. document version SIO_000186 to negatively charge is the capability to add an electron or negatively charged ion to a chemical entity. to negatively charge SIO_000387 A ribonucleic acid is an organic polymer composed of a sequence of ribonucleotide residues. ribonucleic acid SIO_010009 sorrow is the emotion that is characterized by a long term state of intense sadness, distress and a degree of resignation (not accepting). sorrow SIO_000868 depiction An image is an affine projection of a visual entity to a two dimensional surface. image SIO_000081 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 SIO_000608 A logical operator is a unary or binary relation to construct logical expressions. logical operator SIO_000238 A journal is a a peer-reviewed periodical in which scholarship relating to a particular academic discipline is published. http://purl.org/ontology/bibo/Journal journal SIO_000160 The process of maintaining some the frequency, rate or extent of another process. process maintenance SIO_001132 a versioned dataset is a dataset with a particular release date or release number. versioned dataset SIO_001377 A non-cellular organism is an organism that does not contain a cell. non-cellular organism SIO_010378 thickness is the shortest dimensional extent of a 3D projection of an object. thickness SIO_000043 A binding site is a molecular site which when occupied with particular ligands leads to structural transformations that initiatiate new moelcular processes. binding site SIO_010040 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 SIO_000113 ruthenium atom CHEBI:30682 SIO_011043 An open reading frame (ORF) is a part of a gene that encodes a protein but does not contain a stop codon. open reading frame SIO_010073 A probability measure is quantity of how likely it is that some event will occur. probability measure SIO_000638 awe is an emotion produced by that which is grand, sublime or powerful and is characterized by a combination of joy, fear and admiration/reverence/respect. awe SIO_000818 A placebo is a medically ineffectual treatment for a medical condition intended to deceive the recipient. placebo SIO_010429 a immediately derives into b if and only if a or some significant part thereof is consumed in the formation of b and there are no identifiable intermediate entities between a and b. immediately derives into SIO_000246 An antonym is a word with opposite or nearly opposite meaning. antonym SIO_000123 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 SIO_000439 data set A dataset is a data item that is a collection of data items. http://www.w3.org/ns/dcat#Dataset dataset SIO_000089 molecular complex disassociation is the process of dissambly of a molecular complex into its constitutent parts. molecular complex dissociation SIO_010286 An end date is a time instant pertaining to date of the end of a process. end date SIO_000032 female is a biological sex of an individual with female sexual organs. female SIO_010052 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 SIO_000521 A language entity implements some language specification for the visual interpretation and is part of some document. nlp+ language entity SIO_000078 misery is a feeling of great unhappiness, suffering and/or pain. misery SIO_000854 bohrium atom CHEBI:33355 SIO_011078 ecstacy is an emotion characterized by a heightened state of consciousness with total involvement of a subject. ecstasy SIO_000830 volume number is a count of a sequence of periodicals. volume number SIO_000309 A slideshow is a visual presentation of information contained within a collection of slides. slideshow SIO_001170 Pity is the emotion of sadness or sorrow for another. pity SIO_000857 A quote is a excerpt that is attributed to a particular source. quote SIO_000299 to transport is the capability to displace a material from one location to another. to transport SIO_000390 An OWL ontology is an ontology as specified by the W3C OWL specification. OWL ontology SIO_000331 2 to consume is the capability to internalize a material entity. to consume SIO_000492 evidence is the body of facts or information indicating whether a belief or proposition is true or valid. evidence SIO_001394 the regulation of the enzymatic activity. regulation of catalytic capability SIO_000611 SNP SNV single nucleotide variation a single nucleotide variation (SNV) is a nucleotide residue that is a variant compared to some reference nucleic acid sequence. single nucleotide polymorphism SIO_001329 time measurement is a measurement value of the duration of some interval of time or a particular instant of time (against some frame of reference). Time intervals are specified as date/datetime ranges. time measurement the duration of my life; the duration of a surgical procedure, the moment of death SIO_000391 An informational quality is a quality that pertains to information. informational quality SIO_000436 translation is the process of producing a polypeptide from a ribonucleic acid by a ribosome. translation SIO_010301 platinum atom CHEBI:33364 SIO_011063 in relation to is a comparative relation to indicate that the instance of the class holding the relation exists in relation to another entity. core in relation to SIO_000668 An object quality is quality of an object. object quality SIO_000026 A is referred to by B iff B is an informational entity that makes reference to A. is referred to by SIO_000212 A data collection device is a device that collects information about one or more objects. data collection device SIO_001236 1 A is located in B iff the spatialtemporial region occupied by A is part of the spatialtemporal region occupied by B. [T][R] OBO_REL:located_in core is located in A parasite in the interior of a person's intestine is located in their intestinal lumen. SIO_000061 is dissimilar to is a relation between two entities in which one is considered dissimilar to the other based on some criteria. is dissimilar to SIO_000495 circumference is the length of the outline of a circle or ellipse. it is defined as c = 2*pi*r, where r is the radius. circumference SIO_000047 sampling is the act of obtaining a sample, whether through selection, collection or preparation. sampling SIO_001049 has unique identifier is an inverse functional relation between an entity and an identifier that uniquely identifies it. has unique identifier SIO_000673 A diffusion equation describes density fluctuations in a material undergoing diffusion. diffusion equation SIO_000565 A t-statistic based decreased differential gene expression is a differential gene expression ratio in which the t-statistic is less than zero. t-statistic based decreased differential gene expression SIO_001082 gene variant-disease association A gene-disease association in which a sequence variation (a mutation, a SNP) is associated with the disease. gene-disease association linked with genetic variation SIO_001122 An acknowledgements section is a document section that identifies individuals, groups or organizations for their support in the development of the work. acknowledgements section SIO_000189 An epimer is a stereoisomer that differs in configuration at only one stereogenic center. epimer SIO_001336 discouraged Discouragement is the emtion of having lost confidence or enthusiasm. discouragement SIO_001283 Rage is a feeling of intense anger that is associated with the Fight-or-flight response. rage SIO_000860 Humiliation is the abasement of pride, which creates mortification or leads to a state of being humbled or reduced to lowliness or submission. humiliation SIO_001281 The results section is a document section describing the main findings of the study. results section SIO_000200 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 SIO_000909 is measurement value of is a relation between a value and the entity that it is a measurement of. is measurement value of SIO_000215 A character is a language symbol used to construct words. character SIO_000108 is participant in is a relation that describes the participation of the subject in the (processual) object. is participant in a car is a participant in a car race; glucose is a participant in glycolysis SIO_000062 An OBO ontology is an ontology document as specified by the Open Biological Ontology community. OBO ontology SIO_000623 2 A social role is a role that is ascribed to individuals in a community. social role SIO_000676 left-handed helical quality is the quality in which a clockwise screwing motion moves the helix towards the observed along the line of sight along the helix's axis. left-handed helical SIO_001273 metadata is data that provides information about data. metadata SIO_001330 literature curation is the process of an agent selecting and extracting terms and phrases from a document. literature curation SIO_000998 A namespace label is a short name for a namespace. namespace label SIO_000237 character offset The ordinal position of a character in a sequence of characters. character position SIO_001056 An object is an entity that is wholly identifiable at any instant of time during which it exists. core object SIO_000776 a REST web service is a web service that provides functionality according to the Representational State Transfer (REST) specification. REST web service http://en.wikipedia.org/wiki/REST SIO_001190 chemical exposure is a process to expose one or more individuals to a chemical substance. chemical exposure SIO_001399 polonium atom CHEBI:33313 SIO_011069 A medical diagnosis (often simply termed diagnosis) refers to the process of attempting to determine or identify a possible disease or disorder. medical diagnosis SIO_001001 A textual entity is language entity that is manifested as a sequence of one or more distinct characters. textual entity SIO_000651 2 A web service invocation involves the execution of a web service. web service invocation SIO_001192 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 SIO_000444 is transcribed from SIO_010081 is translated into RNA is translated into Protein a relation between two information content entities in which one is translated into (a completely different kind of entity) another through some process. SIO_010082 Precursor mRNA (pre-mRNA) is a single strand of messenger ribonucleic acid (mRNA) that is synthesized from a DNA template throught transcription. pre-mRNA SIO_010097 A medical screening is a medical test or series used to detect or predict the presence of disease in individuals at risk for disease within a defined group, such as a population, family, or workforce medical screening SIO_001023 all of the time always indicates that the event occurs at all times. always SIO_001292 A local maximum stationary point is a point that has a higher value in some axis than adjacent points. local maximum stationary point SIO_000742 A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms. diagnosis SIO_001331 A quantity that extends in two dimensions. 2D extent quantity SIO_000044 A booklet is a document that lacks a named publisher or sponsoring institution. booklet SIO_000169 negative emotion is an emotion that does not feel good. negative emotion SIO_000832 chemical destruction is destruction of a chemical entity to its chemical constituents through one ormore chemical interactions or reactions. chemical destruction SIO_000592 A homonym is a word that sounds the same but has different meaning. homonym SIO_000126 has expression the story 'war of worlds' is expressed as every language edition of the book 'war of the worlds' SIO_000420 A list is any enumeration of a set of items. list SIO_000150 effective specification An action specification is a specification composed of a sequence of instructions to achieve some objective. action specification SIO_000091 protactinium atom CHEBI:33386 SIO_011105 A word is the smallest free form (an item that may be expressed in isolation with semantic or pragmatic content) in a language. word SIO_000114 An enzyme is a protein or protein complex that realizes its disposition to covalently modify some molecule during a chemical reaction. enzyme SIO_010343 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. SIO_001246 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 SIO_001075 A polyhedral skeleton is a collection of polygon edges. polyhedral skeleton SIO_000502 controlled variable extraneous 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. control variable SIO_001070 copper atom CHEBI:28694 SIO_011028 a protein isoform is a protein that is a structural variant (different sequence of amino acids and/or post-translational modifications) of another protein, but encoded by the same gene. protein isoform SIO_001445 A relation between two objects, in which the first object contains information that is used to produce the second object. encodes an open reading frame encodes a protein (it contains information that specifies the amino acid composition and topology) SIO_010078 A streamgraph is a multi-line stacked graph that yields the appearance of continuous y-values across the x-axis. streamgraph SIO_000908 A single displacement reaction where one atom is transferred out of one molecule and into another. single displacement reaction SIO_010514 modification modifying is the process by which an entity gains or loses parts, qualities, roles, dispositions, functions, etc, but maintains their identity through these changes. modifying SIO_000918 A polypeptide is an organic polymer composed of amino acid residues, typically of less than 50 amino acids in length. polypeptide SIO_010007 A right value axis is a value axis that is spatially positioned to the right of the plot area. right value axis SIO_000460 dysfunction is a capability to act in a manner that is abnormal or opposite to the object's typical function. dysfunction SIO_000354 rutherfordium atom CHEBI:33346 SIO_011075 fermium atom CHEBI:33394 SIO_011114 is role of is a relation between a role and the entity that it is a property of. is role of SIO_000227 A television program is a audiovisual media that is produced and broadcast using a television. television program SIO_000924 is cited by is a relation from an object that is referred to by way of example, authority or proof. is cited by SIO_000278 has property is a relation between an entity and the quality, capability or role that it and it alone bears. has property michel's hair has the quality of being brown in colour. SIO_000223 Speed is the rate of change of an object's position. speed SIO_001368 A t-statistic based increased differential gene expression is a differential gene expression ratio in which the t-statistic is greater than zero. t-statistic based increased differential gene expression SIO_001081 A model is a representation of some thing. model SIO_000510 an ordered list is a list in which items are sequentially ordered. ordered list SIO_001316 to inject is the capability to administer a substance into some object through its external barrier. to inject SIO_000372 a duplicate role is a comparative role that holds when one item is an exact copy of another in a specific set. duplicate role SIO_001416 physician A doctor role is the role of an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments. doctor role SIO_000713 A correspondence section is a document section that contains the details for contacting the corresponding author. correspondence section SIO_000194 double stranded nucleic acid is a molecular complex composed of two weakly connected deoxyribonucleic acids. double stranded DNA SIO_001173 selenium atom CHEBI:27568 SIO_011033 The telephone is a communications device that transmits and receives sounds, and are minimally composed of a microphone to speak into, a speaker'which reproduces the voice of the other person and a ringer which makes a sound to alert the owner when a call is coming in. telephone SIO_000927 bioinformatic data is data genereated or used for computer-based investigations of biological phenomena. bioinformatic data SIO_010065 A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes. immediately precedes SIO_000250 a is mutually related to b if and only if the realization of the relation of a necessarily causes the realization of a relation to b. is mutually related to SIO_000709 a work phone number is the number to connect to an phone at a place of work. work phone number SIO_001324 A polygon edge is a line segment joining two polygon vertices. polygon edge SIO_000501 is lesser than to is a comparison relation between two quantities in which the first has a value smaller than the second. is lesser than SIO_000735 A transitive, temporal relation in which one process precedes (has occured earlier than) another process. core precedes SIO_000248 comparison comparing is the process of examining a set of objects and determining their equality or inequality based on one or more features. comparing SIO_000745 2 chaoite is an allotrope of carbon that is slightly harder than graphite with a reflection colour of grey to white. chaoite SIO_010793 A diagnostic opinion is an opinion resulting from a medical diagnostic procedure. diagnostic opinion SIO_001003 A overlaps with B iff there is some C that is part of both A and B. [S][R] overlaps with SIO_000325 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. triangle SIO_000520 is model of is a relation between a model (an artifact) and the entity it purports to represent. is model of the architect builds a model that represents the building she envisions. SIO_000632 has input is a relation between a process and an entity, where the entity is present at the beginning of the process. core sadi has input SIO_000230 has quality is a relation between an entity and the quality that it bears. has quality SIO_000217 to bind to is the capability to physically interact with another object through a set of non-covalent interactions. to bind to SIO_000780 a medical intervention is a medical procedure to treat (to cure or alleviate) a health condition. medical intervention SIO_001398 area is a quantity that pertains to the extent of a two-dimensional surface or shape, or planar lamina, in the plane. area SIO_000045 A process that modulates the frequency, rate or extent of process involved in the destruction of a molecule. regulation of molecular degradation SIO_001129 A legend is a part of a figure that associates textual descriptions with symbols pertaining to plotted entities. legend The colored line segments and the adjacent textual descriptions in Graph 1 of http://tinyurl.com/opwnvm SIO_000468 min A minimal value is smallest value of an attribute for the entities in the defined set. minimal value SIO_001113 not started is the status of a process that is predicted to exist but has not yet begun. not started SIO_000963 reproducing is a process characterized by creation of an entity that is similar or exactly the same as the template from which it is derived. reproducing SIO_000919 ordered list A sequence is an ordered list of entities. Like a set, it contains members (also called elements, or terms). sequence 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. SIO_001118 A is subsequent version of B iff A is a variant of B and A derives from B. is subsequent version of SIO_000286 A primary title is a title that should be first used in describing some entity. primary title SIO_000470 ongoing is the status of a process that is not yet complete. ongoing SIO_000035 to conformationally activate is to modify the conformation of an entity in such a way that it becomes activated or functional. to conformationally activate SIO_010354 A protein complex is a molecular complex composed of at least two polypeptide chains. protein complex SIO_010497 1 A protein-disease association is an association between a protein and a disease. protein-disease association SIO_001439 A submolecular entity is a chemical entity that is a part of a molecule. submolecular entity SIO_010020 A computational entity is an information content entity operated on using some computational system. computational entity SIO_000602 homogeneous is a quality that describes the varied composition of an object. heterogeneous SIO_001091 to measure is the capability to obtain information about some entity by examining its attributes in relation to some reference metric. to measure SIO_000371 sick is the status of a living organism that is behaving at a sub-optimal level. sick SIO_000954 mass is the quality of the amount of substance. mass SIO_000279 a is causally related from b iff there is a causal chain of events from b to a core is causally related from SIO_000352 Frustration is an emotion that arises from the perceived resistance to the fulfillment of individual will. frustration SIO_000838 is equal to is a comparison relation between two quantities whose value are exactly the same. is equal to SIO_000738 moderate is a qualitative intensity value that is more intense than mild, but less intense than strong. moderate SIO_001214 subcellular entity SIO_001400 a salt is a heterogeneous substance that is coposed of positively charged ions (cations) and negatively charged ions (anions) held together by electrostatic forces. salt SIO_001446 A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. sample SIO_001050 A disulfide bond is a bond between two sulfur atoms. disulfide bond SIO_010502 is quality of is a relation between a quality and the entity that it is a property of. is quality of SIO_000218 remorse is an emotion of personal regret felt by a person after he or she has committed an act which they deem to be shameful, hurtful, or violent. remorse SIO_000862 a list item is an item in a list. list item SIO_001260 A database collumn is a column in a database table. database column SIO_000757 A multiple sequence alignment is a sequence alignment involving more than two sequences. multiple sequence alignment SIO_010067 movement is the process in which an object is spatially displaced. core movement SIO_000570 A start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon is almost always preceded by an untranslated region 5' UTR. start codon SIO_010447 bismuth atom CHEBI:33301 SIO_011068 affects SIO_001158 A chapter is a document section of a book or thesis. chapter SIO_000107 satisfaction qualifier SIO_001308 consensus is an acceptable resolution, one that can be supported, even if not the preferred outcome for each individual. consensus SIO_001198 helicity is the quality of being helical helicity SIO_001271 A figure part is a part of a figure. figure part SIO_000448 A temporal relation in which an entity mainstains identity from one state to another. is immediately transformed from SIO_000658 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 SIO_000528 to lose a covalent bond is the capability of a chemical entity to have bonds removed. to lose a covalent bond SIO_001104 worry is the emotion characterized by concer over a real or imaginary issue. worry SIO_000873 germanium atom CHEBI:30441 SIO_011031 rubidium atom CHEBI:33322 SIO_011036 americium atom CHEBI:33389 SIO_011109 homogeneous is a quality that describes the uniform composition of an object. homogeneous SIO_001090 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 SIO_000458 An author section is a document section that lists the contributing authors. author section SIO_000191 Hostility is the intense negative emotion of being in conflict or opposition to someone or something. hostility SIO_000844 envy is an emotion that occurs when a person lacks another's (perceived) superior quality, achievement or possession and wishes that the other lacked it. envy SIO_000834 A processual role is a role that can only be realized in a process. processual role SIO_000677 active movement is the process in which an object is spatially displaced using some chemical energy. active movement SIO_000574 nitrogen atom CHEBI:25555 SIO_011006 exists at is a relation between an entity and a time measurement. core exists at SIO_000687 A consonant is a verbal entity of language that is articulated with complete or partial closure of the vocal tract. consonant SIO_000978 biological reproduction is the biological process by which one or more biological organisms are produced from their "parents". biological reproduction SIO_000587 to conformationally inhibit is to modify the conformation of an entity in such a way that it functionally is reduced or inhibited. to conformationally inhibit SIO_010355 to be passively interacted with is the capability of an object to be observed. to be passively interacted with SIO_000694 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 SIO_000197 A chemical interaction is a biochemical process in which chemical entities interact through some set of attractive forces. biopax:Interaction chemical interaction SIO_010013 An atom is composed of a core of protons and/or neutrons which may be surrounded by a cloud of electrons. atom SIO_010044 A single arrowed line is directed line in which the endpoint is tangentially part of a triangle that bisects the line. single arrowed line segment SIO_000523 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 SIO_000811 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 SIO_000463 A secretary role is the role of an individual that performs administrative tasks to support one or more individuals of the same organization. secretary role SIO_000727 regulation of capability is the regulation of the ability of one party by another. regulation of capability SIO_000610 a is mutual disposition of b if and only if the realization of the disposition a necessarily causes the realization of the disposition b. is mutual disposition of SIO_000697 has proper part is an antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part. has proper part a car has an engine as a proper part; a car has a piston as a proper part; SIO_000053 Annoyance is an unpleasant emtion that is characterized by a abnormal or excessive sensitivity to some external stimulus. annoyance SIO_000814 A vertical bar graph is a bar graph in which the rectangular bars are vertically oriented in space. vertical bar graph Graph 4,5 in http://tinyurl.com/opwnvm SIO_000445 A quantity that extends in three dimensions. 3D extent quantity SIO_000048 a SOAP web service is a web service that implements Simple Object Access Protocol (SOAP). SOAP web service http://en.wikipedia.org/wiki/SOAP SIO_001191 A day is a period of 24 hours. day SIO_000430 A binary compound is a mereological maximum sum of two kinds of weakly connected entities. binary compound SIO_010674 text quality is the quality of a textual entity. text quality SIO_001033 A genome is a collection of nucleic acids. genome SIO_000984 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. valid argument SIO_000266 A population is all the organisms that both belong to the same group or species and live in the same geographical area. population SIO_001061 data transformation is the process of applying an algorithmic procedure to some input data and producing some output data. data transformation SIO_000594 carbon nanofoam is an allotrope of carbon that consists of a low-density cluster-assembly of carbon atoms strung together in a loose three-dimensional web. Each cluster is about 6 nanometers wide and consists of about 4000 carbon atoms linked in graphite-like sheets that are given negative curvature by the inclusion of heptagons among the regular hexagonal pattern. carbon nanofoam SIO_010792 to ionize is the capability to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. to ionize SIO_000350 medical data is data of interest to medicine. medical data SIO_010298 has realizable property SIO_000644 A software entity is a computational entity that can be interpreted by or directly executed by a processing unit. software entity SIO_000097 line chart A line graph is a statistical graph in which lines contains the evaluation of functions or individual points connected by line segments. line graph Graph 1 in http://tinyurl.com/opwnvm SIO_000442 is boundary of is a mereological relation between a boundary located at the periphery of a whole. is boundary of SIO_000096 increased regulation leads to an increase in the number of target objects of a specified type. increased object production from increased regulation SIO_001146 the capability to maintain information such that it can be retrieved in the future. to maintain information SIO_001363 A regulatory authority is an organization responsible for exercising regulatory or supervisory capacity in some area of human activity. regulatory authority SIO_000619 orientation is an angle between the bearer and an axis, or the angle between the bearer and another object. orientation SIO_000057 x is correlated with y when x holds a statistical relationship with y is correlated with SIO_001404 A bottom value axis is a value axis that is spatially positioned to the bottom of the plot area. bottom value axis SIO_000903 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 SIO_000464 An enantiomer is a stereoisomer that is a mirror image of its isomer. enantiomer SIO_010777 Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane latitude SIO_000319 An amino acid polymer submolecule is a submolecule of an amino acid polymer. amino acid polymer submolecule SIO_010471 to cause disease is the capability to materially change a biological object in that it functions abnormally. to cause disease SIO_000547 A molecular complex is a chemical complex composed of at least one weakly interacting molecule. molecular complex SIO_010506 The quality of having a charge. charged SIO_000805 shape is the quality of a bearer that relates to its spatial extent. shape SIO_000055 A heterocyclic ring is a ring containing a hetero atom. heterocyclic ring SIO_010782 A specification for spatial location is an effective specification towards representation spatial position or spatial data. spatial specification SIO_000317 A is broader than B (t) iff for A is broader than B. http://www.w3.org/2004/02/skos/core#narrowerTransitive is broader than (t) SIO_000422 A predicted gene is a gene that was identified through computational method but has not been experimentally validated. predicted gene SIO_000987 A coenzyme role of a chemical entity that is covalently bonded to the enzyme. prosthetic group role SIO_000801 A database key is an informational entity whose value is constructed from one or more database columns. database key SIO_000762 cobalt atom CHEBI:27638 SIO_011026 A catalyst is a molecule that has the capability to reduce the activation energy of a reaction and hence increase the overall rate of reaction. catalyst SIO_010344 is opposite to is a relation between two entities in which one is diametrically opposed to the other. is opposite to hot is the opposite of cold; left is opposite of right SIO_000496 yttrium atom CHEBI:33331 SIO_011038 A movement equation describes the displacement of an object in space over time. movement equation SIO_000566 A scaled value axis is a value axis in which the value range was subject to a mathematic transformation. scaled value axis SIO_000461 A category is a class of entities having particular shared characteristics. category SIO_000137 to ingest is the capability to take into the body by the mouth for digestion or absorption. to ingest SIO_001105 passive transport is the movement of a substance across a membrane and does not require chemical energy. passive transport SIO_000562 Embarrassment is the emotion of intense discomfort with oneself, experienced upon having a socially unacceptable act or condition witnessed by or revealed to other. embarassment SIO_000833 francium atom CHEBI:33323 SIO_011072 A justification is a proposition that defends, explains or excuses some argument. justification SIO_000683 scRNA A small cytoplasmic RNA (scRNA) molecule is a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins. small cytoplasmic RNA (scRNA) SIO_001231 to compare is the capability to examine in order to note the similarities or differences among a set of objects. to compare SIO_000723 angst is the intense feeling of apprehension, anxiety or inner turmoil. angst SIO_000813 is identical to is a relation between two objects that are conceptually the same notwithstanding provenance or other non-intrinsic attributes. is identical to SIO_001242 tin atom CHEBI:27007 SIO_011049 depressed depression is an unpleasant emotion linked to aversion to activity that can affect a person's thoughts, behavior, feelings and physical well-being. Depressed individuals may feel sad, anxious, empty, hopeless, worried, helpless, worthless, guilty, irritable, or restless. depression SIO_000824 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 SIO_001018 contentment is an emotion characterized by acknowledgement and satisfaction of the current state of affairs. contentment SIO_000822 A diary is a document which describes day-to-day experiences. diary SIO_000170 A revision number is a version of a software in which bugs have been fixed from a prior version. revision number SIO_001032 A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation. increased molecular production from increased regulation SIO_001203 vertical axis A y-axis is a Cartesian coordinate axis that is spatially oriented perpendicular to the x-axis. y-axis SIO_000453 is part of is a transitive, reflexive and anti-symmetric mereological relation between a whole and itself or a part and its whole. OBO_REL:part_of core is part of SIO_000068 A role is a realizable entity that describes behaviours, rights and obligations of an entity in some particular circumstance. core role SIO_000016 roentgenium atom CHEBI:33368 SIO_011082 is output of is a relation between an entity and a process, where the entity is present at the end of the process. sadi is output of glucose-6-phosphate and ADP are outputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. SIO_000232 sulfur atom CHEBI:26833 SIO_011015 has function is the relation between an entity and a function that is ascribed to it. has function SIO_000225 A tissue is a mereologically maximal collection of cells that together perform some function. tissue SIO_010002 measured at is a relation between a measurement value and the time measurement. core measured at SIO_000793 realizes is a relation between a process and a realizable entity (role, function, disposition). core realizes SIO_000355 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 SIO_001447 is affected by SIO_001159 regulation of a process duration is a process that modulates the duration of another process relative to some reference process. regulation of process duration SIO_001136 to disassociate is to cease or break association with some thing. to disassociate SIO_000700 agreement quality is a quality that exhibits the degree of consensus for some set of assertions. agreement quality SIO_000965 A is prior version of B iff A is a variant of B and B derives from A. is prior version of SIO_000274 'is data item in' is a relation between an entity that is described or referenced in a dataset. core is data item in SIO_001278 is unique identifier for is a relation between an identifier and an entity that it uniquely identifies is unique identifier for SIO_000674 An RDFS ontology is an ontology that conforms to the syntax and semantics of the Resource Description Framework Schema (RDFS). RDFS ontology SIO_000622 A country is a region legally identified as a distinct entity in political geography. country SIO_000664 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. spherical coordinate system SIO_000330 lawrencium atom CHEBI:33397 SIO_011117 drug-pathway association a chemical-pathway association is an association between a chemical and a pathway. chemical-pathway association SIO_001250 A vocabulary is a collection of terms. vocabulary SIO_001080 1 A transitive temporal relation in which an entity mainstains identity from one state to another. is transformed from SIO_000657 A ligand is a molecule that is part of a complex by weakly interacting with another molecule. ligand SIO_010432 suspended is the status of a process that is no longer progressing towards completion. suspended SIO_000995 A software module is software composed of a collection of software methods. software module SIO_000099 photo A photograph is an image created by light falling on a light-sensitive surface. photograph SIO_000082 scandium atom CHEBI:33330 SIO_011020 A dentist role is the role of an individual that that specializes in the diagnosis, prevention, and treatment of diseases and conditions of the oral cavity. dentist role SIO_000717 ununhexium atom SIO_011087 californium atom CHEBI:33392 SIO_011112 A ring is a submolecule with a circular topology. ring SIO_010780 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 SIO_001043 A percentile (or a centile) is a quantile that divides the given probability distribution, or sample, into 100 equal-sized intervals. percentile SIO_001415 A unicellular organism is a organism that is composed of a single cell. unicellular organism SIO_010376 A is generically related with B iff A is an abstract entity or an information content entity and B is a information content entity or a physical entity, respectively. is generically related with SIO_000425 indium atom CHEBI:30430 SIO_011048 to passively interact with is the capability to interact with another entity in a way that does not require physical contact. to passively interact with SIO_000639 fullerene is a carbon allotrope which take the form of a hollow sphere, ellipsoid, or tube. fullerene SIO_010789 A biological entity is a heterogeneous substance that contains genomic material or is the product of a biological process. chemical- biological entity SIO_010046 silicon atom CHEBI:27573 SIO_011013 to be recorded is the capability of an object to be observed in such a way that information about it can be transcribed in a specified format on some physical medium. to be recorded SIO_000695 The role of an organism in providing resources to maintain the survival and/or reproduction of another organism. host role SIO_000882 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 SIO_001373 A chemical identifier is an identifier for a chemical entity chemical identifier SIO_000728 refers to is a relation between one entity and the entity that it makes reference to. core nlp+ refers to SIO_000628 An article is a publication that is stand-alone section of a larger work. article SIO_000154 hemizygous is the quality of a biological organism in which, based on the ploidy of the organism, there is half the number of alleles than normal at a given locus. hemizygous SIO_001266 A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation. decreased molecular degradation from increased regulation SIO_001202 is greater than to is a comparison relation between two quantities in which the first has a value smaller or equal to the second. is lesser than or equal to SIO_000733 A conference proceedings is a book composed of papers presented at a conference. conference proceedings SIO_000157 A vector line is a line which that is bounded by a startpoint and extends outwards along one dimension. vector line SIO_000540 sodium atom CHEBI:26708 SIO_011010 has capability is a relation between an entity and the capability that it bears. has capability SIO has the capability to semantically integrate data. SIO_000586 A biopolymer is an organic polymer that are typically produced by the cells of living organisms. biopolymer SIO_000092 http://www.w3.org/2004/02/skos/core#closeMatch is close match to SIO_000490 A manual is a document that instructs on the usage of a device. manual SIO_000161 clinical laboratory test A diagnostic test is a procedure performed to confirm, or determine the presence of disease in an individual suspected of having the disease, usually following the report of symptoms, or based on the results of other medical tests. diagnostic test SIO_001022 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 Graphs 6,7 in http://tinyurl.com/opwnvm SIO_000446 An experimentally validated gene is a gene whose existence has been demonstrated through experimental methods. validated gene SIO_000991 width is the shorter dimensional extent perpendicular to a 2D projection of the object. width SIO_000042 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 SIO_001162 is modelled by SIO_000633 An allele is one of a set of sequence variants of a gene. allele SIO_010277 has first part is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. has first part SIO_000971 terbium atom CHEBI:33376 SIO_011097 has frequency is a relation that specifies the occurence of an object or event has frequency SIO_000900 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 SIO_000104 1 homozygous is the quality of a biological organism in which there are two different alleles at a given locus. heterozygous SIO_001265 A z cartesian coordinate is the coordinate of an object onto the z-axis of a cartesian coordinate system. z cartesian coordinate SIO_000402 A diastereomer is a stereoisomer that is not a mirror image of its isomer. diastereomer SIO_010776 is reference for is a relation between a document that provides information about an entity. is referenced by SIO_000252 A rectangle is a quadrilateral in which one pair of line segments are parallel and the other pair are perpendicular to the first pair. rectangle SIO_000518 Hysteria is an unmanageable emotion. hysteria SIO_000846 is weakly interacting with is a symmetric relation between two molecular entities (or any part thereof) that are interacting through some weak force (van der waals, hydrogen bonds, electrostatic interactions) is weakly interacting with (transitive) SIO_000293 technetium atom CHEBI:33353 SIO_011042 example a middle name is a name assigned to an individual that is not the first or last name. middle name SIO_001317 An equation is a mathematical statement that asserts the equality of two expressions. equation SIO_000368 A is match to B iff A and B are terms with similar (related, broad, close, exact) meanings http://www.w3.org/2004/02/skos/core#relatedMatch is match to SIO_000482 An introduction section is a document section that generally provides background, motivation and goals of the work. introduction section SIO_000196 a gene-disease association that is linked with some genomic alteration gene-disease association linked with genomic alterations SIO_001350 A tertiary structure descriptor describes 3D topological patterns in a biopolymer. tertiary structure descriptor SIO_010023 arsenic atom CHEBI:27563 SIO_011032 A medical history is a record of the events of a recipient of medical care. medical history SIO_010673 is comparable to is a relation between two entities that share at least one feature whose value can be compared. core is comparable to SIO_000736 A matrix chart summarizes a multidimensional data set in a grid. matrix chart SIO_000930 A closed interval is an interval that includes its endpoints, and is denoted with square brackets. closed interval [0,1] is a closed interval that is greater than or equal to 0 and less than or equal to 1. SIO_001249 cellular quality is the quality of a cell cellular quality SIO_000476 An apartment number is the number assigned to identify an apartment in a building of apartments. apartment number SIO_000768 A nucleic acid is an organic polymer composed of a sequence of nucleotide residues. nucleic acid SIO_010008 to disassemble is to physically separate the parts of an object. to disassemble SIO_000698 a tensor is a n-dimensional array. tensor SIO_001429 An attribute is a characteristic of some entity. core attribute SIO_000614 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 SIO_001119 Metabolism is the set of chemical processes that occur within a living organism in order to maintain life. metabolism SIO_010308 radon atom CHEBI:33314 SIO_011071 to serve as a template for RNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which an RNA molecule may be produced. to serve as a template for RNA synthesis SIO_010090 gadolinium atom CHEBI:33375 SIO_011096 A nucleic acid part is a component of a nucleic acid. nucleic acid part SIO_010335 aggregate of carbon nanorods is an allotrope of carbon considered to be the least compressible material known, as measured by its isothermal bulk modulus; aggregated diamond nanorods have a modulus of 491 gigapascals (GPa), while a conventional diamond has a modulus of 442 GPa. ADNRs are also 0.3% denser than regular diamond. aggregated carbon nanorods SIO_010790 A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. chemical reaction SIO_010345 An administrative role is the role of an individual that performs administrative tasks for some organization. administrative role SIO_000726 has product is a relation between an process and an entity, where a new entity exists at the end of the process. sadi has product SIO_000312 A peer reviewed article is an article that has undergone peer-review and deemed acceptable for publication. peer reviewed article SIO_001029 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. matrix SIO_001433 A community is a sizeable social unit that shares common values. community SIO_001064 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 SIO_000911 has component part is a relation between a whole and a component part where the component is instrinsic to the whole, and loss of the part would change the kind that it is. has component part a human has blood as a component part SIO_000369 nobelium atom CHEBI:33396 SIO_011116 A displacement reaction is an inorganic reaction in which a elementary substance displaces and sets free a constituent atom from a molecule. displacement reaction SIO_010512 increased duration of process from increased regulation is a process in which the duration of the target process is increased as a result of increased regulation. increased duration of process from increased regulation SIO_001137 A conclusion is a proposition which is reached after considering the evidence, arguments or premises. conclusion SIO_000262 to characterize is the capability to classify the attributes or features of an entity against a reference classification. to characterize SIO_001220 A gene-disease association in which the disease phenotype is associated with post-translational modifications in the protein product. gene-disease association linked with post-translational modification methylation or phosphorylation of protein product SIO_001124 A molecular identifier is an identifier for a molecular entity. molecular identifier SIO_000732 database record A database entry is a single, implicitly structured data item in a table. database entry SIO_000756 A solid-state drive (SSD) is a data storage device that uses solid-state memory to store persistent data. solid state hard drive SIO_000597 is positionally after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity. is positionally after SIO_000211 is translated from SIO_010083 A gene-variant disease association in which a somatic mutation in the gene modifies the clinical presentation of the disease, and it may not be passed on to offspring. gene-disease association linked with somatic modifying mutation SIO_001346 A textual chart is a chart containing text. textual chart SIO_000937 process status is a process quality that describes the state of a process. process status SIO_000033 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. web service SIO_000140 magnesium atom CHEBI:25107 SIO_011011 rank 1 tensor a vector is a rank 1 tensor that is described by n-dimension of scalars. vector SIO_001430 iridium atom CHEBI:49666 SIO_011062 A territory is a non-sovereign geographic region. territory SIO_000663 aborted is a process status in which a started process will not complete as intended. aborted SIO_000997 is frequency of is a relation between a temporal unit and an object or event is frequency of SIO_000901 A quantity that extends in single dimension. 1D extent quantity SIO_000038 diagram A figure is a graphical entity which consists of a visual (n-dimentional) arrangement of information entities. figure SIO_000080 cadmium atom CHEBI:22977 SIO_011047 the capability to retrieve a (digitial/physical/mental) object from a location. to retrieve SIO_001358 A dendrogram is a tree diagram used to illustrate the arrangement of the clusters produced by hierarchical clustering. dendrogram SIO_000948 age is the length of time that a person has lived or a thing has existed. age SIO_001013 A dimensional quantity is a quantity that has an associated unit. dimensional quantity SIO_000258 interest is the emotion of wanting to know or learn about something or someone. interest SIO_000848 is version of is a relation that holds between any two versions in which one is a subsequent or alternate version of (through a branch). is version of SIO_000497 A software version label is a version label for a piece of software. software version label major.minor[.build[.revision]] SIO_000654 to be modified is the capability to be actively interacted with in such a way that it leads to a physical reconfiguration. to be modified SIO_010364 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 SIO_001016 to be a part of is the capability to be assembled into a larger structure that persists in time. to be a part of SIO_000689 An interval is a set of real numbers that includes all numbers between any two numbers in the set. interval SIO_000944 A strain is a genetic variant or kind of microorganism. strain SIO_010055 A concept is term that refers to a generalization of a set of attributes or entities. concept SIO_000326 snRNA A small nuclear RNA (snRNA) is a small RNA molecule that is located in the nucleus of a cell. small nuclear RNA (snRNA) SIO_001233 An amino acid residue is a submolecule of an amino acid that is part of a larger molecule. amino acid residue SIO_010074 evolving is a process that elicits change across successive generations in the inherited characteristics of biological populations. evolving SIO_000703 A linear position is the position of some object against a linear positioning system. linear position SIO_000788 A messenger RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns. messenger RNA SIO_010099 A splice site is a region required for the excision of an intron and connection to another exon. splice site SIO_010451 user account allows a user to authenticate to system services and be granted authorization to access them. user account SIO_001165 has phenotype is a relation between an object and an observable/measurable characteristic. has phenotype SIO_001279 to provide is the capability to make available some object to another that requires it. to provide SIO_000397 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 SIO_001443 paternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the paternal line. paternally transmitted SIO_001270 a replicate is an object that is a facsimile, reproduction, or copy of another item. replicate SIO_001418 scientific data is data obtained from some scientific procedure. scientific data SIO_000472 An ordinary differential equation (ODE) is a differential equation in which the unknown function (also known as the dependent variable) is a function of a single independent variable. ordinary differential equation SIO_000567 A central tendency measure is a central value or a typical value for a probability distribution. centrality measure SIO_001108 is capability of is a relation between a capability and the entity that bears it. is capability of SIO_000646 A nucleic acid sequence is a symbolic sequence of nucleic acid residues in a nucleic acid. nucleic acid sequence SIO_010016 The quality of being polar or not polar. polar quality SIO_001045 A hypernym is a term with a broader meaning. hypernym SIO_000124 A deductive argument is an argument that asserts that the truth of the conclusion is a logical consequence of the premises. deductive argument SIO_000263 polygonal chain, polygonal curve, polygonal path, piecewise linear curve A polyline is a connected sequence of line segments. polyline SIO_000545 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 SIO_001421 A quality is an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary. core quality SIO_000005 A 'is surrounded by' B iff the A 'is contained by' B and A 'is adjacent to' B or A 'is directly connected to' B. is surrounded by SIO_000323 A biological organisn is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). organism SIO_010000 to inhibit to increase the activation energy is to require a larger amount of energy in order to form or break a chemical bond. to increase the activation energy SIO_000550 a little quantifier SIO_001304 increased regulation leads to an decrease in the consumption of an object of specified type. decreased object consumption from increased regulation SIO_001149 very poor quality SIO_001294 The increase of regulation leads to a decreased occurence of processes of the target process type. decreased frequency of process from increased regulation SIO_001134 is covalently connected to is a relation between an atom and another atom. is covalently connected to SIO_000334 A biochemical pathway specifies a series of biochemical modifications and transformations towards achieving some biological outcome. biochemical pathway SIO_010525 guilty Guilt is the emotion borne from feeling responsible for the commission of an offense and arises out of public humiliation. guilt SIO_000841 maintenance of spatial extent of process is a regulation of a process' spatial extent within some specified parameter. maintenance of spatial extent of process SIO_001142 A quaternary structure descriptor describes topological patterns in a multi-unit biopolymer complex. quaternary structure SIO_010024 an ingredient is a chemical substance that forms part of a mixture. ingredient SIO_001428 A horizontal line is a line that is positionally oriented with the horizon. horizontal line SIO_000525 A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression. miRNA microRNA (miRNA) SIO_001397 A liquid solution is a heterogeneous substance in a liquid state. liquid solution SIO_001084 An occupational role is a social role that pertains to an organizational structure. occupational role SIO_000706 A relation between an information content entity and a product that it (directly/indirectly) specifies specifies SIO_000338 Aninactive ingredient is a molecular entity that does not exhibit biological activity. inactive ingredient SIO_010087 A Cartesian coordinate is the signed distance of a point to some referent line. cartesian coordinate SIO_000072 A city is a relatively large and permanent settlement. city SIO_000665 to examine is the capability to make detailed observation. to examine SIO_000724 peer-reviewed is the quality of a textual entity that has been examined and commented by a peer expert reviewer. peer-reviewed SIO_001035 boron atom CHEBI:27560 SIO_011000 An environment is a geographic region that hosts certain processes or objects. environment SIO_000955 A biological fluid is a fluid of biological origin. biological fluid SIO_010051 A bibliography section is a document section that is composed of a list of references used in the development of the work. bibliography section SIO_000192 An issue is a single instance of a periodically published journal, magazine, or newspaper. issue SIO_001169 disordered is a structural quality in which the parts of an object are non-rigid. disordered SIO_000758 ethnicity is the biological quality of membership in a social group based on a common heritage. ethnicity SIO_001014 is regulated by SIO_001155 A deoxyribonucleic acid primer is a deoxyribonucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation. deoxyribonucleic acid primer SIO_010093 A differential gene expression ratio is the ratio of gene expression values from a test sample compared to a control sample. differential gene expression ratio SIO_001078 affection is an emotion characterized with a feeling or type of love for another living thing. affection SIO_000812 is numerically comparable to is a comparison relation between two quantities whose datatype value can be compared. is numerically comparable to SIO_000737 A start date is a time instant pertaining to the date of the beginning of a process. start date SIO_000031 A deoxyribonucleotide residue is a part of a molecule that derives from a deoxyribonucleotide. deoxyribonucleotide residue SIO_010336 An intervention study has the objective of improving the condition of an individual or a group of individuals, and demonstrates the magnitude of that capability by comparing it to a control group. intervention study SIO_001048 none of the time never refers to in none of the occasions. never SIO_001289 hermaphrodite is a biological sex of an individual with both male and female sexual organs. PATO:0001827 hermaphrodite SIO_000784 A start point is a terminal point which is the first of an ordered pair of points. start point SIO_000509 communication communicating is the process of conveying information through the exchange of thoughts, messages, or information, as by speech, visuals, signals, writing, or behaviour. communicating SIO_000969 An mRNA splice variant is an mRNA molecule that varies from another mRNA molecule of the same gene origin but having a different final sequence due to differences in its assembly from splice sites. mRNA splice variant SIO_010098 interacts with A is connected to B iff there exists a fiat, material or temporal path between A and B. [S][T] core nlp is connected to SIO_000203 An independent variable is a variable that may take on different values independent of other elements in a system. independent variable SIO_000920 to be combined is the capability to be modified in a way that the object is merged with another object to form a new object or substance. to be combined SIO_010367 A molecular structure file is a file that contains a description of molecular structure. molecular structure file SIO_011120 to store is the capability to place an object into a medium in which it can be retrieved in the future. to store SIO_001361 A test role is the role of an individual that is a participant in the study and is the target of the intervention. test role SIO_010430 An acid-base reaction is a chemical reaction between an acid and a base. acid-base reaction SIO_010507 written is the quality of information that is embodied as visual glyphs in some material form. written SIO_001039 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 1.62 2026-10-12 sio.owl has direct part is a relation to specify a part at a particular level of granularity has direct part a car has an engine as a direct part SIO_000273 A geolegal region is a geographic region which has causal powers confered by a legal entity. geolegal region The 50 kph zones in Ottawa; the geographic region occupied by France. SIO_000413 A 2D cartesian point is a point whose position is specified along two dimensions using Cartesian coordinates. 2D cartesian point SIO_000437 mixture A chemical substance is a chemical entity composed of two or more weakly (non-covalently) interacting chemical entities. chemical substance CHEMINF:440533 SIO_011126 antiport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in opposite directions simultaneously. antiport enabled secondary active transport SIO_000580 A sequence profile is provides the preference for a character at each position of an abstracted sequence. sequence profile SIO_010531 is annotated with was annotated with has annotation is a relation between an entity and some textual anntotation. has annotation document x is annotated with the keywords 'ontology','semantic web' SIO_000255 has time boundary SIO_000679 A realizable entity is an attribute that is exhibited under some condition and is realized in some process. core realizable entity SIO_000340 A gene-disease association in which the disease phenotype is associated with an altered expression of the gene. gene-disease association linked with altered gene expression SIO_001123 A student advisor role is the role of an individual employed at an academic organization that is involved in advising students. student advisor role SIO_000876 A formal specification is a mathematical description of software or hardware that may be used to develop an implementation. formal specification SIO_000621 A carbohydrate residue is a part of a molecule that was derived from a monosaccharide molecule. carbohydrate residue SIO_010334 amorphous carbon is an allotrope of carbon that does not have any crystalline structure. As with all glassy materials, some short-range order can be observed, but there is no long-range pattern of atomic positions. amorphous carbon SIO_010791 satisfies is a relation between an entity and the specification or objective that it conforms to. satisfies SIO_000362 A process quality is quality that is associated with a process. process quality SIO_000027 virtual is the quality of an entity that exists only in a virtual setting such as a simulation or game environment. virtual SIO_000962 A chemical reaction pathway specifies a series of chemical reactions towards producing some chemical product. chemical reaction pathway SIO_010526 A street name is the token given to identify a particular street. street name SIO_000766 to interact and to be interacted with is a mutual disposition of interacting objects. to interact and to be interacted with SIO_001102 The rate of change of an object's position and the direction of that change velocity SIO_001369 purpose is the reason for which something is done or created or for which something exists. purpose SIO_000359 none quantifier SIO_001303 is product of is a relation between an entity and a process, where the entity is present at the end of the process as a result of a transformation in the process target. sadi is product of glucose-6-phosphate is the product of the hexokinase-mediated conversion of glucose to glucose-6-phosphate. SIO_000311 has data item is a relation between a dataset and any described / referrenced entity. core has data item SIO_001277 An ionic compound is a mereological maximal sum of weakly connected paired positive and negative ions. ionic compound SIO_010784 has start time SIO_000680 An operon is a collection of contiguous genes transcribed as a single (polycistronic) mRNA. SO:0000178 operon SIO_010084 The role of a chemical participant that serves to increase the rate of reaction by lowering the activiation energy. catalytic role SIO_000796 A nucleotide residue is a part of a molecule that derives from a nucleotide. nucleotide residue SIO_010075 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 SIO_000505 A parameter is variable whose value changes the characteristics of a system or a function. parameter SIO_000144 despair is depression, hopelessness or lack of hope. despair SIO_000826 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. polar coordinate system SIO_000327 A positive emotion is an emotion that feels good. positive emotion SIO_000831 pleasure is an emotion of happy satisfaction and enjoyment. pleasure SIO_000858 A chemical-protein association is an association between a chemical and a protein. chemical-protein association SIO_001440 a genomic sequence variant is part of a nucleic acid which is compositionally different than another reference genomic part. variant genomic sequence variant SIO_001381 A is narrower than B (t) iff for A is narrower than B. http://www.w3.org/2004/02/skos/core#broaderTransitive is narrower than (t) SIO_000424 neither satisfied or dissatisfied qualifier SIO_001311 to be covalently modified is the capability of a chemical entity to have bonds added or removed to be covalently modified SIO_010366 A chemical substance role is a chemical entity role held by a chemical substance. chemical substance role SIO_000888 Implication is a logical operator that holds between a set T of propositions and a proposition B, when every model (or interpretation or valuation) of T is also a model of B. implies (->) SIO_000220 A union is a list of all of the values of an attribute for the entities in the defined set. union SIO_001116 A polar solvent is a solvent that exhibits a polar quality. polar solvent SIO_010459 height is the one dimensional extent along the vertical projection of a 3D object from a base plane of reference. height SIO_000040 diamond is a carbon allotrope in which each carbon atom in diamond is covalently bonded to four other carbons in a tetrahedron. These tetrahedrons together form a 3-dimensional network of puckered six-membered rings of atoms. diamond SIO_010787 birthing is the process by which a biological organism is brought into existence. birthing SIO_000582 oligosaccharide saccharide a carbohydrate is an organic molecule composed of two or more monosaccharides. carbohydrate SIO_001395 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 SIO_001347 product SIO_010363 A standard is a socially-agreed upon specification. standard SIO_000618 A synonym is a word with the same or very similar meanings. synonym SIO_000122 an ordered list of authors. author list SIO_001315 A student is an individual who is attends an educational institution. student SIO_000405 A polygon vertex is a terminal point at which two polygon edges meet and are part of a polygon. polygon vertex SIO_000500 nuclear magnetic resonance device A nuclear magnetic resonance (NMR) device is a device that applies a magnetic field to perturb nuclei with an odd number of protons and/or of neutrons in order to hav them absort and re-emit electromagnetic radiation. http://purl.obolibrary.org/obo/OBI_0000566 nmr device SIO_001240 is created by is creator of is a relation between a creator and an entity.. is creator of SIO_000365 describes is a relation between one entity and another entity that it provides a description (detailed account of). core describes SIO_000563 regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is maintained at a steady level. maintenance of level of object consumption SIO_001153 a relation between two entities which indicates their common ancestry. is homologous to SIO_010302 reviewed is the quality of a textual entity that has been examined and commented on by another party. reviewed SIO_001034 to move to translocate is the capability to displace oneself from one location to another. to translocate SIO_000719 quality descriptor SIO_001293 A variable is a value that may change within the scope of a given problem or set of operations. variable SIO_000367 A standard deviation (represented by the symbol σ) is the quantity of variation from the average (mean, or expected value). standard deviation SIO_000770 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. argument SIO_000259 has parameter is a relation between a process and an information content entity which modulates the behaviour of some participant. sadi has parameter SIO_000552 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 SIO_001168 A periodical is a publication that appears on a regular schedule. http://purl.org/ontology/bibo/Periodical periodical SIO_000162 chart A statistical graph is a figure that displays the relationship among numeric data and/or mathematical functions. statistical graph SIO_000083 regulation of information the regulation or maintenance of information information maintenance SIO_001366 A free radical addition is a non-polar addition reaction involving free radicals. free radical addition SIO_010521 irritable irritability is the negative emotion of quick excitability to annoyance, impatience, or anger. irritability SIO_001286 is first part of is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. is first part of SIO_000970 An isomerization reaction is a chemical reaction in which a molecule is converted into its isomer. isomerization reaction SIO_010517 a vector space is a set of vectors. vector space SIO_001432 is trigger for SIO_000636 A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation. increased molecular production from decreased regulation SIO_001205 transporting is a process in which one object physically moves another object from one location to another. transporting SIO_000575 toxic is the quality of a substance imparing the normal functioning of a system. toxic SIO_001009 is directly after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity, and the entities are adjacent to one another. is directly after SIO_000241 pH is a measure of the activity of the (solvated) hydrogen ion. pH is defined as the decimal logarithm of the reciprocal of the hydrogen ion activity, aH+, in a solution. pH SIO_001089 to produce is the capability to create new objects to produce SIO_001106 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. cylindrical coordinate system SIO_000329 is realizable property of SIO_000643 maintenance of quantity of object production is a regulation of object production in which the number of objects produced is held more or less constant. maintenance of quantity of object production SIO_001152 A premise is a proposition of an argument from which the conclusion is drawn. premise SIO_000261 A toxin role is a toxic role of a chemical substance that is poisonous and is produced by an organism. toxin role SIO_000890 OR is a logical operator that results in true whenever one or more of its operands are true. disjunction (or) SIO_000280 A protein coding sequence (CDS) is the region of DNA that is translated to form proteins. The CDS refers to those nucleotides (concatenated exons) that can be divided into codons which are actually translated into amino acids by the ribosomal translation machinery. CDS coding sequence protein coding sequence SIO_001390 A material entity is a physical entity that is spatially extended, exists as a whole at any point in time and has mass. core material entity SIO_000004 A chemical role is a processual role held by a chemical entity. chemical entity role SIO_000795 A chemical-disease association is an association between a chemical and a disease. chemical-disease association SIO_000993 An edited publication is a publication that has been examined and potentially changed by an editor. edited publication SIO_000159 argon atom CHEBI:49475 SIO_011017 plutonium atom CHEBI:33388 SIO_011108 molecular complex formation is the process of forming a molecular complex from its constituent parts. molecular complex formation SIO_010285 to heat is a capability to increase the internal kinetic energy of a material. to heat SIO_000346 A group of people affiliated by consanguinity, affinity, or co-residence. family SIO_001063 A dimensionless quantity is a quantity that has no associated unit. dimensionless quantity SIO_000257 poor quality SIO_001295 xenon atom CHEBI:49957 SIO_011053 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. institute SIO_000688 An expected value (or e-value) is the weighted average of all possible values that a random variable can take on. expected value SIO_001021 A study is a process that realizes the steps of a study design. study SIO_001066 has measurement value is a relation between a quality/realizable and a measurement value. core has measurement value SIO_000216 jealousy is an emotion and typically refers to the negative thoughts and feelings of insecurity, fear, and anxiety over an anticipated loss of something that the person values, particularly in reference to a human connection. jealousy SIO_000849 to supply energy is the capability to transfer energy from a source to a sink. to supply energy SIO_000351 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. collection ovopub SIO_001301 A local minimum stationary point is a point that has a lower value in some axis than adjacent points. local minimum stationary point SIO_000743 A namespace is an informational entity that defines a logical container for a set of symbols or identifiers. namespace SIO_000067 2 study An experiment is an investigation that has the goal of verifying, falsifying, or establishing the validity of a hypothesis. experiment SIO_000994 A default parameter is a parameter which has a default value. default parameter SIO_000952 A nucleic acid strand is a single-stranded nucleic acid that is part of a double stranded nucleic acid complex. nucleic acid strand SIO_001174 2 A relation between a informational entity and its actual value (numeric, date, text, etc). core nlp relations sadi has value SIO_000300 biochemical inhibition is a molecular interaction that decreases the catalytic rate of the target enzyme. biochemical inhibition SIO_010289 An inductive argument is an argument that asserts that the truth of the conclusion is supported by the premises. inductive argument SIO_000264 chemical quality is the quality of a chemical entity. chemical quality SIO_001011 A reagent is a substance that is added to a system in order to bring about a chemical reaction, or added to see if a reaction occurs. reagent SIO_010411 to lose an electron is the capability of a chemical entity to lose an electron. to lose an electron SIO_010371 A millenium is a period of 1000 years millennium SIO_000432 A novel is a fictitious prose narrative of book length, typically representing character and action with some degree of realism. novel SIO_000109 A cellular organism is an organism that contains one or more cells. cellular organism SIO_010377 An idea is a proposition about some object of conceptual thought. idea SIO_000585 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 SIO_000188 A signal is an object that initiates a sequence of events. signal SIO_010438 an arc is a closed segment of a differentiable curve. arc SIO_001333 A positional role is an abstract role which holds by comparing position to another object of reference. positional role SIO_000704 A record is a document containing a collection of statements about some entity. record SIO_000088 cancelled is a process status in which the process, while planned to occur, will not occur. cancelled SIO_000996 has member is a mereological relation between a collection and an item. core has member a collection of cars has as a car as a member SIO_000059 is target in is a relation between an entity and a process, where the entity is present at the beginning of the process and undergoes a change or transformation in the process. is target in glucose is a target in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. SIO_000292 weak is a qualitative intensity value that is more intense than none, but less intense than mild. weak SIO_001218 tellurium atom CHEBI:30452 SIO_011051 An aromatic bond is an interaction between a set of atoms across which pairs of electrons are shared. aromatic bond SIO_010501 a left closed interval is an interval in which there is a real number that is smaller than all its elements. left closed interval SIO_001254 A cation pi interaction is an ionic interaction between the localized negative charge of π orbital electrons, located above and below the plane of an aromatic ring, and a positive charge. cation pi interaction SIO_010034 primary active transport, also called direct active transport, directly uses energy to transport molecules across a membrane. primary active transport SIO_000577 anger is disgust directed toward an equal status individual. anger SIO_000410 to gain a covalent bond is the capability of a chemical entity to have bonds added. to gain a covalent bond SIO_001103 A book series is a collection of books that have been sequentially published. book series SIO_000158 A verbal language is a language that uses sounds to communicate. verbal language SIO_000981 A chemical synthesis pathway is a pathway involved in the assembly of a chemical. chemical synthesis pathway SIO_010527 Frequency is the number of occurrences of a repeating event per unit time frequency SIO_001367 active transport is the movement of a substance across a membrane against its concentration gradient (from low to high concentration) and requires chemical energy. biopax:TransportWithBiochemicalReaction active transport SIO_010284 full agreement is the result of consensus decision making when members of the group unanimously agree. full agreement SIO_001179 is annotation of is a relation between some textual entity and the entity that it annotates. is annotation of SIO_000254 boldness is the trait of being willing to undertake things that involve risk or danger. boldness SIO_000819 written language is a language that is communicated through a writing system. written language SIO_000982 the date at which an information content entity was made public. date of issue SIO_001314 appreciation gratefulness gratification thankfullness Gratitude, thankfulness, gratefulness, or appreciation is a feeling, emotion or attitude in acknowledgment of a benefit that one has received or will receive. gratitude SIO_000839 A low barrier hydrogen bond is a shorter, stronger hydrogen bond that is formed between both heteroatoms. low barrier hydrogen bond SIO_010433 An intervention group is a group of individuals that are subject to an intervention. intervention group SIO_001069 A slide is an visual representation meant to communicate some information. slide SIO_001370 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. last name SIO_000182 A three prime untranslated region (3'-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. 3' untranslated region SIO_010070 A prognosis is a proposition about the likely course of a disease, the chance of recovery or recurrence. prognosis SIO_001025 is base for is a relation between a quality and the realizable entity that it is the basis for. is base for the solubility of salt (the disposition) is based on the molecular structure of NaCl (the quality) that allows the polarized water-molecules (the trigger) to break the ion bonds (the realization). SIO_000642 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 SIO_000030 molecular structure descriptor is data that describes some aspect of the molecular structure (composition) and is about some chemical entity. molecular structure descriptor CHEMINF:000085 SIO_011121 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 SIO_001083 A workflow is an algorithm that is is a depiction of a sequence of operations to achieve one or more objectives. workflow SIO_000127 identifies a relation between an identifier and an entity. is identifier for SIO_000672 genetic data is data pertaining to genetics. genetic data SIO_010028 A molecular regulator is a molecule that regulates the function of another chemical entity. molecular regulator SIO_010436 A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation. increased molecular degradation from decreased regulation SIO_001201 A protein expression value is a quantity obtained from a protein expression experiment. protein expression value SIO_001327 A material boundary is the boundary of a material entity which exists as a lower dimensional entity at exactly the location where its parts no longer extend into space. Every material entity has a boundary, and a boundary is the boundary of exactly 1 material entity. material boundary the external surface of the window; the surface of the p52 protein SIO_000022 lead atom CHEBI:25016 SIO_011067 a SADI semantic web service is a semantic web service that follows the SADI specification sadi SADI semantic web service http://en.wikipedia.org/wiki/SADI SIO_001188 A publication is a document that has been made available by a publisher. publication SIO_000087 to modify is the capability to change some entity. to modify SIO_000343 A foreign database key is a database key that refers to a key in some table. foreign database key SIO_000764 regulation of a participant quantity is the regulation of a process in which the quantity of its partcipants is changed. regulation of object quantity SIO_001145 osmosis is the movement of water molecules through a selectively-permeable membrane down a water potential gradient. osmosis SIO_000572 has target is a relation between a process and an entity, where the entity is present at the beginning of the process and undergoes a change or transformation in the process. has target SIO_000291 A is location of B iff the spatialtemporal region occupied by A has the spatialtemporal region occupied by B as a part. [T][R] nlp+ is location of SIO_000145 A polymer is a molecule composed of a connected set of monomeric residues. polymer SIO_000314 has attribute is a relation that associates a entity with an attribute where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type. core has attribute SIO_000008 to be inhibited is the capability to be modified in such a way that the conformational change leads to an decrease in another capability. to be inhibited SIO_010373 A hyponym is a term with a narrower meaning. hyponym SIO_000125 An anion is an atom or molecule with a net negative electrical charge. anion SIO_010458 A software application is software that can be directly executed by some processing unit. software application SIO_000101 intersex is a biological sex characterised by birth with genitalia and/or secondary sexual characteristics of indeterminate sex, or which combine features of both sexes. intersex SIO_001405 a pharmacokinetic pathway is a metabolic pathway which describes the metabolism of a drug molecule. pharmacokinetic pathway SIO_001255 A base stack is a stabilizing interaction of DNA and RNA between spatially adjacent nucleotides and possibly involving London dispersion, hydrophobic and electrostatic forces. base stack SIO_010505 1 mendelevium atom CHEBI:33395 SIO_011115 has trigger is a relation between a realizable and the factor that causes it to be realized. has trigger SIO_000635 A thesis document is the written research component of a post-secondary institution that contains a statement supported by arguments. thesis document SIO_000165 A verbal language entity is a language entity that is manifested through sound. verbal language entity SIO_000786 A page number is the count of a page in a sequence of pages. page number SIO_000787 mentions references is a relation between one entity and the entity that it makes reference to by name, but is not described by it. core references SIO_000631 sequence variation notation SIO_001388 A primary graph title is a primary title that describes a statistical graph. primary graph title "Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm SIO_000473 subtitle, alternative title A secondary title is a title of lesser importance that should be used after the first title in describing some entity. secondary title SIO_000471 synthetic quality is the quality of a manufactured object that has similar properties as naturally occuring objects. synthetic quality SIO_001410 The increase of regulation leads to a decreased spatial extent of the target process. decreased spatial extent of process from decreased regulation SIO_001141 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. database table SIO_000754 an anatomical entity is an object that is a structural part (material or immaterial) of a biological entity. anatomical entity SIO_001262 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. line SIO_000511 snoRNA A small nucleolar RNA (snoRNA) is a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. small nucleolar RNA (snoRNA) SIO_001234 A letter is a document that contains a personal communication from one part to another. letter SIO_000306 In a controlled observational cohort study, two groups of subjects are selected from two populations that are thought to differ in only one characteristic. The groups of subjects are studied for a specific period and contrasted at the end of the study period. controlled observational cohort study SIO_001067 to be actively interacted with is the capability to be manipulated by some device or agent. to be actively interacted with SIO_000692 length is the longer dimensional extent along a 2D projection of the object. length SIO_000041 A primary database key is a database key that identifies every row of a table. primary database key SIO_000763 electronic configuration 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 structure the electron configuration of the neon atom is 1s2 2s2 2p6. SIO_001099 membrane transport is the movement of molecules across a membrane. membrane transport SIO_000576 increased regulation leads to a decrease in the number of target objects of a specified type. decreased object production from increased regulation SIO_001147 A process mediated by a protein that modulates the frequency, rate or extent of translation. protein mediated regulation of translation SIO_001130 is manifested as is a relation between an expression and its manifestations. is manifested as the english language version of 'war of the worlds' is manifested as a collection of english language versions of the book. SIO_000341 A study group is a group of individuals that are subjects in an observational or intervention study. study group SIO_000403 is refuting evidence for SIO_000775 an oligopeptide is an organic polymer composed of fewer than 10 or 15 amino acids. oligopeptide SIO_001426 A sequence alignment is the character-based alignment of sequences using some method. sequence alignment SIO_010066 An organic polymer is an organic molecule composed of connected set of monomeric units. organic polymer SIO_010346 A versioned record is a record for which there exists another variant based that was derived via modification of the facts. versioned record SIO_000771 A regulatory pathway is a series of biochemical reactions that lead to the increase or decrease of activity of participating molecular components. regulatory pathway SIO_010533 A correlation is a statistical relationship involving dependence between two random variables or datasets. correlation SIO_000923 A medical report is a report prepared by a health care practioner about test outcomes or health status of an individual. medical report SIO_001028 A web page is a document that is published according to World Wide Web standards. web page SIO_000302 perception is the organization, identification, and interpretation of sensory information in order to fabricate a mental representation through the process of transduction, which sensors in the body transform signals from the environment into encoded neural signals. perception SIO_000379 A positional description is a description of location using some system or frame of reference. positional identifier SIO_000328 A vertical line is a line that is positionally oriented perpendicular to the horizon. vertical line SIO_000526 an email address is an identifier to send mail to particular electronic mailbox. email address SIO_001323 A process model is a representation of some process. process model SIO_000647 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. decreasing line SIO_000529 A month is a period of time that divides the year. month SIO_000429 An organic submolecule is connected region of a molecule. organic submolecule SIO_010071 A term variant is a term that is a variant of another term. term variant SIO_000342 mild is a qualitative intensity value that is more intense than weak, but less intense than moderate. mild SIO_001213 europium atom CHEBI:32999 SIO_011095 forward strand The positive nucleic acid strand refers to the strand that is to be read 5' to 3'. positive nucleic acid strand SIO_001175 A small nuclear RNA (snRNA) gene is a gene that encodes a small niuclear RNA molecule. http://purl.obolibrary.org/obo/SO_0001268 small nuclear RNA (snRNA) gene SIO_001228 symport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in the same direction simultaneously. symport enabled secondary active transport SIO_000579 number of objects consumed is a count of objects that were consumed in some process. number of objects consumed SIO_001161 A cisregulatory element is a DNA sequence located on the same DNA strand or chromosome as the gene whose expression it affects. cis regulatory element SIO_001225 A specialized material entity is a material entity that is defined by having some quality, role or capability. specialized material entity SIO_010410 A polygonal face is a polygon bounded by a circuit of polygon edges, and includes the flat (plane) region inside the boundary. polygonal face SIO_000503 interacting is a process characterized by the interaction between two or more entities. core interacting SIO_000593 A homocyclic ring is a ring where the atoms are of a single type. homocyclic ring SIO_010783 a relation between two entities which indicates their common ancestry but due to horizontal gene transfer. is xenologous to SIO_000634 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. therapeutic gene-disease association SIO_001120 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 SIO_001348 A patient role is the role of an individual that is the recepient of medical care. patient role SIO_000715 molybdemum atom CHEBI:28685 SIO_011041 A stereoisomer is an isomer in which the atomic connectivity is the same, but differs in its spatial arrangement of atoms. stereoisomer SIO_010775 A median is the numerical value separating the higher half of a sample, a population, or a probability distribution, from the lower half. median SIO_001110 A worm is a non-arthropod invertebrate animal that typically have a long cylindrical tube-like body and no legs. worm SIO_000488 a derives to b if and only if a or some part thereof is consumed in the formation of b. derives into SIO_000245 a fax number is a number to connect to fax device fax number SIO_001321 structure is the specification that refers to the composition and arrangement of parts of an object. structure SIO_000600 A heatmap is a graphical representation of data where the individual values contained in a matrix are represented as colors. heatmap SIO_000907 A statute is a formal written enactment of a legislative authority that governs a state, city or country. statute SIO_001371 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. syllable SIO_000977 A gene-disease association is an association between a gene and a disease. gene-disease association SIO_000983 A solvent is a substance that can dissolve other substances (solutes). solvent SIO_010417 A sum is the result of adding a set of values together. sum SIO_001112 Molecular modification is chemical alteration of a known and previously characterized lead compound for the purpose of enhancing its usefulness as a drug. This could mean enhancing its specificity for a particular body target site, increasing its potency, improving its rate and extent of absorption, modifying to advantage its time course in the body, reducing its toxicity, changing its physical or chemical properties (like solubility) to provide desired features. molecular modification SIO_010307 A radio receiver is a communication device that receives its input from an antenna, uses electronic filters to separate a wanted radio signal from all other signals picked up by this antenna, amplifies it to a level suitable for further processing, and finally converts through demodulation and decoding the signal into a form usable for the consumer, such as sound, pictures, digital data, measurement values, navigational positions. radio receiver SIO_000926 A phrase net diagram illustrates the relationship between different words used in a text. phrase net diagram SIO_000939 A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation. decreased molecular production from decreased regulation SIO_001206 is attribute of is a relation that associates an attribute with an entity where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type. is attribute of SIO_000011 An address is a position that indicates the physical location of some entity using a social convention. address SIO_000172 A column is a vertical sequence of cells in a cellular automata. column SIO_000753 a mereological quality is a quality of an entity vis-a-vis containment or parthood mereological quality SIO_001338 A statistical graph line is a line used in a statistical graph to communicate some trend or feature of the embedded data. statistical graph line SIO_000535 anxiety is an emotion charactersized by intense feeling of fear and concern coupled with a physical response. anxiety SIO_000815 gesturing is a form of non-verbal communication in which visible bodily actions communicate particular messages, either in place of speech or together and in parallel with spoken words. Gestures include movement of the hands, face, or other parts of the body. gesturing SIO_001059 An evaluation role is a processual role held by an entity during some evaluation. evaluation role SIO_010428 A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation. stop codon SIO_010448 Anabolism is the set of metabolic processes that construct larger chemical entities units from smaller chemical entities. anabolism SIO_010310 euphoria is an emotion characterized by intense feelings of well-being, elation, happiness, ecstasy, excitement, and joy. euphoria SIO_000835 A doctor is an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments. doctor SIO_000394 A standard operating procedure is a specification approved for use in specific environments. standard operating procedure SIO_000964 horizontal axis An x-axis is a Cartesian coordinate axis that is aligned with the horizon. In most figures, this axis represents categories, such as months, market segments, or other non-numeric data. x-axis The horizontal axis in http://tinyurl.com/opwnvm SIO_000452 information translation SIO_001359 diffusion is motion of particles at temperatures above absolute zero. diffusion SIO_000564 arousal is an emotion characterized by state of reactive to stimuli. It involves the activation of the reticular activating system in the brain stem, the autonomic nervous system and the endocrine system, leading to increased heart rate and blood pressure and a condition of sensory alertness, mobility and readiness to respond. arousal SIO_000817 A functional specification is a specification that describes the characteristics of an object. functional specification SIO_000315 A coordinate is a measurement of position in n-dimensional space. coordinate SIO_000071 A cell line is a collection of genetically identifical cells. cell line SIO_010054 A small cytoplasmic RNA (scRNA) gene is a gene that encodes a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins. http://purl.obolibrary.org/obo/SO_0001266 small cytoplasmic RNA (scRNA) gene SIO_001227 A record identifier is an identifier for a database entry. record identifier SIO_000729 is manifestation of SIO_000426 A contains B iff the spatial region occupied by A has the spatial region occupied by B as a part, and B is not part of A. [T] contains SIO_000202 A human is a primates of the family Hominidae and are characterized by having a large brain relative to body size, with a well developed neocortex, prefrontal cortex and temporal lobes, making them capable of abstract reasoning, language, introspection, problem solving and culture through social learning. human SIO_000485 broaderThan A sound wave is a mechanical wave that is an oscillation of pressure transmitted through a solid, liquid, or gas, composed of frequencies within the range of hearing. sound wave SIO_000605 The HGVS (human genome variation society) notation is a notation to specify a sequence variation in dna, rna, proteins, and other biomolecules. hgvs notation SIO_001389 caesium atom CHEBI:30514 SIO_011054 darmstadtium atom CHEBI:33367 SIO_011081 hafnium atom CHEBI:33343 SIO_011057 A Cartesian coordinate axis is an axis whose behavior follows that of a Cartesian coordinate system. Cartesian coordinate axis SIO_000451 2 is provided by is a relation between an entity and the entity that provides it. dc:source has provider SIO_000066 is component part of is a relation between a component and a whole, where the component is instrinsic to the whole, and loss of the part would change the kind that the whole is. core is component part of SIO_000313 A gene-gene association is an association between two genes. gene-gene association SIO_001437 1 A gene that codes for a functional RNA molecule. functional rna coding gene SIO_000986 is realized in the role of a patient is realized in medical examination SIO_000356 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 SIO_001302 A protein domain is a part of a protein that maintains its structure and function independently of the rest of the protein. protein domain SIO_001379 x negatively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an reduced effect on the frequency, rate or extent of y negatively regulates SIO_001402 homepage apprehension is the negative emotion that something unpleasant will occur. apprehension SIO_000949 A province is a territorial unit, almost always an administrative division, within a country or state. province SIO_000661 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. scatterplot SIO_000423 A structural isomer is an isomer in which the atoms are joined together in different ways. structural isomer SIO_010779 biochemical activation is a molecular interaction that increases the catalytic rate of the target enzyme. biochemical activation SIO_010288 reverse strand The negative nucleic acid strand is the strand that is that is complimentary to the forward strand and appears from 3' to 5'. negative nucleic acid strand SIO_001176 An ionic interaction is a weak submolecular interaction between a charged submolecules. ionic interaction SIO_010496 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 SIO_000090 A is concretization of B iff A is a quality of a material entity and B is an informational entity. is concretization of SIO_000214 to gain an electron is the capability of a chemical entity to receive an electron. to gain an electron SIO_010370 A geographic heatmap is a graphical representation of data over a geographic region where individual values are represented as colors. geographic heatmap SIO_000910 iron atom CHEBI:18248 SIO_011025 regulation of a process spatial extent is a process that modulates the spatial extent of another process relative to some reference process. regulation of process spatial extent heating the solution causes greater diffusion of a chemical. SIO_001139 1 is orthologous to is a relation between two biological entities that share a common ancestor and occur in different species. is orthologous to SIO_000558 to boil is the capability to increase the internal kinetic energy of a material such that it changes state from a solid or liquid to a gas. to boil SIO_000373 volume is the quantity of three-dimensional space enclosed by some closed boundary. volume SIO_000049 A pairwise sequence alignment is the alignment of exactly 2 sequences. pairwise sequence alignment SIO_010068 ionsdaleite is a hexagonal allotrope of the carbon allotrope diamond. ionsdaleite SIO_010795 increased chemical destruction is a process in which there is an increase in the amount of chemical destroyed relative to some reference process increased chemical destruction SIO_001207 apathy is an emotion characterized by lack of interest, enthusiasm, or concern. apathy SIO_000816 a duplicate is an object that is an exact copy of another item duplicate SIO_001420 A curve segment is a part of a curve that consists of at least three points. curve segment SIO_000740 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. stationary point SIO_000741 moderately quantifier SIO_001305 thorium atom CHEBI:33385 SIO_011104 is represented by: a relation between an entity and some symbol. is represented by SIO_000205 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. syndrome SIO_001017 non-polar is the quality of not having a dipole. non-polar SIO_001047 An electrophilic addition reaction is a polar addition reaction where a pi bond is removed by the creation of two new covalent bonds. electrophilic addition reaction SIO_010523 A base pair is a weak molecular interaction composed of hydrogen bonds between nucleobases. base pair SIO_010045 curved is the quality of a line that deviates from straightness in a smooth, continuous fashion. curved SIO_001095 to serve as is the capability to act in a manner corresponding to some role. to serve as SIO_000542 is property of is a relation betweena quality, capability or role and the entity that it and it alone bears. is property of SIO_000224 a relation between two information content entities in which one is transcribed into (an exact or similar kind) another through some process. is transcribed into DNA is transcribed into RNA SIO_010080 2 1 A 3D cartesian coordinate is a coordinate that is composed of an x, y and z coordinate. 3D cartesian coordinate SIO_000333 x regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect on the frequency, rate or extent of y regulates SIO_001154 helium atom CHEBI:30217 SIO_011003 max A maximal value is largest value of an attribute for the entities in the defined set. maximal value SIO_001114 vertex a node or vertex is a point in a graph. node SIO_001335 A nominal scale of measurement only specifies a limited set of categories. nomimal scale SIO_000913 software execution is the process of executing software on a computing device. software execution SIO_000667 A century is a period of one hundred years. century SIO_000431 carbon atom CHEBI:27594 SIO_011001 A control role is the role of an individual that is part of a study, but is not subject to the intervention that is to be tested. control role SIO_010431 p-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 probability value SIO_000765 book section SIO_001375 A map is a a visual representation of an area that depicts the relationship between elements of that space. map SIO_000906 lithium atom CHEBI:30145 SIO_011004 reasoning is the agentive process of using knowledge to evaluate the truth value of a proposition. reasoning SIO_000746 A 1D cartesian point is a point whose position is specified along a single dimension using Cartesian coordinates. 1D cartesian point SIO_000441 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. annotation SIO_001166 the ability to reverse an encoding operation to decode information SIO_001364 A molecular pocket is a site on a molecule that appears as a depression into the structure. molecular pocket SIO_010452 A treemap is a chart that fully partitions the area into a set of rectangles whose area represents its relative value. treemap SIO_000935 is result of SIO_001157 http://www.w3.org/2004/02/skos/core#exactMatch is exact match to SIO_000484 A biological quality is a quality held by a biological entity. biological quality SIO_000475 Panic is a sudden emotion of fear which is so strong as to dominate or prevent reason and logical thinking, replacing it with overwhelming feelings of anxiety and frantic agitation consistent with an animalistic fight-or-flight reaction. panic SIO_000855 An excerpt is a contiguous or discontiguous portion of a document. excerpt SIO_000298 to luminesce is to emit light through cold body radiation to luminesce SIO_000894 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. first name SIO_000181 1 A negative charge is a charge where the value is negative. negative charge SIO_010464 replicates a collection of replicates is a collection composed of items that are a facsimile, reproduction, or copy of other items in the collection. a collection of replicates SIO_001419 toxicity is the quality of a chemical substance to cause injury to an organism in a dose dependent manner. toxicity SIO_001008 A process is an entity that is identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists. core process+ process SIO_000006 target SIO_010423 an analyte is a substance or chemical constituent of interest in an analytical procedure. analyte SIO_001378 is direct part of is a relation between a specific part (at some level of granularity) and its whole. core is direct part of SIO_000310 regulation of biochemical process is a process that changes the frequency, rate or extent of a target biochemical process. regulation of biochemical process SIO_010287 A signal transducer is a molecule that responds to and amplifies a signal in a signalling system. signal transducer SIO_010437 antimony atom CHEBI:30513 SIO_011050 A hypothesis is a proposed explanation for a phenomenon. hypothesis SIO_000284 to breathe is the capability to inhale and exhale air into the body during respiration. to breathe SIO_010353 full agreement is the result of consensus decision making when members of the group unanimously disagree. full disagreement SIO_001181 to be examined is the capability of an object to be observed in a detailed manner. to be examined SIO_000725 to demagnify is the capability to decrease the appearance of the size of an object. to demagnify SIO_000377 einsteinium atom CHEBI:33393 SIO_011113 2 A multi-cellular organism is an organism that consists of more than one cell. multicellular organism SIO_010375 A collection of documents is a non-zero set of documents. http://purl.org/ontology/bibo/Collection collection of documents SIO_000295 passive movement is the process in which an object is spatially displaced without an expenditure of energy contained in molecular bonds. passive movement SIO_000573 molecular geometry molecular structure is the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together. molecular structure SIO_000626 truth value is a quality of information that is claimed/verified to be true or false. truth value SIO_000268 A nucleophilic addition reaction is an addition reaction where a pi bond is removed by the creation of two new covalent bonds by the addition from a nucleophile. nucleophilic addition reaction SIO_010522 2 An objective is a proposition that indicates a planned or anticipated outcome. objective SIO_000337 A line segment is a line and a part of a curve that is (inclusively) bounded by two terminal points. line segment SIO_000512 bent is the quality of a line being sharply curved or having an angle. bent SIO_001094 zinc atom CHEBI:27363 SIO_011029 has end time SIO_000681 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. quantile SIO_001414 is generalization of is a relation between a more general instance (in terms of spatial/temporal localization & other attributres) than the other. is generalization of SIO_001097 A geographic image is a photograph of some geographical area. geographic image SIO_000301 is greater than or equal to is a comparison relation between two quantities in which the first has a value larger or equal to the second. is greater than or equal to SIO_000699 results in SIO_001156 A PDB file is a molecular structure file specified by the Protein DataBank (PDB). PDB file SIO_011130 ncRNA gene A non-protein coding RNA (ncRNA) gene is a gene that encodes for a RNA transcript that is not further translated into a protein product. http://purl.obolibrary.org/obo/SO_0001263 non-protein coding RNA (ncRNA) gene SIO_000790 A pattern is a generalized representation of some repeatable concrete or informational item. pattern SIO_000130 epimer association SIO_001337 A geographic position is the coordinate of an entity against some geographic coordinate system. geographic position SIO_000013 depth is the dimensional extent into a plane of a 3D projection of the object. depth SIO_000039 region A spatial region is an object contained in some region of space. spatial region The airspace above Ottawa airport; the band around the northern hemisphere between 50 degrees N and 60 degrees N; the spatial region occupied by a bottle. SIO_000370 a telephone number is an identifier used to connect to a physical device capable of transfering voice or data over a network. telephone number SIO_001319 x positively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect that increases the frequency, rate or extent of y positively regulates SIO_001401 word cloud A tag cloud is a visualization of word frequencies. tag cloud SIO_000938 to change appearance is the capability to change the material composition of an object. to change materially SIO_000376 A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation. decreased molecular degradation from decreased regulation SIO_001200 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 SIO_000079 to regulate the rate of formation is to modify the rate at which an object is formed. to regulate the rate of formation SIO_000536 Email message is a digital document that is composed of a header and a body and is transmitted using the SMTP protocol. email SIO_000304 A symbol is a proposition about what an entity represents. symbol SIO_000105 A bubble chart contains circles whose area corresponds to a value. bubble chart SIO_000933 learning is the agentive process of acquiring knowledge. learning SIO_000744 is described by is a relation between one entity and another entity that provides a description (detailed account) of it. is described by SIO_000557 A disposition is the tendency of a capability to be exhibited under certain conditions or in response to a certain stimulus (trigger). core disposition solubility (to dissolve when put in fluid); fragility (disposition to break when dropped) SIO_000014 is inequal to is a comparison relation between two quantities whose value are not the same. is inequal to SIO_000749 chemical synthesis is synthesis of a chemical entity from physical precursors through one or more chemical interactions or reactions. chemical synthesis SIO_000559 solube RNA (sRNA) gene tRNA gene A transfer RNA (tRNA) gene is a gene that codes for a tRNA used in the translation of a messenger RNA (mRNA) to produce a protein product. http://purl.obolibrary.org/obo/SO_0001272 transfer RNA (tRNA) gene SIO_001230 A is contained in B iff the spatial region occupied by A is part of the spatial region occupied by B and A is not part of B. [T] OBO_REL:contained_in core is contained in SIO_000128 A weak submolecular component is a submolecular component that weakly connects submolecular components. weak submolecular component SIO_010005 A transitive temporal relation in which one entity was materially formed from another non-identical entity. OBO_REL:derives_from core is derived from SIO_000244 suicidal is the emotion of being deeply unhappy or depressed with thoughts of killing one's self. suicidal SIO_001285 The minimal unit of a cellular automaton that can change state and has an associated behavior. cell (informational) SIO_000755 dead is the quality of an object in which there is a cessation of all biological functions. dead SIO_010059 surprise is a brief emotion experienced as the result of an unexpected event. surprise SIO_000870 to activate to reduce the activation energy is to require a smaller amount of energy in order to form or break a chemical bond. to reduce the activation energy SIO_000549 meitnerium atom CHEBI:33361 SIO_011080 A technical report is a publication published by a school or other institution, usually numbered within a series. technical report SIO_000164 non toxic is the quality of a substance having no damaging effect to a system. non toxic SIO_001010 satisfied qualifier SIO_001312 to positively charge is the capability to remove an electron or add a positively charged ion to a chemical entity. to positively charge SIO_000386 Loneliness is an unpleasant emotion in which a person feels a strong sense of emptiness, yearning distress and solitude resulting from inadequate quantity or quality of social relationships. loneliness SIO_000852 to supply electricity is the capability to transfer electricity from a source to a sink. to supply electricity SIO_000375 A referenceing cell is a cell of a cellular automata that refers to another cell. referencing cell SIO_000760 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 SIO_000435 A centrifugation pellet is a solid substance that forms as a result of compaction by a centrifuge. centrifugation pellet SIO_010424 A binary scale is a measurement scale that specifies a choice between two values. binary scale SIO_000914 uranium atom CHEBI:27214 SIO_011106 to cleave is to split or sever an object along a natural line or grain. to cleave SIO_010349 CNV copy number variation refers to the number of deletions/duplications of a DNA region as compared to some reference state. copy number variation SIO_001328 An insertion variant role is the role of an sequence that contains a sub-sequence that is considered to be an addition relative to the frame of reference. insertion variant role SIO_000480 arithmeritic mean average 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. mean SIO_001109 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 SIO_001253 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 SIO_000530 cites is a relation to refer to by way of example, authority or proof. cites SIO_000277 A plot is a part of a figure that corresponds to the spatial region between the set of axes. plot The square portion of the chart bounded by lines that overlap with the two axes in Graph 1 of http://tinyurl.com/opwnvm SIO_000449 0 copernicium atom CHEBI:33517 SIO_011083 An alpha helix is structural region of a protein that is characterized by 3.6 residues per turn, a translation of 1.5 angstroms along the helical axis in which backbone N-H groups form a hydrogen bond to the backbone carboxyl group of the amino acid four residues prior. alpha helix SIO_010468 A note is a brief document. note SIO_000152 a geopolitical region is a geographic region recognized by social or legal convention. geopolitical region The geographic region bounded by Canada; the spatial region occupied by the US embassy in Ottawa. SIO_000415 gallium atom CHEBI:49631 SIO_011030 a right open interval is an interval in which there is no element that is greater than all other elements. right open interval SIO_001252 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 CHEMINF:000123 SIO_011123 observation observing is a process of passive interaction in which one entity makes note of attributes of one or more entities. observing SIO_001055 aluminium atom CHEBI:28984 SIO_011012 niobium atom CHEBI:33344 SIO_011040 A is adjacent to B iff there is a small, but non-zero distance between A and B OBO_REL:adjacent_to core nlp is adjacent to SIO_000204 A base is a molecular entity dissolved in a solvent that is capable of accepting a proton (Bronsted base) or forming a covalent bond with a hydron (Lewis base) . base SIO_010454 fatal is a qualitative intensity value that is more intense than severe, leading to the death/non-functioning of a system. fatal SIO_001216 effective dose is the amount of a substance required to produce an effect on a predefined percentage of a population. effective dose SIO_001020 titanium atom CHEBI:33341 SIO_011021 to serve as a primer for DNA synthesis is the capability of a short nucleic acid to bind to the 5' end of single strand of DNA template and help initiate DNA replication. to serve as a primer for DNA synthesis SIO_010094 A category axis is an axis in which the position along the line is partioned into categories. category axis The horizontal axis corresponding to months of the year in graph 4 of http://tinyurl.com/opwnvm SIO_000455 contempt is disgust towards a lower status individual. contempt SIO_000821 to serve as a template for protein synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a protein may be produced. to serve as a template for protein synthesis SIO_010089 is time boundary of SIO_000029 bromine atom CHEBI:22927 SIO_011034 to be observed is the capability of an object to be perceived. to be observed SIO_000696 A person is an object that has certain capacities or attributes constituting personhood. person SIO_000498 status descriptor is a descriptor for the state of a process or object. status descriptor SIO_001326 data analysis is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making. data analysis SIO_001051 x is associated with y when x and y are logically or statistically related to one another. is associated with SIO_001403 A site is a spatial region bounded (in part or in whole) by material entities and may be occupied by material entities. site A nostril; the interior of the heart valve; the interior of a bottle. SIO_000019 has unit is a relation between a quantity and the unit it is a multiple of. core has unit SIO_000221 A line-bar graph statistical graph that contains both lines and bars. line-bar graph Graph 8 in http://tinyurl.com/opwnvm SIO_000447 zygosity is the quality pertaining to the allelic complement of a biological system at a single locus on the DNA. zygosity SIO_001263 A dose is the quantity of a chemical substance administered to a biological system. dose SIO_001019 homozygous is the quality of a biological organism in which there are two identical alleles at a given locus. homozygous SIO_001264 A redox reaction is a chemical reaction in which there is a net movement of electrons from one reactant to another. redox reaction SIO_010509 history is a sequence of past events. history SIO_001196 A cell is a biological entity that is contained by a plasma membrane. cell SIO_010001 A role of a chemical substance that participates in a chemical reaction as part of some scientific investigation. reagent role SIO_000893 A mouse is a small mammal belonging to the order of rodents, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail. mouse SIO_000486 A specimen is a portion of material for use in testing, examination, or study. specimen SIO_010412 an ontology is a formal specification of entities, their attributes and relationships. ontology SIO_001391 A protein-protein association is an association between two proteins. protein-protein association SIO_001438 The role of a chemical entity present at the beginning of a chemical reaction. reactant role SIO_000879 composition quality is a quality that describes its composition or anatomy. compositional quality SIO_000051 good quality SIO_001297 intent is a desire to realize a particular outcome. intent SIO_000358 gold atom CHEBI:29287 SIO_011064 very dissatisfied qualifier SIO_001309 An acid is a molecular entity in solution capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid). acid SIO_010453 A left value axis is a value axis that is spatially positioned to the left of the plot area. left 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 SIO_000459 dysprosium atom CHEBI:33377 SIO_011098 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 SIO_000515 to record is the capability to detect and transcribe information in a specified format on some physical medium. to record http://purl.obolibrary.org/obo/OBI_0000368 SIO_000344 to modify conformation of is to affect the spatial arrangement of an entity. to modify conformation of SIO_010347 destruction destroying is a process in which something is broken down and/or ceases to exist. destroying SIO_000591 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. major tick mark SIO_000514 A monosaccharide is an organic molecule that consists of a single polyhydroxy aldehyde or ketone group. monosaccharide SIO_010030 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 SIO_000767 A scientific name is a name given through scientific nomenclature. scientific name SIO_000120 has output is a relation between an process and an entity, where the entity is present at the end of the process. core sadi has output SIO_000229 information encoding SIO_001356 rigid is the quality of maintaining structural integrity (and not bending) under pressure. rigid SIO_001093 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 SIO_001117 is input in is a relation between an entity and a process, where the entity is present at the beginning of the process. sadi is input in glucose and ATP are inputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. SIO_000231 A molecular activator is a molecular regulator that realizes its disposition to conformationally change a target molecule and increase its functionality. activator SIO_010434 hassium atom CHEBI:33357 SIO_011079 A Gantt chart is a bar chart that illustrates a project schedule. Gantt chart SIO_000922 A Master's thesis is a thesis prepared as a requirement for a Master's degree. master's thesis SIO_000167 A variant role is a comparative role in which the value of an attribute differs when compared to another entity variant role SIO_000479 a collection item is an item in a collection. collection item SIO_001259 to reduce is the capability to add an electron or an decrease in oxidation state of a chemical entity. to reduce SIO_010359 A differential diagnosis (sometimes abbreviated DDx, ddx, DD, D/Dx, or ΔΔ) is a systematic diagnostic method used to identify the presence of an entity where multiple alternatives are possible (and the process may be termed differential diagnostic procedure), and may also refer to any of the included candidate alternatives (which may also be termed candidate condition). differential diagnosis SIO_001002 Altitude is a distance above sea level. altitude SIO_000438 2 A quality that has a value that is normal or average. PATO:0000461 normal SIO_000554 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 SIO_000308 positive is an assertional qualifier that expresses the validity or truth of a basic assertion. positive SIO_001210 ytterbium atom CHEBI:33381 SIO_011102 modified A mass spectrometry experiment is an experiment that involves the use of a mass spectrometer. mass spectrometry experiment SIO_001180 http://www.w3.org/2004/02/skos/core#narrower is broader than SIO_000477 to observe is the capability to watch attentively. to observe SIO_000353 is member of is a mereological relation between a item and a collection. is member of SIO_000095 is phenotype of is a relation between an observable/measurable characteristic and an object. is phenotype of SIO_001280 A t-statistic is a ratio of the departure of an estimated parameter from its notional value and its standard error. t-statistic SIO_001074 resentment is disgust directed toward a higher status individual. resentment SIO_000950 is function of is a relation between a function and an entity that it is a property of. is function of SIO_000226 A citation is a textual entity which denotes a source described in the bibliography or reference section of a document. citation SIO_000174 set item is an item in a set. set item SIO_001258 A chemical complex is a chemical substance composed of weakly connected molecules and ions in a known stoichiometry. chemical complex SIO_010342 a circularly helical quality is the quality of a helix that is connected in a circle or loop. circularly helical SIO_001272 An investigational role is a role held by participants involved in an investigation. investigational role SIO_000881 polar is the quality of having a dipole. polar SIO_001046 lutetium atom CHEBI:33382 SIO_011103 a temporal qualifier is pertains to the frequency of the event of interest. temporal qualifier SIO_001288 has boundary is a mereological relation between a whole and boundary located at its periphery. has boundary the surface of an apple is a 2D boundary of the apple. SIO_000054 is ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. is ordered part of SIO_000975 Density (volumetric mass density) is the quantity of mass per unit volume of a substance. density SIO_001406 to identify is the capability to determine the identity of something. to identify SIO_001239 A chemical entity is a material entity that pertains to chemistry. CHEBI:23367 chemical+ chemical entity atom, ion, molecule, chemical substance, SIO_010004 a notation to describe a chemical entity chemical notation SIO_001386 equivalentTo A sequence end position is the position of the last character in a sequence of characters relative to some linear frame of reference. sequence end position SIO_000792 unutrium atom SIO_011084 An intron is a region of a gene that is removed from the final protein open reading frame. intron SIO_010443 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. 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. axis The left vertical and bottom horizontal lines with tickmarks in Graph 1 http://tinyurl.com/opwnvm SIO_000450 An academic is an individual that participates in education and scholarship. academic SIO_000406 3 passion is the intense desire for something. passion SIO_000856 A moleclar site is a spatial region bounded (in part or in whole) by a molecule and may be occupied by other material entities (e.g. drugs). molecular site SIO_010049 DNA sequence A deoxyribonucleic acid sequence is a symbolic sequence of deoxyribonucleic acid residues in a deoxyribonucleic acid. deoxyribonucleic acid sequence SIO_010018 strontium atom CHEBI:33324 SIO_011037 A preferred name is the name that is generally used by some organization. preferred name SIO_000117 A newspaper is a periodical publication containing news regarding current events, informative articles, diverse features, editorials, and advertising. http://purl.org/ontology/bibo/Newspaper newspaper SIO_000163 A polar addition reaction is an addition reaction involving polar residues. polar addition reaction SIO_010519 A wave is a physical entity that travels through space and time, consist of oscillations or vibrations and may be accompanied by the transfer of energy. wave SIO_000650 An exclusion criterion is a criterion that must be absent to satistify the objective. exclusion criterion SIO_000143 A numeric scale of measurement is one that only specifies numeric values. numeric scale SIO_000915 is expression of is a relation between more concrete expression of some conceptualization. is expression of every language edition of 'war of the worlds' are expressions of the story of 'war of the worlds' SIO_000421 A comment is a verbal or written remark often related to an added piece of information, or an observation or statement. comment SIO_001167 is alternate of relates two specialized instances. http://www.w3.org/ns/prov#alternateOf is alternate of two weather forecasts for the city of London produced at different times or by different organizations (etc) are alternates of each other, and instances of / specializations of forecasts for the city of London. SIO_001098 A page total is a textual entity that is about the number of pages in some informational entity. page total SIO_000178 2 A transitive, symmetric, temporal relation in which one entity is causally related with another non-identical entity. core is causally related with SIO_000243 straight is a quality of a bearer that is free of curves, bends, or angles. straight PATO:0002180 [for material entities] SIO_000538 manganese atom CHEBI:18291 SIO_011024 A global minimum data point is a data point that corresponds to a measurement value is smaller than that of all other plotted datapoints. global minimal stationary point SIO_000467 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 SIO_000321 A social relation is a social entity that describes a relationship between two or more individuals or groups. social relation SIO_000287 core#exactMatch joy is an emotion of intense happiness. joy SIO_000850 an open interval is an interval that does not include its endpoints. open interval (0,1) is an open interval that is greater than 0 and less than 1. SIO_001248 to filter is the capability to retain certain entities based on selected attribute(s) while allowing other entities to pass through. to filter SIO_000382 A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms. math+ mathematical entity SIO_000075 An hour is a period of 60 minutes. hour SIO_000433 neptunium atom CHEBI:33387 SIO_011107 is denoted by SIO_000060 A document section is a component of a document. document section SIO_000111 A proposition is a sentence expressing something true or false. proposition SIO_000256 rhodium atom CHEBI:33359 SIO_011044 An active site is a molecular site in which a chemical event occurs (structural transformation or conformational change). active site SIO_010041 A plan is a set of intended actions, through which one expects to achieve a goal. plan SIO_000076 An aromatic ring is a ring in which the electrons are delocalized across all atoms in the ring. aromatic ring SIO_010781 a peptide is an organic polymer composed of between two and fifty amino acids. peptide SIO_001425 a is causally related to b iff there is a causal chain of events from a to b is causally related to SIO_000294 dying is a process in which a biological entity ceases to exist. dying SIO_000583 to infect is the capability to administer a disease-causing organism into some object. to infect SIO_000544 to serve as a template for DNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a DNA molecule may be produced. to serve as a template for DNA synthesis SIO_010091 An antigen is a molecule that can be bound by a major histocompatibility complex (MHC) and presented to a T-cell receptor. antigen SIO_010419 A radar is an object-detection system which uses radio waves to determine the range, altitude, direction, or speed of objects. radar SIO_000928 an amino acid polymer is an organic polymer composed of two or more amino acid residues. amino acid polymer SIO_001427 calcium atom CHEBI:22984 SIO_011019 A document title is a textual entity that summarizes the topic of the document in one sentence. document title SIO_000175 male is a biological sex of an individual with male sexual organs. PATO:0000384 male SIO_010048 nickel atom CHEBI:28112 SIO_011027 A unique identifier is an identifier that uniquely identifies some thing. unique identifier SIO_000675 disappointed disappointing disappointment is the feeling of dissatisfaction that follows the failure of expectations or hopes to manifest. disappointment SIO_000827 is proper part of is an asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole. OBO_REL:proper_part_of core is proper part of SIO_000093 An inorganic reaction is a chemical reaction that involves the transformation of inorganic molecules. inorganic reaction SIO_010510 to be compared is the capability of an object to be examined in order to note the similarities or differences among a set of objects. to be compared SIO_000722 phosphorus atom CHEBI:28659 SIO_011014 is paralogous to is a relation between two entities which indicates their common ancestry as a result of a gene duplication. is paralogous to SIO_000630 a replicate role is a comparative role that holds when one item is a reproduction, facsimile, or a copy of another. replicate role SIO_001417 A mereological chart is a chart that illustrates the parts in the context of the whole. mereological chart SIO_000940 A structural quality is a quality of an object that describes its structure. structural quality SIO_001092 A corporation is an organization that is granted a charter recognizing it as a separate legal entity. corporation SIO_000693 A chemical element is a (effectively) homogeneous substance composed of one type of atom. chemical element SIO_010037 An isomer is a molecule that is compositionally identical to another molecule as a result of a different atomic connectivity. isomer SIO_010455 A function is a capability that satisfies some agentive objective, or (evolutionary) optimization. core function SIO_000017 tRNA A transfer RNA (tRNA) is an RNA molecule that aids in the translation of a messenger RNA (mRNA) to produce a protein product. transfer RNA (tRNA) SIO_001232 A procedure is a process that attempts to achieve one or more objectives by following an established set of actions. procedure SIO_000999 Disgust is a feeling of revulsion or profound disapproval aroused by something unpleasant or offensive. disgust SIO_000828 A clause consists of a subject and a predicate. clause SIO_000493 NOT is a logical operator in that has the value true if its operand is false. negation (not) SIO_000281 to increase the rate of formation is to regulate the rate of formation in a manner that increases this rate relative to a reference process. to increase the rate of formation SIO_000407 A haplotype is one of a set of genomic sequence variants. haplotype SIO_010042 Fear is a negative emotion induced by a perceived threat that induces one to hide or move quickly away from the location of the perceived threat. fear SIO_000837 1 citesAsAuthority A network diagram consists of a set of vertices connected by edges. network diagram SIO_000931 healthy is an organismal state of complete physical, mental and social well-being. healthy SIO_001012 neodymium atom CHEBI:33372 SIO_011092 z-value, z-score, normal score, standardadized variable. A standard score is the (signed) number of standard deviations an observation or datum is above the mean. standard score SIO_001245 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 SIO_000531 A book is a publication composed of a large number of entries. book SIO_000106 An exact cross-reference is a database cross-reference in which one entity is equivalent to the other based on all the entitie's attributes (minus the source). exact cross-reference SIO_001172 mercury atom CHEBI:25195 SIO_011065 zirconium atom CHEBI:33342 SIO_011039 study investigation is the process of carrying out a plan or procedure so as to discover facts or information about the object of study. investigation SIO_000747 to covalently modify is to materially change a molecule by adding or removing covalent bonds between atoms. to covalently modify SIO_010340 A row represents a single, implicitly structured data item in a table. row SIO_000752 life status is the quality of whether something is alive or dead. life status SIO_010057 to modify electronically is the capability to change the electronic properties of an object. to modify electronically SIO_001087 alive is the state of a biological organism that exhibits biological functions. alive SIO_010058 object relational quality refers to a quality in relation to one or more objects object relational quality SIO_001409 a in relation from b is a comparative relation in a is the object of reference in a relation with b. in relation from SIO_000892 An y cartesian coordinate is the coordinate of an object onto the y-axis of a cartesian coordinate system. y cartesian coordinate SIO_000401 an edge is a line connecting two graph vertices. edge SIO_001334 rank 0 tensor a scalar is a rank 0 tensor and is an element of a field that is used to define a vector space. scalar SIO_001431 has agent is a relation between a process and an entity, where the entity is present throughout the process and is a causal participant in the process. OBO_REL:has_agent core sadi has agent SIO_000139 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 SIO_001057 A sound argument is a valid argument with true premises. sound argument SIO_000265 A 3D structure model is a representation of the spatial arrangement of one or more chemical entities. 3d structure model SIO_010530 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 SIO_000469 A linear value axis is a value axis that corresponds to a scaling factor of 1 of the value range. linear value axis SIO_000462 A township is a rural or sub-urban settlement. township SIO_000666 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 SIO_010053 information decoding SIO_001360 An academic department is a division of a university or school faculty devoted to a particular academic discipline. academic department SIO_000686 A database row is a row that is part of a database table. database row SIO_001187 is source of is a relation between a source of information about some entity. is source of SIO_000219 A referent cell is a cell that is the referent of some function or pointer. referent cell SIO_000761 A start position is the proximal position of an object relative to an origin in a linear system. start position SIO_000943 A pharmaceutical ingredient is a part of a pharmaceutical preparation. pharmaceutical ingredient SIO_010338 predicted is the quality of an entity that is thought to exist, as evidenced by some rational procedure. predicted SIO_000036 A liquid solution component is a part of a liquid solution. liquid solution component SIO_010427 A process that modulates the frequency, rate or extent of process involved in the consumption of an object. regulation of object consumption SIO_001150 is implementation of is a relation between an information entity and a specification that it conforms to. is implementation of SIO_000233 A protein is an organic polymer that is composed of one or more linear polymers of amino acids. CHEBI:36080 protein SIO_010043 maternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the maternal line. maternally transmitted SIO_001269 The self-propelled movement of an object. GO:0040011 locomotion SIO_000581 is specialization of is a relation between a more specific instance (in terms of spatial/temporal localization & other attributres) than the other. http://www.w3.org/ns/prov#specializationOf is specialization of a weather forecast for the city of London produced at a specific time is a specialization of a weather forecast for the city of London. SIO_001096 text span start position is the position (offset) of the first character of a text span in relation the text it is from. text span start position SIO_001071 1 A substrate is a molecule that is consumed in the course of a biochemical reaction. substrate SIO_010362 neither good nor poor quality SIO_001296 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) SIO_000282 the capability to encode information in a different representation to encode information SIO_001362 A title is a textual entity that summarily describes some entity. title SIO_000185 subset an ordered list item is an item in an ordered list. ordered list item SIO_001261 a coding frame offset is a numeric value that indicates the number of bases from a reference start codon position. coding frame offset SIO_001275 to combine is the capability to modify a set of objects in a way that the object is merged with another object to form a new object or substance. to combine SIO_010351 a real number is a complex number whose imaginary part is zero, e.g. a + 0i. real number SIO_001442 A centrifugation substance is a substance that is the target or product of centrifugation. centrifugation substance SIO_010426 to extract is the capability to remove certain entities based on selected attribute(s) while allowing other entities to remain. to extract SIO_000389 is provider of is a relation between a source and the entity it makes available. is provider of SIO_000064 physical dimensional quantity A spatial quantity is a quantity obtained from measuring the spatial extent of an entity spatial quantity SIO_000037 unsupported is an existence quality in which there is no evidence to support the existence of the entity in any world (real or hypothetical) unsupported SIO_000992 http://www.w3.org/2004/02/skos/core#broadMatch is broad match to SIO_000491 An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. ion SIO_010456 IP address an IP number is an number to connect to a device on the internet. IP number SIO_001322 to reduce energy is the capability to remove energy from a source. to reduce energy SIO_000374 a is mutual capability of b if and only if the realization of capability a necessarily causes the realization of capability b. is mutual capability of SIO_001101 family history is the systematic narrative and research of past events relating to a specific family, or specific families. family history SIO_010060 A spatial boundary is the closure minus the interior of a subset of a topological space. spatial boundary SIO_000783 has last part is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. has last part SIO_000972 An undergraduate student advisor role is the role of an individual employed at an academic organization that is involved in advising undergraduate students. undergraduate student advisor role SIO_000877 A primer is a nucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation. primer SIO_000779 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. coordinate system SIO_000320 A gene that contains an open reading frame which codes for a protein. http://purl.obolibrary.org/obo/SO_0001217 protein coding gene SIO_000985 A medical health record is a record of a single patient's medical history. medical health record SIO_001027 A quality that has a value that is outside normal or average. abnormal SIO_000555 A state is a set of governing and supportive institutions that have sovereignty over a definite territory and population. state SIO_000662 has evidence is a relation between a proposition and something that demonstrates the truth of the assertion. has evidence SIO_000772 concentration is the amount of substance per unit volume of a solution concentration SIO_001088 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. primary category axis The category axis that corresponds to years in Graph 1 of http://tinyurl.com/opwnvm SIO_000456 A double displacement reaction is a displacement reaction in which two molecules swap ions, effectively displacing each other to form two new molecules. double displacement reaction SIO_010513 to distort is the capability to change the appearance of an entity by some transformation. to distort SIO_000778 race is a characteristic of an individual by heritable phenotypic characteristics, geographic ancestry, physical appearance, ethnicity, and social status. race SIO_001015 An amino acid is an organic molecule composed of a carbon bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom. In the case of glycine, the R group is another hydrogen atom. amino acid SIO_001224 A minute is a period of 60 seconds. minute SIO_000434 a statement of consequence is a statement concerning the result or effect of an action or condition. statement of consequence SIO_001384 specialized object SIO_001353 chlorine atom CHEBI:23116 SIO_011016 Log likelihood is the natural logarithm of the likelihood function log likelihood SIO_001244 very good quality SIO_001298 2 a weak chemical salt is a chemical salt composed of weak eletrolytes. weak chemical salt SIO_001424 A non-transitive temporal relation in which one process is immediately preceded by another process, such that there is no interval of time between the two processes. is immediately preceded by SIO_000251 A word tree is a chart that links phrases with contexts through a tree-like branching structure. word tree SIO_000936 A description is language entity in which elements of a language (formal or natural) are used to characterize an entity. description SIO_000136 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 SIO_000201 A bibliographic attribute is an attribute related to publications. document component SIO_000171 has role is a relation between an entity and a role that it bears. has role SIO_000228 regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is increased. regulation of object production SIO_001151 A unit of measurement is a definite magnitude of a physical quantity, defined and adopted by convention and/or by law, that is used as a standard for measurement of the same physical quantity. unit of measurement SIO_000074 A buffer is a dissolved chemical substance that resists change in pH upon addition of small amounts of acid or base. buffer SIO_010416 A brand name is a trademarked and marketed name of a product. brand name SIO_000119 A publisher role is the role of an individual that prepares and issues creative works. publisher role SIO_000885 A major version number is a version of a software that exhibits a significant change in functionalilty from a prior version. major version number SIO_001030 a containment quality is a quality of being able to contain another entity. containment quality SIO_001341 to be cleaved is the capability to be modified in a way that splits one part of the object from the other. to be cleaved SIO_010365 observational study draws inferences about the possible effect of a treatment on subjects, where the assignment of subjects into a treated group versus a control group is outside the control of the investigator observational study SIO_000976 A gene expression value is a measured value obtained from a gene expression experiment. gene expression value SIO_001077 A website is a collection of documents published on the World Wide Web. website SIO_000296 An author contribution section is a document section that describes the contribution of the authors. author contribution section SIO_000190 right-handed helical quality is the quality in which a clockwise screwing motion moves the helix away from the observed along the line of sight along the helix's axis. right-handed helical SIO_001274 The methods section is a document section containing a description of the methods used in the study. methods section SIO_000199 A mesenger is a molecule involved in either signal detection or signal propagation from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus. messenger SIO_010439 to change appearance is the capability to change the visual attributes of an object. to change appearance SIO_000378 The 3' splice site is the terminal region of an exon that is 3' to the intron that is to be excised. 3' splice site SIO_001223 A keyword is a descriptor in which the association of the word with the entity facilitates information retrieval. keyword SIO_000147 A reference is a textual entity that describes a single source used in the preparation or development of the work. reference SIO_000176 A disease-disease association is an association between two diseases. disease-disease association SIO_001436 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. tree diagram SIO_000945 A sequence start position is the start position for a sequence of characters. sequence start position SIO_000791 A geographic region is a spatial region whose boundaries are typically defined against some material frame of reference (like the earth). geographic region The spatial region occupied by the province of ontario; the spatial region occupied by a lake. SIO_000414 A process that modulates the frequency, rate or extent of translation. regulation of translation SIO_001126 A blog is a publication accessible at some website and is typically about various experiences. blog SIO_000155 vanadium atom CHEBI:27698 SIO_011022 A dependent variable is one whose value changes as a consequence of changes in other values in the system. dependent variable SIO_000921 A human population refers to a collection of human beings. human population SIO_001062 planned is a process status for a process that has not yet started, but is referred to in a plan. planned SIO_001060 A molecule is a single chemical entity composed of fully covalently bonded atoms. molecule CHEBI:23367 SIO_011125 An informational entity identifier is an identifier for an informational entity. informational entity identifier SIO_000731 A catalyzed reaction is a chemical reaction that is facilitated by a catalyst. catalyzed reaction SIO_010508 A sequence variant role is a comparative role in which the composition of characters in a sequence differs when compared to another entity of similar type. sequence variant role SIO_000478 graphite is an allotrope of carbon which is a conductor, and is the most stable form of solid carbon. graphite SIO_010788 An organic reaction is a chemical reaction involving at least one organic molecule. organic reaction SIO_010516 secondary active transport or co-transport uses electrochemical potential difference created by pumping ions out of the cell to transport molecules across a membrane. secondary active transport SIO_000578 A chromosome is a molecular complex of circular or linear DNA and bound proteins. chromosome SIO_000899 to cool is the capability to decrease the internal kinetic energy of a material. to cool http://purl.obolibrary.org/obo/OBI_0000387 SIO_000347 barium atom CHEBI:32594 SIO_011055 has ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. has ordered part SIO_000974 is positionally before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity. is positionally before SIO_000240 A microarray experiment is an experiment that involves a microarray device to measure the expression of one or more genes. microarray experiment SIO_001076 has basis is a relation between a realizable entity and the quality that forms the basis for it. has basis the solubility of salt (the disposition) is based on the molecular structure of NaCl (the quality) that allows the polarized water-molecules (the trigger) to break the ion bonds (the realization). SIO_000641 A unique cell is a cell that contains a unique value in the cellular automaton. unique cell SIO_000759 A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. software method SIO_000098 nullizygous is the quality of a biological organism in which there are no allelles at a given locus. nullizygous SIO_001267 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 SIO_001351 0 is disposition of is a relation between a disposition and the entity that it is a property of. is disposition of SIO_000236 A secondary structure descriptor describes local topological patterns in a biopolymer. secondary structure descriptor SIO_010022 to be transported is the disposition to undergo motion. to be transported SIO_010368 has participant is a relation that describes the participation of the object in the (processual) subject. OBO_REL:has_participant core has participant SIO_000132 full is the quality of contain an entity such that there is no more space for any additional entity. full SIO_001340 is last part of is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. is last part of SIO_000973 bioassay An assay is an investigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte) which can be a drug or biochemical substance or a cell in an organism or organic sample. assay SIO_001007 The quality of having a charge that is not a full multiple of 1 unit charge. partial charge SIO_000809 negative regulation process down-regulation is a process that decreases the frequency, rate or extent of one or more processes in relation to a reference state. process down-regulation SIO_010296 A legal name is a name given at birth, or which appears on their birth certificate, marriage certificate, or change of name certificate. legal name SIO_000184 agreement is the result of consensus decision making when members of the group do not all agree. disagreement SIO_000967 desire is a strong emotion of wanting to have something or wishing for something to happen. desire SIO_000825 A triple bond is a covalent bond between a pair of atoms in which three pairs of electrons are shared. triple bond SIO_010500 A gene regulatory component is a gene component that exerts a regulatory function. gene regulatory component SIO_010085 to excite is the capability to supply energy to a materila by bombarding it with energetic particles (e.g., photons). to excite SIO_000383 regulation of a process is a process that modulates the duration, frequency, spatial extent of a target process. regulation of process SIO_000609 to emit is the capability to release some physical entity (light, pollution, etc). to emit SIO_000384 A measurement value is a quantitative description that reflects the magnitude of some attribute. measurement value SIO_000070 A differential equation is a mathematical equation for an unknown function of one or several variables that relates the values of the function itself and its derivatives of various orders. differential equation SIO_000569 A common name is a name that is commonly used. common name SIO_000118 shock is an emotion of sudden upset or surprise. shock SIO_000866 to change the activation energy is to change the amount of energy required to form or break a chemical bond. to change the activation energy SIO_000551 A supernatent is a liquid substance that remains after centrifugation. supernatant SIO_010425 A phenotype is an observable characteristic of an individual. phenotype SIO_010056 Specific gravity is the ratio of the density of a substance to the density of a reference substance; equivalently, it is the ratio of the mass of a substance to the mass of a reference substance for the same given volume. specific gravity SIO_001355 to investigate is the capability to uncover facts. to investigate SIO_000408 completely quantifier SIO_001307 A table is a figure that consists of an ordered arrangement of columns and rows. table SIO_000419 to assemble is the capability to combine entities together into a larger object that persists in time. to assemble SIO_000388 A phrase is a group of words functioning as a single unit in the syntax of a sentence. phrase SIO_000483 radium atom CHEBI:33325 SIO_011073 negative is an assertional qualifier that expresses the falsity or lack of truth of a basic assertion. negative SIO_001211 A department chain role is the role of an individual that heads a department at a academic organization. department chair role SIO_000875 selector A text span is a subset of contiguous sequence of characters of a textual entity. text span SIO_001073 The role of a chemical entity that increases the rate of reaction. activator role SIO_000804 ploidy is the cellular quality relating to the amount of DNA contained in a cell. ploidy SIO_010278 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. point SIO_000507 An academic organization is a lawfully recognized organization that confers diplomas, degrees and other forms of recognition of academic achievement. academic organization SIO_000285 samarium atom CHEBI:33374 SIO_011094 number of objects produced is a count of objects that were produced in some process. number of objects produced SIO_001160 A ribonucleotide residue is a part of a molecule that derives from a ribonucleotide. ribonucleotide residue SIO_010337 a cellular phone number is a number to connect to a mobile device cellular phone number SIO_001320 1 neon atom CHEBI:33310 SIO_011009 Pain is an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. pain SIO_000951 A start time is a time instant pertaining to the time at which a process begins. start time SIO_000669 A dipole-dipole interaction is a weak submolecular interaction between strongly electronegative atoms. dipole-dipole interaction SIO_010503 A biochemical reaction is a biochemical process that involves the conversion of at least one chemical participant (target) into another (product) by an enzyme (agent). biopax:BiochemicalReaction biopax:Conversion biochemical reaction SIO_010036 A morpheme is the smallest semantically meaningful unit in a language. morpheme SIO_001040 a middle initial is an abbreviated middle name. middle initial SIO_001318 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 SIO_001349 A co-factor role in which the chemical entity is modified during catalysis and must be regenerated. co-enzyme role SIO_000800 The DisGeNET pleiotropy index is a measure of specificity as it pertains to classes of disease. The disease pleotropy index is computed from the ratio of the number of disease classes associated with an entity over the total number of disease classes multplied by 100. The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pleiotropy DisGeNET Pleiotropy Index SIO_001352 planning is the agentive process of developing a plan that specifies a set of actions in order to meet a set of goals or objectives. planning SIO_000739 drafted draft is the quality of text that has not yet complete. draft SIO_001036 An decrease in the number of objects produced is the negative value of a difference in number of objects produced. decrease in number of objects produced SIO_001164 A drug-drug interaction is an interaction in which two drugs interact in such a way to produce a non-additive biological response. drug drug interaction SIO_001006 2 to fluoresce is to emit light as a result of absorbing light or other electromagnetic radiation. to fluoresce SIO_000895 RNA sequence A ribonucleic acid sequence is a symbolic sequence of ribonucleic acid residues in a ribonucleic acid. ribonucleic acid sequence SIO_010017 a notation is a series or system of written symbols used to represent numbers, amounts, or elements. notation SIO_001385 2 A measurement of a spatial location relative to a frame of reference or other objects. position SIO_000056 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 SIO_000946 has implementation is a relation between a specification and an implementation that conforms to it. has implementation SIO_000234 chromium atom CHEBI:28073 SIO_011023 A slope or gradient of a line describes its steepness, incline, or grade. A higher slope value indicates a steeper incline. Slope is normally described by the ratio of the "rise" divided by the "run" between two points on a line. slope SIO_001184 to test a hypothesis is the capability to evaluate the truth value of a proposition based on gathered evidence. to test a hypothesis SIO_001219 A book volume is a book that is part of a collection. book volume SIO_000156 A beta strand is structural region of a protein that is characterized by a roughly planar sequence of amino acid residues forming hydrogen bonds between the N-O and the C=O of another part of the peptide and having their side chains perpendicular to the planar axis. beta strand SIO_010469 A molecular inhibitor is a molecular regulator that realizes its disposition to conformationally change a target molecule and decrease its functionality. inhibitor SIO_010435 A class is a collection of sets which can be unambiguously defined by a property that all its members share. class SIO_000138 grief is an emotion in response to loss, whether physical or abstract including death, unemployment, ill health or the end of a relationship. grief SIO_000842 The number of elements of a finite set of objects. count SIO_000794 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 SIO_001344 A homogeneous substance is a substance that is composed of a uniform type of entity. homogeneous substance SIO_010463 a semantic web service is a web service that provides a formal, machine understanble description of its functionality. semantic web service SIO_001189 A process that modulates the frequency, rate or extent of transcription. regulation of transcription SIO_001125 data collection is the process of acquiring information. data collection SIO_001052 A pie chart is a circular chart divided into sectors each of whose length is proportional to the quantity it represents. pie chart SIO_000929 loathing is an intense dislike or disgust. loathing SIO_000851 A deoxyribonucleic acid is an organic polymer composed of a sequence of deoxyribonucleotide residues. deoxyribonucleic acid SIO_010010 An honor's thesis is a thesis prepared as a requirement for an honor's undergraduate degree. honor's thesis SIO_000166 media are audo/visual/audiovisual modes of communicating information for mass consumption. media SIO_001194 An active ingredient is a molecular entity that exhibits biological activity. active ingredient SIO_010077 A partial negative charge is a negative charge where the value of the charge is negative. partial positive charge SIO_000807 severe is a qualitative intensity value that is more intense than strong, but less intense than fatal. severe SIO_001215 A nurse is an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations. nurse SIO_000398 2 A capability is a realizable entity whose basis lies in one or more parts or qualities and reflects possibility of an entity to behave in a specified way under certain conditions or in response to a certain stimulus (trigger). capability+ core capability SIO_000112 An invalid argument is an argument where the truth of the conclusion is false because it is not a logical consequence of the premises. invalid argument SIO_000267 1 A SADI web service invocation is the excution of a SADI web service. sadi SADI web service invocation SIO_001193 is start time of SIO_000682 double stranded nucleic acid is a molecular complex composed of two weakly connected ribonucleic acids. double stranded RNA SIO_001178 An assertional qualifier is the quality of affirmation, either being positive or negative. assertional qualifier SIO_001209 excellent quality SIO_001313 The role of a chemical entity present at the end of a chemical reaction. product role SIO_000798 has substrate is a relation between a process and an object where the object is destroyed by its participation in the process. has substrate SIO_000905 existence quality is the quality of an entity that describe in what environment it is known to exist. existence quality SIO_000959 full name A personal name is a name to identify an individual person and usually comprises of a first name and a last name. personal name SIO_000183 A non-protein coding RNA (ncRNA) is a RNA molecular that cannot be used as a template for generating a protein product. non-protein coding RNA (ncRNA) SIO_001235 is greater than to is a comparison relation between two quantities in which the first has a value larger than the second. is greater than SIO_000734 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 SIO_000153 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. block histogram SIO_000932 A name is a label used to identify an entity. name SIO_000116 A file is an information-bearing object that contains a physical embodiment of some information using a particular character encoding. http://www.w3.org/ns/dcat#Distribution file SIO_000396 A chemical-chemical association is an association between two chemical entities. chemical-chemical association SIO_001435 A decimal scale of measurement is one that only specifies decimal values. decimal scale SIO_000916 An inclusion criterion is a criterion that must be present to satisfy some objective. inclusion criterion SIO_000142 positive regulation process up-regulation is a process that increases the frequency, rate or extent of one or more processes in relation to a reference state. process up-regulation SIO_010295 1 information content entity is an object that requires some background knowledge or procedure to correctly interpret. core ice+ information content entity SIO_000015 A perimeter is a length of the outline that surrounds a two-dimensional shape. length of perimeter SIO_000046 A legal document proposing or enacting a law or a group of laws. legislation SIO_001372 A transitive temporal relation in which an entity mainstains identity from one state to another. transforms into SIO_000655 a relation between a product and the information content entity that specifies it. is specified by SIO_000339 A non-polar addition reaction is an addition reaction involving non-polar residues. non-polar addition reaction SIO_010520 A is spatiotemporally related to B iff A is in the spatial or temporal vicinity of B core is spatiotemporally related to SIO_000322 The uncertainty value (margin of error) of a measurement is a range of values likely to enclose the true value. uncertainty value SIO_000769 fictional is the quality of an entity that exists only in a creative work of fiction. fictional SIO_000961 to change spatially is the capability to affect the physical movement of some entity. to change spatially SIO_000392 A temporal relation in which an entity mainstains identity from one state to another. immediately transforms into SIO_000656 not implemented in standard distribution ovopub is transitively related to SIO_001247 A page range denotes the start and end page in some document. page range SIO_000177 A data storage device is a device that is capable of storing information. data storage device SIO_000596 oxygen atom CHEBI:25805 SIO_011007 increased regulation leads to an increase in the consumption of an object of specified type. increased object consumption from increased regulation SIO_001148 predicting is the process of formulating a proposition about a state of affairs which might be realized in the future. predicting SIO_000748 A drug regulatory authority is a regulatory authority which acts to control what substances may be used to treat individuals. drug regulatory authority SIO_010383 A primary structure descriptor describes a biomolecular object in terms of a 1D or 2D topology. primary structure descriptor SIO_010014 A descriptor (index term, subject term, subject heading) is a term that captures the essence of the topic of a document. descriptor SIO_000133 glassy carbon is an allotrope of carbon which is widely used as an electrode material in electrochemistry, as well as for high temperature crucibles and as a component of some prosthetic devices. glassy carbon SIO_010794 to separate is the capability to i) distinguish some entities based on some attribute(s) and ii) subsequently physically displace them. to separate SIO_000349 a label is a term that is associated with some entity label SIO_000179 a home phone number is the number to connect to an phone at a place of residence. home phone number SIO_001325 1 A hydrogen bond is a weak submolecular interaction formed between a hydrogen atom and a electronegative atom. hydrogen bond SIO_010033 A molecular orbital (or MO) is a mathematical function describing the wave-like behavior of an electron in a molecule. molecular orbital SIO_000561 A statistical association is any relationship between two measured quantities that renders them statistically dependent. statistical association SIO_000898 A molecular entity role is a chemical entity role held by a molecule. molecular entity role SIO_000889 A gene promoter is a region of DNA that initiates transcription of a particular gene. gene promoter SIO_010446 shame is the emotion borne from feeling responsible for the commission of an offense. shame SIO_000865 film moving pictures A movie is a series of images that are displayed in rapid succession to give the impression of movement. movie SIO_000297 A data item consists of information that has been collected/generated towards some purpose. data item SIO_000069 A magazine is a periodical that typically contains essays, stories, poems, etc., by many writers, and often photographs and drawings, frequently specializing in a particular subject or area, as hobbies, news, or sports. http://purl.org/ontology/bibo/Magazine magazine SIO_000121 a rank nonzero tensor is a tensor with a rank greater than zero. rank nonzero tensor SIO_001434 is satisfied by SIO_000363 An ontology document is a document that contains an ontology. ontology document SIO_000129 Hate is a deep and emotional extreme dislike, directed against a certain object or class of objects. hate SIO_000411 to serve as a template for molecular synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which another molecule may be produced. to serve as a template for molecular synthesis SIO_010088 A is directly connected to B iff there exists a path direclty between A and B. is directly connected to SIO_000652 1 A mature RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns. mature mRNA SIO_010096 0 amino acid sequence polypeptide sequence A protein sequence is a symbolic sequence of amino acid residues in a protein or class of proteins. protein sequence SIO_010015 A collection of points is a geometric entity that contains a non-zero set of geometric points. collection of points SIO_000546 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. vowel SIO_000979 A process mediated by rna that modulates the frequency, rate or extent of translation. rna mediated regulation of translation SIO_001131 genetic polymorphism is the description of a difference in genetic composition at some location. genetic polymorphism SIO_010026 alternative A is narrower than B iff the meaning of term A is narrower in scope than the meaning of term B http://www.w3.org/2004/02/skos/core#broader is narrower than SIO_000427 A gene is part of a nucleic acid that contains all the necessary elements to encode a functional transcript. biopax:Gene http://purl.obolibrary.org/obo/SO_0000704 gene SIO_010035 A gene enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster. gene enhancer SIO_010086 iodine atom CHEBI:24859 SIO_011052 A chemical effect is a chemical interaction in which a chemical elicits a marked characteristic of a biological system. chemical effect SIO_001005 A mass spectrometer is a device that identifies ions based on their mass to charge ratio using an electromagnetic field. http://purl.obolibrary.org/obo/OBI_0000049 mass spectrometer SIO_001237 a strong chemical salt is a chemical salt that is composed of strong electrolytes. Strong chemical salts contain Na,K,NH4 or NO3, CIO4, CH3COO. strong chemical salt SIO_001423 potassium atom CHEBI:26216 SIO_011018 A relation between two objects, in which the first object is produced from the information contained in the second object. is encoded by SIO_010079 A reason is a justification that specifies the motive for an action or a determination. reason SIO_001053 A trans-regulatory element is a DNA sequence associated with the regulation of a gene located outside the genomic region supporting the corresponding structural DNA region of the trans-regulatory element (i.e., a different DNA strand or different chromosome). trans-regulatory element SIO_001226 A count of the instances of a class or members in a collection. member count SIO_001115 maintenance of duration of process is a process that regulates a target process to maintain its duration within an expected interval. maintenance of duration of process SIO_001143 A hole is a site that is opening into or through something. hole SIO_000660 conversing a form of interactive, spontaneous communication between two or more agents who are following rules of etiquette. conversing SIO_000941 A solute is a substance that becomes dissolved in a solvent. solute SIO_010418 biological sex is the quality of a biological organism based on reproductive function or organs. biological sex SIO_010029 A subject role is the role of an individual that is the target of the study. subject role SIO_000883 process number is a number associated with a process that denotes its ordinal position in a set of processes. process number SIO_000305 maintenance of frequency of process is a process that regulates the number of occurences of a target process type to a specified number or interval. maintenance of frequency of process SIO_001144 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 SIO_000513 A medical procedure is a procedure to identify, examine, alleviate or eliminate an undesirable biological disease or disorder. medical procedure SIO_001024 dag 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. directed acyclic graph SIO_001332 An end time is a time instant pertaining to the time at which a process ends. end time SIO_000670 speculation is an opinion based on incomplete evidence. speculation SIO_001065 real is the quality of an entity that exists in real space and time. real SIO_000960 An affiliation is a social relation which indicates the partnership between two or more entities. affiliation SIO_000173 A lipid residue is a part of an organic molecule that was derived from a lipid molecule. lipid residue SIO_000556 palladium atom CHEBI:33363 SIO_011045 A parameterized data transformation is a data transformation whose behaviour may be modified by one or more parameters. parameterized data transformation SIO_000595 fluorine atom CHEBI:24061 SIO_011008 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 SIO_000989 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 SIO_000418 A metabolic pathway is a series of biochemical reactions that begins with one or more substrates and ends with one or more products. metabolic pathway SIO_010532 A percentage is a number that is a ratio expressed as a fraction of 100. It is denoted using the percent sign "%". percentage SIO_001413 silver atom CHEBI:30512 SIO_011046 A is related to B iff there is some relation between A and B. 'is related to' is the top level relation in SIO core relations+ is related to SIO_000001 An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) organic molecule SIO_010072 dread is the instense negative emotion that induces fear and apprehension. dread SIO_000829 information processing is a process that involves the generation or use of information. information processing SIO_000649 A covalent bond is a strong submolecular interaction between atoms. covalent bond CHEMINF:000063 SIO_011118 A representation is a entity that in some way represents another entity (or attribute thereof). representation SIO_000612 is covalently connected to (transitive) SIO_000288 2 biological pathway A pathway is an effective specification that outlines a set of actions that forms a way to achieve an objective. pathway SIO_001107 fitness is the quality of an object with respect to some stated functions or evolutionary adaptation. fitness SIO_000357 A recipe is a set of instructions that describe how to prepare or make something. recipe SIO_001042 A clinical trial is an intervention trial to determine the safety and efficacy of medical interventions (e.g., drugs, diagnostics, devices, therapy protocols). clinical trial SIO_001000 A student role is the role of an individual that is enrolled in courses at an academic institution. student role SIO_000707 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 SIO_000616 A crystal structure is the arrangement of atoms or molecules in a crystalline liquid or solid. crystal structure SIO_001100 finalized is the quality of a textual entity that is in its final form. finalized SIO_001037 to describe is the capabilty to communicate facts about an entity. to describe SIO_001221 2 A terminology is a set of terms used for a specified application. terminology SIO_001396 is evidence for SIO_000773 regulation of a process duration is a process that modulates the frequency of another process relative to some reference process. regulation of process frequency SIO_001135 biosynthesis is the synthesis of an organic compound in a living organism, usually aided by enzymes. biosynthesis SIO_000590 A chemical degradation pathway is a pathway involved in the disassembly of a chemical. chemical degradation pathway SIO_010528 replica quality is the quality of an object that is an exact copy of another object. replica quality SIO_001412 A PDB chain identifier is a alphabetical label to identify a molecule in a structure provided by the Protein DataBank . PDB chain identifier SIO_010031 A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation. decreased molecular production from increased regulation SIO_001204 core#example A biomolecular structure descriptor is structure description for organic compounds. biomolecular structure descriptor SIO_011119 to remove a covalent bond is the capability to covalently modify a chemical entity by removing a covalent bond. to remove a covalent bond SIO_001085 A molecular tracer role is a reactant role of a molecular entity that serves as a marker for the presence, abundance, or location of a molecular target that it associates with. molecular tracer role SIO_000896 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 SIO_000318 A bar graph is a statistical graph with rectangular bars of lengths proportional to that value that they represent. bar graph Graphs 3,4,5 in http://tinyurl.com/opwnvm SIO_000443 A co-enzyme role of a chemical entity that is transiently associated, and is regenerated in a separate reaction. co-substrate role SIO_000802 van der Waals' interaction is an a weak submolecular interaction between an instantaneous dipole and induced dipole. van der Waals interaction SIO_010504 sad unhappiness unhappy sadness is emotional pain associated with, or characterized by feelings of disadvantage, loss, despair, helplessness, sorrow, and rage. sadness SIO_000863 erbium atom CHEBI:33379 SIO_011100 actinium atom CHEBI:33337 SIO_011074 A measurement scale is a functional specification that specifies an allowed range of categories or values. measurement scale SIO_000912 quantity modifier SIO_001299 denotes is a relation between an entity and what it is a sign or indication of, or what specifically means. denotes the symbol '%' denotes a proportion in relation to a whole. SIO_000020 A biologic, also known as a biologic medical product, biological, or biopharmaceutical, is any pharmaceutical drug product manufactured in, extracted from, or semisynthesized from biological sources. biologic SIO_001392 A question is a linguistic expression used to make a request for information. question SIO_000085 tantalum atom CHEBI:33348 SIO_011058 An association is a relationship between two or more entities derived by some informational analysis. association SIO_000897 rRNA gene A ribosomal RNA gene is a gene that codes for a ribosomal RNA molecule. http://purl.obolibrary.org/obo/SO_0001637 ribosomal RNA gene SIO_001182 A decomposition reaction is an inorganic reaction in which molecule is fragmented into submolecules or atoms. decomposition reaction SIO_010511 0.0 parental transmition is the quality of a biological organism in which the (genetic) material is transmitted from a parental unit. parental transmission SIO_001268 title InCHI notation SIO_001387 mostly quantifier SIO_001306 cerium atom CHEBI:33369 SIO_011090 A non-polar solvent is a solvent that exhibits a non-polar quality. nonpolar solvent SIO_010460 The amount of change accumulated per unit time. rate of change SIO_001365 ununoctium atom SIO_011089 true is a truth value that indicates that it holds under all possible worlds. true SIO_000269 a unigene cluster is a collection of transcripts (ESTs and mRNAs) that map to a particular genomic region. cluster of transcripts unigene cluster SIO_001382 to be activated is the capability to be modified in such a way that the conformational change leads to an increase in another capability. to be activated SIO_010372 An allotrope is a structural variant of a chemical element. allotrope SIO_010785 2 satisfaction is an emotion of fulfillment of one's wishes, expectations, or needs, or the pleasure derived from this. satisfaction SIO_000864 intensity is a quality that represents the strength or degree of something. intensity SIO_001212 An x cartesian coordinate is the coordinate of an object onto the x-axis of a cartesian coordinate system. x cartesian coordinate SIO_000400 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 SIO_001300 An identifier is a label that specifically refers to (identifies) an entity (instance/type). identifier SIO_000115 A nurse role is the role of an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations. nurse role SIO_000714 decreased chemical destruction is a process in which there is a decrease in the amount of chemical destroyed relative to some reference process decreased chemical destruction SIO_001208 dbxref A database cross-reference is an association between one data item and another. database cross-reference SIO_001171 empty is the quality of not containing some thing empty SIO_001339 A gene component is a component of a gene. gene component SIO_010444 A belief is a proposition that is believed to be true. belief SIO_000360 curium atom CHEBI:33390 SIO_011110 is unit of is a relation between a unit and a quantity that it is a multiple of. is unit of SIO_000222 has disputing evidence is a relation between a proposition and something that disputes (does not directly support) the truth of the assertion. is disputed by SIO_000207 boredom is the emotion experience by those not interested in their surroundings or available activities. boredom SIO_000820 to contain is the capability to bound or constrain a physical entity in some site. to contain SIO_000380 A minor version number is a version of a software that exhibits minor features or significant fix from a prior version. minor version number SIO_001031 chemical transport is the directed movement of a chemical entity by some agent (e.g. transporter). biopax:Transport chemical transport SIO_010283 A quality that has a value that is decreased compared to normal or average. PATO:0002301 decreased SIO_000751 chemical structure is the structure of a chemical entity in terms of its molecular geometry and electronic structure. chemical structure SIO_000625 group 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. collective SIO_000620 1 has part is a transitive, reflexive and antisymmetric relation between a whole and itself or a whole and its part. has part a collection of cars has as a car as a part;a car has an engine as a part; a car has a piston as a part; SIO_000028 chemical group A chemical functional group is a submolecule that confers specific chemical properties. chemical functional group SIO_000624 sample quality is the quality of an object that is drawn from a larger population. sample quality SIO_001411 description contentment pleasure satisfaction is the emotion of fulfillling one's wishes, expectations, or needs. satisfaction SIO_001284 Escherichia coli (e coli) is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms. e.coli SIO_000489 The role of a chemical entity involved in the mechanism for enzyme-mediated catalysis. cofactor role SIO_000799 A terminal point is a point that defines the finite extension of a line. terminal point SIO_000532 to magnify is the capability to increase the appearance of the size of an object. to magnify SIO_000345 A medical role is the role of an individual that is a participant in the delivery of medical care. medical role SIO_000712 most of the time most refers to in the majority of occasions most of the time SIO_001291 a represents b when a serves as a sign, symbol or model of b. core represents SIO_000210 A communication device is a device that facilitates the transmission of information through encoded in an audio or digital signal between a sender and a receiver. communication device SIO_000957 A carbon allotrope is a chemical substance composed of carbon. carbon allotrope SIO_010786 has evidence is a relation between a proposition and something that refutes (is incompatible with) the truth of the assertion. is refuted by SIO_000774 A quality that has a value that is increased compared to normal or average. PATO:0002300 increased SIO_000640 A top value axis is a value axis that is spatially positioned to the top of the plot area. top value axis SIO_000902 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 SIO_001058 hypothetical is the quality of an entity that is conjectured to exist. hypothetical SIO_001186 holmium atom CHEBI:49648 SIO_011099 a is mutual role of b if and only if the realization of role a necessarily causes the realization of role b. is mutual role of SIO_000710 Anabolism is the set of metabolic processes that take apart larger chemical entities units into smaller chemical entities. catabolism SIO_010309 An answer is a reply to a question. answer SIO_000785 agreement is the result of consensus decision making when members of the group agree. agreement SIO_000966 An infinite line is a line that extends outwards in both directions of a single dimensional and is not bounded by terminal points. infinite line SIO_000539 seaborgium atom CHEBI:33351 SIO_011077 hurt is an unpleasant feeling, emotion or sensation. hurt SIO_000845 The role of a chemical entity that modifies the rate of reaction. regulator role SIO_000880 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. quadrilateral SIO_000517 description 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. 5i is an imaginary number, and its square is -25. imaginary number SIO_001441 a relation between an entity and an identifier. has identifier SIO_000671 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 SIO_000465 protege#defaultLanguage is variant of: a relationship indicating that two entities are different (by some measure), but either achieve the same objectives in different ways or are permutations of one another (temporal, logical or otherwise) core is variant of SIO_000272 rhenium atom CHEBI:49882 SIO_011060 A mode is the value that appears most often in a set of data. mode SIO_001111 A gene-disease association in which a gene mutation is known to modify the clinical presentation of the disease. gene-disease association linked with modifying mutation SIO_001342 A gene that is located on DNA. dna gene SIO_010100 A poison is a drug that is harzardous or toxic to an organism when ingested at a certain quantity. poison SIO_010076 A bill is proposed legislation under consideration by a legislature. bill SIO_001376 ununpentium atom SIO_011086 An abstract role is a role whose basis lies in spatial/temporal or comparative relations. abstract role SIO_000678 A deletion variant role is the role of an sequence that lacks a sub-sequence relative to the frame of reference. deletion variant role SIO_000481 A gene-disease association in which the gene/protein is involved in the etiology or maintenance of the disease. gene-disease biomarker association SIO_001121 is similar to is a relation between two entities that share one or more features. is similar to SIO_000283 Brownian motion is the seemlingly random movement of particles suspended in a fluid. brownian motion SIO_000571 Suffering is the unpleasant emotion and aversion associated with the perception of harm or threat of harm in an individual. suffering SIO_000869 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. trend line SIO_000527 A 'surrounds' B iff the A 'contains' B and A 'is adjacent to' B or A 'is directly connected to' B. surrounds SIO_000324 is parameter in is a relation between a data item and some data transformation process. is parameter in SIO_000553 A language label is a label that denotes the language of a textual entity. language label SIO_000180 A patient is an individual that is the recepient of medical care. patient SIO_000393 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 SIO_001068 promethium atom CHEBI:33373 SIO_011093 A polyhedral surface is composed of polygonal faces. polyhedral surface SIO_000504 A comparative role is an abstract role which holds by comparing some attribute of another object of reference. comparative role SIO_000721 A year is a period of time taken by a planet to make one revolution around the sun. year SIO_000428 to immobilize is the capability to contain an entity in such a way that it may not move in space. to immobilize SIO_000381 A secondary graph title is a secondary title that describes a statistical graph. secondary graph title SIO_000474 The five prime untranslated region (5' UTR) is a section of messenger RNA (mRNA) and the DNA that codes for it that starts at the +1 position (where transcription begins) and ends one nucleotide before the start codon (usually AUG) of the coding region. 5' untranslated region SIO_010064 praseodymium atom CHEBI:49828 SIO_011091 registry A catalog is a systemic collection of items of the same type. catalog SIO_001241 XMLSchema#date charge quality is the quality pertaining to electric charge. charge quality SIO_010442 A complete charge is a charge where the value of the charge is a multiple of 1. complete charge SIO_000810 is disputing evidence for SIO_000209 lust is the strong desire for sex. lust SIO_000853 regret is a feeling of sadness, repentance, or disappointment over something that has happened or been done. regret SIO_000861 An allosteric site is a binding site that when bound to particular ligand changes the conformational state and affects its functionality. allosteric site SIO_010050 contributor completed is that status of a process that successfully unfolds. completed SIO_000034 A receptor molecule is a molecule that has the capability to bind to a signal and propogate a response to that signal. receptor SIO_010420 A report is a textual document made that present focused, salient content to a specific audience. report SIO_001026 to associate is the capability to physically interact with another object. to associate SIO_000690 A single bond is a covalent bond between a pair of atoms in which one pair of electrons are shared. single bond SIO_010498 A publishing role is the role of an individual that is involved in the preparation and issue of creative works for consumption by a wider audience. publishing role SIO_000884 indecisiveness indecision is the emotion of being unable to choose between two or more possible courses of action. indecision SIO_001287 A non-transitive temporal relation in which one entity is immediately derived from a non-identical entity such that there are no intermediate entities between them. is immediately derived from SIO_000247 thulium atom CHEBI:33380 SIO_011101 berkelium atom CHEBI:33391 SIO_011111 hunger is the craving for food. hunger SIO_001282 An addition reaction is an organic reaction where two or more molecules combine to form a larger one. Addition reactions are limited to chemical compounds that have multiply-bonded atoms: * Molecules with carbon-carbon double bonds or triple bonds * Molecules with carbon - hetero double bonds like C=O or C=N addition reaction SIO_010518 excitement is a positive emotion of feeling great enthusiasm and eagerness. excitement SIO_000836 A set is a collection of entities, for which there may be zero members. set SIO_000289 An RNA transcript is an RNA molecule that is produced from transcription of a nucleic acid template. RNA transcript SIO_010450 An optical isomer is a stereoisomer that rotates the plane of polarization of a beam of plane polarized light. optical isomer SIO_010778 a pharmacodynamic pathay is a regulatory pathway in which a drug molecule regulates the activity of one or more components organized in a pathway. pharmacodynamic pathway SIO_001256 An object model is a representation of an object. object model SIO_000648 A document is a bounded physical or digital representation of a body of information designed with the capacity (and usually intent) to communicate. document SIO_000148 A buffer role is the role of a chemical substance which maintains a pH at a near constant value. buffer role SIO_000887 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 The category axis that corresponds to months in Graph 1 of http://tinyurl.com/opwnvm SIO_000457 2 osmium atom CHEBI:30687 SIO_011061 The increase of regulation leads to a increased spatial extent of the target process. increased spatial extent of process from increased regulation SIO_001140 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 SIO_000980 transcription is the process of creating a complementary RNA copy of a sequence of DNA. transcription SIO_010300 Likelihood is the hypothetical probability that an event that has already occurred would yield a specific outcome. likelihood SIO_001243 2 An RNA transcript component is a region of an RNA transcript. RNA transcript component SIO_010095 A social entity pertains to the interaction among individuals and groups. social entity SIO_000009 indifference is an emotion characterized by lack of interest, concern, or sympathy. indifference SIO_000847 A graduate student advisor role is the role of an individual employed at an academic organization that is involved in advising graduate students. graduate student advisor role SIO_000878 a left open interval is an interval in which there is no element that is smaller than all other elements. left open interval SIO_001251 to decrease the rate of formation is to regulate the rate of formation in a manner that decreases this rate relative to a reference process. to decrease the rate of formation SIO_000499 A double bond is a covalent bond between a pair of atoms in which two pairs of electrons are shared. double bond SIO_010499 A gene that is located on RNA. rna gene SIO_010101 is supporting evidence for SIO_000208 to add a covalent bond is the capability to covalently modify a chemical entity by adding a covalent bond. to add a covalent bond SIO_001086 A hard disk drive (HDD) is a non-volatile, random access device for digital data. It features rotating rigid platters on a motor-driven spindle within a protective enclosure. Data is magnetically read and written on the platter by read/write heads that float on a film of air above the platters. hard disk drive SIO_000598 to actively interact with is the capability to interact with another entity in a way that requires physical contact. to actively interact with SIO_000494 A rat is a medium-sized, long-tailed rodent of the superfamily Muroidea. rat SIO_000487 to modify the oxidation state of is to change the number of electrons of a molecule, atom or ion. to modify oxidation state of SIO_010360 A global maximum stationary point is a data point that corresponds to a measurement value is larger than that of all other plotted datapoints. global maximal stationary point SIO_000466 text span end position is the position (offset) of the last character of a text span in relation the text it is from. text span end position SIO_001072 A design specification is a specification that provides precise and explicit information about the requirements for a product design. design specification SIO_000316 a chemical-gene association is an association between a chemical and a gene. chemical-gene association SIO_001257 A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation. increased molecular degradation from increased regulation SIO_001199 to be electronically modified is the capability of a chemical entity to have electrons added or removed. to be electronically modified SIO_010369 rank 0 tensor A number is a tensor of rank 0. number SIO_000366 A positive charge is a charge where the value is positive. positive charge SIO_010461 A ray is a line which that is bounded by a startpoint and extends outwards infinitely along one dimension. ray SIO_000516 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. brief SIO_001374 astatine atom CHEBI:30415 SIO_011070 A toxic role is the role of a chemical substance that is poisonous. toxic role SIO_000891 A genotype is a functional specification of a biological entity in terms of its genetic composition (or lack thereof). genotype SIO_001079 A collection of 3D molecular structure models is just that. collection of 3d molecular structure models SIO_011131 dissatisfied qualifier SIO_001310 beryllium atom CHEBI:30501 SIO_011005 A synthesis reaction is an inorganic reaction in which two or more molecules are chemically bonded together to produce a single product. synthesis reaction SIO_010515 A Venn diagram is a chart that illustrates all possible logical relations between a finite collection of sets as overlapping circles. venn diagram SIO_000947 A medical practioner is an individual that provides medical care. medical practitioner SIO_000716 A geometric entity is an information content entity that pertains to the structure and topology of a space. geometry+ geometric entity SIO_000506 A poison role is the role of a substance that causes some negative disturbance in an organism. poison role SIO_000968 has source is a relation between an entity and another entity from which it stems from. has source SIO_000253 is subject of SIO_000629 2 the quality of existing only in the imagination. it can be used to describe concepts, ideas, or things that are the product of a cognitive process. imaginary SIO_001444 A sequence motif is a pattern of nucleotides in a DNA sequence or amino acids in a protein. sequence motif SIO_000131 A double arrowed line is an arrowed line in which both terminal points are tangentially part of different triangles that bisect the line. double arrowed line segment SIO_000524 decreased duration of process from increased regulation is a process in which the duration of the target process is decreased as a result of increased regulation. decreased duration of process from increased regulation SIO_001138 A host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. host SIO_010415 AND is a logical operator that has the value true if both of its operands are true, otherwise a value of false. conjunction (and) SIO_000239 double stranded nucleic acid is a molecular complex composed of two weakly connected nucleic acids. double stranded nucleic acid SIO_001177 offset A ordinal position is a number that designates the position of an entity from the first entity in an ordered sequence of entities. ordinal position SIO_000613 An endpoint is a terminal point that is the last of an ordered pair of points. endpoint SIO_000508 true A professor role is the role of an individual that is involved in teaching of students (undergraduate and/or graduate) at a post-secondary academic institution. professor role SIO_000708 A lipid is a water-insoluable organic molecule. lipid SIO_010011 generation number is a count of the number of biological reproduction events elapsed from some starting reference point. generation number SIO_010061 The increase of regulation leads to a increased occurence of processes of the target type. increased frequency of process from increased regulation SIO_001133 is supported by is a relation between a proposition and something that supports the truth of the assertion. is supported by SIO_000206 curvature is a quality of a bearer that relates to the presence of curves, bends, or angles. curvature SIO_000537 A polar coordinate is a position characterized by a distance from a fixed point and an angle from a fixed direction. polar coordinate SIO_000073 ununquadium atom SIO_011085 microarray platform A microarray device is a device that identifies the binding of a target substance to a physically immobile substrate placed in an array or lattice. http://purl.obolibrary.org/obo/OBI_0000052 microarray device SIO_001238 A software script is software whose instructions can be executed using a software interpreter. software script SIO_000103 0.0 preferredNamespaceUri 2 some of the time some refers to in the minority of occasions some of the time SIO_001290 An algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. algorithm SIO_000094 2 A mutual disposition is a disposition that simulataneously invokes another disposition when realized. mutual disposition SIO_000409 A 3D cartesian point is a point whose position is specified along three dimensions using Cartesian coordinates. 3D cartesian point SIO_000440 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 SIO_000290 disease is the outward manifestation of one or more disorders. disease SIO_010299 An exon is a nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after introns have been removed by RNA splicing. exon SIO_010445 is end time of SIO_000684 a gene symbol is a short name assigned to a gene. gene symbol SIO_001383 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 SIO_000100 An integer scale of measurement is one that only specifies integer values. integer scale SIO_000917 is weakly interacting with SIO_000335 A process that modulates the frequency, rate or extent of process involved in the production of a molecule. regulation of molecular production SIO_001128 A criterion is a specification to describe properties used for evaluation. criterion SIO_000141 2 lanthanum atom CHEBI:33336 SIO_011056 to oxidize is the capability to remove an electron or an increase in oxidation state of a chemical entity. to oxidize SIO_010358 to be conformationally changed is the capability to be modified in such a way that the object's conformation is changed. to be conformationally changed SIO_010374 The role of a chemical entity that reduces the rate of reaction. inhibitor role SIO_000803 krypton atom CHEBI:49696 SIO_011035 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 SIO_000519 a coding sequence is a sequence of nucleotides which encode a RNA or protein product.. coding sequence SIO_001276 A PDB record identifier is an identifier for a PDB generated record. PDB record identifier SIO_010032 An antibody (also known as immunoglobulins, abbreviated Ig) are gamma globulin proteins that are used by the immune system to identify and neutralize foreign objects. They are typically made of two large heavy chains and two small light chains. antibody SIO_010465 false is a truth value in that indicates that it is not true. false SIO_000270 shyness is an emotion of apprehension, lack of comfort, or awkwardness experienced when in proximity to, approaching, or being approached by other individuals, especially in new situations or with unfamiliar individuals. shyness SIO_000867 hasSynonym speech is the expression of thoughts and feelings by sound. speech SIO_001357 is created by was created by has creator is a relation between an entity and that which created it. dc:creator has creator the iPhone was created by Apple Inc SIO_000364 1.0 An increase in the number of objects produced is the positive value of a difference in number of objects produced. increase in number of objects produced SIO_001163 A second messenger is a molecule that relay signals from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus. second messenger SIO_010440 measurement measuring is the process of determining the size, amount, or degree of (something) by using an instrument or device marked in standard units measuring SIO_001054 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 SIO_000934 2 A strong submolecular component is a submolecular component that strongly connects submolecular components. strong submolecular component SIO_010047 An opinion is a belief that is the result of emotion or interpretation of facts. opinion SIO_001004 A software process identifier is an identifier for a software process in some operating system. software process identifier SIO_001185 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 SIO_000568 biological data is scientific data relevant to biology. biological data SIO_010019 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 SIO_001183 regulation regulating is a process that modulates the attributes of an object or process. regulating SIO_000589 An emotion is a process (experience) that arises internally or from an involuntary physiological response to a stimulus. emotion++ emotion SIO_000276 The 5' splice site is the terminal region of an exon that is 5' to the intron that is to be excised. 5' splice site SIO_001222 A virus is a non-cellular organism that can replicate only inside the living cells of an organism. virus SIO_010379 An organization is a collective with a complex articulation of tasks, roles and responsibilities. organization SIO_000012 A software interpreter is a software application that executes some specified input software. software interpreter SIO_000102 license A sequence element position is the position of an element of a linear sequence. sequence element position SIO_000789 A study subject is an individual that is the subject of the study. study subject SIO_000399 wonder is an emotion of perceiving something very rare or unexpected, but not threatening. wonder SIO_000872 2 a post-translational modification is a part of a protein that was added, removed, or modified as a result of a chemical reaction after synthesis. post-translational modification SIO_001393 The surface area of a is a measure of the total area that the surface of the object occupies. surface area SIO_001407 pride is an emotion of satisfaction of attachment toward one's own or another's choices and actions, or toward a whole group of people, and is a product of praise, independent self-reflection, or a fulfilled feeling of belonging. pride SIO_000859 A surface normal is a vector that is perpendicular to a flat surface. surface normal SIO_000533 A term is a word or phrase used to denote one or more entities. term SIO_000275 A manuscript is a document prior to publication. manuscript SIO_000151 A paragraph is a self-contained unit of written discourse consisting of one or more sentences. paragraph SIO_000110 A gene-disease association in which a germline mutation in the gene predisposes to the development of the disease, and it is necessary but not sufficient for the manifestation of the disease. gene-disease association linked with susceptibility mutation SIO_001343 hope is an emotion of belief in a positive outcome related to events and circumstances in one's life. hope SIO_000843 A version label is a label for a particular form or variation of an earlier or original type. version label SIO_000653 Every thing is an entity. core entity SIO_000000 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 SIO_000705 tungsten atom CHEBI:27998 SIO_011059 to freeze is the capability to decrease the internal kinetic energy of a material such that it changes state from a gas or liquid to a solid. to freeze http://purl.obolibrary.org/obo/OBI_0000375 SIO_000348 null A heterogeneous substance is a chemical substance that is composed of more than one different kind of component. heterogeneous substance SIO_010462 strong is a qualitative intensity value that is more intense than moderate, but less intense than severe. strong SIO_001217 A device is usually a constructed tool. device SIO_000956 false hydrogen atom CHEBI:49637 SIO_011002 A z-axis is a Cartesian coordinate axis that is spatially oriented normal to the plane formed by the x- and y-axes. z-axis SIO_000454 A positionally oriented line is a line that is positioned against some axis of reference. positionally oriented line SIO_000534 An anion is an atom or molecule with a net positive electrical charge. cation SIO_010457 A pathogen or infectious agent is a microorganism that causes disease in its host. pathogen SIO_010414 creator stop position An end position is the distal position of an object relative to an origin in a linear system. end position SIO_000953 0.0 issued 2 contributor A small nucleolar RNA (snoRNA) gene is a gene that encodes a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. http://purl.obolibrary.org/obo/SO_0001267 small nucleolar RNA (snoRNA) gene SIO_001229 The materials section is a document section containing a description of the materials used in the study. materials section SIO_000198 creator A viroid is a molecule of RNA that does not code for and is not protected by a protein coat. viroid SIO_001044 A numeric label is a number used as a label. numeric label SIO_000942 love is an emotion of a strong affection and personal attachment. love SIO_000412 1 An author role is the role of an individual that creates a creative, written work. author role SIO_000886 curiosity is the strong desire to know or learn something. curiosity SIO_000823 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. discussion section SIO_000195 preferredNamespacePrefix The aspect ratio of a geometric shape is the ratio of its sizes in different dimensions. aspect ratio SIO_001408 similarTo happiness is an emotion characterized by positive or pleasant emotions ranging from contentment to intense joy. happiness SIO_000840 rights