TODO: Long term goals: Adding compatibility with SBML, BrainML, NeuroML various Entrez databases... TODO: Add better undestandable comments to the classes and properties from DOLCE. TODO: Representation of stoichometry through n-ary relations? TODO: Clarify the semantics of "states" in the DOLCE ontology. TODO: Change units from kJ/mol to J/mol ? TODO: Representation of conformational changes? bio-zen ontology. This ontology is under development and is NOT intended for use. Please use the BioPAX ontology instead. See: http://biopax.org Matthias Samwald 2006 For more information, visit http://neuroscientific.net TODO: Meaning of qualities of qualities? TODO: Clarify the distinctions between different 'constituent' properties. TODO: Creative Commons / Science Commons (should stay in OWL DL, though) TODO: Relationship between realness and evidence? TODO: Temporality and temporal indexing of properties? 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'. Experimental modification concept A concept describing the experimental (i.e. artificial, human-made) modification of a molecule. Concept about the binding of a catalytic molecule that has modulatory effect A solution (e.g. a liquid inside a cell or inside a petri dish). Note: Things that are dissolved in the solution (e.g. a molecule population) can be described as PARTS of the solution. Abstract thing Object, feature etc. ('endurant') 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: The support for a particular assertion, such as the existence of an interaction or pathway. Examples: A description of a molecular binding assay that was used to detect a protein-protein interaction. 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. A quality inherent in a physical endurant. Quality of physical endurant 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⁺]). (Definition from EcoCyc) 1 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). Quality of perdurant A quality inherent in a perdurant. 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. 1 1 1 1 Cross reference 1 A cross reference is a reference to an object in an external resource (e.g. a database entry). 1 Luminous intensity measured in candela. Unit: candela (cd). An organism. In the context of this ontology, immortalized cell-lines (e.g. HeLa cells) can be classified as organisms, too. Organism Population of nucleotides that are parts of DNA molecules 1 The location of the nucleotides on the RNA strands can be defined through its sequence-position (given as a number). 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: kJ/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) Correlation between two qualities. Additionally to the description of correlations in MathML, this class allows the description of the correlation using concepts (e.g. "positive correlation", "negative correlation"). Correlation between two qualities 2 0 0 0 0 0 0 0 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 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. 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 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. A concept that can be used to describe a molecular interaction. Molecular process concept An occurrence-type is stative or eventive according to whether it holds of the mereological sum of two of its instances, i.e. if it is cumulative or not. A sitting occurrence is stative since the sum of two sittings is still a sitting occurrence.In general, events differ from situations because they are not assumed to have a description from which they depend. They can be sequenced by some course, but they do not require a description as a unifying criterion.On the other hand, at any time, one can conceive a description that asserts the constraints by which an event of a certian type is such, and in this case, it becomes a situation.Since the decision of designing an explicit description that unifies a perdurant depends on context, task, interest, application, etc., when aligning an ontology do DLP, there can be indecision on where to align an event-oriented class. For example, in the WordNet alignment, we have decided to put only some physical events under 'event', e.g. 'discharge', in order to stress the social orientedness of DLP. But whereas we need to talk explicitly of the criteria by which we conceive discharge events, these will be put under 'situation'.Similar considerations are made for the other types of perdurants in DOLCE.A different notion of event (dealing with change) is currently investigated for further developments: being 'achievement', 'accomplishment', 'state', 'event', etc. can be also considered 'aspects' of processes or of parts of them. For example, the same process 'rock erosion in the Sinni valley' can be conceptualized as an accomplishment (what has brought the current state that e.g. we are trying to explain), as an achievement (the erosion process as the result of a previous accomplishment), as a state (if we collapse the time interval of the erosion into a time point), or as an event (what has changed our focus from a state to another).In the erosion case, we could have good motivations to shift from one aspect to another: a) causation focus, b) effectual focus, c) condensation d) transition (causality).If we want to consider all the aspects of a process together, we need to postulate a unifying descriptive set of criteria (i.e. a 'description'), according to which that process is circumstantiated in a 'situation'. The different aspects will arise as a parts of a same situation. Concept The concentration of physical entities in a solution, measured in moles. Units: mol/L Concentration Mass measured in kilograms. Unit: kilogram (kg). Mass Temperature measured in Kelvin. Unit: Kelvin. Temperature 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. In general, processes differ from situations because they are not assumed to have a description from which they depend. They can be sequenced by some course, but they do not require a description as a unifying criterion. On the other hand, at any time, one can conceive a description that asserts the constraints by which a process of a certian type is such, and in this case, it becomes a situation. Since the decision of designing an explicit description that unifies a perdurant depends on context, task, interest, application, etc., when aligning an ontology do DLP, there can be indecision on where to align a process-oriented class. For example, in the WordNet alignment, we have decided to put only some physical processes under 'process', e.g. 'organic process', in order to stress the social orientedness of DLP. But whereas we need to talk explicitly of the criteria by which we conceive organic processes, these will be put under 'situation'. Similar considerations are made for the other types of perdurants in DOLCE. A different notion of event (dealing with change) is currently investigated for further developments: being 'achievement', 'accomplishment', 'state', 'event', etc. can be also considered 'aspects' of processes or of parts of them. For example, the same process 'rock erosion in the Sinni valley' can be conceptualized as an accomplishment (what has brought the current state that e.g. we are trying to explain), as an achievement (the erosion process as the result of a previous accomplishment), as a state (if we collapse the time interval of the erosion into a time point), or as an event (what has changed our focus from a state to another). In the erosion case, we could have good motivations to shift from one aspect to another: a) causation focus, b) effectual focus, c) condensation d) transition (causality). If we want to consider all the aspects of a process together, we need to postulate a unifying descriptive set of criteria (i.e. a 'description'), according to which that process is circumstantiated in a 'situation'. The different aspects will arise as a parts of a same situation. URL Sequence type or feature concept pH 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) 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). Definition: 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. Spatio-temporal-particular (a particular thing located in certain places at certain times) Dummy class for optimizing some property universes. It includes all entities that are not reifications of universals ('abstracts'), i.e. those entities that are in space-time. 0 Uncatalyzed (spontaneous) chemical conversion process. Organismal classification concept A concept from the taxonomy of species in biology (e.g. Homo, Homo sapiens, Rattus, Eukaryota). Features that are relevant parts of their host, like a bump or an edge. 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 Concept describing a certain database Examples: 'Uniprot', 'Ensembl', 'Entrez Gene' are examples for biological database systems. 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. delta-G'^o = delta-H'^o - T delta-S'^o (This definition from EcoCyc) The measured equilibrium constant for a biochemical reaction, encoded by the slot KEQ, is actually the apparent equilibrium constant, K'. UNIT: (dimensionless) 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⁺]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K' T I pH pMg). This property may have multiple values, representing different measurements for K' obtained under the different experimental conditions listed in the 5-tuple. (This definition adapted from EcoCyc) Molecular function concept Concept describing a cell type (e.g. "hepatocyte", "neuron", "HeLa cell"). Celltype concept A concept from the general lexical reference system Wordnet. See http://wordnet.princeton.edu/ Concept from Wordnet Population of either molecules, molecular complexes, parts of molecules or parts of molecular complexes A concept about a correlation (e.g. 'positive correlation', 'negative correlation'). Correlation concept 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). A concept that describes the type of a molecular interaction (e.g. van-der-Waals interactions, ionic interactions). Molecular binding type concept AKA arbitrary-collection.The mereological sum of any two or more endurants (physical or not). Arbitrary sums have no unity criterion (they are 'extensional'). Chemical conversion process A process in which molecules undergo covalent changes to become other molecules (thereby becoming part of another molecule population). Examples: ATP + H2O = ADP + Pi Note: When writing biochemical reactions, it is not necessary to attach charges to the biochemical reactants or to include ions such as H+ and Mg2+ in the equation. 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. 1 1 Species A species, e.g. 'Homo sp.', 'Homo sapiens', 'Rattus rattus', 'Arabidopsis thaliana'. Biological process type (concept) Mean molecular mass of molecules in population of molecules / molecular complexes Instances of this class describe observed correlations between qualities. Optionally, this can contain MATHEMATICAL correlations expressed in MathML that can be used for numeric simulation. 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. Additionally to the description of correlations in MathML, this class allows the description of the correlation using concepts (e.g. "positive correlation", "negative correlation"). 1 1 1 1 1 1 1 1 An observed correlation of the qualities of some things. 1 2 Definition: A molecular-binding-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. The assembly or disassembly of a complex is often a spontaneous process, in which case the direction of the complexAssembly (toward either assembly or disassembly) should be specified via the SPONTANEOUS property. Synonyms: aggregation, complex formation Examples: Assembly of the TFB2 and TFB3 proteins into the TFIIH complex, and assembly of the ribosome through aggregation of its subunits. Note: The following are not examples of complex assembly: Covalent phosphorylation of a protein (this is a biochemicalReaction); the TFIIH complex itself (this is an instance of the complex class, not the complexAssembly class). 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. Comment: It is possible to define a pathway without specifying the interactions within the pathway. In this case, the pathway instance could consist simply of a name and could be treated as a 'black box'. Synonyms: network Examples: glycolysis, valine biosynthesis, synthesis of serotonin from tryptophan. Chemical pathway Electrical current (quality) Electrical current measured in Ampere. Unit: Ampere (A). A concept from the sequence ontology. See http://song.sourceforge.net/ Definition of RNA: A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid. Examples: messengerRNA, microRNA, ribosomalRNA. A specific example is the let-7 microRNA. Population of RNA molecules. 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. Synonyms: translocation. Examples: The exocytosis of a neurotransmitter from a cellular vesicle into the synaptic cleft. 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. Concept from EC enzyme nomenclature pMg A measure of the concentration of magnesium (Mg) in solution. (pMg = -log₁₀[Mg²⁺]) A population of either molecules, molecular complexes, parts of molecules, parts of molecular complexes 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. 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). Event, process, state etc. ('perdurant') Small molecule concept Definition: Describes a small molecule, optionally giving its structure. A physical quality, q-located in (whose value is given within) ordinary spaces (geographical coordinates, cosmological positions, anatomical axes, etc.). An endurant having a direct physical (at least spatial) quality. Catalyzed chemical conversion process 1 Population of molecules A genus, e.g. 'Homo', 'Rattus' or 'Escherichia'. Genus The duration of a perdurant. UNIT: s Duration The location of the nucleotides on the DNA strands can be defined through its sequence-position (given as a number). Population of nucleotides that are parts of DNA molecules 1 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. Length measured in meters. Unit: meter (m). Population of DNA molecules Definition of DNA: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid. Comment: This is not a 'gene', since gene is a genetic concept, not a physical entity. Note: This should NOT be used to refer to e.g. a chromosome! A chromosome has many other parts (histones etc.) that are not part of the DNA (which is a polymer of amino acids). DNA is a physical part of a chromosome. A temporal location quality. 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. Population of parts of RNA molecules 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.In general, states differ from situations because they are not assumed to have a description from which they depend. They can be sequenced by some course, but they do not require a description as a unifying criterion.On the other hand, at any time, one can conceive a description that asserts the constraints by which a state of a certian type is such, and in this case, it becomes a situation.Since the decision of designing an explicit description that unifies a perdurant depends on context, task, interest, application, etc., when aligning an ontology do DLP, there can be indecision on where to align a state-oriented class. For example, in the WordNet alignment, we have decided to put only some physical states under 'state', e.g. 'turgor', in order to stress the social orientedness of DLP. But whereas we need to talk explicitly of the criteria by which we conceive turgor states, these will be put under 'situation'.Similar considerations are made for the other types of perdurants in DOLCE.A different notion of event (dealing with change) is currently investigated for further developments: being 'achievement', 'accomplishment', 'state', 'event', etc. can be also considered 'aspects' of processes or of parts of them. For example, the same process 'rock erosion in the Sinni valley' can be conceptualized as an accomplishment (what has brought the current state that e.g. we are trying to explain), as an achievement (the erosion process as the result of a previous accomplishment), as a state (if we collapse the time interval of the erosion into a time point), or as an event (what has changed our focus from a state to another).In the erosion case, we could have good motivations to shift from one aspect to another: a) causation focus, b) effectual focus, c) condensation d) transition (causality).If we want to consider all the aspects of a process together, we need to postulate a unifying descriptive set of criteria (i.e. a 'description'), according to which that process is circumstantiated in a 'situation'. The different aspects will arise as a parts of a same situation. Concept from MeSH A concept from the Medical Subject Headings - taxonomy. See http://www.nlm.nih.gov/mesh/meshhome.html 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: kJ/mol delta-G'^o = delta-H'^o - T delta-S'^o (This definition from EcoCyc) delta-H (enthalpy difference) Stoichiometry The stoichiometry of a chemical reaction regarding to one of the reaction participants. 1 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 would typically not be described using instances of this class. Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules. Population of molecular complexes Cell (in the biological sense) Quality of non-physical endurant A quality inherent in a non-physical endurant. Chemical reaction direction and speed 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 'left' to 'right', negative values meant that the direction is 'right' to 'left'. NOTE: When a reaction is in equilibrium, this value should be 0. An occurrence-type is stative or eventive according to whether it holds of the mereological sum of two of its instances, i.e. if it is cumulative or not. A sitting occurrence is stative since the sum of two sittings is still a sitting occurrence. 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). Population of subsequence-parts of DNA molecules. AKA 'entity'.Any individual in the DOLCE domain of discourse. The extensional coverage of DOLCE is as large as possible, since it ranges on 'possibilia', i.e all possible individuals that can be postulated by means of DOLCE axioms. Possibilia include physical objects, substances, processes, qualities, conceptual regions, non-physical objects, collections and even arbitrary sums of objects.The class 'particular' features a covering partition that includes: endurant, perdurant, quality, and abstract. There are also some subclasses defined as unions of subclasses of 'particular' for special purposes: spatio-temporal-particular (any particular except abstracts)- physical-realization (any realization of an information object, defined in the ExtendedDnS ontology). Tissue (biological) 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. Biological compartment (including its contents) Definition: A xref that represents a publication such as a book, journal article, web page, or software manual. The reference may or may not be in a database, although references to PubMed are preferred when possible. The publication should make a direct reference to the instance it is attached to. Comment: Publication xrefs should make use of PubMed IDs wherever possible. Publication cross reference Population of parts of small molecules 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. Population of parts of DNA molecules Population of parts of protein molecules Population of protein molecules. Definition of protein: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain. Examples: The epidermal growth factor receptor (EGFR) protein. Cellular component type (concept) Definition of a small molecule: Any bioactive molecule that is not a peptide, DNA, or RNA. Generally these are non-polymeric, but complex carbohydrates are not explicitly modeled as classes in this version of the ontology, thus are forced into this class. Comment: Recently, a number of small molecule databases have become available to cross-reference from this class. Examples: glucose, penicillin, phosphatidylinositol Population of small molecules 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. An extension of the 'skos:broader' property to specify an instantiation (instance of) relationship between two concepts. broader (instantive) Temporal connection between perdurants: p1 ending part is connected to p2 beginning part. 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 Broader concepts are typically rendered as parents in a concept hierarchy (tree).