No Current Link To VocabularyCoded With ExtensionsCoded No Extensions
POCP_HD082100UV01
E_SubstanceChemical

(Link to Excel View)
Derived from RMIM: POCP_RM082100UV01
 
Substance

Design Comments: The main substance entity that is being defined.

classCode [1..1] (M)
ManufacturedMaterial (CS) {CNE:V:EntityClassManufacturedMaterial, root= "MMAT"}

Design Comments: Fixed to MMAT (manufactured material, "material" meaning simply "thing".)

determinerCode [1..1] (M)
ManufacturedMaterial (CS) {CNE:V:EntityDeterminerDetermined, root= "KIND"}

Design Comments: Fixed to KIND (kind of substance, class, never a particular instance of a molecule.)

code [1..1] (M)
ManufacturedMaterial (CV) {CNE:D:SubstanceEntityType}

Design Comments: The code of the substance to be defined. The purpose of this specification is to define substance codes with all necessary detail. So, this is the code to which a definition is assigned.

name [0..*]
ManufacturedMaterial (DSET<EN>)

Design Comments: The primary name of the substance used in this specification. See also NamedEntity.

desc [0..1]
ManufacturedMaterial (ED)

Design Comments: A brief description of the substance.

asNamedEntity [0..*] (NamedEntity)

Design Comments: Allows assigning name variants for the substance for use in different regions and by different organizations (such as pharmacopoieas or organizations with authority to define established names.)

asEquivalentSubstance [0..*] (EquivalentSubstance)

Design Comments: Specifies essentially the same substance in other substance registries. This is often referred to as "cross-reference". It must be noted, however, that different substance specification schemas might no have the exact same conceptionalizations, e.g., whether tautomers are distinguished, hence the relation is an "equivalence" relation (similartity) rather than an exact equality.

asSpecializedKind [0..*] (R_SpecializedKindUniversal)
moiety [0..*] (Moiety)

Design Comments: A relationship linking a substance (molecule) to its parts (moieties).

ingredient [0..*] (Ingredient)

Design Comments: A role linking a constituent to a mixed substance. A substance is a mixed substance if the ingredients are synthesized or extracted together. Conversely, a mixture as a result of combining component substances is not considered a substance but a product made up of those substances.

 
NamedEntity

Design Comments: Allows assigning name variants for the substance for use in different regions and by different organizations (such as pharmacopoieas or organizations with authority to define established names.)

classCode [1..1] (M)
Role (CS) {CNE:V:RoleClassIdentifiedEntity, root= "IDENT"}

Design Comments: Fixed to IDENT (identified entity), as naming is one way of identifying an entity.

code [0..1]
Role (CV) {CWE:D:IdentifiedEntityType}

Design Comments: A code allowing to further specify the kind of naming (e.g., systemic name, established name, common/primary name.)

name [0..*]
Role (DSET<TN>)

Design Comments: A text name for the substance so assigned.

statusCode [0..1]
Role (CS) {CNE:V:RoleStatus}

Design Comments: Specifies if the name is currently used (active) or no longer used historical (completed). Note that the NamedEntity can be subjectOf a Policy, a naming Policy, which allows to control more specifically when and under what circumstances this name was or is valid.

effectiveTime [0..1]
Role (IVL<TS>)

Design Comments: Specifies the time range at which this name was actively used. Note that the NamedEntity can be subjectOf a Policy, a naming Policy, which allows to control more specifically when and under what circumstances this name was or is valid.

assigningAuthority [0..1] (Authority)
subjectOf [0..*] (Subject1)
 
Authority
choice of Territory

Design Comments: A politically organized body of people bonded by territory, culture, or ethnicity, having sovereignty (to a certain extend) granted by other states (enclosing or neighboring states). This includes countries (nations), provinces (e.g., one of the United States of America or a French department), counties or municipalities. Refine using, e.g., ISO country codes, FIPS-PUB state codes, etc.

          or Organization

Design Comments: An organization that is responsible for the name or descriptor of the substance.

 
Territory

Design Comments: A politically organized body of people bonded by territory, culture, or ethnicity, having sovereignty (to a certain extend) granted by other states (enclosing or neighboring states). This includes countries (nations), provinces (e.g., one of the United States of America or a French department), counties or municipalities. Refine using, e.g., ISO country codes, FIPS-PUB state codes, etc.

classCode [1..1] (M)
Organization (CS) {CNE:V:EntityClassState, root= "STATE"}

Design Comments: Fixed to STATE, indicating any political region.

determinerCode [1..1] (M)
Organization (CS) {CNE:V:EntityDeterminerSpecific, root= "INSTANCE"}

Design Comments: Fixed to INSTANCE.

code [1..1] (M)
Organization (CD) {CWE:V:CountryEntityType}

Design Comments: A code to identify the country or other relevant geographic entity, e.g., European Union.

name [0..1]
Organization (TN)

Design Comments: The country name, if not coded.

asTerritorialAuthority [0..*] (TerritorialAuthority1)

Design Comments: A Role linking an organization of authority to a country or region for which it has authority.

 
TerritorialAuthority1

Design Comments: A Role linking an organization of authority to a country or region for which it has authority.

classCode [1..1] (M)
Role (CS) {CNE:V:RoleClassTerritoryOfAuthority, root= "TERR"}

Design Comments: Fixed to TERR.

governingOrganization [1..1] (Organization)

Design Comments: An organization that is responsible for the name or descriptor of the substance.

 
Organization

Design Comments: An organization that is responsible for the name or descriptor of the substance.

classCode [1..1] (M)
Organization (CS) {CNE:V:EntityClassOrganization, root= "ORG"}

Design Comments: Fixed to ORG (organization).

determinerCode [1..1] (M)
Organization (CS) {CNE:V:EntityDeterminerSpecific, root= "INSTANCE"}

Design Comments: Fixed to INSTANCE.

id [0..1]
Organization (II)

Design Comments: A unique identifier for the organization.

name [0..1]
Organization (ON)

Design Comments: A text name for the organization.

territorialAuthority [0..*] (TerritorialAuthority)

Design Comments: A Role linking the organization naming the substance with its country or region for which it has authority.

 
TerritorialAuthority

Design Comments: A Role linking the organization naming the substance with its country or region for which it has authority.

classCode [1..1] (M)
Role (CS) {CNE:V:RoleClassTerritoryOfAuthority, root= "TERR"}

Design Comments: Fixed to TERR.

territory [1..1] (Territory)
 
EquivalentSubstance

Design Comments: Specifies essentially the same substance in other substance registries. This is often referred to as "cross-reference". It must be noted, however, that different substance specification schemas might no have the exact same conceptionalizations, e.g., whether tautomers are distinguished, hence the relation is an "equivalence" relation (similartity) rather than an exact equality.

classCode [1..1] (M)
Role (CS) {CNE:V:RoleClassEquivalentEntity, root= "EQUIV"}
code [0..1]
Role (CD) {CWE:D:RoleCode}

Design Comments: Specifies in which way the two substance (records) are considered equivalent. Examples: same, mapping, etc.

quantity [0..1]
Role (RTO<PQ,PQ>)

Design Comments: Allows specifying a quantity relation between equivalent substances.

definingSubstance [1..1] (Substance)
subjectOf [0..*] (Subject1)

Design Comments: A link between a reaction or derivation process and documentarions and characteristics about them.

 
Subject1

Design Comments: A link between a reaction or derivation process and documentarions and characteristics about them.

typeCode [1..1] (M)
Participation (CS) {CNE:V:ParticipationTargetSubject, root= "SBJ"}

Design Comments: Fixed to SUBJ (subject)

information1 [1..1] (Information1)
 
Information1
choice of HorizontalBox
          or Information
 
HorizontalBox
choice of Policy

Design Comments: A policy under which a substance name is to be used. Can distinguish the name to be used as an active ingredient from one to be used as an excipient for the same substance (e.g., flurescein)

          or A_SubstanceSpecificationUniversal
 
Policy

Design Comments: A policy under which a substance name is to be used. Can distinguish the name to be used as an active ingredient from one to be used as an excipient for the same substance (e.g., flurescein)

classCode [1..1] (M)
Act (CS) {CNE:V:ActClassPolicy, root= "POLICY"}
moodCode [1..1] (M)
Act (CS) {CNE:V:ActMoodEventOccurrence, root= "EVN"}
code [0..1]
Act (CD) {CWE:D:ActCode}

Design Comments: The code specifying the policy in most specific detail.

statusCode [0..1]
Act (CS) {CNE:V:ActStatus}

Design Comments: The status of this Policy, active means the policy currently holds, completed means the Policy no longer holds. New could be used for draft Policies that do not hold yet. But also note that effectiveTime should be used to manage the temporal aspect of changing Policies, i.e., policies that will apply in the future, etc. This is analogous to the Marketing act.

effectiveTime [0..1]
Act (IVL<TS>)

Design Comments: Specifies a time range for which this Policy applies.

 
Information
choice of A_ReferencedDocumentUniversal
          or A_CharacteristicUniversal
 
Moiety

Design Comments: A relationship linking a substance (molecule) to its parts (moieties).

classCode [1..1] (M)
Role (CS) {CNE:V:RoleClassPart, root= "PART"}

Design Comments: Fixed to PART.

code [0..1]
Role (CD) {CWE:D:MolecularPartRoleType}

Design Comments: Specifies the sense in which a molecule is being conceptually or actually divided into parts.

Examples: (1) sub-unit of a protein (i.e., sequences held together usually by disulfide bonds); (2) domain of a protein or component of a nucleic acid sequence (i.e., a sub-sequence identified to have a certain folding structure or function, e.g. signaling peptide of a protein precursor or promoter and open reading frame of a nucleic acid); (3) residue on a molecular base skeleton; atom of a molecule (e.g., to identify substitution with a radioactive isotope), (4) dissociable ion.

UsageNote: the specific code system and concepts are left to be externally defined. However, when the positionNumber attribute is to be used with the part role to indicate where the part is placed, the part role code must specify how the position number vector is to be interpreted. For example, for subunits of a protein oligomer (such as fibrinogen) held together by disulfide bonds, the part relationship would need to specify the position of the links.

quantity [0..1]
Role (RTO<PQ,PQ>){default= "1:1"}

Design Comments: The amount of the moiety (numerator) in the comple substance (denominator). May be specified as counts (e.g., 2 parts per one molecule) which is the same as "mole ratio" (2 mol of the moiety in one mol of the substance) or in mass ratios (2 gram of the moiety in 100 gram of the substance.)

positionNumber [0..*]
Role (LIST<INT.NONNEG>)

Design Comments: Specifies the position of the moiety part with respect to the whole. Would be used particularly for sub-moieties, where a base skeletton is defined in one moiety, and then the position of another functional group is given (e.g., amino-group in gamma position.) The interpretation of the positionNumber is dependent on the moiety code, and must be specified for the definition of moiety codes.

partMoiety [1..1] (Moiety1)

Design Comments: A moiety is a part of a molecule. Molecules are made up from such parts. The parts may be specified as the elements (atoms) or as higher order sub-units, e.g., functional groups.

subjectOf [0..*] (Subject1)
productOf [0..*] (Product)
participation [0..*] (Interactor1)
 
Moiety1

Design Comments: A moiety is a part of a molecule. Molecules are made up from such parts. The parts may be specified as the elements (atoms) or as higher order sub-units, e.g., functional groups.

classCode [1..1] (M)
ManufacturedMaterial (CS) {CNE:V:EntityClassManufacturedMaterial, root= "MMAT"}

Design Comments: Fixed to MMAT (manufactured material, "material" meaning simply "thing".)

determinerCode [1..1] (M)
ManufacturedMaterial (CS) {CNE:V:EntityDeterminerDetermined, root= "KIND"}

Design Comments: Fixed to KIND (kind of substance, class, never a particular instance of a molecule.)

id [0..1]
ManufacturedMaterial (II)

Design Comments: A unique identifier MUST be specified when a moitey is specified based on a molecule (substance) code. In that case, the moiety is not actually the so specified molecule, but the molecule bonded together with the other moieties that make up the substance. It is perfectly fine to specify moieties (functional groups) based on the base substance, specifying a unique id then indicatese specifically that this substance is meant only inasmuch as it is a moiety of the to be defined substance.

code [0..1]
ManufacturedMaterial (CD) {CWE:D:MoleculeEntityType}

Design Comments: The code for the moiety. May be from the same code system as substances and may actually reference complete molecules even if taken only as a functional group. In that case an id must also be specified.

name [0..*]
ManufacturedMaterial (DSET<TN>)

Design Comments: The name of the moiety.

asSpecializedKind [0..*] (R_SpecializedKindUniversal)
bond [0..*] (Bond)

Design Comments: A bond is a connection between two specified moieties. Normally, moiety structures can be specified simply by breaking down the molecule into its part moieties and breaking those moieties down further. However, when multiple bonds exists between moieties, those may be specified. This can also be used to specify all the bonds in case where the moieties are provided as a parts list. For instance, in the most general case, a substance is specified by all its elements and all its bonds (this is, for example, how the MDL/MOLFILE format works.) Specific examples of the use of the bond role is to specify a protein based on its sub-units (chains) as moieties and the disulfide bridges specified as bonds connecting the subunits.

moiety [0..*] (Moiety)
 
Bond

Design Comments: A bond is a connection between two specified moieties. Normally, moiety structures can be specified simply by breaking down the molecule into its part moieties and breaking those moieties down further. However, when multiple bonds exists between moieties, those may be specified. This can also be used to specify all the bonds in case where the moieties are provided as a parts list. For instance, in the most general case, a substance is specified by all its elements and all its bonds (this is, for example, how the MDL/MOLFILE format works.) Specific examples of the use of the bond role is to specify a protein based on its sub-units (chains) as moieties and the disulfide bridges specified as bonds connecting the subunits.

classCode [1..1] (M)
Role (CS) {CNE:V:RoleClassMolecularBond, root= "BOND"}

Design Comments: Fixed to BOND.

code [0..1]
Role (CD) {CWE:D:MolecularBondRoleType}

Design Comments: A code specifying the nature of the bond by which two molecular parts are connected.

Examples: (1) simple bonds such as, single bond, double bond, triple bond, (2) specialized bonds such as peptide bond, disulfide bond, etc., (3) weak bonds such as van-der-Waals, chelate, and ion-associations.

quantity [0..1]
Role (RTO<PQ,PQ>)
positionNumber [0..*]
Role (LIST<INT.NONNEG>)

Design Comments: Specifies the detailed position of the bond in the two sub-units, if that is known. The interpretation of the positionNumber depends on the specific bond code. E.g., disulfide bonds are positioned by amino-acid position in the subunit.

distalMoiety [1..1] (Moiety1)
subjectOf [0..*] (Subject1)
productOf [0..*] (Product)
participation [0..*] (Interactor1)
 
Ingredient

Design Comments: A role linking a constituent to a mixed substance. A substance is a mixed substance if the ingredients are synthesized or extracted together. Conversely, a mixture as a result of combining component substances is not considered a substance but a product made up of those substances.

classCode [1..1] (M)
Role (CS) {CNE:V:RoleClassIngredientEntity, root= "INGR"}

Design Comments: Fixed to INGR, or, rarely, specializations thereof.

id [0..1]
Role (II)

Design Comments: A unique identifier to the ingredient relationship for later reference.

confidentialityCode [0..1]
Role (CD) {CWE:D:Confidentiality}

Design Comments: Specified as 'B' if the ingredient role is to be considered a trade secret.

quantity [0..1]
Role (RTO<PQ,PQ>)

Design Comments: The amount of the ingredient substance in the micture, if that is known.

ingredientSubstance [1..1] (Substance)
subjectOf [0..*] (Subject1)
productOf [0..*] (Product)
participation [0..*] (Interactor1)

Design Comments: Links a reaction with other reactands.

 
Interactor1

Design Comments: Links a reaction with other reactands.

typeCode [1..1] (M)
Participation (CS) {CNE:V:ReactionParticipant}

Design Comments: Reaction participant can be CSM (input substrate), PRD (output substrate), and CAT (catalyst). For an antigen-antibody reaction, both are considered input substrates (and the antigen antibody complexes would be output substrates.)

functionCode [0..1]
Participation (CD) {CWE:D:MolecularInteractionFunction}

Design Comments: Further specifies the function of the substrate in the interaction (e.g., to clearly mark an antibody from an antigen input substrate, or specify receptor agents as effectors vs. inhibitors, etc.)

quantity [0..1]
Participation (PQ)

Design Comments: Specifies, if relevant, the amount of the reactand interacting in the interaction.

interaction [1..1] (Interaction)

Design Comments: A molecular interaction (reaction) that a defined substance undergoes with other substances, particularly if that information is definitional to the nature of the substance (e.g., links an antibody to the antigen-antibody reaction in which it participates.)

 
Interaction

Design Comments: A molecular interaction (reaction) that a defined substance undergoes with other substances, particularly if that information is definitional to the nature of the substance (e.g., links an antibody to the antigen-antibody reaction in which it participates.)

classCode [1..1] (M)
Act (CS) {CNE:V:ActClassRoot, root= "ACT"}
moodCode [1..1] (M)
Act (CS) {CNE:V:ActMoodDefinition, root= "DEF"}

Design Comments: Fixed as DEF.

code [1..1] (M)
Act (CD) {CNE:D:MolecularInteractionType}

Design Comments: The reaction code, as specific as known and possible. Note that a generalization link is available ot specify reaction classes.

participation [1..*] (Interactor2)

Design Comments: Links a substance with an interaction that it undergoes with other substances, particularly if that information is definitional to the nature of the substance (e.g., links an antibody to the antigen-antibody reaction in which it participates.)

generalization [0..*] (Generalization2)

Design Comments: Allows specifying a generalization (class) of an interaction (e.g., "receptor binding" in general for a specific receptor binding interaction.)

subjectOf [0..*] (Subject2)
 
Interactor2

Design Comments: Links a substance with an interaction that it undergoes with other substances, particularly if that information is definitional to the nature of the substance (e.g., links an antibody to the antigen-antibody reaction in which it participates.)

typeCode [1..1] (M)
Participation (CS) {CNE:V:ReactionParticipant}

Design Comments: Reaction participant can be CSM (input substrate), PRD (output substrate), and CAT (catalyst). For an antigen-antibody reaction, both are considered input substrates (and the antigen antibody complexes would be output substrates.)

functionCode [0..1]
Participation (CD) {CWE:D:MolecularInteractionFunction}

Design Comments: Further specifies the function of the substrate in the interaction (e.g., to clearly mark an antibody from an antigen input substrate, or specify receptor agents as effectors vs. inhibitors, etc.)

quantity [0..1]
Participation (PQ)

Design Comments: Specifies, if relevant, the amount of the substance interacting in the interaction.

identifiedOrPresentSubstance [1..1] (IdentifiedOrPresentSubstance)
 
IdentifiedOrPresentSubstance
choice of IdentifiedSubstance

Design Comments: A role assigning an identifier to the substance.

          or R_PresentSubstanceUniversal
 
IdentifiedSubstance

Design Comments: A role assigning an identifier to the substance.

classCode [1..1] (M)
Role (CS) {CNE:V:RoleClassIdentifiedEntity, root= "IDENT"}

Design Comments: Fixed to IDENT.

id [1..1] (M)
Role (II)

Design Comments: The identifier of the substance so assigned. Note that this may often be the same identifier as given in the Substance.id attribute and the identifier should indeed be specified both places. This has the advantage of clearly indicating that the substance identifier may indeed be referred to from Entity id as well as from Role id references.

code [0..1]
Role (CV) {CWE:D:IdentifiedEntityType}

Design Comments: A code that may be specifying how the substance identifier is being assigned. Used rarely.

statusCode [0..1]
Role (CS) {CNE:V:RoleStatus}

Design Comments: Specifies if this identification or name for the substance is currently active or outdated (completed). Note that the NamedEntity can be subjectOf a Policy, a naming Policy, which allows to control more specifically when and under what circumstances this name was or is valid.

effectiveTime [0..1]
Role (IVL<TS>)

Design Comments: Specifies the time range during which this identification or name was used for the substance. Note that the NamedEntity can be subjectOf a Policy, a naming Policy, which allows to control more specifically when and under what circumstances this name was or is valid.

identifiedSubstance [0..1] (Substance)
assigningAuthority [0..1] (Authority)
subjectOf [0..*] (Subject1)
productOf [0..*] (Product)

Design Comments: Links the derivation process description to the substance.

participation [0..*] (Interactor1)
 
Product

Design Comments: Links the derivation process description to the substance.

typeCode [1..1] (M)
Participation (CS) {CNE:V:ParticipationProduct, root= "PRD"}

Design Comments: Fixed to PRD (product).

functionCode [0..1]
Participation (CD) {CWE:D:MolecularInteractionFunction}
quantity [0..1]
Participation (PQ)

Design Comments: Allows specifying the amount of the product yield given the specified amounts of the substrates (consumables) used for the process step.

derivationProcess [1..1] (DerivationProcess)

Design Comments: A process which might be used or is actually used to produce the substance by synthesis or extraction or other method.

 
DerivationProcess

Design Comments: A process which might be used or is actually used to produce the substance by synthesis or extraction or other method.

classCode [1..1] (M)
Procedure (CS) {CNE:V:ActClassProcedure, root= "PROC"}

Design Comments: Fixed to PROC (procedure).

moodCode [1..1] (M)
Procedure (CS) {CNE:V:ActMoodDefinition, root= "DEF"}

Design Comments: Fixed to DEF.

code [1..1] (M)
Procedure (CD) {CNE:D:ActSubstanceDerivation}

Design Comments: A code for the process general or specific, as specific as known.

effectiveTime [0..1]
Procedure (IVL<TS>)
participation [1..*] (Interactor2)
generalization [0..*] (Generalization1)

Design Comments: Allows specifying a generalization (class) of a derivation process (e.g., "cold water extraction" in general for a specific extraction method.)

controlVariable [0..*] (ControlVariable)

Design Comments: Links a derivation process to a control condition under which a derivation process is operated, e.g., to the temperature of the reactor.

subjectOf [0..*] (Subject2)

Design Comments: A link between a substance and documentarions and characteristics about them.

UsageNotes: This is the link to the Information choice (Document / Characteristic)

componentOf [0..*] (Component)

Design Comments: Allows further detailing the derivation process into process steps.

 
Generalization1

Design Comments: Allows specifying a generalization (class) of a derivation process (e.g., "cold water extraction" in general for a specific extraction method.)

typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasGeneralization, root= "GEN"}
derivationProcess [1..1] (DerivationProcess)
 
ControlVariable

Design Comments: Links a derivation process to a control condition under which a derivation process is operated, e.g., to the temperature of the reactor.

typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasControlVariable, root= "CTRLV"}

Design Comments: Fixed to CTRLV.

characteristic [1..1] (A_CharacteristicUniversal)
 
Subject2

Design Comments: A link between a substance and documentarions and characteristics about them.

UsageNotes: This is the link to the Information choice (Document / Characteristic)

typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasSubject, root= "SUBJ"}

Design Comments: Fixed to SUBJ (subject)

information [1..1] (Information)
 
Component

Design Comments: Allows further detailing the derivation process into process steps.

typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}

Design Comments: Fixed to COMP (component).

sequenceNumber [0..1]
ActRelationship (INT.NONNEG)

Design Comments: Specifies the sequencing of process steps 1 for first, 2 for second, etc. If process steps sequenceNumbers are the same, it means these steps are executed in parallel or as alternatives (see splitCode in the RIM).

splitCode [0..1]
ActRelationship (CS) {CNE:V:ActRelationshipSplit}
joinCode [0..1]
ActRelationship (CS) {CNE:V:ActRelationshipJoin}
derivationProcess [1..1] (DerivationProcess)
 
Generalization2

Design Comments: Allows specifying a generalization (class) of an interaction (e.g., "receptor binding" in general for a specific receptor binding interaction.)

typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasGeneralization, root= "GEN"}
interaction [1..1] (Interaction)