SIO_000844 Hostility is the intense negative emotion of being in conflict or opposition to someone or something. hostility line A line is curve that extends in a single dimension (e.g. straight line; exhibits no curvature), and is composed of at least two fully connected points. SIO_000511 3d structure model A 3D structure model is a representation of the spatial arrangement of one or more chemical entities. SIO_010530 SIO_000482 A is match to B iff A and B are terms with similar (related, broad, close, exact) meanings is match to http://www.w3.org/2004/02/skos/core#relatedMatch A chemical role is a processual role held by a chemical entity. SIO_000795 chemical entity role 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 excitement is a positive emotion of feeling great enthusiasm and eagerness. SIO_000836 excitement left-handed helical SIO_001273 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. is alternate of relates two specialized instances. SIO_001098 is alternate of http://www.w3.org/ns/prov#alternateOf 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. protein coding gene http://purl.obolibrary.org/obo/SO_0001217 SIO_000985 A gene that contains an open reading frame which codes for a protein. SIO_000829 dread dread is the instense negative emotion that induces fear and apprehension. SIO_000309 volume number is a count of a sequence of periodicals. volume number A parameter is variable whose value changes the characteristics of a system or a function. SIO_000144 parameter intersex SIO_001405 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. has member SIO_000059 core a collection of cars has as a car as a member has member is a mereological relation between a collection and an item. 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. SIO_000722 to be compared 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 A Cartesian coordinate axis is an axis whose behavior follows that of a Cartesian coordinate system. Cartesian coordinate axis SIO_000451 selector text span A text span is a subset of contiguous sequence of characters of a textual entity. SIO_001073 affection is an emotion characterized with a feeling or type of love for another living thing. affection SIO_000812 ecstasy ecstacy is an emotion characterized by a heightened state of consciousness with total involvement of a subject. SIO_000830 probability value SIO_000765 A p-value or probability value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true p-value A numeric scale of measurement is one that only specifies numeric values. numeric scale SIO_000915 2 to interact with is a capabililty that involves another object. to interact with SIO_000701 SIO_001229 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. small nucleolar RNA (snoRNA) gene http://purl.obolibrary.org/obo/SO_0001267 primary title SIO_000470 A primary title is a title that should be first used in describing some entity. the surface of an apple is a 2D boundary of the apple. has boundary has boundary is a mereological relation between a whole and boundary located at its periphery. SIO_000054 is version of SIO_000497 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). SIO_000964 A standard operating procedure is a specification approved for use in specific environments. standard operating procedure SIO_000703 evolving is a process that elicits change across successive generations in the inherited characteristics of biological populations. evolving slope SIO_001184 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. dead is the quality of an object in which there is a cessation of all biological functions. dead SIO_010059 drug A drug is a chemical substance that contains one or more active ingredients that regulate one or more biological processes. SIO_010038 SIO_011069 CHEBI:33313 polonium atom SIO_000047 circumference circumference is the length of the outline of a circle or ellipse. it is defined as c = 2*pi*r, where r is the radius. SIO_000338 A relation between an information content entity and a product that it (directly/indirectly) specifies specifies A small nuclear RNA (snRNA) gene is a gene that encodes a small niuclear RNA molecule. small nuclear RNA (snRNA) gene SIO_001228 http://purl.obolibrary.org/obo/SO_0001268 to associate is the capability to physically interact with another object. SIO_000690 to associate pathogen A pathogen or infectious agent is a microorganism that causes disease in its host. SIO_010414 is refuting evidence for SIO_000775 is greater than to is a comparison relation between two quantities in which the first has a value smaller or equal to the second. SIO_000733 is lesser than or equal to SIO_000767 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 hate SIO_000411 Hate is a deep and emotional extreme dislike, directed against a certain object or class of objects. CHEBI:25107 SIO_011011 magnesium atom ununhexium atom SIO_011087 chemical reaction A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. SIO_010345 non-polar non-polar is the quality of not having a dipole. SIO_001047 2 regulation of biochemical process is a process that changes the frequency, rate or extent of a target biochemical process. SIO_010287 regulation of biochemical process Every thing is an entity. SIO_000000 entity core note SIO_000152 A note is a brief document. A chemical substance role is a chemical entity role held by a chemical substance. chemical substance role SIO_000888 An acid-base reaction is a chemical reaction between an acid and a base. SIO_010507 acid-base reaction SIO_010338 pharmaceutical ingredient A pharmaceutical ingredient is a part of a pharmaceutical preparation. SIO_011094 samarium atom CHEBI:33374 SIO_000681 has end time is refuted by has evidence is a relation between a proposition and something that refutes (is incompatible with) the truth of the assertion. SIO_000774 SIO_001065 speculation speculation is an opinion based on incomplete evidence. hysteria SIO_000846 Hysteria is an unmanageable emotion. SIO_000073 A polar coordinate is a position characterized by a distance from a fixed point and an angle from a fixed direction. polar coordinate peer-reviewed peer-reviewed is the quality of a textual entity that has been examined and commented by a peer expert reviewer. SIO_001035 dissatisfied qualifier SIO_001310 cerium atom SIO_011090 CHEBI:33369 SIO_010309 catabolism Anabolism is the set of metabolic processes that take apart larger chemical entities units into smaller chemical entities. curved is the quality of a line that deviates from straightness in a smooth, continuous fashion. SIO_001095 curved 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 SIO_010451 splice site A splice site is a region required for the excision of an intron and connection to another exon. a peptide is an organic polymer composed of between two and fifty amino acids. peptide SIO_001425 SIO_000664 country A country is a region legally identified as a distinct entity in political geography. regulation of transcription A process that modulates the frequency, rate or extent of transcription. SIO_001125 primary category axis The category axis that corresponds to years in Graph 1 of http://tinyurl.com/opwnvm SIO_000456 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. copy number variation SIO_001328 CNV copy number variation refers to the number of deletions/duplications of a DNA region as compared to some reference state. SIO_000496 hot is the opposite of cold; left is opposite of right is opposite to is opposite to is a relation between two entities in which one is diametrically opposed to the other. medical report SIO_001028 A medical report is a report prepared by a health care practioner about test outcomes or health status of an individual. character SIO_000108 A character is a language symbol used to construct words. 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 medical screening 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 SIO_001023 is paralogous to is paralogous to is a relation between two entities which indicates their common ancestry as a result of a gene duplication. SIO_000630 SIO_010036 biopax:BiochemicalReaction biopax:Conversion biochemical reaction 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). has data item has data item is a relation between a dataset and any described / referrenced entity. SIO_001277 core depth is the dimensional extent into a plane of a 3D projection of the object. depth SIO_000039 SIO_000832 negative emotion negative emotion is an emotion that does not feel good. bromine atom CHEBI:22927 SIO_011034 SIO_000550 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 to inhibit to separate SIO_000349 to separate is the capability to i) distinguish some entities based on some attribute(s) and ii) subsequently physically displace them. A measurement of a spatial location relative to a frame of reference or other objects. position SIO_000056 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 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. non-protein coding RNA (ncRNA) gene ncRNA gene SIO_000790 http://purl.obolibrary.org/obo/SO_0001263 SIO_000734 is greater than is greater than to is a comparison relation between two quantities in which the first has a value larger than the second. SIO_010051 biological fluid A biological fluid is a fluid of biological origin. has source is a relation between an entity and another entity from which it stems from. SIO_000253 has source to filter to filter is the capability to retain certain entities based on selected attribute(s) while allowing other entities to pass through. SIO_000382 SIO_011020 scandium atom CHEBI:33330 increased SIO_000640 PATO:0002300 A quality that has a value that is increased compared to normal or average. 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. 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 SIO_001096 is specialization of ununoctium atom SIO_011089 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 arithmeritic mean average mean SIO_001109 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. creation development production synthesis formulation SIO_000588 creating creating is the process in which an entity comes into existence. A process quality is quality that is associated with a process. process quality SIO_000027 dimensionless quantity SIO_000257 A dimensionless quantity is a quantity that has no associated unit. 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 is role of is role of is a relation between a role and the entity that it is a property of. SIO_000227 thickness SIO_000043 thickness is the shortest dimensional extent of a 3D projection of an object. 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 is transformed from SIO_000657 A transitive temporal relation in which an entity mainstains identity from one state to another. SIO_000675 unique identifier A unique identifier is an identifier that uniquely identifies some thing. realizes SIO_000355 core realizes is a relation between a process and a realizable entity (role, function, disposition). dag directed acyclic graph a directed acyclic graph or DAG is a network digram that contains directed edges in which nodes may have multiple parents, but there are no cycles. SIO_001332 is inequal to SIO_000749 is inequal to is a comparison relation between two quantities whose value are not the same. written is the quality of information that is embodied as visual glyphs in some material form. written SIO_001039 SIO_000313 is component part of 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 learning SIO_000744 learning is the agentive process of acquiring knowledge. 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 An operon is a collection of contiguous genes transcribed as a single (polycistronic) mRNA. SIO_010084 SO:0000178 operon antibody 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. SIO_010465 SIO_001156 results in web service invocation A web service invocation involves the execution of a web service. SIO_001192 A co-factor role in which the chemical entity is modified during catalysis and must be regenerated. SIO_000800 co-enzyme role is equal to is a comparison relation between two quantities whose value are exactly the same. SIO_000738 is equal to double stranded RNA double stranded nucleic acid is a molecular complex composed of two weakly connected ribonucleic acids. SIO_001178 SIO_000476 cellular quality cellular quality is the quality of a cell A role of a chemical substance that participates in a chemical reaction as part of some scientific investigation. SIO_000893 reagent role document component SIO_000171 A bibliographic attribute is an attribute related to publications. SIO_000087 publication A publication is a document that has been made available by a publisher. SIO_000436 informational quality An informational quality is a quality that pertains to information. A lipid residue is a part of an organic molecule that was derived from a lipid molecule. SIO_000556 lipid residue transcription is the process of creating a complementary RNA copy of a sequence of DNA. SIO_010300 transcription barium atom CHEBI:32594 SIO_011055 SIO_001252 right open interval a right open interval is an interval in which there is no element that is greater than all other elements. euphoria is an emotion characterized by intense feelings of well-being, elation, happiness, ecstasy, excitement, and joy. euphoria SIO_000835 nobelium atom CHEBI:33396 SIO_011116 SIO_000088 record A record is a document containing a collection of statements about some entity. functional specification A functional specification is a specification that describes the characteristics of an object. SIO_000315 to investigate SIO_000408 to investigate is the capability to uncover facts. bubble chart SIO_000933 A bubble chart contains circles whose area corresponds to a value. 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 telephone number SIO_001319 a telephone number is an identifier used to connect to a physical device capable of transfering voice or data over a network. SIO_000269 true is a truth value that indicates that it holds under all possible worlds. true A molecular pocket is a site on a molecule that appears as a depression into the structure. molecular pocket SIO_010452 The results section is a document section describing the main findings of the study. SIO_000200 results section SIO_001251 a left open interval is an interval in which there is no element that is smaller than all other elements. left open interval 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. SIO_000528 increasing line bent is the quality of a line being sharply curved or having an angle. SIO_001094 bent doctor SIO_000394 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. is member of is member of is a mereological relation between a item and a collection. SIO_000095 A television program is a audiovisual media that is produced and broadcast using a television. television program SIO_000924 SIO_001082 t-statistic based decreased differential gene expression A t-statistic based decreased differential gene expression is a differential gene expression ratio in which the t-statistic is less than zero. SIO_000354 dysfunction is a capability to act in a manner that is abnormal or opposite to the object's typical function. dysfunction SIO_001291 most of the time most refers to in the majority of occasions most of the time has capability SIO has the capability to semantically integrate data. has capability is a relation between an entity and the capability that it bears. SIO_000586 is broader than (t) http://www.w3.org/2004/02/skos/core#narrowerTransitive SIO_000422 A is broader than B (t) iff for A is broader than B. SIO_000045 area is a quantity that pertains to the extent of a two-dimensional surface or shape, or planar lamina, in the plane. area A positional description is a description of location using some system or frame of reference. positional identifier SIO_000328 diastereomer SIO_010776 A diastereomer is a stereoisomer that is not a mirror image of its isomer. SIO_010782 heterocyclic ring A heterocyclic ring is a ring containing a hetero atom. SIO_000449 The square portion of the chart bounded by lines that overlap with the two axes in Graph 1 of http://tinyurl.com/opwnvm A plot is a part of a figure that corresponds to the spatial region between the set of axes. plot SIO_000360 belief A belief is a proposition that is believed to be true. terror is the extreme feeling of fear. SIO_000871 terror scaled value axis A scaled value axis is a value axis in which the value range was subject to a mathematic transformation. SIO_000461 A cellular organism is an organism that contains one or more cells. SIO_010377 cellular organism medical data medical data is data of interest to medicine. SIO_010298 SIO_001360 information decoding SIO_001410 synthetic quality is the quality of a manufactured object that has similar properties as naturally occuring objects. synthetic quality satisfies SIO_000362 satisfies is a relation between an entity and the specification or objective that it conforms to. An ionic compound is a mereological maximal sum of weakly connected paired positive and negative ions. ionic compound SIO_010784 An x-axis is a Cartesian coordinate axis that is aligned with the horizon. SIO_000452 horizontal axis x-axis In most figures, this axis represents categories, such as months, market segments, or other non-numeric data. The horizontal axis in http://tinyurl.com/opwnvm SIO_010460 A non-polar solvent is a solvent that exhibits a non-polar quality. nonpolar solvent SIO_000841 guilt guilty Guilt is the emotion borne from feeling responsible for the commission of an offense and arises out of public humiliation. a collection of replicates is a collection composed of items that are a facsimile, reproduction, or copy of other items in the collection. replicates SIO_001419 a collection of replicates CHEBI:29287 gold atom SIO_011064 glucose and ATP are inputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. sadi SIO_000231 is input in is a relation between an entity and a process, where the entity is present at the beginning of the process. is input in A versioned record is a record for which there exists another variant based that was derived via modification of the facts. SIO_000771 versioned record SIO_000623 An OBO ontology is an ontology document as specified by the Open Biological Ontology community. OBO ontology SIO_010278 ploidy is the cellular quality relating to the amount of DNA contained in a cell. ploidy assertional qualifier An assertional qualifier is the quality of affirmation, either being positive or negative. SIO_001209 SIO_010335 nucleic acid part A nucleic acid part is a component of a nucleic acid. consensus SIO_001198 consensus is an acceptable resolution, one that can be supported, even if not the preferred outcome for each individual. a duplicate is an object that is an exact copy of another item duplicate SIO_001420 SIO_000648 An object model is a representation of an object. object model SIO_001430 a vector is a rank 1 tensor that is described by n-dimension of scalars. rank 1 tensor vector A hydrogen bond is a weak submolecular interaction formed between a hydrogen atom and a electronegative atom. hydrogen bond SIO_010033 triangle SIO_000520 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. carbohydrate oligosaccharide saccharide SIO_001395 a carbohydrate is an organic molecule composed of two or more monosaccharides. A patient role is the role of an individual that is the recepient of medical care. patient role SIO_000715 CDS coding sequence 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. protein coding sequence SIO_001390 SIO_001222 5' splice site The 5' splice site is the terminal region of an exon that is 5' to the intron that is to be excised. SIO_001127 regulation of molecular quantity A process that modulates the frequency, rate or extent of process involved in the creation or destruction of a molecule. SIO_000512 A line segment is a line and a part of a curve that is (inclusively) bounded by two terminal points. line segment SIO_000016 role core A role is a realizable entity that describes behaviours, rights and obligations of an entity in some particular circumstance. 1 SIO_001357 speech is the expression of thoughts and feelings by sound. speech SIO_010094 to serve as a primer for DNA synthesis 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. behaviour behaviour+ core SIO_001195 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. SIO_011086 ununpentium atom (0,1) is an open interval that is greater than 0 and less than 1. SIO_001248 an open interval is an interval that does not include its endpoints. open interval CHEBI:25195 mercury atom SIO_011065 SIO_010787 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 A z cartesian coordinate is the coordinate of an object onto the z-axis of a cartesian coordinate system. SIO_000402 z cartesian coordinate contentment contentment is an emotion characterized by acknowledgement and satisfaction of the current state of affairs. SIO_000822 SIO_000015 core ice+ information content entity is an object that requires some background knowledge or procedure to correctly interpret. information content entity A quaternary structure descriptor describes topological patterns in a multi-unit biopolymer complex. SIO_010024 quaternary structure generic name SIO_000077 A generic name is the preferred name provided by manufacturer. OBO_REL:contained_in core 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] is contained in SIO_000128 SIO_000486 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 inclusion criterion An inclusion criterion is a criterion that must be present to satisfy some objective. SIO_000142 physician SIO_000713 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_001317 middle name a middle name is a name assigned to an individual that is not the first or last name. 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. SIO_001347 gene-disease association linked with germline modifying mutation monomer SIO_000146 A monomer is a submolecule that is proper part of some polymer, and is a building block for such polymer. SIO_000946 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 desire desire is a strong emotion of wanting to have something or wishing for something to happen. SIO_000825 core SIO_000068 OBO_REL:part_of is part of is a transitive, reflexive and anti-symmetric mereological relation between a whole and itself or a part and its whole. is part of SIO_001267 nullizygous nullizygous is the quality of a biological organism in which there are no allelles at a given locus. A centrifugation pellet is a solid substance that forms as a result of compaction by a centrifuge. SIO_010424 centrifugation pellet chaoite is an allotrope of carbon that is slightly harder than graphite with a reflection colour of grey to white. SIO_010793 chaoite 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 SIO_000013 A geographic position is the coordinate of an entity against some geographic coordinate system. geographic position not started is the status of a process that is predicted to exist but has not yet begun. not started SIO_000963 SIO_001165 user account allows a user to authenticate to system services and be granted authorization to access them. user account SIO_000335 is weakly interacting with SIO_000989 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_001257 chemical-gene association a chemical-gene association is an association between a chemical and a gene. A map is a a visual representation of an area that depicts the relationship between elements of that space. map SIO_000906 SIO_000944 SIO_001246 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. An interval is a set of real numbers that includes all numbers between any two numbers 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. A positive emotion is an emotion that feels good. SIO_000831 positive emotion sound wave 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. SIO_000605 SIO_010444 A gene component is a component of a gene. gene component patient A patient is an individual that is the recepient of medical care. SIO_000393 chemical reaction pathway SIO_010526 A chemical reaction pathway specifies a series of chemical reactions towards producing some chemical product. 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 photograph is an image created by light falling on a light-sensitive surface. SIO_000082 photograph photo is disposition of is disposition of is a relation between a disposition and the entity that it is a property of. SIO_000236 fatal is a qualitative intensity value that is more intense than severe, leading to the death/non-functioning of a system. SIO_001216 fatal 2 is directly after 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. SIO_000241 SIO_001174 A nucleic acid strand is a single-stranded nucleic acid that is part of a double stranded nucleic acid complex. nucleic acid strand SIO_000903 bottom value axis A bottom value axis is a value axis that is spatially positioned to the bottom of the plot area. SIO_000337 An objective is a proposition that indicates a planned or anticipated outcome. objective positive SIO_001210 positive is an assertional qualifier that expresses the validity or truth of a basic assertion. A paragraph is a self-contained unit of written discourse consisting of one or more sentences. paragraph SIO_000110 SIO_000617 An empty set is a set for which there are exactly 0 members. empty set has direct part SIO_000273 has direct part is a relation to specify a part at a particular level of granularity a car has an engine as a direct part A binary scale is a measurement scale that specifies a choice between two values. SIO_000914 binary scale gene enhancer 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. SIO_010086 An intron is a region of a gene that is removed from the final protein open reading frame. intron SIO_010443 A standard score is the (signed) number of standard deviations an observation or datum is above the mean. standard score z-value, z-score, normal score, standardadized variable. SIO_001245 SIO_010438 signal A signal is an object that initiates a sequence of events. SIO_001250 drug-pathway association chemical-pathway association a chemical-pathway association is an association between a chemical and a pathway. rate of change SIO_001365 The amount of change accumulated per unit time. the architect builds a model that represents the building she envisions. is model of is a relation between a model (an artifact) and the entity it purports to represent. is model of SIO_000632 Pity is the emotion of sadness or sorrow for another. pity SIO_000857 structure structure is the specification that refers to the composition and arrangement of parts of an object. SIO_000600 concentration is the amount of substance per unit volume of a solution concentration SIO_001088 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 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 to transport SIO_000390 to transport is the capability to displace a material from one location to another. corporation SIO_000693 A corporation is an organization that is granted a charter recognizing it as a separate legal entity. to reduce SIO_010359 to reduce is the capability to add an electron or an decrease in oxidation state of a chemical entity. CHEBI:28073 SIO_011023 chromium atom SIO_000114 A word is the smallest free form (an item that may be expressed in isolation with semantic or pragmatic content) in a language. word A hyponym is a term with a narrower meaning. hyponym SIO_000125 criterion SIO_000141 A criterion is a specification to describe properties used for evaluation. SIO_010513 double displacement reaction A double displacement reaction is a displacement reaction in which two molecules swap ions, effectively displacing each other to form two new molecules. planning SIO_000739 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. notation SIO_001385 a notation is a series or system of written symbols used to represent numbers, amounts, or elements. SIO_000935 treemap A treemap is a chart that fully partitions the area into a set of rectangles whose area represents its relative value. SIO_000297 A movie is a series of images that are displayed in rapid succession to give the impression of movement. movie film moving pictures decreased frequency of process from increased regulation SIO_001134 The increase of regulation leads to a decreased occurence of processes of the target process type. legislation A legal document proposing or enacting a law or a group of laws. SIO_001372 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 SIO_000965 agreement quality is a quality that exhibits the degree of consensus for some set of assertions. agreement quality SIO_000199 methods section The methods section is a document section containing a description of the methods used in the study. SIO_010088 to serve as a template for molecular synthesis 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. SIO_011047 CHEBI:22977 cadmium atom effective specification action specification SIO_000091 An action specification is a specification composed of a sequence of instructions to achieve some objective. SIO_000157 A conference proceedings is a book composed of papers presented at a conference. conference proceedings document version A document version is a version of a work in some sequence of derivative works. SIO_000186 process up-regulation is a process that increases the frequency, rate or extent of one or more processes in relation to a reference state. positive regulation SIO_010295 process up-regulation text span start position text span start position is the position (offset) of the first character of a text span in relation the text it is from. SIO_001071 SIO_000353 to observe is the capability to watch attentively. to observe SIO_000720 to be moved to be translocated to be translocated is the capability to be physically displaced from one location to another the role of a patient is realized in medical examination SIO_000356 is realized in SIO_010378 non-cellular organism A non-cellular organism is an organism that does not contain a cell. gadolinium atom CHEBI:33375 SIO_011096 SIO_000373 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 is capability of SIO_000646 is capability of is a relation between a capability and the entity that bears it. subject role SIO_000883 A subject role is the role of an individual that is the target of the study. The materials and methods section is a document section containing a description of the materials and methods used in the study. SIO_000197 materials and methods section An occupational role is a social role that pertains to an organizational structure. occupational role SIO_000706 discouragement discouraged SIO_001283 Discouragement is the emtion of having lost confidence or enthusiasm. 2 nlp+ core refers to is a relation between one entity and the entity that it makes reference to. SIO_000628 refers to SIO_000960 real real is the quality of an entity that exists in real space and time. The geographic region bounded by Canada; the spatial region occupied by the US embassy in Ottawa. geopolitical region a geopolitical region is a geographic region recognized by social or legal convention. SIO_000415 SIO_000728 A chemical identifier is an identifier for a chemical entity chemical identifier information processing information processing is a process that involves the generation or use of information. SIO_000649 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 SIO_000736 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_000123 An antonym is a word with opposite or nearly opposite meaning. antonym SIO_001150 regulation of object consumption A process that modulates the frequency, rate or extent of process involved in the consumption of an object. vector line SIO_000540 A vector line is a line which that is bounded by a startpoint and extends outwards along one dimension. SIO_000966 agreement agreement is the result of consensus decision making when members of the group agree. 2 joy SIO_000850 joy is an emotion of intense happiness. A submolecular entity is a chemical entity that is a part of a molecule. submolecular entity SIO_010020 passive transport SIO_000562 passive transport is the movement of a substance across a membrane and does not require chemical energy. a relation between two entities which indicates their common ancestry. SIO_010302 is homologous to SIO_000624 chemical group A chemical functional group is a submolecule that confers specific chemical properties. chemical functional group SIO_000954 sick sick is the status of a living organism that is behaving at a sub-optimal level. e.coli Escherichia coli (e coli) is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms. SIO_000489 A standard is a socially-agreed upon specification. standard SIO_000618 SIO_000557 is described by is described by is a relation between one entity and another entity that provides a description (detailed account) of it. implies (->) Implication is a logical operator that holds between a set T of propositions and a proposition B, when every model (or interpretation or valuation) of T is also a model of B. SIO_000220 conclusion SIO_000262 A conclusion is a proposition which is reached after considering the evidence, arguments or premises. SIO_001352 DisGeNET Pleiotropy Index The DisGeNET pleiotropy index is a measure of specificity as it pertains to classes of disease. The disease pleotropy index is computed from the ratio of the number of disease classes associated with an entity over the total number of disease classes multplied by 100. The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pleiotropy SIO_011039 CHEBI:33342 zirconium atom chemical salt salt a chemical salt is a molecular complex composed of an ionic assembly of cations and anions. SIO_001422 to record to record is the capability to detect and transcribe information in a specified format on some physical medium. SIO_000344 http://purl.obolibrary.org/obo/OBI_0000368 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 tag cloud is a visualization of word frequencies. word cloud tag cloud SIO_000938 medical intervention SIO_001398 a medical intervention is a medical procedure to treat (to cure or alleviate) a health condition. SIO_000447 A line-bar graph statistical graph that contains both lines and bars. Graph 8 in http://tinyurl.com/opwnvm line-bar graph SIO_010780 A ring is a submolecule with a circular topology. ring SIO_010788 graphite graphite is an allotrope of carbon which is a conductor, and is the most stable form of solid carbon. 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 Frequency is the number of occurrences of a repeating event per unit time SIO_001367 frequency suffering SIO_000869 Suffering is the unpleasant emotion and aversion associated with the perception of harm or threat of harm in an individual. purpose is the reason for which something is done or created or for which something exists. purpose SIO_000359 alive SIO_010058 alive is the state of a biological organism that exhibits biological functions. A medical practioner is an individual that provides medical care. medical practitioner SIO_000716 A ribonucleotide residue is a part of a molecule that derives from a ribonucleotide. ribonucleotide residue SIO_010337 A chemical degradation pathway is a pathway involved in the disassembly of a chemical. chemical degradation pathway SIO_010528 dimensional quantity SIO_000258 A dimensional quantity is a quantity that has an associated unit. A primary database key is a database key that identifies every row of a table. primary database key SIO_000763 SIO_000092 A biopolymer is an organic polymer that are typically produced by the cells of living organisms. biopolymer title SIO_000185 A title is a textual entity that summarily describes some entity. 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 SIO_010518 addition reaction 'is related to' is the top level relation in SIO core relations+ SIO_000001 is related to A is related to B iff there is some relation between A and B. A database row is a row that is part of a database table. SIO_001187 database row A hypernym is a term with a broader meaning. hypernym SIO_000124 regulation of object quantity regulation of a participant quantity is the regulation of a process in which the quantity of its partcipants is changed. SIO_001145 is satisfied by SIO_000363 cell A cell is a biological entity that is contained by a plasma membrane. SIO_010001 number of objects consumed SIO_001161 number of objects consumed is a count of objects that were consumed in some process. polygonal chain, polygonal curve, polygonal path, piecewise linear curve A polyline is a connected sequence of line segments. polyline SIO_000545 An academic is an individual that participates in education and scholarship. SIO_000406 academic SIO_001368 speed Speed is the rate of change of an object's position. A graph title is a title that describes a graph. SIO_000469 graph title Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm SIO_001345 gene-disease association linked with somatic causal mutation A gene-variant disease association in which a somatic mutation in the gene/protein results in the development or maintenance of the disease, and it may not be passed on to offspring. A computational entity is an information content entity operated on using some computational system. computational entity SIO_000602 to change appearance is the capability to change the material composition of an object. SIO_000376 to change materially SIO_010373 to be inhibited to be inhibited is the capability to be modified in such a way that the conformational change leads to an decrease in another capability. core SIO_000793 measured at is a relation between a measurement value and the time measurement. measured at author role An author role is the role of an individual that creates a creative, written work. SIO_000886 decreased duration of process from increased regulation 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. SIO_001138 SIO_000501 A polygon edge is a line segment joining two polygon vertices. polygon edge is direct part of core is direct part of is a relation between a specific part (at some level of granularity) and its whole. SIO_000310 moderate SIO_001214 moderate is a qualitative intensity value that is more intense than mild, but less intense than strong. A numeric label is a number used as a label. SIO_000942 numeric label 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 has part has part is a transitive, reflexive and antisymmetric relation between a whole and itself or a whole and its part. SIO_000998 literature curation is the process of an agent selecting and extracting terms and phrases from a document. literature curation http://www.w3.org/2004/02/skos/core#narrower SIO_000477 is broader than SIO_000593 interacting is a process characterized by the interaction between two or more entities. interacting core some of the time some of the time SIO_001290 some refers to in the minority of occasions SIO_001113 min minimal value A minimal value is smallest value of an attribute for the entities in the defined set. measurement value SIO_000070 A measurement value is a quantitative description that reflects the magnitude of some attribute. a coding sequence is a sequence of nucleotides which encode a RNA or protein product.. SIO_001276 coding sequence medical history A medical history is a record of the events of a recipient of medical care. SIO_010673 SIO_000616 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_001236 A data collection device is a device that collects information about one or more objects. data collection device maintenance of spatial extent of process SIO_001142 maintenance of spatial extent of process is a regulation of a process' spatial extent within some specified parameter. 2 dc:creator has creator the iPhone was created by Apple Inc was created by is created by SIO_000364 has creator is a relation between an entity and that which created it. SIO_000692 to be actively interacted with is the capability to be manipulated by some device or agent. to be actively interacted with SIO_001340 full is the quality of contain an entity such that there is no more space for any additional entity. full The table of contents is a document section that lists all sections (and optionally subsections) in a sequential order along with their page number. SIO_000201 table of contents to negatively charge SIO_000387 to negatively charge is the capability to add an electron or negatively charged ion to a chemical entity. A manuscript is a document prior to publication. manuscript SIO_000151 statistical graph A statistical graph is a figure that displays the relationship among numeric data and/or mathematical functions. SIO_000083 chart tree diagram A tree diagram is a hierarchical network diagram in which a root vertex is connected to one or more other vertices through a directed edge, which in turn may be connected to other vertices. SIO_000945 is mutual role of a is mutual role of b if and only if the realization of role a necessarily causes the realization of role b. SIO_000710 SIO_011026 cobalt atom CHEBI:27638 SIO_000306 letter A letter is a document that contains a personal communication from one part to another. SIO_011040 CHEBI:33344 niobium atom is unique identifier for is a relation between an identifier and an entity that it uniquely identifies is unique identifier for SIO_000674 to modify electronically SIO_001087 to modify electronically is the capability to change the electronic properties of an object. A molecular regulator is a molecule that regulates the function of another chemical entity. SIO_010436 molecular regulator A curve segment is a part of a curve that consists of at least three points. SIO_000740 curve segment SIO_001014 ethnicity ethnicity is the biological quality of membership in a social group based on a common heritage. to modify the oxidation state of is to change the number of electrons of a molecule, atom or ion. SIO_010360 to modify oxidation state of A nucleotide residue is a part of a molecule that derives from a nucleotide. SIO_010075 nucleotide residue SIO_000473 A primary graph title is a primary title that describes a statistical graph. "Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm primary graph title reference A reference is a textual entity that describes a single source used in the preparation or development of the work. SIO_000176 has time boundary SIO_000679 to test a hypothesis to test a hypothesis is the capability to evaluate the truth value of a proposition based on gathered evidence. SIO_001219 biopax:TransportWithBiochemicalReaction SIO_010284 active transport active transport is the movement of a substance across a membrane against its concentration gradient (from low to high concentration) and requires chemical energy. core process+ SIO_000006 process 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. SIO_000245 derives into a derives to b if and only if a or some part thereof is consumed in the formation of b. SIO_010013 A chemical interaction is a biochemical process in which chemical entities interact through some set of attractive forces. chemical interaction biopax:Interaction major version number A major version number is a version of a software that exhibits a significant change in functionalilty from a prior version. SIO_001030 is narrower than (t) http://www.w3.org/2004/02/skos/core#broaderTransitive SIO_000424 A is narrower than B (t) iff for A is narrower than B. The role of a chemical entity that modifies the rate of reaction. SIO_000880 regulator role SIO_000238 A logical operator is a unary or binary relation to construct logical expressions. logical operator SIO_000261 A premise is a proposition of an argument from which the conclusion is drawn. premise SIO_000798 product role The role of a chemical entity present at the end of a chemical reaction. arc an arc is a closed segment of a differentiable curve. SIO_001333 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 family history family history is the systematic narrative and research of past events relating to a specific family, or specific families. SIO_010060 decreased molecular production from increased regulation A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation. SIO_001204 loathing is an intense dislike or disgust. loathing SIO_000851 glucose-6-phosphate is the product of the hexokinase-mediated conversion of glucose to glucose-6-phosphate. 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. SIO_000311 is product of sadi SIO_000549 to reduce the activation energy to reduce the activation energy is to require a smaller amount of energy in order to form or break a chemical bond. to activate SIO_000279 mass is the quality of the amount of substance. mass to demagnify to demagnify is the capability to decrease the appearance of the size of an object. SIO_000377 SIO_001404 x is correlated with y when x holds a statistical relationship with y is correlated with OBO_REL:adjacent_to nlp core SIO_000204 is adjacent to A is adjacent to B iff there is a small, but non-zero distance between A and B has product is a relation between an process and an entity, where a new entity exists at the end of the process. SIO_000312 has product sadi SIO_000918 modifying is the process by which an entity gains or loses parts, qualities, roles, dispositions, functions, etc, but maintains their identity through these changes. modification modifying SIO_000192 bibliography section A bibliography section is a document section that is composed of a list of references used in the development of the work. scientific name A scientific name is a name given through scientific nomenclature. SIO_000120 human SIO_000485 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. SIO_001062 human population A human population refers to a collection of human beings. polymer A polymer is a molecule composed of a connected set of monomeric residues. SIO_000314 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 SIO_000619 A regulatory authority is an organization responsible for exercising regulatory or supervisory capacity in some area of human activity. regulatory authority SIO_000167 A Master's thesis is a thesis prepared as a requirement for a Master's degree. master's thesis hurt is an unpleasant feeling, emotion or sensation. SIO_000845 hurt SIO_001157 is result of CHEBI:49957 xenon atom SIO_011053 to decode information the ability to reverse an encoding operation SIO_001364 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. SIO_001274 right-handed helical A spatial boundary is the closure minus the interior of a subset of a topological space. SIO_000783 spatial boundary charge quality SIO_010442 charge quality is the quality pertaining to electric charge. statistical association SIO_000898 A statistical association is any relationship between two measured quantities that renders them statistically dependent. A quality that has a value that is outside normal or average. SIO_000555 abnormal CHEBI:33322 SIO_011036 rubidium atom SIO_011119 A biomolecular structure descriptor is structure description for organic compounds. biomolecular structure descriptor an anatomical entity is an object that is a structural part (material or immaterial) of a biological entity. SIO_001262 anatomical entity deoxyribonucleotide residue SIO_010336 A deoxyribonucleotide residue is a part of a molecule that derives from a deoxyribonucleotide. to contain to contain is the capability to bound or constrain a physical entity in some site. SIO_000380 A class is a collection of sets which can be unambiguously defined by a property that all its members share. class SIO_000138 question A question is a linguistic expression used to make a request for information. SIO_000085 SIO_000651 A textual entity is language entity that is manifested as a sequence of one or more distinct characters. textual entity wave 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. SIO_000650 2 appreciation thankfullness gratification gratefulness SIO_000839 Gratitude, thankfulness, gratefulness, or appreciation is a feeling, emotion or attitude in acknowledgment of a benefit that one has received or will receive. gratitude cylindrical coordinate system A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis. SIO_000329 chemical-disease association A chemical-disease association is an association between a chemical and a disease. SIO_000993 SIO_000622 RDFS ontology An RDFS ontology is an ontology that conforms to the syntax and semantics of the Resource Description Framework Schema (RDFS). verbal language A verbal language is a language that uses sounds to communicate. SIO_000981 SIO_000756 database entry database record A database entry is a single, implicitly structured data item in a table. promethium atom SIO_011093 CHEBI:33373 Graphs 3,4,5 in http://tinyurl.com/opwnvm bar graph A bar graph is a statistical graph with rectangular bars of lengths proportional to that value that they represent. SIO_000443 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 SIO_011061 CHEBI:30687 osmium atom phrase net diagram A phrase net diagram illustrates the relationship between different words used in a text. SIO_000939 hafnium atom SIO_011057 CHEBI:33343 A 3D cartesian coordinate is a coordinate that is composed of an x, y and z coordinate. 3D cartesian coordinate SIO_000333 anion An anion is an atom or molecule with a net negative electrical charge. SIO_010458 is directly connected to A is directly connected to B iff there exists a path direclty between A and B. SIO_000652 SIO_000351 to supply energy to supply energy is the capability to transfer energy from a source to a sink. SIO_001186 hypothetical hypothetical is the quality of an entity that is conjectured to exist. A sequence motif is a pattern of nucleotides in a DNA sequence or amino acids in a protein. SIO_000131 sequence motif SIO_001414 quantile A quantile is a quantity that divides the range of a probability distribution into continuous intervals with equal probabilities, or dividing the observations in a sample in the same way. SIO_000233 is implementation of is a relation between an information entity and a specification that it conforms to. is implementation of is cited by is cited by is a relation from an object that is referred to by way of example, authority or proof. SIO_000278 time measurement is a measurement value of the duration of some interval of time or a particular instant of time (against some frame of reference). the duration of my life; the duration of a surgical procedure, the moment of death time measurement SIO_000391 Time intervals are specified as date/datetime ranges. SIO_000287 social relation A social relation is a social entity that describes a relationship between two or more individuals or groups. 2 sadi has parameter has parameter is a relation between a process and an information content entity which modulates the behaviour of some participant. SIO_000552 collection of 3d molecular structure models SIO_011131 A collection of 3D molecular structure models is just that. A medical procedure is a procedure to identify, examine, alleviate or eliminate an undesirable biological disease or disorder. medical procedure SIO_001024 composition quality is a quality that describes its composition or anatomy. compositional quality SIO_000051 annoyance SIO_000814 Annoyance is an unpleasant emtion that is characterized by a abnormal or excessive sensitivity to some external stimulus. has concretization A has concretization B iff A is an informational entity and B is the a quality of some material entity. SIO_000213 molecular orbital SIO_000561 A molecular orbital (or MO) is a mathematical function describing the wave-like behavior of an electron in a molecule. SIO_010434 A molecular activator is a molecular regulator that realizes its disposition to conformationally change a target molecule and increase its functionality. activator 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 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. SIO_000407 to increase the rate of formation SIO_000428 A year is a period of time taken by a planet to make one revolution around the sun. year A mode is the value that appears most often in a set of data. mode SIO_001111 SIO_000375 to supply electricity to supply electricity is the capability to transfer electricity from a source to a sink. SIO_000490 is close match to http://www.w3.org/2004/02/skos/core#closeMatch CHEBI:33353 technetium atom SIO_011042 introduction section SIO_000196 An introduction section is a document section that generally provides background, motivation and goals of the work. SIO_000326 A concept is term that refers to a generalization of a set of attributes or entities. concept SIO_011046 CHEBI:30512 silver atom SIO_011001 carbon atom CHEBI:27594 false 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. SIO_010089 to serve as a template for protein synthesis neither satisfied or dissatisfied qualifier SIO_001311 SIO_000678 abstract role An abstract role is a role whose basis lies in spatial/temporal or comparative relations. SIO_000237 A namespace label is a short name for a namespace. namespace label SIO_010030 A monosaccharide is an organic molecule that consists of a single polyhydroxy aldehyde or ketone group. monosaccharide SIO_000856 passion passion is the intense desire for something. SIO_010005 weak submolecular component A weak submolecular component is a submolecular component that weakly connects submolecular components. 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. SIO_001058 word end position a statement of consequence is a statement concerning the result or effect of an action or condition. SIO_001384 statement of consequence none of the time never refers to in none of the occasions. SIO_001289 never measurement scale SIO_000912 A measurement scale is a functional specification that specifies an allowed range of categories or values. curium atom SIO_011110 CHEBI:33390 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. SIO_000435 second has property is a relation between an entity and the quality, capability or role that it and it alone bears. michel's hair has the quality of being brown in colour. SIO_000223 has property 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 chemical element is a (effectively) homogeneous substance composed of one type of atom. chemical element SIO_010037 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 http://purl.org/ontology/bibo/Newspaper A newspaper is a periodical publication containing news regarding current events, informative articles, diverse features, editorials, and advertising. SIO_000163 newspaper SIO_000365 is creator of is a relation between a creator and an entity.. is creator of is created by stereoisomer SIO_010775 A stereoisomer is an isomer in which the atomic connectivity is the same, but differs in its spatial arrangement of atoms. 1 SIO_000961 fictional is the quality of an entity that exists only in a creative work of fiction. fictional SIO_000060 is denoted by SIO_001435 chemical-chemical association A chemical-chemical association is an association between two chemical entities. is supporting evidence for SIO_000208 SIO_000283 is similar to is a relation between two entities that share one or more features. is similar to 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 a human has blood as a component part has component part 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. SIO_000369 An anion is an atom or molecule with a net positive electrical charge. cation SIO_010457 An object is an entity that is wholly identifiable at any instant of time during which it exists. core object SIO_000776 process number is a number associated with a process that denotes its ordinal position in a set of processes. process number SIO_000305 SIO_001117 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 5i is an imaginary number, and its square is -25. An imaginary number is a complex number whose real part is zero e.g. 0 + bi, and is expressed as a multiple of the square root of -1. imaginary number SIO_001441 SIO_010433 A low barrier hydrogen bond is a shorter, stronger hydrogen bond that is formed between both heteroatoms. low barrier hydrogen bond A common name is a name that is commonly used. common name SIO_000118 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 comparison SIO_011099 CHEBI:49648 holmium atom written language is a language that is communicated through a writing system. SIO_000982 written language nmr device http://purl.obolibrary.org/obo/OBI_0000566 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. nuclear magnetic resonance device SIO_001240 SIO_010522 nucleophilic addition reaction 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. website SIO_000296 A website is a collection of documents published on the World Wide Web. SIO_000198 materials section The materials section is a document section containing a description of the materials used in the study. geometric entity A geometric entity is an information content entity that pertains to the structure and topology of a space. SIO_000506 geometry+ SIO_010531 A sequence profile is provides the preference for a character at each position of an abstracted sequence. sequence profile SIO_000639 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 An RNA transcript is an RNA molecule that is produced from transcription of a nucleic acid template. RNA transcript SIO_010450 2 SIO_010785 allotrope An allotrope is a structural variant of a chemical element. SIO_000910 A geographic heatmap is a graphical representation of data over a geographic region where individual values are represented as colors. geographic heatmap SIO_001043 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 fear SIO_000837 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. SIO_001338 mereological quality a mereological quality is a quality of an entity vis-a-vis containment or parthood SIO_011029 CHEBI:27363 zinc atom mild SIO_001213 mild is a qualitative intensity value that is more intense than weak, but less intense than moderate. association SIO_000897 An association is a relationship between two or more entities derived by some informational analysis. is causally related from a is causally related from b iff there is a causal chain of events from b to a core SIO_000352 SIO_011113 einsteinium atom CHEBI:33393 SIO_000062 a car is a participant in a car race; glucose is a participant in glycolysis is participant in is a relation that describes the participation of the subject in the (processual) object. is participant in SIO_000847 indifference indifference is an emotion characterized by lack of interest, concern, or sympathy. transporting SIO_000575 transporting is a process in which one object physically moves another object from one location to another. SIO_000417 A time internval is a contiguous temporal region having some duration. time interval exists at is a relation between an entity and a time measurement. SIO_000687 core exists at empty is the quality of not containing some thing SIO_001339 empty SIO_001409 object relational quality object relational quality refers to a quality in relation to one or more objects 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 is translated into The colored line segments and the adjacent textual descriptions in Graph 1 of http://tinyurl.com/opwnvm A legend is a part of a figure that associates textual descriptions with symbols pertaining to plotted entities. SIO_000468 legend 1 experiment An experiment is an investigation that has the goal of verifying, falsifying, or establishing the validity of a hypothesis. SIO_000994 study 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 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 diagnostic test SIO_001022 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. sequence start position SIO_000791 A sequence start position is the start position for a sequence of characters. A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation. SIO_001203 increased molecular production from increased regulation SIO_001232 transfer RNA (tRNA) A transfer RNA (tRNA) is an RNA molecule that aids in the translation of a messenger RNA (mRNA) to produce a protein product. tRNA SIO_001020 effective dose effective dose is the amount of a substance required to produce an effect on a predefined percentage of a population. 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. SIO_000318 longitude SIO_000858 pleasure pleasure is an emotion of happy satisfaction and enjoyment. SIO_001234 snoRNA small nucleolar RNA (snoRNA) A small nucleolar RNA (snoRNA) is a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. SIO_010418 solute A solute is a substance that becomes dissolved in a solvent. is parameter in is parameter in is a relation between a data item and some data transformation process. SIO_000553 IP address SIO_001322 IP number an IP number is an number to connect to a device on the internet. regulation regulating regulating is a process that modulates the attributes of an object or process. SIO_000589 has start time SIO_000680 A dependent variable is one whose value changes as a consequence of changes in other values in the system. dependent variable SIO_000921 SIO_001115 member count A count of the instances of a class or members in a collection. glucose-6-phosphate and ADP are outputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. is output of SIO_000232 sadi is output of is a relation between an entity and a process, where the entity is present at the end of the process. chemical transport is the directed movement of a chemical entity by some agent (e.g. transporter). biopax:Transport SIO_010283 chemical transport CHEBI:30513 antimony atom SIO_011050 chemical destruction is destruction of a chemical entity to its chemical constituents through one ormore chemical interactions or reactions. chemical destruction SIO_000592 SIO_000508 endpoint An endpoint is a terminal point that is the last of an ordered pair of points. Rage is a feeling of intense anger that is associated with the Fight-or-flight response. SIO_000860 rage thorium atom CHEBI:33385 SIO_011104 francium atom CHEBI:33323 SIO_011072 A group of people affiliated by consanguinity, affinity, or co-residence. family SIO_001063 SIO_001091 homogeneous is a quality that describes the varied composition of an object. heterogeneous 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. SIO_001230 tRNA gene solube RNA (sRNA) gene http://purl.obolibrary.org/obo/SO_0001272 transfer RNA (tRNA) gene ionsdaleite ionsdaleite is a hexagonal allotrope of the carbon allotrope diamond. SIO_010795 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. SIO_001048 intervention study SIO_000281 NOT is a logical operator in that has the value true if its operand is false. negation (not) SIO_000112 capability capability+ core 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). has basis has basis is a relation between a realizable entity and the quality that forms the basis for it. 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 SIO_000288 is covalently connected to (transitive) SIO_001173 double stranded nucleic acid is a molecular complex composed of two weakly connected deoxyribonucleic acids. double stranded DNA quantity modifier SIO_001299 A biological entity is a heterogeneous substance that contains genomic material or is the product of a biological process. biological entity SIO_010046 chemical- SIO_010054 A cell line is a collection of genetically identifical cells. cell line A realizable entity is an attribute that is exhibited under some condition and is realized in some process. core realizable entity SIO_000340 SIO_001189 semantic web service a semantic web service is a web service that provides a formal, machine understanble description of its functionality. SIO_000794 count The number of elements of a finite set of objects. 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. SIO_000379 perception is identical to is a relation between two objects that are conceptually the same notwithstanding provenance or other non-intrinsic attributes. SIO_001242 is identical to SIO_001346 gene-disease association linked with somatic modifying mutation A gene-variant disease association in which a somatic mutation in the gene modifies the clinical presentation of the disease, and it may not be passed on to offspring. http://www.w3.org/2004/02/skos/core#exactMatch SIO_000484 is exact match to SIO_001377 versioned dataset a versioned dataset is a dataset with a particular release date or release number. regulation of molecular production A process that modulates the frequency, rate or extent of process involved in the production of a molecule. SIO_001128 http://purl.obolibrary.org/obo/SO_0001637 SIO_001182 rRNA gene A ribosomal RNA gene is a gene that codes for a ribosomal RNA molecule. ribosomal RNA gene a collection item is an item in a collection. SIO_001259 collection item core SIO_000668 in relation to in relation to is a comparative relation to indicate that the instance of the class holding the relation exists in relation to another entity. SIO_000285 academic organization An academic organization is a lawfully recognized organization that confers diplomas, degrees and other forms of recognition of academic achievement. SIO_001383 a gene symbol is a short name assigned to a gene. gene symbol SIO_011044 rhodium atom CHEBI:33359 is lesser than to is a comparison relation between two quantities in which the first has a value smaller than the second. SIO_000735 is lesser than SIO_000067 A namespace is an informational entity that defines a logical container for a set of symbols or identifiers. namespace SIO_000400 x cartesian coordinate An x cartesian coordinate is the coordinate of an object onto the x-axis of a cartesian coordinate system. SIO_000022 the external surface of the window; the surface of the p52 protein 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 periodical SIO_000162 http://purl.org/ontology/bibo/Periodical A periodical is a publication that appears on a regular schedule. integer scale An integer scale of measurement is one that only specifies integer values. SIO_000917 replica quality is the quality of an object that is an exact copy of another object. replica quality SIO_001412 drug regulatory authority SIO_010383 A drug regulatory authority is a regulatory authority which acts to control what substances may be used to treat individuals. pharmacodynamic pathway SIO_001256 a pharmacodynamic pathay is a regulatory pathway in which a drug molecule regulates the activity of one or more components organized in a pathway. SIO_000789 sequence element position A sequence element position is the position of an element of a linear sequence. protein-protein association A protein-protein association is an association between two proteins. SIO_001438 data storage device SIO_000596 A data storage device is a device that is capable of storing information. SIO_000826 despair despair is depression, hopelessness or lack of hope. SIO_000518 rectangle A rectangle is a quadrilateral in which one pair of line segments are parallel and the other pair are perpendicular to the first pair. polar coordinate system SIO_000327 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 is the quality of having a dipole. polar SIO_001046 The spatial region occupied by the province of ontario; the spatial region occupied by a lake. SIO_000414 geographic region A geographic region is a spatial region whose boundaries are typically defined against some material frame of reference (like the earth). SIO_000316 design specification A design specification is a specification that provides precise and explicit information about the requirements for a product design. SIO_000454 z-axis A z-axis is a Cartesian coordinate axis that is spatially oriented normal to the plane formed by the x- and y-axes. scatterplot scatter chart scatter diagram scatter graph SIO_000423 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. charged The quality of having a charge. SIO_000805 SIO_000324 surrounds A 'surrounds' B iff the A 'contains' B and A 'is adjacent to' B or A 'is directly connected to' B. A structural motif is a pattern in a structure formed by a spatial arrangement of objects (e.g. atoms). structural motif SIO_001197 SIO_000708 professor role 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. SIO_000030 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_010791 amorphous carbon 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. major.minor[.build[.revision]] A software version label is a version label for a piece of software. software version label SIO_000654 SIO_001389 The HGVS (human genome variation society) notation is a notation to specify a sequence variation in dna, rna, proteins, and other biomolecules. hgvs notation aggregated carbon nanorods SIO_010790 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. SIO_000885 publisher role A publisher role is the role of an individual that prepares and issues creative works. Log likelihood is the natural logarithm of the likelihood function SIO_001244 log likelihood envy 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. SIO_000834 SIO_011081 darmstadtium atom CHEBI:33367 SIO_001119 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 OWL ontology SIO_000331 An OWL ontology is an ontology as specified by the W3C OWL specification. SIO_000029 is time boundary of clause SIO_000493 A clause consists of a subject and a predicate. is causally related to a is causally related to b iff there is a causal chain of events from a to b SIO_000294 2 SIO_000042 width width is the shorter dimensional extent perpendicular to a 2D projection of the object. Disgust is a feeling of revulsion or profound disapproval aroused by something unpleasant or offensive. SIO_000828 disgust broaderThan A pathway is an effective specification that outlines a set of actions that forms a way to achieve an objective. biological pathway SIO_001107 pathway replicate a replicate is an object that is a facsimile, reproduction, or copy of another item. SIO_001418 increase in number of objects produced An increase in the number of objects produced is the positive value of a difference in number of objects produced. SIO_001163 ongoing is the status of a process that is not yet complete. ongoing SIO_000035 SIO_000625 chemical structure is the structure of a chemical entity in terms of its molecular geometry and electronic structure. chemical structure 0 SIO_001175 The positive nucleic acid strand refers to the strand that is to be read 5' to 3'. positive nucleic acid strand forward strand A mature RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns. mature mRNA SIO_010096 angst angst is the intense feeling of apprehension, anxiety or inner turmoil. SIO_000813 binding site SIO_010040 A binding site is a molecular site which when occupied with particular ligands leads to structural transformations that initiatiate new moelcular processes. negative nucleic acid strand The negative nucleic acid strand is the strand that is that is complimentary to the forward strand and appears from 3' to 5'. SIO_001176 reverse strand is quality of SIO_000218 is quality of is a relation between a quality and the entity that it is a property of. The quality of having a charge that is not a full multiple of 1 unit charge. partial charge SIO_000809 is boundary of is a mereological relation between a boundary located at the periphery of a whole. is boundary of SIO_000096 an edge is a line connecting two graph vertices. SIO_001334 edge happiness is an emotion characterized by positive or pleasant emotions ranging from contentment to intense joy. happiness SIO_000840 maternally transmitted maternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the maternal line. SIO_001269 to serve as a host SIO_000543 to serve as host is the capability to act in a manner that provides hospitality, serves to harbour an organism in or on itself. SIO_000105 A symbol is a proposition about what an entity represents. symbol SIO_010783 A homocyclic ring is a ring where the atoms are of a single type. homocyclic ring SIO_010432 A ligand is a molecule that is part of a complex by weakly interacting with another molecule. ligand radon atom SIO_011071 CHEBI:33314 2 A specification for spatial location is an effective specification towards representation spatial position or spatial data. spatial specification SIO_000317 biological reproduction is the biological process by which one or more biological organisms are produced from their "parents". biological reproduction SIO_000587 A top value axis is a value axis that is spatially positioned to the top of the plot area. SIO_000902 top value axis toxin role SIO_000890 A toxin role is a toxic role of a chemical substance that is poisonous and is produced by an organism. primer 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. SIO_000779 core nlp A is connected to B iff there exists a fiat, material or temporal path between A and B. [S][T] interacts with SIO_000203 is connected to information translation SIO_001359 is last part of SIO_000973 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. assay SIO_001007 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. SNV SNP single nucleotide variation SIO_001329 single nucleotide polymorphism a single nucleotide variation (SNV) is a nucleotide residue that is a variant compared to some reference nucleic acid sequence. A catalog is a systemic collection of items of the same type. registry SIO_001241 catalog homozygous is the quality of a biological organism in which there are two identical alleles at a given locus. SIO_001264 homozygous A Gantt chart is a bar chart that illustrates a project schedule. SIO_000922 Gantt chart SIO_000475 biological quality A biological quality is a quality held by a biological entity. SIO_000509 A start point is a terminal point which is the first of an ordered pair of points. start point SIO_000788 A linear position is the position of some object against a linear positioning system. linear position A nostril; the interior of the heart valve; the interior of a bottle. A site is a spatial region bounded (in part or in whole) by material entities and may be occupied by material entities. site SIO_000019 2 polypeptide sequence amino acid sequence A protein sequence is a symbolic sequence of amino acid residues in a protein or class of proteins. protein sequence SIO_010015 boredom SIO_000820 boredom is the emotion experience by those not interested in their surroundings or available activities. software method A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. SIO_000098 unique cell SIO_000759 A unique cell is a cell that contains a unique value in the cellular automaton. SIO_000879 reactant role The role of a chemical entity present at the beginning of a chemical reaction. A set is a collection of entities, for which there may be zero members. SIO_000289 set SIO_011100 CHEBI:33379 erbium atom mereological chart SIO_000940 A mereological chart is a chart that illustrates the parts in the context of the whole. SIO_000205 is represented by is represented by: a relation between an entity and some symbol. A linear value axis is a value axis that corresponds to a scaling factor of 1 of the value range. SIO_000462 linear value axis SIO_000683 justification A justification is a proposition that defends, explains or excuses some argument. SIO_001218 weak weak is a qualitative intensity value that is more intense than none, but less intense than mild. satisfaction is an emotion of fulfillment of one's wishes, expectations, or needs, or the pleasure derived from this. satisfaction is the emotion of fulfillling one's wishes, expectations, or needs. satisfaction SIO_000864 SIO_001284 contentment pleasure 2 SIO_000119 brand name A brand name is a trademarked and marketed name of a product. SIO_000148 document A document is a bounded physical or digital representation of a body of information designed with the capacity (and usually intent) to communicate. the date at which an information content entity was made public. SIO_001314 date of issue 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 2 contributor always always indicates that the event occurs at all times. SIO_001292 all of the time molecular structure descriptor SIO_011121 molecular structure descriptor is data that describes some aspect of the molecular structure (composition) and is about some chemical entity. CHEMINF:000085 SIO_001235 non-protein coding RNA (ncRNA) A non-protein coding RNA (ncRNA) is a RNA molecular that cannot be used as a template for generating a protein product. SIO_000381 to immobilize to immobilize is the capability to contain an entity in such a way that it may not move in space. activator role SIO_000804 The role of a chemical entity that increases the rate of reaction. SIO_000748 predicting is the process of formulating a proposition about a state of affairs which might be realized in the future. predicting SIO_010017 RNA sequence ribonucleic acid sequence A ribonucleic acid sequence is a symbolic sequence of ribonucleic acid residues in a ribonucleic acid. SIO_001313 excellent quality SIO_001285 suicidal is the emotion of being deeply unhappy or depressed with thoughts of killing one's self. suicidal A document section is a component of a document. document section SIO_000111 protege#defaultLanguage SIO_010417 solvent A solvent is a substance that can dissolve other substances (solutes). diffusion diffusion is motion of particles at temperatures above absolute zero. SIO_000564 matrix rank 2 tensor SIO_001433 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. process model SIO_000647 A process model is a representation of some process. SIO_000682 is start time of is referenced by is reference for is a relation between a document that provides information about an entity. SIO_000252 A millenium is a period of 1000 years millennium SIO_000432 SIO_000971 has first part 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. reagent 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. SIO_010411 software module SIO_000099 A software module is software composed of a collection of software methods. 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. SIO_001168 audio recording SIO_000862 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 material entity core SIO_000004 A material entity is a physical entity that is spatially extended, exists as a whole at any point in time and has mass. A signal transducer is a molecule that responds to and amplifies a signal in a signalling system. SIO_010437 signal transducer SIO_000999 procedure A procedure is a process that attempts to achieve one or more objectives by following an established set of actions. CHEBI:33392 californium atom SIO_011112 phosphorus atom CHEBI:28659 SIO_011014 CHEMINF:440533 mixture SIO_011126 chemical substance A chemical substance is a chemical entity composed of two or more weakly (non-covalently) interacting chemical entities. CHEBI:27698 SIO_011022 vanadium atom differential diagnosis SIO_001002 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). SIO_000861 regret regret is a feeling of sadness, repentance, or disappointment over something that has happened or been done. transforms into SIO_000655 A transitive temporal relation in which an entity mainstains identity from one state to another. lithium atom SIO_011004 CHEBI:30145 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. SIO_000480 insertion variant role 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 SIO_001139 heating the solution causes greater diffusion of a chemical. SIO_000899 chromosome A chromosome is a molecular complex of circular or linear DNA and bound proteins. A decomposition reaction is an inorganic reaction in which molecule is fragmented into submolecules or atoms. decomposition reaction SIO_010511 SIO_000667 software execution software execution is the process of executing software on a computing device. SIO_000726 An administrative role is the role of an individual that performs administrative tasks for some organization. administrative role parameterized data transformation SIO_000595 A parameterized data transformation is a data transformation whose behaviour may be modified by one or more parameters. A variable is a value that may change within the scope of a given problem or set of operations. SIO_000367 variable 1 uncertainty value SIO_000769 The uncertainty value (margin of error) of a measurement is a range of values likely to enclose the true value. SIO_001415 A percentile (or a centile) is a quantile that divides the given probability distribution, or sample, into 100 equal-sized intervals. percentile An honor's thesis is a thesis prepared as a requirement for an honor's undergraduate degree. honor's thesis SIO_000166 SIO_001075 A microarray probe set identifier is an identifier for a set of probe pairs selected to represent expressed sequences on an array. microarray probe set identifier A description is language entity in which elements of a language (formal or natural) are used to characterize an entity. SIO_000136 description is disputed by SIO_000207 has disputing evidence is a relation between a proposition and something that disputes (does not directly support) the truth of the assertion. to consume is the capability to internalize a material entity. to consume SIO_000492 is manifested as is a relation between an expression and its manifestations. the english language version of 'war of the worlds' is manifested as a collection of english language versions of the book. is manifested as SIO_000341 SIO_000104 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 decrease in number of objects produced An decrease in the number of objects produced is the negative value of a difference in number of objects produced. SIO_001164 SIO_010429 placebo A placebo is a medically ineffectual treatment for a medical condition intended to deceive the recipient. to store is the capability to place an object into a medium in which it can be retrieved in the future. SIO_001361 to store physical entity identifier SIO_000730 A physical entity identifier is an identifier for a physical entity. 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 SIO_000155 A blog is a publication accessible at some website and is typically about various experiences. blog SIO_000855 panic 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. to inject is the capability to administer a substance into some object through its external barrier. to inject SIO_000372 A start date is a time instant pertaining to the date of the beginning of a process. start date SIO_000031 1 molecular complex A molecular complex is a chemical complex composed of at least one weakly interacting molecule. SIO_010506 SIO_000970 is first part of 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. to oxidize is the capability to remove an electron or an increase in oxidation state of a chemical entity. to oxidize SIO_010358 XMLSchema#date ytterbium atom CHEBI:33381 SIO_011102 to change spatially SIO_000392 to change spatially is the capability to affect the physical movement of some entity. SIO_000401 y cartesian coordinate An y cartesian coordinate is the coordinate of an object onto the y-axis of a cartesian coordinate system. SIO_010504 van der Waals' interaction is an a weak submolecular interaction between an instantaneous dipole and induced dipole. van der Waals interaction SIO_000234 has implementation has implementation is a relation between a specification and an implementation that conforms to it. SIO_000008 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. has attribute core A gene promoter is a region of DNA that initiates transcription of a particular gene. gene promoter SIO_010446 drug drug interaction A drug-drug interaction is an interaction in which two drugs interact in such a way to produce a non-additive biological response. SIO_001006 fullerene fullerene is a carbon allotrope which take the form of a hollow sphere, ellipsoid, or tube. SIO_010789 SIO_001215 severe is a qualitative intensity value that is more intense than strong, but less intense than fatal. severe disappointment is the feeling of dissatisfaction that follows the failure of expectations or hopes to manifest. disappointed disappointing disappointment SIO_000827 SIO_000504 A polyhedral surface is composed of polygonal faces. polyhedral surface curiosity is the strong desire to know or learn something. curiosity SIO_000823 SIO_000322 is spatiotemporally related to A is spatiotemporally related to B iff A is in the spatial or temporal vicinity of B core SIO_001295 poor quality SIO_010039 A pharmaceutical preparation is a chemical substance that is approved for use in the medical diagnosis, cure, treatment, or prevention of disease. medicine pharmaceutical drug A synonym is a word with the same or very similar meanings. SIO_000122 synonym has unique identifier is an inverse functional relation between an entity and an identifier that uniquely identifies it. has unique identifier SIO_000673 an ordered list item is an item in an ordered list. ordered list item SIO_001261 SIO_001027 medical health record A medical health record is a record of a single patient's medical history. 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 SIO_001280 is phenotype of is a relation between an observable/measurable characteristic and an object. is phenotype of to ingest SIO_001105 to ingest is the capability to take into the body by the mouth for digestion or absorption. 1 SIO_010455 isomer An isomer is a molecule that is compositionally identical to another molecule as a result of a different atomic connectivity. osmosis SIO_000572 osmosis is the movement of water molecules through a selectively-permeable membrane down a water potential gradient. SIO_000320 coordinate system A coordinate system is a specification for spatial location that uses a set of numbers, or coordinates, to uniquely determine the position of a point or other geometric element. SIO_010308 metabolism Metabolism is the set of chemical processes that occur within a living organism in order to maintain life. 0.0 to fluoresce to fluoresce is to emit light as a result of absorbing light or other electromagnetic radiation. SIO_000895 is subject of SIO_000629 core function SIO_000017 A function is a capability that satisfies some agentive objective, or (evolutionary) optimization. SIO_000345 to magnify to magnify is the capability to increase the appearance of the size of an object. sum A sum is the result of adding a set of values together. SIO_001112 A century is a period of one hundred years. century SIO_000431 A SADI web service invocation is the excution of a SADI web service. SADI web service invocation SIO_001193 sadi 2 SIO_001393 post-translational modification 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. A collection of points is a geometric entity that contains a non-zero set of geometric points. collection of points SIO_000546 A database is a set of tables. SIO_000750 database http://purl.obolibrary.org/obo/SO_0000336 SIO_000988 pseudogene A pseudo gene is a region of a nucleic acid that either cannot be transcribed, or its RNA transcript cannot be translated. A positional role is an abstract role which holds by comparing position to another object of reference. SIO_000704 positional role SIO_000450 The value of a plotted geometric objects (e.g. point) can be obtained from the perpendicular projection of the position of the object onto the axis. Axis may also be associated with a textual description of what the values on the axis represents. An axis is a line segment that is part of a statistical graph in which the position along the line corresponds to a numeric or categorical value. axis The left vertical and bottom horizontal lines with tickmarks in Graph 1 http://tinyurl.com/opwnvm has identifier a relation between an entity and an identifier. SIO_000671 A vertext normal is the normalized average of the surface normals of the faces that contain that vertex. vertex normal SIO_000541 CHEBI:30217 SIO_011003 helium atom SIO_000274 A is prior version of B iff A is a variant of B and B derives from A. is prior version of SIO_000229 has output sadi core has output is a relation between an process and an entity, where the entity is present at the end of the process. SIO_001074 A t-statistic is a ratio of the departure of an estimated parameter from its notional value and its standard error. t-statistic professor SIO_000404 A professor is an individual that is a scholarly teacher. A tertiary structure descriptor describes 3D topological patterns in a biopolymer. tertiary structure descriptor SIO_010023 iodine atom CHEBI:24859 SIO_011052 A correspondence section is a document section that contains the details for contacting the corresponding author. correspondence section SIO_000194 SIO_000448 A figure part is a part of a figure. figure part is preceded by SIO_000249 OBO_REL:preceded_by referent cell SIO_000761 A referent cell is a cell that is the referent of some function or pointer. hassium atom CHEBI:33357 SIO_011079 SIO_001166 annotation An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information. A 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 gene-disease association linked with modifying mutation SIO_001342 A gene-disease association in which a gene mutation is known to modify the clinical presentation of the disease. 0 A base pair is a weak molecular interaction composed of hydrogen bonds between nucleobases. SIO_010045 base pair 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. SIO_000499 to decrease the rate of formation SIO_000495 is dissimilar to is dissimilar to is a relation between two entities in which one is considered dissimilar to the other based on some criteria. A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation. stop codon SIO_010448 is trigger for SIO_000636 regulates 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 SIO_001154 A base stack is a stabilizing interaction of DNA and RNA between spatially adjacent nucleotides and possibly involving London dispersion, hydrophobic and electrostatic forces. SIO_010505 base stack An amino acid polymer submolecule is a submolecule of an amino acid polymer. amino acid polymer submolecule SIO_010471 SIO_000130 pattern A pattern is a generalized representation of some repeatable concrete or informational item. regulation of object production regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is increased. SIO_001151 SIO_001067 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 organic polymer An organic polymer is an organic molecule composed of connected set of monomeric units. SIO_010346 SIO_010464 A negative charge is a charge where the value is negative. negative charge SIO_010347 to modify conformation of to modify conformation of is to affect the spatial arrangement of an entity. http://purl.obolibrary.org/obo/SO_0000704 biopax:Gene SIO_010035 A gene is part of a nucleic acid that contains all the necessary elements to encode a functional transcript. gene SIO_000884 publishing role 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. stop position SIO_000953 An end position is the distal position of an object relative to an origin in a linear system. end position A bill is proposed legislation under consideration by a legislature. bill SIO_001376 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. SIO_000531 drop line PATO:0001827 hermaphrodite is a biological sex of an individual with both male and female sexual organs. SIO_000784 hermaphrodite secondary structure descriptor SIO_010022 A secondary structure descriptor describes local topological patterns in a biopolymer. measurement measuring is the process of determining the size, amount, or degree of (something) by using an instrument or device marked in standard units SIO_001054 measuring SIO_000009 social entity A social entity pertains to the interaction among individuals and groups. is greater than or equal to 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. SIO_000699 has quality SIO_000217 has quality is a relation between an entity and the quality that it bears. 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 SIO_000529 decreasing line An decreasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is negative. poison A poison is a drug that is harzardous or toxic to an organism when ingested at a certain quantity. SIO_010076 is concretization of A is concretization of B iff A is a quality of a material entity and B is an informational entity. SIO_000214 specialized object SIO_001353 hope hope is an emotion of belief in a positive outcome related to events and circumstances in one's life. SIO_000843 SIO_000714 nurse role 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. A non-polar addition reaction is an addition reaction involving non-polar residues. non-polar addition reaction SIO_010520 SIO_000321 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_001059 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 differential equation A differential equation is a mathematical equation for an unknown function of one or several variables that relates the values of the function itself and its derivatives of various orders. SIO_000569 life status SIO_010057 life status is the quality of whether something is alive or dead. apathy is an emotion characterized by lack of interest, enthusiasm, or concern. SIO_000816 apathy chemical synthesis SIO_000559 chemical synthesis is synthesis of a chemical entity from physical precursors through one or more chemical interactions or reactions. SIO_010363 product SIO_000573 passive movement is the process in which an object is spatially displaced without an expenditure of energy contained in molecular bonds. passive movement core OBO_REL:has_participant SIO_000132 has participant is a relation that describes the participation of the object in the (processual) subject. has participant CHEMINF:000063 SIO_011118 A covalent bond is a strong submolecular interaction between atoms. covalent bond An organic submolecule is connected region of a molecule. SIO_010071 organic submolecule An academic role is a social role that pertains to the academic institution. academic role SIO_000711 SIO_011120 A molecular structure file is a file that contains a description of molecular structure. molecular structure file CHEBI:22984 SIO_011019 calcium atom SIO_001437 gene-gene association A gene-gene association is an association between two genes. SIO_010296 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 negative regulation SIO_001287 indecision is the emotion of being unable to choose between two or more possible courses of action. indecision indecisiveness SIO_001036 draft is the quality of text that has not yet complete. draft drafted SIO_001392 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 is located in 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 A parasite in the interior of a person's intestine is located in their intestinal lumen. SIO_000061 core has frequency is a relation that specifies the occurence of an object or event SIO_000900 has frequency SIO_010289 biochemical inhibition is a molecular interaction that decreases the catalytic rate of the target enzyme. biochemical inhibition SIO_010786 A carbon allotrope is a chemical substance composed of carbon. carbon allotrope SIO_000905 has substrate has substrate is a relation between a process and an object where the object is destroyed by its participation in the process. manual SIO_000161 A manual is a document that instructs on the usage of a device. PATO:0002180 [for material entities] SIO_000538 straight straight is a quality of a bearer that is free of curves, bends, or angles. is positionally before 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. SIO_000240 SIO_001181 full disagreement full agreement is the result of consensus decision making when members of the group unanimously disagree. mass spectrometer http://purl.obolibrary.org/obo/OBI_0000049 SIO_001237 A mass spectrometer is a device that identifies ions based on their mass to charge ratio using an electromagnetic field. SIO_000975 is ordered part of 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. SIO_010441 A submolecule is any part of a molecule. submolecule SIO_011027 nickel atom CHEBI:28112 imaginary SIO_001444 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. SIO_001304 a little quantifier 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 SIO_001072 text span end position text span end position is the position (offset) of the last character of a text span in relation the text it is from. SIO_000873 worry is the emotion characterized by concer over a real or imaginary issue. worry has phenotype is a relation between an object and an observable/measurable characteristic. has phenotype SIO_001279 to be electronically modified is the capability of a chemical entity to have electrons added or removed. to be electronically modified SIO_010369 SIO_000686 academic department An academic department is a division of a university or school faculty devoted to a particular academic discipline. SIO_000926 radio receiver 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. 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. SIO_000817 arousal 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 ray is a line which that is bounded by a startpoint and extends outwards infinitely along one dimension. ray SIO_000516 SIO_000705 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 molecule CHEBI:23367 SIO_011125 A molecule is a single chemical entity composed of fully covalently bonded atoms. left closed interval SIO_001254 a left closed interval is an interval in which there is a real number that is smaller than all its elements. A citation is a textual entity which denotes a source described in the bibliography or reference section of a document. citation SIO_000174 SIO_011010 sodium atom CHEBI:26708 to be interacted with SIO_000702 to be interacted with is the capability of an object to be target of a physical interaction. 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 peer reviewed article is an article that has undergone peer-review and deemed acceptable for publication. peer reviewed article SIO_001029 A social role is a role that is ascribed to individuals in a community. social role SIO_000676 CHEBI:26833 SIO_011015 sulfur atom A province is a territorial unit, almost always an administrative division, within a country or state. SIO_000661 province A name is a label used to identify an entity. name SIO_000116 is provider of is provider of is a relation between a source and the entity it makes available. SIO_000064 intensity SIO_001212 intensity is a quality that represents the strength or degree of something. 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 subtitle, alternative title Humiliation is the abasement of pride, which creates mortification or leads to a state of being humbled or reduced to lowliness or submission. SIO_001281 humiliation informational entity identifier SIO_000731 An informational entity identifier is an identifier for an informational entity. gene-disease association linked with post-translational modification methylation or phosphorylation of protein product A gene-disease association in which the disease phenotype is associated with post-translational modifications in the protein product. SIO_001124 deoxyribonucleic acid SIO_010010 A deoxyribonucleic acid is an organic polymer composed of a sequence of deoxyribonucleotide residues. finalized finalized is the quality of a textual entity that is in its final form. SIO_001037 A nucleic acid sequence is a symbolic sequence of nucleic acid residues in a nucleic acid. SIO_010016 nucleic acid sequence female is a biological sex of an individual with female sexual organs. SIO_010052 female 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 article SIO_000154 An article is a publication that is stand-alone section of a larger work. scalar a scalar is a rank 0 tensor and is an element of a field that is used to define a vector space. rank 0 tensor SIO_001431 has last part SIO_000972 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. web service A web service is a software application that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services. SIO_000140 SIO_001306 mostly quantifier The category axis that corresponds to months in Graph 1 of http://tinyurl.com/opwnvm A secondary category axis is a category axis that defines a finer granular part (or subset) of the value range of the primary category axis. SIO_000457 secondary category axis SIO_011091 praseodymium atom CHEBI:49828 tissue A tissue is a mereologically maximal collection of cells that together perform some function. SIO_010002 history is a sequence of past events. SIO_001196 history title 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 to ionize 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. SIO_000350 CHEBI:27007 tin atom SIO_011049 dying SIO_000583 dying is a process in which a biological entity ceases to exist. A gene that is located on RNA. rna gene SIO_010101 5' untranslated region SIO_010064 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. SIO_000179 label a label is a term that is associated with some entity neodymium atom SIO_011092 CHEBI:33372 CHEBI:28685 molybdemum atom SIO_011041 SIO_000891 toxic role A toxic role is the role of a chemical substance that is poisonous. a duplicate role is a comparative role that holds when one item is an exact copy of another in a specific set. SIO_001416 duplicate role SIO_000396 file http://www.w3.org/ns/dcat#Distribution A file is an information-bearing object that contains a physical embodiment of some information using a particular character encoding. Graphs 6,7 in http://tinyurl.com/opwnvm A stacked bar graph is a bar graph in which each rectangular bar is partioned by the categorical value of each series of data. SIO_000446 stacked bar graph electronic structure is the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals. electronic configuration SIO_001099 the electron configuration of the neon atom is 1s2 2s2 2p6. electronic structure SIO_011035 CHEBI:49696 krypton atom to serve as SIO_000542 to serve as is the capability to act in a manner corresponding to some role. A start time is a time instant pertaining to the time at which a process begins. SIO_000669 start time CHEBI:33382 SIO_011103 lutetium atom 1.0 node SIO_001335 a node or vertex is a point in a graph. vertex strontium atom SIO_011037 CHEBI:33324 SIO_001172 exact cross-reference An exact cross-reference is a database cross-reference in which one entity is equivalent to the other based on all the entitie's attributes (minus the source). homogeneous homogeneous is a quality that describes the uniform composition of an object. SIO_001090 SIO_001324 work phone number a work phone number is the number to connect to an phone at a place of work. SIO_001056 character offset The ordinal position of a character in a sequence of characters. character position to lose a covalent bond is the capability of a chemical entity to have bonds removed. SIO_001104 to lose a covalent bond deoxyribonucleic acid template SIO_010092 A deoxyribonucleic acid template is a deoxyribonucleic acid that provides the template to synthesize a complementary strand of DNA through transcription. SIO_001407 The surface area of a is a measure of the total area that the surface of the object occupies. surface area SIO_001135 regulation of process frequency regulation of a process duration is a process that modulates the frequency of another process relative to some reference process. is proper part of is an asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole. is proper part of SIO_000093 OBO_REL:proper_part_of core isomerization reaction An isomerization reaction is a chemical reaction in which a molecule is converted into its isomer. SIO_010517 decreased PATO:0002301 SIO_000751 A quality that has a value that is decreased compared to normal or average. to reduce energy is the capability to remove energy from a source. to reduce energy SIO_000374 SIO_000526 A vertical line is a line that is positionally oriented perpendicular to the horizon. vertical line has annotation is a relation between an entity and some textual anntotation. was annotated with is annotated with document x is annotated with the keywords 'ontology','semantic web' SIO_000255 has annotation 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. SIO_001397 miRNA microRNA (miRNA) displacement reaction A displacement reaction is an inorganic reaction in which a elementary substance displaces and sets free a constituent atom from a molecule. SIO_010512 SIO_010508 catalyzed reaction A catalyzed reaction is a chemical reaction that is facilitated by a catalyst. A union is a list of all of the values of an attribute for the entities in the defined set. SIO_001116 union SIO_000189 An acknowledgements section is a document section that identifies individuals, groups or organizations for their support in the development of the work. acknowledgements section 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 cell (informational) SIO_000755 The minimal unit of a cellular automaton that can change state and has an associated behavior. SIO_010461 positive charge A positive charge is a charge where the value is positive. SIO_000889 A molecular entity role is a chemical entity role held by a molecule. molecular entity role 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 A student is an individual who is attends an educational institution. SIO_000405 student An author section is a document section that lists the contributing authors. SIO_000191 author section SIO_000870 surprise is a brief emotion experienced as the result of an unexpected event. surprise in relation from a in relation from b is a comparative relation in a is the object of reference in a relation with b. SIO_000892 dendrogram SIO_000948 A dendrogram is a tree diagram used to illustrate the arrangement of the clusters produced by hierarchical clustering. SIO_010095 An RNA transcript component is a region of an RNA transcript. RNA transcript component SIO_011084 unutrium atom SIO_010048 male is a biological sex of an individual with male sexual organs. male PATO:0000384 generation number generation number is a count of the number of biological reproduction events elapsed from some starting reference point. SIO_010061 A binary compound is a mereological maximum sum of two kinds of weakly connected entities. SIO_010674 binary compound is subsequent version of SIO_000286 A is subsequent version of B iff A is a variant of B and A derives from B. SIO_000292 glucose is a target in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. is target in 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. represents a represents b when a serves as a sign, symbol or model of b. core SIO_000210 An end date is a time instant pertaining to date of the end of a process. end date SIO_000032 SIO_000934 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_001083 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 resentment SIO_000950 resentment is disgust directed toward a higher status individual. A dataset is a data item that is a collection of data items. data set http://www.w3.org/ns/dcat#Dataset SIO_000089 dataset primary active transport, also called direct active transport, directly uses energy to transport molecules across a membrane. SIO_000577 primary active transport structural quality A structural quality is a quality of an object that describes its structure. SIO_001092 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 SIO_000427 is narrower than dbxref database cross-reference SIO_001171 A database cross-reference is an association between one data item and another. selenium atom CHEBI:27568 SIO_011033 single bond SIO_010498 A single bond is a covalent bond between a pair of atoms in which one pair of electrons are shared. standard deviation A standard deviation (represented by the symbol σ) is the quantity of variation from the average (mean, or expected value). SIO_000770 example translation translation is the process of producing a polypeptide from a ribonucleic acid by a ribosome. SIO_010301 secondary graph title SIO_000474 A secondary graph title is a secondary title that describes a statistical graph. 2 SIO_000206 is supported by is a relation between a proposition and something that supports the truth of the assertion. is supported by SIO_000833 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 A verbal language entity is a language entity that is manifested through sound. SIO_000786 verbal language entity cites cites is a relation to refer to by way of example, authority or proof. SIO_000277 1 SIO_000695 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_000033 process status process status is a process quality that describes the state of a process. existence quality is the quality of an entity that describe in what environment it is known to exist. SIO_000959 existence quality to be passively interacted with to be passively interacted with is the capability of an object to be observed. SIO_000694 A deoxyribonucleic acid sequence is a symbolic sequence of deoxyribonucleic acid residues in a deoxyribonucleic acid. DNA sequence deoxyribonucleic acid sequence SIO_010018 is numerically comparable to is a comparison relation between two quantities whose datatype value can be compared. SIO_000737 is numerically comparable to software entity SIO_000097 A software entity is a computational entity that can be interpreted by or directly executed by a processing unit. An intervention group is a group of individuals that are subject to an intervention. SIO_001069 intervention group 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 to extract is the capability to remove certain entities based on selected attribute(s) while allowing other entities to remain. to extract SIO_000389 sadi core relations nlp A relation between a informational entity and its actual value (numeric, date, text, etc). SIO_000300 has value to conformationally inhibit to conformationally inhibit is to modify the conformation of an entity in such a way that it functionally is reduced or inhibited. SIO_010355 allele An allele is one of a set of sequence variants of a gene. SIO_010277 a fax number is a number to connect to fax device fax number SIO_001321 syndrome SIO_001017 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. surface normal A surface normal is a vector that is perpendicular to a flat surface. SIO_000533 SIO_000121 magazine http://purl.org/ontology/bibo/Magazine A magazine is a periodical that typically contains essays, stories, poems, etc., by many writers, and often photographs and drawings, frequently specializing in a particular subject or area, as hobbies, news, or sports. SIO_000700 to disassociate is to cease or break association with some thing. to disassociate is generalization of is generalization of is a relation between a more general instance (in terms of spatial/temporal localization & other attributres) than the other. SIO_001097 SIO_000472 scientific data is data obtained from some scientific procedure. scientific data SIO_000139 OBO_REL:has_agent 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. has agent sadi core social structure A social structure is a social entity which consists of relationships between two or more entities. SIO_000010 increased object production from increased regulation SIO_001146 increased regulation leads to an increase in the number of target objects of a specified type. SIO_001394 evidence is the body of facts or information indicating whether a belief or proposition is true or valid. evidence communication communicating is the process of conveying information through the exchange of thoughts, messages, or information, as by speech, visuals, signals, writing, or behaviour. SIO_000969 communicating target SIO_010423 SIO_000195 discussion section The discussion section is a document section containing a summary of the findings, a reflection on the significance of findings, comparison with related work, among others. vowel SIO_000979 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. very dissatisfied qualifier SIO_001309 SIO_000732 A molecular identifier is an identifier for a molecular entity. molecular identifier to assemble is the capability to combine entities together into a larger object that persists in time. SIO_000388 to assemble host role SIO_000882 The role of an organism in providing resources to maintain the survival and/or reproduction of another organism. apprehension is the negative emotion that something unpleasant will occur. SIO_000949 apprehension A dipole-dipole interaction is a weak submolecular interaction between strongly electronegative atoms. dipole-dipole interaction SIO_010503 is causally related with A transitive, symmetric, temporal relation in which one entity is causally related with another non-identical entity. core SIO_000243 2 SIO_000635 has trigger is a relation between a realizable and the factor that causes it to be realized. has trigger SIO_000725 to be examined is the capability of an object to be observed in a detailed manner. to be examined SIO_001206 decreased molecular production from decreased regulation A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation. A homonym is a word that sounds the same but has different meaning. SIO_000126 homonym sad unhappiness unhappy sadness is emotional pain associated with, or characterized by feelings of disadvantage, loss, despair, helplessness, sorrow, and rage. sadness SIO_000863 beryllium atom CHEBI:30501 SIO_011005 SIO_000005 core quality 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. homozygous is the quality of a biological organism in which there are two different alleles at a given locus. SIO_001265 heterozygous references references is a relation between one entity and the entity that it makes reference to by name, but is not described by it. core mentions SIO_000631 SIO_001060 planned planned is a process status for a process that has not yet started, but is referred to in a plan. toxic is the quality of a substance imparing the normal functioning of a system. toxic SIO_001009 SIO_001066 study A study is a process that realizes the steps of a study design. core is data item in SIO_001278 'is data item in' is a relation between an entity that is described or referenced in a dataset. dose A dose is the quantity of a chemical substance administered to a biological system. SIO_001019 SIO_000467 global minimal stationary point A global minimum data point is a data point that corresponds to a measurement value is smaller than that of all other plotted datapoints. descriptor A descriptor (index term, subject term, subject heading) is a term that captures the essence of the topic of a document. SIO_000133 receptor A receptor molecule is a molecule that has the capability to bind to a signal and propogate a response to that signal. SIO_010420 SIO_010368 to be transported to be transported is the disposition to undergo motion. polygon vertex A polygon vertex is a terminal point at which two polygon edges meet and are part of a polygon. SIO_000500 SIO_000621 A formal specification is a mathematical description of software or hardware that may be used to develop an implementation. formal specification maintenance of duration of process SIO_001143 maintenance of duration of process is a process that regulates a target process to maintain its duration within an expected interval. SIO_000848 interest interest is the emotion of wanting to know or learn about something or someone. SIO_010439 messenger 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. increased molecular degradation from increased regulation SIO_001199 A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation. an ingredient is a chemical substance that forms part of a mixture. SIO_001428 ingredient SIO_000909 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_000263 A deductive argument is an argument that asserts that the truth of the conclusion is a logical consequence of the premises. deductive argument 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 SIO_001121 A gene-disease association in which the gene/protein is involved in the etiology or maintenance of the disease. gene-disease biomarker association A city is a relatively large and permanent settlement. city SIO_000665 unit of measurement SIO_000074 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. chemical effect A chemical effect is a chemical interaction in which a chemical elicits a marked characteristic of a biological system. SIO_001005 An algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. algorithm SIO_000094 SIO_000684 is end time of hunger is the craving for food. SIO_001282 hunger molecular complex formation molecular complex formation is the process of forming a molecular complex from its constituent parts. SIO_010285 mutual disposition SIO_000409 A mutual disposition is a disposition that simulataneously invokes another disposition when realized. SIO_000537 curvature is a quality of a bearer that relates to the presence of curves, bends, or angles. curvature depression 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. depressed SIO_000824 is regulated by SIO_001155 SIO_000156 A book volume is a book that is part of a collection. book volume 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. SIO_001447 symbolic sequence 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 SIO_001191 SOAP web service http://en.wikipedia.org/wiki/SOAP a SOAP web service is a web service that implements Simple Object Access Protocol (SOAP). SIO_000614 attribute An attribute is a characteristic of some entity. core buffer role SIO_000887 A buffer role is the role of a chemical substance which maintains a pH at a near constant value. A terminology is a set of terms used for a specified application. terminology SIO_001396 page total SIO_000178 A page total is a textual entity that is about the number of pages in some informational entity. A disposition is the tendency of a capability to be exhibited under certain conditions or in response to a certain stimulus (trigger). disposition SIO_000014 solubility (to dissolve when put in fluid); fragility (disposition to break when dropped) core SIO_001015 race is a characteristic of an individual by heritable phenotypic characteristics, geographic ancestry, physical appearance, ethnicity, and social status. race A data series is a data set composed of related values displayed in a statistical graph. SIO_000464 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_010462 A heterogeneous substance is a chemical substance that is composed of more than one different kind of component. heterogeneous substance SIO_000612 representation A representation is a entity that in some way represents another entity (or attribute thereof). A temporal relation in which an entity mainstains identity from one state to another. SIO_000656 immediately transforms into SIO_010074 amino acid residue An amino acid residue is a submolecule of an amino acid that is part of a larger molecule. pain Pain is an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. SIO_000951 reproducing SIO_000919 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. velocity SIO_001369 The rate of change of an object's position and the direction of that change textual chart A textual chart is a chart containing text. SIO_000937 SIO_000901 is frequency of is a relation between a temporal unit and an object or event is frequency of is broad match to http://www.w3.org/2004/02/skos/core#broadMatch SIO_000491 SIO_000268 truth value is a quality of information that is claimed/verified to be true or false. truth value dysprosium atom CHEBI:33377 SIO_011098 SIO_000159 An edited publication is a publication that has been examined and potentially changed by an editor. edited publication A document title is a textual entity that summarizes the topic of the document in one sentence. SIO_000175 document title strong chemical salt SIO_001423 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. 2 every language edition of 'war of the worlds' are expressions of the story of 'war of the worlds' is expression of is a relation between more concrete expression of some conceptualization. SIO_000421 is expression of Brownian motion is the seemlingly random movement of particles suspended in a fluid. brownian motion SIO_000571 A web page is a document that is published according to World Wide Web standards. web page SIO_000302 SIO_001220 to characterize to characterize is the capability to classify the attributes or features of an entity against a reference classification. SIO_000535 statistical graph line A statistical graph line is a line used in a statistical graph to communicate some trend or feature of the embedded data. SIO_000339 a relation between a product and the information content entity that specifies it. is specified by SIO_011080 meitnerium atom CHEBI:33361 SIO_000135 A definition is a description that succintly characterizes an entity. definition SIO_000036 predicted is the quality of an entity that is thought to exist, as evidenced by some rational procedure. predicted very good quality SIO_001298 SIO_010079 is encoded by A relation between two objects, in which the first object is produced from the information contained in the second object. 3D extent quantity A quantity that extends in three dimensions. SIO_000048 nitrogen atom CHEBI:25555 SIO_011006 SIO_001366 regulation of information information maintenance the regulation or maintenance of information A sequence alignment is the character-based alignment of sequences using some method. SIO_010066 sequence alignment an amino acid polymer is an organic polymer composed of two or more amino acid residues. SIO_001427 amino acid polymer 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 1 the regulation of the enzymatic activity. regulation of catalytic capability SIO_000611 SIO_000503 A polygonal face is a polygon bounded by a circuit of polygon edges, and includes the flat (plane) region inside the boundary. polygonal face 1 berkelium atom SIO_011111 CHEBI:33391 SIO_000366 A number is a tensor of rank 0. number rank 0 tensor to gain an electron to gain an electron is the capability of a chemical entity to receive an electron. SIO_010370 SIO_010026 genetic polymorphism is the description of a difference in genetic composition at some location. genetic polymorphism SIO_000403 study group A study group is a group of individuals that are subjects in an observational or intervention study. CHEBI:33348 SIO_011058 tantalum atom is derived from OBO_REL:derives_from core SIO_000244 A transitive temporal relation in which one entity was materially formed from another non-identical entity. A keyword is a descriptor in which the association of the word with the entity facilitates information retrieval. SIO_000147 keyword 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. SIO_000519 bar CHEBI:33325 radium atom SIO_011073 small nuclear RNA (snRNA) A small nuclear RNA (snRNA) is a small RNA molecule that is located in the nucleus of a cell. snRNA SIO_001233 model A model is a representation of some thing. SIO_000510 SIO_000517 quadrilateral A quadrilateral is a polygon with composed of four points and four line segments, in which each point is fully connected to two other points. completely quantifier SIO_001307 germanium atom CHEBI:30441 SIO_011031 shame SIO_000865 shame is the emotion borne from feeling responsible for the commission of an offense. A nominal scale of measurement only specifies a limited set of categories. SIO_000913 nomimal scale global maximal stationary point A global maximum stationary point is a data point that corresponds to a measurement value is larger than that of all other plotted datapoints. SIO_000466 SIO_000455 category axis The horizontal axis corresponding to months of the year in graph 4 of http://tinyurl.com/opwnvm A category axis is an axis in which the position along the line is partioned into categories. to measure SIO_000371 to measure is the capability to obtain information about some entity by examining its attributes in relation to some reference metric. 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 SIO_001402 negatively regulates control role 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. SIO_010431 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 A 1D cartesian point is a point whose position is specified along a single dimension using Cartesian coordinates. 1D cartesian point SIO_000441 A diary is a document which describes day-to-day experiences. SIO_000170 diary student role A student role is the role of an individual that is enrolled in courses at an academic institution. SIO_000707 1.61 sio-subset-dash-labels.owl http://www.jbiomedsem.com/content/5/1/14 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 free to use,share,modify. modify with attribution [http://creativecommons.org/licenses/by/4.0/]. Semanticscience Integrated Ontology (SIO) 2026-05-01 en 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' Michel Dumontier sio sio.owl 2010-03-29 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 http://semanticscience.org/resource/ http://sio.semanticscience.org movement is the process in which an object is spatially displaced. SIO_000570 core movement SIO_010100 dna gene A gene that is located on DNA. has measurement value is a relation between a quality/realizable and a measurement value. has measurement value core SIO_000216 SIO_000610 regulation of capability regulation of capability is the regulation of the ability of one party by another. SIO_010419 antigen An antigen is a molecule that can be bound by a major histocompatibility complex (MHC) and presented to a T-cell receptor. SIO_001355 specific gravity Specific gravity is the ratio of the density of a substance to the density of a reference substance; equivalently, it is the ratio of the mass of a substance to the mass of a reference substance for the same given volume. valid argument A valid argument is an argument where the truth of the conclusion is a logical consequence of the premises and (consequently) its corresponding conditional is a necessary truth. SIO_000266 likelihood SIO_001243 Likelihood is the hypothetical probability that an event that has already occurred would yield a specific outcome. A strong submolecular component is a submolecular component that strongly connects submolecular components. strong submolecular component SIO_010047 to be observed SIO_000696 to be observed is the capability of an object to be perceived. data collection SIO_001052 data collection is the process of acquiring information. SIO_001064 A community is a sizeable social unit that shares common values. community anger is disgust directed toward an equal status individual. anger SIO_000410 SIO_001238 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. microarray device microarray platform http://purl.obolibrary.org/obo/OBI_0000052 hole SIO_000660 A hole is a site that is opening into or through something. lawrencium atom CHEBI:33397 SIO_011117 zygosity is the quality pertaining to the allelic complement of a biological system at a single locus on the DNA. zygosity SIO_001263 A correlation is a statistical relationship involving dependence between two random variables or datasets. correlation SIO_000923 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 to emit SIO_000384 to emit is the capability to release some physical entity (light, pollution, etc). SIO_001331 diagnosis A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms. SIO_010288 biochemical activation biochemical activation is a molecular interaction that increases the catalytic rate of the target enzyme. SIO_000173 affiliation An affiliation is a social relation which indicates the partnership between two or more entities. is identifier for identifies a relation between an identifier and an entity. SIO_000672 modified SIO_001224 amino acid 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. has provider dc:source SIO_000066 is provided by is a relation between an entity and the entity that provides it. SIO_001170 A slideshow is a visual presentation of information contained within a collection of slides. slideshow SIO_000772 has evidence is a relation between a proposition and something that demonstrates the truth of the assertion. has evidence SIO_010410 A specialized material entity is a material entity that is defined by having some quality, role or capability. specialized material entity SIO_000544 to infect to infect is the capability to administer a disease-causing organism into some object. address SIO_000172 An address is a position that indicates the physical location of some entity using a social convention. A centrifugation substance is a substance that is the target or product of centrifugation. centrifugation substance SIO_010426 last name SIO_000182 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. metabolic pathway SIO_010532 A metabolic pathway is a series of biochemical reactions that begins with one or more substrates and ends with one or more products. A horizontal bar graph is a bar graph in which the rectangular bars are horizontally oriented in space. horizontal bar graph SIO_000444 Graph 3 in http://tinyurl.com/opwnvm volume is the quantity of three-dimensional space enclosed by some closed boundary. SIO_000049 volume SIO_011016 CHEBI:23116 chlorine atom ion 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. SIO_010456 description A homogeneous substance is a substance that is composed of a uniform type of entity. homogeneous substance SIO_010463 environment An environment is a geographic region that hosts certain processes or objects. SIO_000955 2 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 SIO_000956 A device is usually a constructed tool. device [0,1] is a closed interval that is greater than or equal to 0 and less than or equal to 1. closed interval SIO_001249 A closed interval is an interval that includes its endpoints, and is denoted with square brackets. 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 SIO_000978 consonant A consonant is a verbal entity of language that is articulated with complete or partial closure of the vocal tract. analyte SIO_001378 an analyte is a substance or chemical constituent of interest in an analytical procedure. observing is a process of passive interaction in which one entity makes note of attributes of one or more entities. observation SIO_001055 observing statute SIO_001371 A statute is a formal written enactment of a legislative authority that governs a state, city or country. intent SIO_000358 intent is a desire to realize a particular outcome. A liquid solution component is a part of a liquid solution. SIO_010427 liquid solution component SIO_000079 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_001177 double stranded nucleic acid is a molecular complex composed of two weakly connected nucleic acids. double stranded nucleic acid boldness boldness is the trait of being willing to undertake things that involve risk or danger. SIO_000819 SIO_000304 email Email message is a digital document that is composed of a header and a body and is transmitted using the SMTP protocol. positionally oriented line SIO_000534 A positionally oriented line is a line that is positioned against some axis of reference. virus SIO_010379 A virus is a non-cellular organism that can replicate only inside the living cells of an organism. good quality SIO_001297 SIO_000598 hard disk drive 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. 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. SIO_001227 small cytoplasmic RNA (scRNA) gene http://purl.obolibrary.org/obo/SO_0001266 CHEBI:27563 SIO_011032 arsenic atom CHEBI:18248 iron atom SIO_011025 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 author list an ordered list of authors. SIO_001315 SIO_000357 fitness fitness is the quality of an object with respect to some stated functions or evolutionary adaptation. vector space a vector space is a set of vectors. SIO_001432 A study subject is an individual that is the subject of the study. study subject SIO_000399 an ordered list is a list in which items are sequentially ordered. SIO_001316 ordered list regulation of a process is a process that modulates the duration, frequency, spatial extent of a target process. SIO_000609 regulation of process SIO_000291 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 negative negative is an assertional qualifier that expresses the falsity or lack of truth of a basic assertion. SIO_001211 database key A database key is an informational entity whose value is constructed from one or more database columns. SIO_000762 a containment quality is a quality of being able to contain another entity. containment quality SIO_001341 SIO_000052 quantity A quantity is an informational entity that gives the magnitude of a property. A reason is a justification that specifies the motive for an action or a determination. SIO_001053 reason A buffer is a dissolved chemical substance that resists change in pH upon addition of small amounts of acid or base. buffer SIO_010416 carbohydrate residue A carbohydrate residue is a part of a molecule that was derived from a monosaccharide molecule. SIO_010334 to distort SIO_000778 to distort is the capability to change the appearance of an entity by some transformation. gene-disease association linked with genomic alterations a gene-disease association that is linked with some genomic alteration SIO_001350 SIO_000838 Frustration is an emotion that arises from the perceived resistance to the fulfillment of individual will. frustration therapeutic gene-disease association gene-disease association arising from a therapeutic role of the gene/protein A gene disease association in which the gene is a therapeutic marker for the disease. SIO_001120 A term is a word or phrase used to denote one or more entities. term SIO_000275 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. SIO_010053 evolutionary lineage SIO_000202 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 opinion SIO_001004 An opinion is a belief that is the result of emotion or interpretation of facts. 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 SIO_000594 data transformation is the process of applying an algorithmic procedure to some input data and producing some output data. data transformation streamgraph SIO_000908 A streamgraph is a multi-line stacked graph that yields the appearance of continuous y-values across the x-axis. SIO_011083 CHEBI:33517 copernicium atom SIO_000785 answer An answer is a reply to a question. SIO_000574 active movement is the process in which an object is spatially displaced using some chemical energy. active movement is transcribed into SIO_010080 DNA is transcribed into RNA a relation between two information content entities in which one is transcribed into (an exact or similar kind) another through some process. default parameter SIO_000952 A default parameter is a parameter which has a default value. irritability irritability is the negative emotion of quick excitability to annoyance, impatience, or anger. irritable SIO_001286 exon SIO_010445 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. SIO_011082 CHEBI:33368 roentgenium atom chemical exposure is a process to expose one or more individuals to a chemical substance. chemical exposure SIO_001399 A language label is a label that denotes the language of a textual entity. SIO_000180 language label SIO_000876 student advisor role A student advisor role is the role of an individual employed at an academic organization that is involved in advising students. SIO_000235 has disposition has disposition is the relation between an entity and a disposition that it bears. A PhD thesis is a thesis prepared as a requirement for a doctoral degree. phd thesis SIO_000168 2 An arrowed line is a directed line segment in which one or both endpoints is tangentially part of a triangle that bisects the line. SIO_000522 arrowed line segment SIO_010093 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_000076 A plan is a set of intended actions, through which one expects to achieve a goal. plan SIO_010029 biological sex is the quality of a biological organism based on reproductive function or organs. biological sex An organic reaction is a chemical reaction involving at least one organic molecule. SIO_010516 organic reaction regulation of molecular degradation A process that modulates the frequency, rate or extent of process involved in the destruction of a molecule. SIO_001129 SIO_001201 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 A coordinate is a measurement of position in n-dimensional space. coordinate SIO_000071 chapter A chapter is a document section of a book or thesis. SIO_000107 SIO_001185 software process identifier A software process identifier is an identifier for a software process in some operating system. 1 cartesian coordinate SIO_000072 A Cartesian coordinate is the signed distance of a point to some referent line. database column SIO_000757 A database collumn is a column in a database table. heatmap SIO_000907 A heatmap is a graphical representation of data where the individual values contained in a matrix are represented as colors. A protein complex is a molecular complex composed of at least two polypeptide chains. SIO_010497 protein complex is generically related with SIO_000425 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. to cause disease SIO_000547 to cause disease is the capability to materially change a biological object in that it functions abnormally. An aromatic bond is an interaction between a set of atoms across which pairs of electrons are shared. aromatic bond SIO_010501 metadata SIO_001330 metadata is data that provides information about data. platinum atom CHEBI:33364 SIO_011063 A synthesis reaction is an inorganic reaction in which two or more molecules are chemically bonded together to produce a single product. SIO_010515 synthesis reaction 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 to luminesce is to emit light through cold body radiation SIO_000894 to luminesce SIO_000465 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 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 to be a member of to be a member of is the capability to be considered a part of a collection. SIO_000777 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. SIO_000100 software library SIO_000554 PATO:0000461 normal A quality that has a value that is normal or average. control variable SIO_001070 extraneous variable controlled variable A control variable that is believed to alter the dependent or independent variables, but may not actually be the focus of the experiment. So that variable will be kept constant or monitored to try to minimise its effect on the experiment. clinical trial A clinical trial is an intervention trial to determine the safety and efficacy of medical interventions (e.g., drugs, diagnostics, devices, therapy protocols). SIO_001000 A row represents a single, implicitly structured data item in a table. SIO_000752 row data item SIO_000069 A data item consists of information that has been collected/generated towards some purpose. A start position is the proximal position of an object relative to an origin in a linear system. start position SIO_000943 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 to modify is the capability to change some entity. to modify SIO_000343 SIO_001275 a coding frame offset is a numeric value that indicates the number of bases from a reference start codon position. coding frame offset SIO_011017 CHEBI:49475 argon atom SIO_000226 is function of is a relation between a function and an entity that it is a property of. is function of CHEBI:33349 SIO_011076 dubnium atom SIO_000020 denotes the symbol '%' denotes a proportion in relation to a whole. denotes is a relation between an entity and what it is a sign or indication of, or what specifically means. SIO_001130 A process mediated by a protein that modulates the frequency, rate or extent of translation. protein mediated regulation of translation biological data biological data is scientific data relevant to biology. SIO_010019 SIO_000115 identifier An identifier is a label that specifically refers to (identifies) an entity (instance/type). A foreign database key is a database key that refers to a key in some table. foreign database key SIO_000764 to provide SIO_000397 to provide is the capability to make available some object to another that requires it. study investigation SIO_000747 investigation is the process of carrying out a plan or procedure so as to discover facts or information about the object of study. CHEBI:30514 SIO_011054 caesium atom 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. SIO_000398 nurse optical isomer SIO_010778 An optical isomer is a stereoisomer that rotates the plane of polarization of a beam of plane polarized light. SIO_010510 inorganic reaction An inorganic reaction is a chemical reaction that involves the transformation of inorganic molecules. SIO_000368 equation An equation is a mathematical statement that asserts the equality of two expressions. SIO_001424 weak chemical salt a weak chemical salt is a chemical salt composed of weak eletrolytes. genotype A genotype is a functional specification of a biological entity in terms of its genetic composition (or lack thereof). SIO_001079 A double bond is a covalent bond between a pair of atoms in which two pairs of electrons are shared. SIO_010499 double bond SIO_011078 bohrium atom CHEBI:33355 CHEBI:33341 SIO_011021 titanium atom SIO_001010 non toxic is the quality of a substance having no damaging effect to a system. non toxic 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 is unit of is unit of is a relation between a unit and a quantity that it is a multiple of. SIO_000222 neon atom SIO_011009 CHEBI:33310 a rank nonzero tensor is a tensor with a rank greater than zero. SIO_001434 rank nonzero tensor SIO_010514 single displacement reaction A single displacement reaction where one atom is transferred out of one molecule and into another. SIO_000992 unsupported unsupported is an existence quality in which there is no evidence to support the existence of the entity in any world (real or hypothetical) the capability to encode information in a different representation SIO_001362 to encode information to produce is the capability to create new objects SIO_001106 to produce SIO_010343 An enzyme is a protein or protein complex that realizes its disposition to covalently modify some molecule during a chemical reaction. enzyme PDB file A PDB file is a molecular structure file specified by the Protein DataBank (PDB). SIO_011130 A lipid is a water-insoluable organic molecule. lipid SIO_010011 SIO_000460 A right value axis is a value axis that is spatially positioned to the right of the plot area. right value axis a genomic sequence variant is part of a nucleic acid which is compositionally different than another reference genomic part. SIO_001381 genomic sequence variant variant SIO_000620 A collective is a group of entities that share or are motivated by at least one common issue or interest, or work together on a specific project(s) to achieve a common objective. group collective 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 has proper part has proper part is an antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part. a car has an engine as a proper part; a car has a piston as a proper part; SIO_000053 SIO_001443 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_001387 InCHI notation SIO_001108 A central tendency measure is a central value or a typical value for a probability distribution. centrality measure 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 CHEBI:49637 SIO_011002 hydrogen atom SIO_001013 age is the length of time that a person has lived or a thing has existed. age SIO_000815 anxiety is an emotion charactersized by intense feeling of fear and concern coupled with a physical response. anxiety CHEBI:33395 SIO_011115 mendelevium atom Graph 1 in http://tinyurl.com/opwnvm A line graph is a statistical graph in which lines contains the evaluation of functions or individual points connected by line segments. line graph line chart SIO_000442 SIO_001386 a notation to describe a chemical entity chemical notation morpheme SIO_001040 A morpheme is the smallest semantically meaningful unit in a language. SIO_000697 is mutual disposition of a is mutual disposition of b if and only if the realization of the disposition a necessarily causes the realization of the disposition b. hasSynonym creator A report is a textual document made that present focused, salient content to a specific audience. report SIO_001026 molecular complex dissociation molecular complex disassociation is the process of dissambly of a molecular complex into its constitutent parts. SIO_010286 increased object consumption from increased regulation SIO_001148 increased regulation leads to an increase in the consumption of an object of specified type. astatine atom SIO_011070 CHEBI:30415 to translocate is the capability to displace oneself from one location to another. SIO_000719 to translocate to move SIO_001406 Density (volumetric mass density) is the quantity of mass per unit volume of a substance. density SIO_001162 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 day A day is a period of 24 hours. SIO_000430 thulium atom CHEBI:33380 SIO_011101 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 quote A quote is a excerpt that is attributed to a particular source. SIO_000299 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 probability measure SIO_000638 A probability measure is quantity of how likely it is that some event will occur. to change appearance is the capability to change the visual attributes of an object. SIO_000378 to change appearance A revision number is a version of a software in which bugs have been fixed from a prior version. SIO_001032 revision number SIO_000498 A person is an object that has certain capacities or attributes constituting personhood. person seaborgium atom SIO_011077 CHEBI:33351 SIO_001293 quality descriptor SIO_000433 An hour is a period of 60 minutes. hour 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 software script A software script is software whose instructions can be executed using a software interpreter. SIO_000103 week SIO_001354 A week is a period of 7 consecutive days. A three prime untranslated region (3'-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. SIO_010070 3' untranslated region terminal point SIO_000532 A terminal point is a point that defines the finite extension of a line. beta strand 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. SIO_010469 SIO_000188 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_000221 core has unit is a relation between a quantity and the unit it is a multiple of. has unit healthy is an organismal state of complete physical, mental and social well-being. healthy SIO_001012 study protocol study design SIO_001041 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. SIO_000248 precedes core A transitive, temporal relation in which one process precedes (has occured earlier than) another process. to bind to SIO_000780 to bind to is the capability to physically interact with another object through a set of non-covalent interactions. SIO_000929 A pie chart is a circular chart divided into sectors each of whose length is proportional to the quantity it represents. pie chart SIO_001308 satisfaction qualifier An exclusion criterion is a criterion that must be absent to satistify the objective. SIO_000143 exclusion criterion Graph 4,5 in http://tinyurl.com/opwnvm SIO_000445 vertical bar graph A vertical bar graph is a bar graph in which the rectangular bars are vertically oriented in space. CHEBI:33337 actinium atom SIO_011074 SIO_001126 A process that modulates the frequency, rate or extent of translation. regulation of translation real number SIO_001442 a real number is a complex number whose imaginary part is zero, e.g. a + 0i. SIO_001348 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 media media are audo/visual/audiovisual modes of communicating information for mass consumption. SIO_001194 1 has function is the relation between an entity and a function that is ascribed to it. has function SIO_000225 SIO_001344 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 oxygen atom SIO_011007 CHEBI:25805 The process of maintaining some the frequency, rate or extent of another process. SIO_001132 process maintenance A partial positive charge is a partial charge where the value of the charge is positive. partial negative charge SIO_000808 conversing a form of interactive, spontaneous communication between two or more agents who are following rules of etiquette. SIO_000941 conversing is immediately transformed from SIO_000658 A temporal relation in which an entity mainstains identity from one state to another. apartment number SIO_000768 An apartment number is the number assigned to identify an apartment in a building of apartments. SIO_000224 is property of is property of is a relation betweena quality, capability or role and the entity that it and it alone bears. point SIO_000507 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. gene-disease association linked with altered gene expression SIO_001123 A gene-disease association in which the disease phenotype is associated with an altered expression of the gene. SIO_001258 set item set item is an item in a set. A free radical addition is a non-polar addition reaction involving free radicals. free radical addition SIO_010521 chemical+ SIO_010004 A chemical entity is a material entity that pertains to chemistry. CHEBI:23367 atom, ion, molecule, chemical substance, chemical entity gallium atom CHEBI:49631 SIO_011030 SIO_000334 is covalently connected to is a relation between an atom and another atom. is covalently connected to parental transmission parental transmition is the quality of a biological organism in which the (genetic) material is transmitted from a parental unit. SIO_001268 SIO_001021 expected value An expected value (or e-value) is the weighted average of all possible values that a random variable can take on. An image is an affine projection of a visual entity to a two dimensional surface. image SIO_000081 depiction A term variant is a term that is a variant of another term. SIO_000342 term variant SIO_000075 mathematical entity math+ A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms. SIO_000957 communication device 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. organ SIO_010003 An organ is a collection of tissues joined in structural unit to serve a common function. A proposition is a sentence expressing something true or false. proposition SIO_000256 solid state hard drive A solid-state drive (SSD) is a data storage device that uses solid-state memory to store persistent data. SIO_000597 the capability to maintain information such that it can be retrieved in the future. to maintain information SIO_001363 SIO_001440 chemical-protein association A chemical-protein association is an association between a chemical and a protein. The role of a chemical entity that reduces the rate of reaction. inhibitor role SIO_000803 SIO_001255 a pharmacokinetic pathway is a metabolic pathway which describes the metabolism of a drug molecule. pharmacokinetic pathway core 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) SIO_000272 is variant of trend line A trend line is a line, line segment or ray that is part of a statistical graph which indicates a statistical or visual direction across categorical or value data. SIO_000527 SIO_000930 matrix chart A matrix chart summarizes a multidimensional data set in a grid. 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 CHEBI:25016 lead atom SIO_011067 maintenance of frequency of process 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. SIO_001144 SIO_000046 A perimeter is a length of the outline that surrounds a two-dimensional shape. length of perimeter SIO_001421 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 the story 'war of worlds' is expressed as every language edition of the book 'war of the worlds' SIO_000420 has expression rights SIO_000670 end time An end time is a time instant pertaining to the time at which a process ends. 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 spatial quantity A spatial quantity is a quantity obtained from measuring the spatial extent of an entity SIO_000037 physical dimensional quantity neither good nor poor quality SIO_001296 A supernatent is a liquid substance that remains after centrifugation. supernatant SIO_010425 A multiple sequence alignment is a sequence alignment involving more than two sequences. multiple sequence alignment SIO_010067 An author contribution section is a document section that describes the contribution of the authors. author contribution section SIO_000190 A PDB record identifier is an identifier for a PDB generated record. PDB record identifier SIO_010032 cellular phone number SIO_001320 a cellular phone number is a number to connect to a mobile device core#exactMatch SIO_001439 protein-disease association A protein-disease association is an association between a protein and a disease. SIO_000799 cofactor role The role of a chemical entity involved in the mechanism for enzyme-mediated catalysis. decreased spatial extent of process from decreased regulation SIO_001141 The increase of regulation leads to a decreased spatial extent of the target process. sequence end position SIO_000792 A sequence end position is the position of the last character in a sequence of characters relative to some linear frame of reference. SIO_001136 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_000265 A sound argument is a valid argument with true premises. sound argument A preferred name is the name that is generally used by some organization. preferred name SIO_000117 SIO_010073 open reading frame An open reading frame (ORF) is a part of a gene that encodes a protein but does not contain a stop codon. SIO_000219 is source of is a relation between a source of information about some entity. is source of A copyright section is a document section that contains a notice of copyright. SIO_000193 copyright section inhibitor SIO_010435 A molecular inhibitor is a molecular regulator that realizes its disposition to conformationally change a target molecule and decrease its functionality. SIO_000576 membrane transport membrane transport is the movement of molecules across a membrane. 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. SIO_001152 maintenance of quantity of object production SIO_000494 to actively interact with to actively interact with is the capability to interact with another entity in a way that requires physical contact. text quality is the quality of a textual entity. SIO_001033 text quality block histogram SIO_000932 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. A y-axis is a Cartesian coordinate axis that is spatially oriented perpendicular to the x-axis. vertical axis y-axis SIO_000453 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 to breathe is the capability to inhale and exhale air into the body during respiration. to breathe SIO_010353 A structural isomer is an isomer in which the atoms are joined together in different ways. SIO_010779 structural isomer SIO_001388 sequence variation notation a temporal qualifier is pertains to the frequency of the event of interest. temporal qualifier SIO_001288 SIO_001103 to gain a covalent bond is the capability of a chemical entity to have bonds added. to gain a covalent bond describes SIO_000563 core describes is a relation between one entity and another entity that it provides a description (detailed account of). SIO_000090 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_001356 information encoding A viroid is a molecule of RNA that does not code for and is not protected by a protein coat. SIO_001044 viroid protein family a protein family is a collection of proteins that share a common evolutionary origin, reflected by their related function and similarity in composition or structure. SIO_001380 SIO_001131 rna mediated regulation of translation A process mediated by rna that modulates the frequency, rate or extent of translation. SIO_011085 ununquadium atom first name SIO_000181 A first name is a name that denotes a specific individual between members of a group of individuals, whose members usually share the same surname. A gene expression value is a measured value obtained from a gene expression experiment. gene expression value SIO_001077 minute A minute is a period of 60 seconds. SIO_000434 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 reviewed reviewed is the quality of a textual entity that has been examined and commented on by another party. SIO_001034 personal name full name SIO_000183 A personal name is a name to identify an individual person and usually comprises of a first name and a last name. protein domain A protein domain is a part of a protein that maintains its structure and function independently of the rest of the protein. SIO_001379 brief A brief is a written legal document used in various legal adversarial systems that is presented to a court arguing why one party to a particular case should prevail. SIO_001374 is transitively related to SIO_001247 ovopub not implemented in standard distribution SIO_000041 length is the longer dimensional extent along a 2D projection of the object. length SIO_001147 decreased object production from increased regulation increased regulation leads to a decrease in the number of target objects of a specified type. gene regulatory component A gene regulatory component is a gene component that exerts a regulatory function. SIO_010085 orientation SIO_000057 orientation is an angle between the bearer and an axis, or the angle between the bearer and another object. A phrase is a group of words functioning as a single unit in the syntax of a sentence. SIO_000483 phrase tungsten atom SIO_011059 CHEBI:27998 SIO_000567 ordinary differential equation An ordinary differential equation (ODE) is a differential equation in which the unknown function (also known as the dependent variable) is a function of a single independent variable. SIO_010525 biochemical pathway A biochemical pathway specifies a series of biochemical modifications and transformations towards achieving some biological outcome. locomotion SIO_000581 GO:0040011 The self-propelled movement of an object. 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 SIO_000319 latitude Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane A predicted gene is a gene that was identified through computational method but has not been experimentally validated. SIO_000987 predicted gene CHEBI:27573 SIO_011013 silicon atom SIO_001401 positively regulates 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 SIO_000295 A collection of documents is a non-zero set of documents. collection of documents http://purl.org/ontology/bibo/Collection word tree A word tree is a chart that links phrases with contexts through a tree-like branching structure. SIO_000936 to be conformationally changed to be conformationally changed is the capability to be modified in such a way that the object's conformation is changed. SIO_010374 SIO_000585 An idea is a proposition about some object of conceptual thought. idea full agreement is the result of consensus decision making when members of the group unanimously agree. full agreement SIO_001179 A version label is a label for a particular form or variation of an earlier or original type. SIO_000653 version label SIO_001370 A slide is an visual representation meant to communicate some information. slide anabolism SIO_010310 Anabolism is the set of metabolic processes that construct larger chemical entities units from smaller chemical entities. destroying destruction SIO_000591 destroying is a process in which something is broken down and/or ceases to exist. list SIO_000150 A list is any enumeration of a set of items. The role of a chemical entity that is modified in a chemical reaction. SIO_000797 substrate role sorrow is the emotion that is characterized by a long term state of intense sadness, distress and a degree of resignation (not accepting). SIO_000868 sorrow CHEBI:30430 indium atom SIO_011048 2 affects SIO_001158 offset ordinal position SIO_000613 A ordinal position is a number that designates the position of an entity from the first entity in an ordered sequence of entities. SIO_001085 to remove a covalent bond to remove a covalent bond is the capability to covalently modify a chemical entity by removing a covalent bond. to disassemble is to physically separate the parts of an object. to disassemble SIO_000698 A 3D cartesian point is a point whose position is specified along three dimensions using Cartesian coordinates. SIO_000440 3D cartesian point A worm is a non-arthropod invertebrate animal that typically have a long cylindrical tube-like body and no legs. worm SIO_000488 SIO_001327 protein expression value A protein expression value is a quantity obtained from a protein expression experiment. SIO_010043 protein CHEBI:36080 A protein is an organic polymer that is composed of one or more linear polymers of amino acids. An issue is a single instance of a periodically published journal, magazine, or newspaper. issue SIO_001169 SIO_000853 lust lust is the strong desire for sex. 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 SIO_001260 list item a list item is an item in a list. SIO_000459 The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm left value axis A left value axis is a value axis that is spatially positioned to the left of the plot area. investigational role An investigational role is a role held by participants involved in an investigation. SIO_000881 alternative SIO_000437 A 2D cartesian point is a point whose position is specified along two dimensions using Cartesian coordinates. 2D cartesian point SIO_000821 contempt contempt is disgust towards a lower status individual. moderately quantifier SIO_001305 SIO_010007 polypeptide A polypeptide is an organic polymer composed of amino acid residues, typically of less than 50 amino acids in length. SIO_010777 enantiomer An enantiomer is a stereoisomer that is a mirror image of its isomer. increased spatial extent of process from increased regulation The increase of regulation leads to a increased spatial extent of the target process. SIO_001140 reasoning is the agentive process of using knowledge to evaluate the truth value of a proposition. SIO_000746 reasoning SIO_000346 to heat is a capability to increase the internal kinetic energy of a material. to heat rigid is the quality of maintaining structural integrity (and not bending) under pressure. rigid SIO_001093 record identifier SIO_000729 A record identifier is an identifier for a database entry. SIO_010440 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 A Venn diagram is a chart that illustrates all possible logical relations between a finite collection of sets as overlapping circles. SIO_000947 venn diagram aluminium atom CHEBI:28984 SIO_011012 cation pi interaction SIO_010034 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. disordered is a structural quality in which the parts of an object are non-rigid. SIO_000758 disordered sadi a SADI semantic web service is a semantic web service that follows the SADI specification SIO_001188 SADI semantic web service http://en.wikipedia.org/wiki/SADI A host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. host SIO_010415 An undergraduate student advisor role is the role of an individual employed at an academic organization that is involved in advising undergraduate students. SIO_000877 undergraduate student advisor role SIO_000332 is about is a relation between an information content entity and the entity that its primary subject. is about A is referred to by B iff B is an informational entity that makes reference to A. SIO_000212 is referred to by A co-enzyme role of a chemical entity that is transiently associated, and is regenerated in a separate reaction. co-substrate role SIO_000802 SIO_000106 A book is a publication composed of a large number of entries. book has realizable property SIO_000644 CHEBI:33388 SIO_011108 plutonium atom SIO_011088 ununseptium atom 1 uranium atom SIO_011106 CHEBI:27214 SIO_000634 is xenologous to a relation between two entities which indicates their common ancestry but due to horizontal gene transfer. SIO_001336 An epimer is a stereoisomer that differs in configuration at only one stereogenic center. epimer 1 SIO_000247 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 diagnostic opinion A diagnostic opinion is an opinion resulting from a medical diagnostic procedure. SIO_001003 SIO_011068 CHEBI:33301 bismuth atom horizontal line SIO_000525 A horizontal line is a line that is positionally oriented with the horizon. copper atom SIO_011028 CHEBI:28694 chart SIO_000904 A chart is a figure that displays the relationship among tabular numeric data, functions or some kinds of qualitative structures. 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 to combine SIO_010351 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. SIO_001226 trans-regulatory element 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). The aspect ratio of a geometric shape is the ratio of its sizes in different dimensions. aspect ratio SIO_001408 SIO_000426 is manifestation of SIO_001076 microarray experiment A microarray experiment is an experiment that involves a microarray device to measure the expression of one or more genes. fermium atom SIO_011114 CHEBI:33394 nlp+ SIO_000078 language entity A language entity implements some language specification for the visual interpretation and is part of some document. 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 A poison role is the role of a substance that causes some negative disturbance in an organism. SIO_000968 poison role to be covalently modified SIO_010366 to be covalently modified is the capability of a chemical entity to have bonds added or removed 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 SIO_000298 excerpt An excerpt is a contiguous or discontiguous portion of a document. bioinformatic data SIO_010065 bioinformatic data is data genereated or used for computer-based investigations of biological phenomena. A chemical synthesis pathway is a pathway involved in the assembly of a chemical. chemical synthesis pathway SIO_010527 CHEBI:49666 SIO_011062 iridium atom A territory is a non-sovereign geographic region. territory SIO_000663 to freeze SIO_000348 http://purl.obolibrary.org/obo/OBI_0000375 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. altitude Altitude is a distance above sea level. SIO_000438 A diffusion equation describes density fluctuations in a material undergoing diffusion. diffusion equation SIO_000565 SIO_001301 collection ovopub A collection ovopub is an ovopub that contains and links to one or more assertion subgraphs and/or ovopubs, as well as statements describing its provenance. It is used to share a specific set of items or restrict a search to the resources contained therein. core#example creator 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 SIO_001411 sample quality is the quality of an object that is drawn from a larger population. sample quality conjunction (and) SIO_000239 AND is a logical operator that has the value true if both of its operands are true, otherwise a value of false. SIO_000215 is measurement value of is a relation between a value and the entity that it is a measurement of. is measurement value of SIO_001081 t-statistic based increased differential gene expression A t-statistic based increased differential gene expression is a differential gene expression ratio in which the t-statistic is greater than zero. SIO_000539 infinite line An infinite line is a line that extends outwards in both directions of a single dimensional and is not bounded by terminal points. A 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 book section SIO_001375 height is the one dimensional extent along the vertical projection of a 3D object from a base plane of reference. height SIO_000040 validated gene An experimentally validated gene is a gene whose existence has been demonstrated through experimental methods. SIO_000991 A polar solvent is a solvent that exhibits a polar quality. SIO_010459 polar solvent molecular structure molecular structure is the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together. molecular geometry SIO_000626 A disulfide bond is a bond between two sulfur atoms. SIO_010502 disulfide bond A column is a vertical sequence of cells in a cellular automata. column SIO_000753 A partial negative charge is a negative charge where the value of the charge is negative. SIO_000807 partial positive charge a home phone number is the number to connect to an phone at a place of residence. home phone number SIO_001325 null SIO_001358 to retrieve the capability to retrieve a (digitial/physical/mental) object from a location. to examine is the capability to make detailed observation. SIO_000724 to examine A maximal value is largest value of an attribute for the entities in the defined set. maximal value SIO_001114 max ribonucleic acid SIO_010009 A ribonucleic acid is an organic polymer composed of a sequence of ribonucleotide residues. 1 An active ingredient is a molecular entity that exhibits biological activity. SIO_010077 active ingredient homepage SIO_001133 The increase of regulation leads to a increased occurence of processes of the target type. increased frequency of process from increased regulation disease SIO_010299 disease is the outward manifestation of one or more disorders. ordered list A sequence is an ordered list of entities. Like a set, it contains members (also called elements, or terms). SIO_001118 For example, (M, A, R, Y) is a sequence of letters that differs from (A, R, M, Y), as the ordering matters, and (1, 1, 2, 3, 5, 8), which contains the number 1 at two different positions, is a valid sequence. sequence SIO_000984 genome A genome is a collection of nucleic acids. specimen SIO_010412 A specimen is a portion of material for use in testing, examination, or study. is orthologous to is a relation between two biological entities that share a common ancestor and occur in different species. SIO_000558 is orthologous to SIO_011075 rutherfordium atom CHEBI:33346 book series A book series is a collection of books that have been sequentially published. SIO_000158 SIO_000267 invalid argument An invalid argument is an argument where the truth of the conclusion is false because it is not a logical consequence of the premises. 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. scRNA SIO_001231 small cytoplasmic RNA (scRNA) editor reviewed SIO_001038 editor reviewed is the quality of a textual entity that has been examined and commented on by an editor. SIO_001025 prognosis A prognosis is a proposition about the likely course of a disease, the chance of recovery or recurrence. http://purl.org/ontology/bibo/Journal SIO_000160 journal A journal is a a peer-reviewed periodical in which scholarship relating to a particular academic discipline is published. gene-disease association linked with genetic variation A gene-disease association in which a sequence variation (a mutation, a SNP) is associated with the disease. SIO_001122 gene variant-disease association SIO_001110 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_000852 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_000996 cancelled cancelled is a process status in which the process, while planned to occur, will not occur. normality normality is the quality in which the value may differ from normal or average SIO_000307 A relation between two objects, in which the first object contains information that is used to produce the second object. SIO_010078 an open reading frame encodes a protein (it contains information that specifies the amino acid composition and topology) encodes A figure is a graphical entity which consists of a visual (n-dimentional) arrangement of information entities. figure diagram SIO_000080 SIO_000063 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. is agent in hexokinase is an agent in the conversion of glucose to glucose-6-phosphate sadi 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 SIO_000164 A technical report is a publication published by a school or other institution, usually numbered within a series. technical report 1 genetic data is data pertaining to genetics. genetic data SIO_010028 nucleic acid A nucleic acid is an organic polymer composed of a sequence of nucleotide residues. SIO_010008 A radar is an object-detection system which uses radio waves to determine the range, altitude, direction, or speed of objects. SIO_000928 radar is transcribed from SIO_010081 wonder SIO_000872 wonder is an emotion of perceiving something very rare or unexpected, but not threatening. A quantity that extends in single dimension. 1D extent quantity SIO_000038 gene-disease association linked with susceptibility mutation SIO_001343 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. 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 SIO_001303 none quantifier SIO_010794 glassy carbon 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. fluorine atom SIO_011008 CHEBI:24061 to identify is the capability to determine the identity of something. SIO_001239 to identify 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 A test role is the role of an individual that is a participant in the study and is the target of the intervention. SIO_010430 test role A novel is a fictitious prose narrative of book length, typically representing character and action with some degree of realism. novel SIO_000109 love is an emotion of a strong affection and personal attachment. love SIO_000412 SIO_000962 virtual virtual is the quality of an entity that exists only in a virtual setting such as a simulation or game environment. substrate A substrate is a molecule that is consumed in the course of a biochemical reaction. SIO_010362 tensor a tensor is a n-dimensional array. SIO_001429 SIO_001326 status descriptor status descriptor is a descriptor for the state of a process or object. object quality SIO_000026 An object quality is quality of an object. suspended is the status of a process that is no longer progressing towards completion. SIO_000995 suspended middle initial a middle initial is an abbreviated middle name. SIO_001318 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. SIO_000709 is mutually related to A complete charge is a charge where the value of the charge is a multiple of 1. SIO_000810 complete charge CHEBI:27560 SIO_011000 boron atom is modelled by SIO_000633 software application A software application is software that can be directly executed by some processing unit. SIO_000101 SIO_011109 CHEBI:33389 americium atom SIO_001337 epimer association x is associated with y when x and y are logically or statistically related to one another. SIO_001403 is associated with polyhedral skeleton SIO_000502 A polyhedral skeleton is a collection of polygon edges. An active site is a molecular site in which a chemical event occurs (structural transformation or conformational change). active site SIO_010041 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. SIO_000717 dentist role similarTo A quantity that extends in two dimensions. 2D extent quantity SIO_000044 gene-disease association SIO_000983 A gene-disease association is an association between a gene and a disease. A secretary role is the role of an individual that performs administrative tasks to support one or more individuals of the same organization. SIO_000727 secretary role An organization is a collective with a complex articulation of tasks, roles and responsibilities. organization SIO_000012 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. SIO_000246 immediately derives into SIO_000385 to change energetically to change energetically is the capability to change the energetic aspects of an object. 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+ SIO_000145 is location of single arrowed line segment A single arrowed line is directed line in which the endpoint is tangentially part of a triangle that bisects the line. SIO_000523 SIO_001373 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 functional rna coding gene SIO_000986 A gene that codes for a functional RNA molecule. SIO_010342 chemical complex A chemical complex is a chemical substance composed of weakly connected molecules and ions in a known stoichiometry. SIO_010509 redox reaction A redox reaction is a chemical reaction in which there is a net movement of electrons from one reactant to another. decreased object consumption from increased regulation SIO_001149 increased regulation leads to an decrease in the consumption of an object of specified type. A medical role is the role of an individual that is a participant in the delivery of medical care. medical role SIO_000712 A primary structure descriptor describes a biomolecular object in terms of a 1D or 2D topology. primary structure descriptor SIO_010014 SIO_001167 A comment is a verbal or written remark often related to an added piece of information, or an observation or statement. comment potassium atom SIO_011018 CHEBI:26216 A pairwise sequence alignment is the alignment of exactly 2 sequences. SIO_010068 pairwise sequence alignment SIO_000323 is surrounded by 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. disagreement agreement is the result of consensus decision making when members of the group do not all agree. SIO_000967 CHEBI:33331 SIO_011038 yttrium atom CHEBI:30452 tellurium atom SIO_011051 to modulate to regulate is to control or maintain the rate or speed of an object or process. to regulate SIO_000395 geographic image A geographic image is a photograph of some geographical area. SIO_000301 SIO_001160 number of objects produced number of objects produced is a count of objects that were produced in some process. polar quality The quality of being polar or not polar. SIO_001045 SIO_000818 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_010496 An ionic interaction is a weak submolecular interaction between a charged submolecules. ionic interaction false SIO_000270 false is a truth value in that indicates that it is not true. evaluation role SIO_010428 An evaluation role is a processual role held by an entity during some evaluation. SIO_000419 A table is a figure that consists of an ordered arrangement of columns and rows. table SIO_011060 rhenium atom CHEBI:49882 SIO_010031 PDB chain identifier A PDB chain identifier is a alphabetical label to identify a molecule in a structure provided by the Protein DataBank . referencing cell SIO_000760 A referenceing cell is a cell of a cellular automata that refers to another cell. SIO_001080 vocabulary A vocabulary is a collection of terms. 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 circularly helical quality is the quality of a helix that is connected in a circle or loop. circularly helical SIO_001272 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 subset chemical quality is the quality of a chemical entity. SIO_001011 chemical quality CHEMINF:000123 SIO_011123 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 SIO_001101 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 2 very poor quality SIO_001294 has role is a relation between an entity and a role that it bears. has role SIO_000228 differential gene expression ratio A differential gene expression ratio is the ratio of gene expression values from a test sample compared to a control sample. SIO_001078 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 multicellular organism A multi-cellular organism is an organism that consists of more than one cell. SIO_010375 A page range denotes the start and end page in some document. page range SIO_000177 to lose an electron is the capability of a chemical entity to lose an electron. to lose an electron SIO_010371 SIO_000259 argument An argument is a set of one or more declarative sentences (or propositions) known as the premises along with another declarative sentence (or proposition) known as the conclusion. CHEBI:33386 protactinium atom SIO_011105 true major tick mark A major tick mark is a tick mark that indicates the position of a specific numeric value and is adjacent to its value label on the value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value indicated by an adjacent category label on the categorical axis. SIO_000514 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. region SIO_000370 A spatial region is an object contained in some region of space. spatial region SIO_001271 helicity helicity is the quality of being helical SIO_000582 birthing is the process by which a biological organism is brought into existence. birthing biosynthesis is the synthesis of an organic compound in a living organism, usually aided by enzymes. biosynthesis SIO_000590 sampling is the act of obtaining a sample, whether through selection, collection or preparation. SIO_001049 sampling SIO_010792 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 an oligopeptide is an organic polymer composed of fewer than 10 or 15 amino acids. oligopeptide SIO_001426 preferredNamespaceUri SIO_011107 CHEBI:33387 neptunium atom decreased molecular degradation from increased regulation SIO_001202 A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation. SIO_000723 to compare is the capability to examine in order to note the similarities or differences among a set of objects. to compare grief grief is an emotion in response to loss, whether physical or abstract including death, unemployment, ill health or the end of a relationship. SIO_000842 street name A street name is the token given to identify a particular street. SIO_000766 An ontology document is a document that contains an ontology. SIO_000129 ontology document crystal structure SIO_001100 A crystal structure is the arrangement of atoms or molecules in a crystalline liquid or solid. A department chain role is the role of an individual that heads a department at a academic organization. department chair role SIO_000875 completed SIO_000034 completed is that status of a process that successfully unfolds. disjunction (or) SIO_000280 OR is a logical operator that results in true whenever one or more of its operands are true. SIO_010349 to cleave is to split or sever an object along a natural line or grain. to cleave triple bond SIO_010500 A triple bond is a covalent bond between a pair of atoms in which three pairs of electrons are shared. 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. SIO_001018 ratio SIO_000137 category A category is a class of entities having particular shared characteristics. ontology an ontology is a formal specification of entities, their attributes and relationships. SIO_001391 SIO_000487 A rat is a medium-sized, long-tailed rodent of the superfamily Muroidea. rat SIO_000127 A workflow is an algorithm that is is a depiction of a sequence of operations to achieve one or more objectives. workflow population A population is all the organisms that both belong to the same group or species and live in the same geographical area. SIO_001061 shyness SIO_000867 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. to excite is the capability to supply energy to a materila by bombarding it with energetic particles (e.g., photons). to excite SIO_000383 license SIO_000429 A month is a period of time that divides the year. month SIO_000662 A state is a set of governing and supportive institutions that have sovereignty over a definite territory and population. state An atom is composed of a core of protons and/or neutrons which may be surrounded by a cloud of electrons. atom SIO_010044 is annotation of SIO_000254 is annotation of is a relation between some textual entity and the entity that it annotates. SIO_011095 CHEBI:32999 europium atom 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 SIO_000184 legal name A legal name is a name given at birth, or which appears on their birth certificate, marriage certificate, or change of name certificate. SIO_010056 phenotype A phenotype is an observable characteristic of an individual. 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 1 inactive ingredient Aninactive ingredient is a molecular entity that does not exhibit biological activity. SIO_010087 SIO_011043 ruthenium atom CHEBI:30682 A unicellular organism is a organism that is composed of a single cell. SIO_010376 unicellular organism shape is the quality of a bearer that relates to its spatial extent. SIO_000055 shape A percentage is a number that is a ratio expressed as a fraction of 100. It is denoted using the percent sign "%". SIO_001413 percentage is affected by SIO_001159 independent variable SIO_000920 An independent variable is a variable that may take on different values independent of other elements in a system. institute institute is a society or organization having a object or common factor, and is normally applied to those with a scientific, educational, or social objective. SIO_000688 SIO_000325 A overlaps with B iff there is some C that is part of both A and B. [S][R] overlaps with SIO_000916 decimal scale A decimal scale of measurement is one that only specifies decimal values. 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. SIO_001153 maintenance of level of object consumption 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 a unigene cluster is a collection of transcripts (ESTs and mRNAs) that map to a particular genomic region. SIO_001382 unigene cluster cluster of transcripts 1 REST web service a REST web service is a web service that provides functionality according to the Representational State Transfer (REST) specification. SIO_001190 http://en.wikipedia.org/wiki/REST A strain is a genetic variant or kind of microorganism. SIO_010055 strain SIO_000102 A software interpreter is a software application that executes some specified input software. software interpreter SIO_000481 A deletion variant role is the role of an sequence that lacks a sub-sequence relative to the frame of reference. deletion variant role 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. SIO_000568 partial differential equation A movement equation describes the displacement of an object in space over time. SIO_000566 movement equation SIO_000801 A coenzyme role of a chemical entity that is covalently bonded to the enzyme. prosthetic group role preferredNamespacePrefix syllable A syllable is a verbal entity of language having one vowel sound, with or without surrounding consonants, forming the whole or a part of a word. SIO_000977 SIO_001400 subcellular entity SIO_001436 disease-disease association A disease-disease association is an association between two diseases. 1 2 paternally transmitted SIO_001270 paternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the paternal line. CHEBI:33336 SIO_011056 lanthanum atom SIO_001225 cis regulatory element A cisregulatory element is a DNA sequence located on the same DNA strand or chromosome as the gene whose expression it affects. geolegal region A geolegal region is a geographic region which has causal powers confered by a legal entity. The 50 kph zones in Ottawa; the geographic region occupied by France. SIO_000413 SIO_001042 A recipe is a set of instructions that describe how to prepare or make something. recipe satisfied qualifier SIO_001312 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. SIO_010090 to serve as a template for RNA synthesis SIO_000796 The role of a chemical participant that serves to increase the rate of reaction by lowering the activiation energy. catalytic role An inductive argument is an argument that asserts that the truth of the conclusion is supported by the premises. inductive argument SIO_000264 to be combined SIO_010367 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. mass spectrometry experiment SIO_001180 A mass spectrometry experiment is an experiment that involves the use of a mass spectrometer. manganese atom SIO_011024 CHEBI:18291 spherical coordinate system A spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane. SIO_000330 SIO_000284 A hypothesis is a proposed explanation for a phenomenon. hypothesis SIO_000643 is realizable property of 2 SIO_001084 liquid solution A liquid solution is a heterogeneous substance in a liquid state. to add a covalent bond is the capability to covalently modify a chemical entity by adding a covalent bond. SIO_001086 to add a covalent bond SIO_000677 processual role A processual role is a role that can only be realized in a process. is translated from SIO_010083 has input has input is a relation between a process and an entity, where the entity is present at the beginning of the process. sadi core SIO_000230 SIO_000478 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 polar addition reaction SIO_010519 A polar addition reaction is an addition reaction involving polar residues. terbium atom CHEBI:33376 SIO_011097 A local minimum stationary point is a point that has a lower value in some axis than adjacent points. SIO_000743 local minimum stationary point A township is a rural or sub-urban settlement. SIO_000666 township SIO_000608 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 palladium atom SIO_011045 CHEBI:33363 SIO_001221 to describe to describe is the capabilty to communicate facts about an entity. An aromatic ring is a ring in which the electrons are delocalized across all atoms in the ring. aromatic ring SIO_010781 2 SIO_000209 is disputing evidence for SIO_000931 A network diagram consists of a set of vertices connected by edges. network diagram SIO_000787 A page number is the count of a page in a sequence of pages. page number SIO_001253 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 3' splice site The 3' splice site is the terminal region of an exon that is 3' to the intron that is to be excised. SIO_001223 2 0 shock is an emotion of sudden upset or surprise. shock SIO_000866 SIO_000276 An emotion is a process (experience) that arises internally or from an involuntary physiological response to a stimulus. emotion emotion++ to interact and to be interacted with SIO_001102 to interact and to be interacted with is a mutual disposition of interacting objects. 1 aborted is a process status in which a started process will not complete as intended. SIO_000997 aborted The quality of not having a charge. uncharged SIO_000806 pH pH is a measure of the activity of the (solvated) hydrogen ion. SIO_001089 pH is defined as the decimal logarithm of the reciprocal of the hydrogen ion activity, aH+, in a solution. 2 SIO_001323 email address an email address is an identifier to send mail to particular electronic mailbox. CHEBI:49920 SIO_011066 thallium atom toxicity is the quality of a chemical substance to cause injury to an organism in a dose dependent manner. SIO_001008 toxicity SIO_000741 stationary point A stationary point is a point that is part of a curve in which the derivative at that point is zero, and hence its value is at least a local maximum or minimum. 2 SIO_010072 organic molecule An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) is evidence for SIO_000773 strong is a qualitative intensity value that is more intense than moderate, but less intense than severe. SIO_001217 strong issued SIO_000578 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 A thesis document is the written research component of a post-secondary institution that contains a statement supported by arguments. SIO_000165 thesis document organism SIO_010000 A biological organisn is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). A booklet is a document that lacks a named publisher or sponsoring institution. SIO_000169 booklet immediately precedes 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. SIO_000250 SIO_000721 comparative role A comparative role is an abstract role which holds by comparing some attribute of another object of reference. 2 database table A database table is a set of named columns with zero or more rows composed of cells that contain column values and is part of a database. SIO_000754 to covalently modify to covalently modify is to materially change a molecule by adding or removing covalent bonds between atoms. SIO_010340 description A haplotype is one of a set of genomic sequence variants. haplotype SIO_010042 3 0.0 double arrowed line segment A double arrowed line is an arrowed line in which both terminal points are tangentially part of different triangles that bisect the line. SIO_000524 contributor SIO_000854 misery is a feeling of great unhappiness, suffering and/or pain. misery 2 0.0 equivalentTo comment citesAsAuthority