Molecular transport concept has size (in byte) A metric to state how valid the assertions made by an entity are, i.e. how probable it is that this entity is really found in nature. The value should lie between (inclusively) 0 and 1. If a user applies a realness-value of 1 to an entity this essentially means that he or she is sure that the entity exists in nature. Lower values mean that he or she is less certain. A value of 0 means that the entity is not a valid representation of reality at all. However, this should NOT be understood as a NEGATION of any assertions we can associate with the entity. It just means that the entity described in OWL is useless for our understanding of reality. Scores for interestingness and realness can be meaningfully combined. For instance, an interesting but unproven new theory might be assigned a high interestingness score but a low realness score. realness has participant-B Non physical object Formerly known as description. A unitary endurant with no mass (non-physical), generically constantly depending on some agent, on some communication act, and indirectly on some agent participating in that act. Both descriptions (in the now current sense) and concepts are non-physical objects. 1 delta-S quality For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o. UNIT: J/K delta-G'^o = delta-H'^o - T delta-S'^o (This definition from EcoCyc) participant The immediate relation holding between endurants and perdurants (e.g. in 'the car is running').Participation can be constant (in all parts of the perdurant, e.g. in 'the car is running'), or temporary (in only some parts, e.g. in 'I'm electing the president').A 'functional' participant is specialized for those forms of participation that depend on the nature of participants, processes, or on the intentionality of agentive participants. Traditional 'thematic role' should be mapped to functional participation.For relations holding between participants in a same perdurant, see the co-participates relation. interestingness A subjective metric that lets users state how interesting or meaningul they find an entity. The value should lie between (inclusively) 0 and 1. Scores for interestingness and realness can be meaningfully combined. For instance, an interesting but unproven new theory might be assigned a high interestingness score but a low realness score. Liquid solution A liquid, homogeneous mixture of two or more substances. Note: Things that are dissolved in the solution (e.g. a molecule population) can be described as PARTS of the solution. Examples: a liquid inside a cell or inside a petri dish Population of either molecules, molecular complexes, parts of molecules or parts of molecular complexes Caenorhabditis elegans Genus A genus, e.g. 'Homo', 'Rattus' or 'Escherichia'. A process in which at least one participant is a molecule or a part of a molecule, e.g. a binding event. Example: Two proteins observed to interact in a yeast-two-hybrid experiment where there is not enough experimental evidence to suggest that the proteins are forming a complex by themselves without any indirect involvement of other proteins. This is the case for most large-scale yeast two-hybrid screens. Molecular process A process. Within stative occurrences, we distinguish between states and processes according to homeomericity: sitting is classified as a state but running is classified as a process, since there are (very short) temporal parts of a running that are not themselves runnings. (definition from DOLCE ontology) Process Instances of this class describe observed correlations between qualities. Optionally, such descriptions can contain mathematical statements expressed in MathML that can be used for numeric simulation. Additionally to the description of correlations in MathML, this class allows the description of the correlation using concepts (e.g. "positive correlation", "negative correlation"). Exemplary use cases: "Concentration of metabolite A is positively correlated with concentration of metabolite B", "Concentration of metabolite A is negatively correlated with the conversion rate of the enzymatic reaction B", "The rate of influx of metabolite A into compartment B is equal to 123,4 times the first derivative of the concentration of metabolite B minus the second derivative of the concentration of metabolite C" etc. An observed correlation of the qualities of some things. A date associated with an event in the life cycle of the resource. Date 1 1 A string in SMILES format describing the structure of a molecule (see URL www.daylight.com/dayhtml/smiles/ for more info). SMILES structure data correlates quality Electrical current (quality) Electrical current measured in Ampere. UNIT: Ampere (A). Evidence description concept A concept from an external controlled vocabulary such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'. Note: The bio-zen ontology contains terms from the OBO evidence codes ontology made by Michael Ashburner. They are represented as individuals belonging to this class. See http://obo.sourceforge.net/cgi-bin/detail.cgi?evidence_code for the original version of evidence codes ontology. Species A species, e.g. 'Homo sp.', 'Homo sapiens', 'Rattus rattus', 'Arabidopsis thaliana'. Duration The duration of a perdurant. UNIT: s correlates-H A 'population of parts of molecular complexes' can be thought of as a population of many similar sites on molecular complexes in a molecular-complex-population. Note: this refers to populations of molecular complex parts, NOT to sub-populations of molecular-complex-populations. Population of parts of molecular complexes Organism concept standard deviation of value 0 Format The physical or digital manifestation of the resource. Negative correlation (signed) Signed negative correlation: A ~ (-B) mathML A mathematical description of the correlation of one-dimensional-qualities in MathML (using variables A, B, C, D, E, F, G, H and I). has mime-type 1 Title A name given to the resource. A string in InChI format describing a molecular structure (see URL http://www.iupac.org/inchi/ for more info). InChI structure data A concept that can be used to describe a molecular interaction. Molecular process concept Chemical conversion process concept An entity responsible for making the resource available Publisher Luminous intensity measured in candela. Unit: candela (cd). Luminous intensity has cofactor Any cofactor(s) or coenzyme(s) required for catalysis of the (probably enzymatic) chemical-reaction-event. 1 Molecule type concept has sequence start position is life of Dependent place A feature that is not part of its host, like a hole in a piece of cheese, the underneath of a table, the front of a house, or the shadow of a tree. Reactome Biological compartment (including its contents) A compartment in the biological is in most cases a structure filled with liquid that is confined by a tight barrier. Note: Things that are inside the compartment can be described as PARTS of the compartment. A concept from the Medical Subject Headings - taxonomy. See http://www.nlm.nih.gov/mesh/meshhome.html Concept from MeSH Molecular transport process A process in which molecules of a certain molecule population change their location and become part of another molecule population (which is located elsewhere). Transporters are linked to transport interactions via the catalyzed-by property. Example: The exocytosis of a neurotransmitter from a cellular vesicle into the synaptic cleft. By strong connection here we mean a connection between two entities that share a boundary. has strong connection with Coverage The extent or scope of the content of the resource. has sibling part Mereological sibling: having a common whole 0 Molecular function concept 1 A part that is in fact one of many ('uncountable') similar parts. Example: "<liver-tissue> <exemplary-part> <typical-liver-cell>". typical-liver-cell here stands as an example for many other, similar liver cells that are also part of the liver-tissue, but which are not described. exemplary part This property is the inverse of the 'broaderPartitive' property. narrower (partitive) regards For biochemical reactions, this quality refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o. UNIT: J/mol delta-G'^o = delta-H'^o - T delta-S'^o (This definition from EcoCyc) delta-H (enthalpy difference) Rights Management Information about rights held in and over the resource. Positive correlation (unsigned) Unsigned Positive correlation: |A| ~ |B| 0 ID version The version number of the identifier (ID). E.g. The RefSeq accession number NM_005228.3 should be split into NM_005228 as the ID and 3 as the ID-version. has sequence position AKA 'co-occurs'. Temporal coincidence between perdurants. temporally coincides with Population of nucleotides that are parts of DNA molecules The location of the nucleotides on the DNA strands can be defined through its sequence-position (given as a number). Concept about the binding of a catalytic molecule that has modulatory effect Population of nucleotides that are parts of DNA molecules The location of the nucleotides on the RNA strands can be defined through its sequence-position (given as a number). In biology and ecology, an organism is an assembly of molecules that influence each other in such a way that they function as a more or less stable whole and have properties of life [1]. In the context of this ontology, immortalized cell-lines (e.g. HeLa cells) can also be classified as organisms. Examples: a bacterium, a mouse, a human. [1] from en.wikipedia.org/wiki/Organism Organism KEQ quality The measured equilibrium constant for a biochemical reaction, encoded by the slot KEQ, is actually the apparent equilibrium constant, K'. UNIT: (dimensionless) It is a function of temperature (T), ionic strength (I), pH, and pMg, which have to be given as properties of the containing solution. Population of subsequence-parts of DNA molecules. A 'subsequence-part' of a macromolecule is a part of a molecule to which we can assign a sequence (which is a subsequence of the sequence of the whole macromolecule). Concept from EC enzyme nomenclature A concept from the EC nomenclature of enzymes / enzymatic reactions. The EC number is a unique number assigned to a reaction or an enzyme by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology. has sequence length Length of the sequence of a polymer (i.e. the number of monomers that make up the polymer). Temperature Temperature measured in Kelvin. Unit: Kelvin. 1 has generic location The most generic location relation (e.g. containment for exact location, proximity for approximate location). This is meant to reason on generalized, common sense as well as formal locations, including naive localization, between any kinds of entities. An event. A perdurant is stative or eventive depending on whether it is cumulative or not. A sitting occurrence is stative (and not eventive) since the sum of two sittings is still a sitting occurrence. Event The common trait of amounts of matter is that they are endurants with no unity (according to Gangemi et a. 2001 none of them is an essential whole). Amounts of matter - 'stuffs' referred to by mass nouns like 'gold', 'iron', 'wood', 'sand', 'meat', etc. - are mereologically invariant, in the sense that they change their identity when they change some parts. Amount of matter correlates-B A process that has several molecular interaction processes as its parts, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical or other reasons. Examples: glycolysis, synthesis of serotonin from tryptophan. Chemical pathway Negative correlation (unsigned) Unsigned negative correlation: |A| ~ |B| * (-1) has generic constituent 'Constituent' should depend on some layering of the ontology. For example, scientific granularities or ontological 'strata' are typical layerings. A constituent is a part belonging to a lower layer. Since layering is actually a partition of the ontology, constituents are not properly classified as parts, although this kinship can be intuitive for common sense. Example of specific constant constituents are the entities constituting a setting (a situation), whilethe entities constituting a collection are examples of generic constant constituents. catalyzed by has constant-participant Anytime x is present, x has participant y. In other words, all parts of x have a same participant.Participation can be constant (in all parts of the perdurant, e.g. in 'the car is running'), or temporary (in only some parts, e.g. in 'I'm electing the president'). correlates-D 1 Spatial length Length measured in meters. Unit: meter (m). A string in CML format for the description of molecular structures (see URL http://www.xml-cml.org for more info). CML structure data Small molecule concept Definition: Describes a small molecule, optionally giving its structure. Pubmed This property is the inverse of the 'broaderInstantive' property. narrower (instantive) An unambiguous reference to the resource within a given context. Resource Identifier described by data The status code (e.g. 201, 404) that was received when a resolution of the URL was last attempted. status code received An extension of the 'skos:broader' property to specify an instantiation (instance of) relationship between two concepts. broader (instantive) temporally meets Temporal connection between perdurants: p1 ending part is connected to p2 beginning part. Uncatalyzed (spontaneous) chemical conversion process. Non-physical endurant An endurant with no mass, generically constantly depending on some agent. Non-physical endurants can have physical constituents (e.g. in the case of members of a collection). Temporal coincidence between perdurants, the life of endurants and qualities. This property can be used to put things into a common timeframe. coincidence of life Population of parts of RNA molecules Arbitrary sum AKA arbitrary-collection.The mereological sum of any two or more endurants (physical or not). Arbitrary sums have no unity criterion (they are 'extensional'). Narrower concepts are typically rendered as children in a concept hierarchy (tree). narrower concept 1 Arabidopsis thaliana has MD5 hash value Stoichiometry The stoichiometry of a chemical reaction regarding to one of the reaction participants. correlates-F This important property should be used to relate things to 'clones' of these things we have made in OWL. Example: A biological sequence database holds many sequences of proteins from the human proteome (in the form of sequence-qualities that are not assigned to any particular protein). A scientist wants to describe the sequence of a certain protein he is investigating, and thinks that the sequence-quality of this protein is similar to the sequence-quality described in the sequence database. He makes a copy of the sequence-quality and assigns this quality to his protein. In order to state that this new sequence quality was derived from the database, he adds a statement like '{copied-sequence-quality} inf:prototype {sequence-quality-in-database}' has prototype The relation between an entity (playing the role of example, sample, prototype, master, etc.), and another that has all the properties of the first (or a given set of them), except space-time. The description of the first entity should be 'sharper' or at least 'more accurate' than that of the prototype. Definition: A process that has both a molecular-transport-process and a chemical-conversion-process as its parts. Through such a process, one or more molecules change both their location and their physical structure. Active transport reactions that use ATP as an energy source fall under this category, even if the only covalent change is the hydrolysis of ATP to ADP. Examples: In the PEP-dependent phosphotransferase system, transportation of sugar into an E. coli cell is accompanied by the sugar's phosphorylation as it crosses the plasma membrane. Molecular transport with chemical conversion process 0 Population of DNA molecules A population of physical entities, each consisting of a sequence of deoxyribonucleotide monophosphates. Note: Be careful when you are trying to describe genes with individuals of this class, since 'gene' is a genetic concept that sometimes does not refer to a physical entity. Note: This should NOT be used to refer to a chromosome. A chromosome has many other parts (histones etc.). DNA is a physical part of a chromosome. Mass measured in kilograms. Unit: kilogram (kg). Mass Perdurant (event, process, state etc.) Perdurants (AKA occurrences) comprise what are variously called events, processes, phenomena, activities and states. They can have temporal parts or spatial parts. For instance, the first movement of (an execution of) a symphony is a temporal part of the symphony. On the other hand, the play performed by the left side of the orchestra is a spatial part. In both cases, these parts are occurrences themselves. We assume that objects cannot be parts of occurrences, but rather they participate in them. Perdurants extend in time by accumulating different temporal parts, so that, at any time they are present, they are only partially present, in the sense that some of their proper temporal parts (e.g., their previous or future phases) may be not present. E.g., the piece of paper you are reading now is wholly present, while some temporal parts of your reading are not present yet, or any more. Philosophers say that endurants are entities that are in time, while lacking temporal parts (so to speak, all their parts flow with them in time). Perdurants, on the contrary, are entities that happen in time, and can have temporal parts (all their parts are fixed in time). (definition from DOLCE ontology) Spatial location quality A physical quality, whose value is given within ordinary spaces (geographical coordinates, cosmological positions, anatomical axes, etc.). A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution. (Definition from Merriam-Webster Dictionary) pH Physical endurant An endurant having a direct physical (at least spatial) quality. The ionic strength is defined as half of the total sum of the concentration (ci) of every ionic species (i) in the solution times the square of its charge (zi). For example, the ionic strength of a 0.1 M solution of CaCl2 is 0.5 x (0.1 x 22 + 0.2 x 12) = 0.3 M (Definition from http://www.lsbu.ac.uk/biology/enztech/ph.html) Ionic strength Metabolic pathway concept Cellular component concept This property can be used to state that a quality has a constant value (i.e. the value does not change in the whole existance of the quality). has constant value preferred label NOTE: Parts of a complex should be defined via its 'proper-part' property. NOTE: 'Sub-complexes' should not be defined in this ontology. Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA). Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. Comment: Complexes cannot be defined recursively so that smaller complexes exist within larger complexes. The boundaries on the size of complexes described by this class are not defined here, although elements of the cell as large and dynamic as, e.g., a mitochondrion should not be described using individuals belonging to this class. Examples: Ribosome, RNA polymerase, complexes of multiple protein monomers, complexes of proteins and small molecules. Population of molecular complexes A state. Within stative occurrences, we distinguish between states and processes according to homeomericity: sitting is classified as a state but running is classified as a process, since there are (very short) temporal parts of a running that are not themselves runnings. (definition from DOLCE ontology) State Celltype concept Concept describing a cell type (e.g. "hepatocyte", "neuron", "HeLa cell"). is partly compresent with A composed (mediated) relation used here to make relations 'temporary': by adding it as a superrelation, the effect is that the two related endurants cannot be present at all the same time intervals, but are compresent at least at some time interval (see related axiom).In FOL, the same constraint can be stated directly by coreference.This workaround can be used to index time of relations that involve reciprocal dependency, but it cannot be used in general with relations involving multiple strata of reality. For example, _about_ relation can be temporally indexed, without involving that the time of the information object overlaps with the time of the entity the information is about (but this works for e.g. the _realizes_ relation between information objects and entities whatsoever). The different temporal constraints of about vs. expresses probably derive from the dependency of aboutness from conception (to be about x, an information object should also express a description d that is satisfied by a situation including x, then temporal overlapping of _about_ is true in virtue of d). On the other hand, even conceives cannot be indexed in this way, because overlapping does not hold between the time og the conceiving agent, and the conceived description (or situation). Correlation between two qualities. Correlation between two qualities Particular thing Population of amino acids that are parts of protein molecules The location of the amino acids on the protein strands can be defined through its sequence-position (given as a number). maximum deviation of value 1 Broader concepts are typically rendered as parents in a concept hierarchy (tree). has broader causes Population of molecules A reference to a related resource. Relation Population of subsequence-parts of RNA molecules. A 'subsequence-part' of a macromolecule is a part of a molecule to which we can assign a sequence (which is a subsequence of the sequence of the whole macromolecule). A concept about a correlation (e.g. 'positive correlation', 'negative correlation'). Correlation concept corresponding schema can be downloaded from Points to the URL of a schema corresponding to the data. Example: the location of a DTD or and XML schema for XML data. broader (generic) An extension of the 'broader' property to specify the class subsumption (sub-class/super-class) relationship between two concepts. The process of the binding of molecules from different molecule populations to each other. Events of 'unbinding' (molecules that are bound lose their bonds) are also parts of such a process. If you want to emphasise that an interaction results in the formation of a complex, you should consider using the subclass complex-assembly-process instead. Molecular binding process Quality of perdurant A quality inherent in a perdurant. is host of feature 1 Molecular binding concept 0.0 A quality that always has the value 0. related to has weak connection with The basic connection, not requiring a common boundary. Temporal overlap: having a (partly) common temporal location. temporally overlaps has sequence end position 1 Cell (in the biological sense) Concept 2 An extension of the 'broader' property to specify a partitive (part of) relationship between two concepts. broader (partitive) Any concept describing data (which, in the context of this ontology, refers to individuals belonging to the class biozen:data). Data concept A reference to a resource from which the present resource is derived. Source Nucleotide concept Spatio-temporal-particular (a particular thing located in certain places at certain times) This class includes all entities that are not reifications of universals ('abstracts'), i.e. those entities that are in space-time. All temporal locations of perdurant x are also temporal locations of perdurant y. temporally includes Cell concept Relevant part / feature Features that are relevant parts of their host, like a bump or an edge. Population of parts of molecules A 'population of parts of molecules' can be thought of as a population of many similar sites on molecules in a molecule-population. Note: this refers to populations of molecular parts, NOT to sub-populations of molecular-populations. can be downloaded from has temporary part Being part at time t. It holds for endurants only. This is important to model parts that can change or be lost over time without affecting the identity of the whole. In FOL, this is expressed as a ternary relation, but in DLs we only can reason with binary relations, then only the necessary axiom of compresence is represented here. Experimental modification concept A concept describing the experimental (i.e. artificial, human-made) modification of a molecule. Subject and Keywords The topic of the content of the resource. Tissue concept Language A language of the intellectual content of the resource. Signed positive correlation: A ~ B Positive correlation (signed) started by Population of parts of DNA molecules 1 Mean molecular mass of molecules in population of molecules / molecular complexes 1 This value is the initial value of the quality (e.g. a concentration). 'Initial' here means at the start of the life of the quality. has initial value Human-readable document data Any document intended to be read by persons, e.g. a HTML document, a MS Word document or a PDF document. The speed and direction of a chemical reaction. UNIT: mol/h (Mol per hour) Note: Positive values mean that the direction of the direction is from group 'A' of participants to group 'B', negative values mean that the direction is from group 'B' to group 'A' Note: When a reaction is in equilibrium, this value should be 0. Chemical reaction direction and speed Homo sapiens A string describing a polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, G. Note: The string should contain only the sequence string, NOT additional data or characters (e.g. a FASTA header). Nucleotide sequence string Population of small molecules A population of small molecules. Small molecules are not a polymers (e.g. a peptide, DNA, or RNA are not small molecules). Examples: glucose, penicillin, phosphatidylinositol Chemical conversion process type concept 0 1 Population of either molecules, molecular complexes, parts of molecules, parts of molecular complexes is in termporal relation to Any mediated relation that composes temporal locations of perdurants with mereotopological relations between those locations.Mereotopological relations are those specified in the J. Allen's theory of time intervals. This property is the inverse of the 'broaderGeneric' property. narrower (generic) Population of RNA molecules. A population of physical entities, each consisting of a sequence of ribonucleotide monophosphates. Examples: mRNA, microRNA, rRNA. precedes Temporal precedence between two perdurants. No further dependence is implied (e.g. mereological, causal). has participant-A semantic relation This property should not be used directly, but as a super-property for all properties denoting a relationship of meaning between concepts. Biological process concept An entity responsible for making contributions to the content of the resource. Contributor has part OR participant A population of physical entities, each consisting of a sequence of amino acids. Example: The epidermal growth factor receptor (EGFR) protein Population of protein molecules. Compartment concept BIND (Biomolecular Interaction Network Database) A 'subsequence-part' of a macromolecule is a part of a molecule to which we can assign a sequence (which is a subsequence of the sequence of the whole macromolecule). Each subsequence-part of a molecule has two sequence-sites as boundaries. Population of subsequence-parts of protein molecules. Stative A stative perdurant (e.g. a process or a state). A perdurant is stative or eventive depending on whether it is cumulative or not. A sitting occurrence is stative (and not eventive) since the sum of two sittings is still a sitting occurrence. Chemical conversion process A process in which molecules undergo covalent changes to become other molecules (thereby becoming part of another molecule population). Example: ATP + H2O = ADP + Pi Note: Polymerization reactions involving large polymers whose structure is not explicitly captured should generally be represented as unbalanced reactions in which the monomer is consumed but the polymer remains unchanged, e.g. glycogen + glucose = glycogen. The main characteristic of physical objects is that they are endurants with unity. However, they have no common unity criterion, since different subtypes of objects may have different unity criteria. Differently from aggregates, (most) physical objects change some of their parts while keeping their identity, they can have therefore temporary parts. Often physical objects (indeed, all endurants) are ontologically independent from occurrences (discussed below). However, if we admit that every object has a life, it is hard to exclude a mutual specific constant dependence between the two. Nevertheless, we may still use the notion of dependence to (weakly) characterize objects as being not specifically constantly dependent on other objects. Physical object Tissue (biological) An aggregate of cells having a similar function or structure. pMg A measure of the concentration of magnesium (Mg) in solution. (pMg = -log₁₀[Mg²⁺]) One-dimensional quality A quality that can be fully described by a single value. Examples: Location of an event in time, diameter of an object, velocity of an object, charge of an object. Note: The spatial location of an object in three dimensional space is not a one-dimensional-quality, because three values are needed to describe this quality. To describe spatial locations as one-dimensional-qualities, its location should be described with x, y and z coordinates according to an initial system. concluded by A concept from the taxonomy of species in biology (e.g. Homo, Homo sapiens, Rattus, Eukaryota). Organismal classification concept Abstract thing Endurant (object, feature etc.) The main characteristic of endurants is that all of them are independent essential wholes. This does not mean that the corresponding property (being an endurant) carries proper unity, since there is no common unity criterion for endurants. Endurants can 'genuinely' change in time, in the sense that the very same endurant as a whole can have incompatible properties at different times. To see this, suppose that an endurant - say 'this paper' - has a property at a time t 'it's white', and a different, incompatible property at time t' 'it's yellow': in both cases we refer to the whole object, without picking up any particular part of it. Within endurants, we distinguish between physical and non-physical endurants, according to whether they have direct spatial qualities. Within physical endurants, we distinguish between amounts of matter, objects, and features. (definition from DOLCE ontology) has quality The concentration of physical entities in a solution, measured in moles. Units: mol/L Concentration Resource Type The nature or genre of the content of the resource. A string describing a polymer sequence in uppercase letters, usually the letters corresponding to the 20 letter IUPAC amino acid code. Note:The string should contain only the sequence string, NOT additional data or characters (e.g. a FASTA header). Aminoacid sequence string Data about a small molecule or a group of small molecules (e.g. molecular structure). Small molecule structure data A quality inherent in a physical endurant. Quality of physical endurant alternative label Creator An entity primarily responsible for making the content of the resource. Description An account of the content of the resource. Population of parts of small molecules 'Constituent' should depend on some layering of the ontology. For example, scientific granularities or ontological 'strata' are typical layerings. A constituent is a part belonging to a lower layer. Since layering is actually a partition of the ontology, constituents are not properly classified as parts, although this kinship can be intuitive for common sense. Example of specific constant constituents are the entities constituting a setting (a situation), whilethe entities constituting a collection are examples of generic constant constituents. has specific constant constituent Rattus sp. delta-G-prime-O quality For biochemical reactions, this quality refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o. UNIT: J/mol delta-G'^o = -RT lnK' and delta-G'^o = delta-H'^o - T delta-S'^o delta-G'^o has units of kJ/mol. Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'^o T I pH pMg). (This definition from EcoCyc) 2 Definition: A process in which molecules from different molecule populations, at least one being a population of macromolecules (e.g. protein, RNA, DNA), aggregate via non-covalent interactions. One of the participants of molecular-binding-process must be an instance of the class complex-population. Comment: This class is also used to represent complex disassembly. Examples: Assembly of the TFB2 and TFB3 proteins into the TFIIH complex; assembly of the ribosome through aggregation of its subunits. Complex assembly process The most generic part relation, reflexive, asymmetric, and transitive. has part correlates-A 0 0 Concept describing a certain database Examples: 'Uniprot', 'Ensembl', 'Entrez Gene' are examples for biological database systems. Database system concept A unified resource locator (URL) that can be resolved via HTTP. URL correlates-assign Qualities can be seen as the basic entities we can perceive or measure: shapes, colors, sizes, sounds, smells, as well as weights, lengths, electrical charges... 'Quality' is often used as a synonymous of 'property', but this is not the case in this upper ontology: qualities are particulars, properties are universals. Qualities inhere to entities: every entity (including qualities themselves) comes with certain qualities, which exist as long as the entity exists. Quality Escherichia coli Sequence type, sequence feature or genomic concept Example: The HTML version of a text is an alternative representation of the PDF version of the same text. The binary representations are different, but the content is the same. has alternative representation overlaps with Mereological overlap: having a common part. Data type concept Population of parts of protein molecules correlates-C Data described by concept 1 correlates-G ID The primary identifier in the external database in which this data can be found. Note: The name of the external database can be stated with the 'DB' property. 1 Concept from Wordnet A concept from the general lexical reference system Wordnet. See http://wordnet.princeton.edu/ 0 correlates-E Having the same parts at time t. mereologically coincides with contains data The value of this property can contain the data represented by this resource (e.g. a sequence of characters). Note: Additionally / alternatively, you can use the 'download' property to point to a URL where the data can be downloaded. 1 1 Feature Features are 'parasitic entities', that exist insofar their host exists. Typical examples of features are holes, bumps, boundaries, or spots of color. Features may be relevant parts of their host, like a bump or an edge, or dependent regions like a hole in a piece of cheese, the underneath of a table, the front of a house, or the shadow of a tree, which are not parts of their host. All features are essential wholes, but no common unity criterion may exist for all of them. However, typical features have a topological unity, as they are singular entities.Here only features of physical endurants are considered. bio-zen ontology The bio-zen ontology is an ontology for the life sciences. In its current version, it is focussed on the representation and mathematical modelling of molecular structures, biochemical and physiological processes and interaction networks. bio-zen is based on foundational ontologies and metadata standards (DOLCE, SKOS, Dublin Core). bio-zen is unique in that it unifies a high degree of ontological consistency with a maximum of flexibility and simplicity in its design. A large collection of extensions is available (e.g. extensions containing concepts from the Gene Ontology, Medical Subject Headings, Cell Ontology, Evidence Codes, Chemical Entities of Biological Interest, Sequence Ontology, NCBI Taxonomy). - Matthias Samwald, 2006 For more information, visit http://neuroscientific.net/semantic 1.0 boundary A temporal location quality. Temporal location quality is derived from '<A> <derives from> <B>' means that a significant portion of the matter of entity B becomes part of the newly created entity A. The lifetimes of A and B might overlap; at least they meet in a certain instant of time. Examples: <cake> <derives-from> <mass-of-dough> <Frog> <derives-from> <Newt> <Blood-cell> <derives-from> <Reticulocyte> <new-cell-1> <derives-from> <cell-undergoing-mitosis>, <new-cell-2> <derives-from> <cell-undergoing-mitosis> Quality of non-physical endurant A quality inherent in a non-physical endurant. Mus musculus This is a superproperty of the 'described-by' and the 'narrower' property. It can be used to make the broader/narrower - hierarchies of SKOS accessible for automated reasoning about entities annotated with a SKOS concept. described by OR narrower The apparent equilibrium constant K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate: K' = [ADP][P_i]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [MgHATP^-] + [Mg₂ATP]. The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm³) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]). These can be represented as qualities of the liquid solution. (Definition from EcoCyc) K-prime quality