Recommendation for HL7 RIM and/or
Vocabulary Changes
RECOMMENDATION ID1:
For Harmonization During: MAR2010
SUB1
Sponsor’s Draft3:
Sponsored by2: OO
Date Approved by Sponsor: 2010-02-11
1
Sponsor’s Status4 Pending
Editor/ Author: Gunther Schadow
PROPOSALNAME: Substance Vocabulary
Class Model Change
Datatypes Change
Structural Vocabulary Change
Other Vocabulary Change
SUMMARY RECOMMENDATION
This is adding vocabulary domains as needed for completing the Substances CMET ballot
preparation. Mostly external code systems will be used for the content. However, there are some
additions to structural codes required.
VOCABULARY OBJECTS CHANGE SUMMARY
<<REQUIRED – fill in the numbers in the rightmost three columns that total the number of
vocabulary changes in the proposal. This is used to cross-check the accuracy of capturing and
applying the requested changes>>
Abbrev. Description
# to add
# to remove # to change
D
Concept Domains
12
2
S
Code Systems
4
C
Concept Codes in a Code System
5
V
Value Sets
2
2
B
Context Bindings
POSITION OF CONCERNED ORGANIZATIONS:
<<REQUIRED - This table should contain one row for each organization (e.g., TC, SIG, other
SDO) known to be interested, and should outline any consultation with – and feedback from – the
organization. Overwrite the examples below. >>
ORG
RECOMMENDATION APPROVAL STATUS
AFFECTED ELEMENTS OF INTEREST TO
ORG
OO - Primary
Sponsor
CPM project
members Pharmacy
WG, Patient Safety
WG
Joint ISO IDMP
project team
SPL Industry
Working Group
Pending
All
Content being circulated, to be endorsed
for ballot with the entire ballot package.
All
Content being circulated, to be endorsed
for ballot with the entire ballot package.
May be an interested party
Drug and Substances
All
ISSUE:
1
identifier by which proposal is known to sponsor
must be sponsored by an HL7 TC, the HL7 International Committee, an HL7 SIG, or an ANSI or ISO
accredited SDO
3
for sponsor tracking only; not for Harmonization identification
4
for sponsor tracking only, Sponsor’s status must be “Approved” for submission to Harmonization
2
Recommendation for HL7 RIM Change (continued)
There is new ballot content being developed and specific vocabulary domains need to be created.
Those are simple and trivially related to the attribute definitions.
For the Substances project, there are some structural code changes required, a few new
Participation types, a few Role class codes, and Act class codes, and Entity classes.
CURRENT STATE:
The existing approach has been to use existing, more general vocabulary domains and place a
Note box into the RMIMs to indicate where further specific domains need to be added. In this
ballot we intend to bring all the necessary detail forward in time for harmonization.
OPTIONS CONSIDERED:
We are very aware of using code rather than class code wherever possible and our decisions to
add structural codes are conservative after having considered reusing generic alternatives.
RATIONALE:
To specifically support the new ballot content, these code systems are required. The final
submission of this harmonization will be supported with details from models that are going into
the ballot.
RECOMMENDATION DETAILS:
New Vocabulary Domains
MoleculePartRoleType is-a Part
includes code moiety MOIT, parent of Active Moiety, ACTM. (see also a the Partitive Role class
code revision proposal)
Molecular entity classes:
- MolecularEntity – any molecular entity or compound or complex
- SmallMoleculeEntity – small molecules are most metabolites and signaling substances
(except if peptide hormone) defined, pharmaceutical compounds and all their building blocks,
including individual elements.
- ElementNuclideEntity – The chemical elements (periodic system) in general
and their specific isotopes.
- AminoAcidEntity – An amino acid molecule (one of 20 plus some odd ones,
including all possible modifications.)
- NucleotideEntityType – One of the 5 base nucleotides (Adenosine, Guanosine,
Cytidine, Thymidine, and Uracil)
- PolymerEntityCode - A macro-molecule, the structure of which essentially comprises
the multiple repetition of units derived, actually or conceptually, from molecules of low relative
molecular mass. (IUPAC Gold Book)
- AminoAcidSequenceEntityCode – A polymer consisting of Amino Acid
components chained together in a linear fashion through peptide bonds. Includes short
peptides and sequences of any length (proteins).
- NucleicAcidSequenceEntityCode – A polymer consisting of ribonucleic acids
(RNA and DNA).
- PolysaccharideEntity – A polymer consisting of saccharide (sugar-like,
carbohydrate) components joined together by glycosidic bonds often in chains and branches,
includes starch, cellulose, chitin and glycanes.
- ComplexMolecularEntity - A molecular entity that combines several other molecular
entities of same or different kinds. Includes protein complexes, protein RNA complexes,
lipoproteins. The exact structure of complex molecular entities can sometimes not be defined
exactly.
Parts of molecules (i.e., sub-units) are often considered molecules even though they may not
exist independent from the whole or are highly instable as radicals. One may argue whether a
Recommendation for HL7 RIM Change (continued)
radical should be considered to be the same kind of entity as the same structure bound to a
whole molecule (they certainly act very differently), however, existing external code systems do
not necessarily make the distinction.
The rationale for defining these sets is that they are described differently (e.g., simple element
symbol, structure formula, sequence notation), and are enumerated in different external code
systems (e.g., Element symbols, Amino Acid and Ribonucleic Base symbols, ChEBI for small
molecules, IPI for proteins, EntrezGene for Genes, etc.)
MolecularPartTypeCode
-
MolecularPartTypeCode – the different aspects by which molecules may be actually or
conceptually composed or divided into sub-units.
o AminoAcidSequencePartTypeCode – e.g., subunit, domain, signaling peptide
o NucleicAcidSequencePartTypeCode – e.g., promoter, open reading frame, etc.
o MolecularBondRoleType – specifies the nature by which a molecular sub-unit is
connected to a whole molecule, e.g. a glycane polysaccharide may be joined to
an Amino Acid (AminoAcidSequencePartType) through an N- or O- link. Even
though arbitrary and relative, one can consider this the Glycane to be a part of
the Amino-Acid-Glycane compound, the amino-acid glycane compound being a
part of the overall molecule.
Value Sets
- ActiveMoietyEntityCode – a molecule or part of a molecule which is comprised of the
MolecularEntityTypes recognized as having a known pharmacological effect.
New Structural Codes
MolecularParticipationType
- substrate - DIR
o input - SBJ
o output - PRD
- catalyst – PRF?
- co-factor - DIR
- modulator - DIR
o (non-competitive) inhibitor
o effector
Acts
-
MolecularInteraction
o Transcription - creating mRNA from a DNA (gene)
o Translation – creating an AminoAcidSequence from mRNA
o Post-TranslationalModification
 Cleavage – e.g., hydrolysis of a peptide
 Addition – glycosylation, phosphorylation
o ReceptorBinding
-
SubstanceCharacteristic (Observation), a domain including, probably from LOINC:
o ChemicalStructure - SMILES, MolFile, InChi - ED
o MolecularFormula - CV “structured” code system
o
- SumFormula, e.g. “C2H5OH”
o
- NucleicAcidCode, e.g. “GTAATCTGTATGTA...”
o
- AminoAcidCode, e.g., “MPATCHLLIAT…"
o Stereochemistry - CV - racemic, meso, mixed, axial, absolute
o OpticalActivity - CV - +, -, +/o MolecularMass - PQ ~ 1 g/mol
o pH - PQ ~ 1 [pH]
Recommendation for HL7 RIM Change (continued)
o
o
viscosity - PQ
enzymatic activity - PQ ~ 1 mol/s
DISCUSSION:
These proposals are not forwarded in a hurry or in a vacuum. Parties who will work these out in
the following weeks have been working in this field for years and mapped and integrated biochemical knowledge. However, not all detail is defined at this point.
There are external ontologies for molecular structures and interactions which have been and are
being consulted. The intention for defining these domains codes in HL7 is exclusively in order to
be able to create predictable RMIM models without relying solely on clone names for distinction. It
is expected that codes (apart from a few structural codes) would be used from these external
systems.
MaterialKind
1..1 scoper *
classCode*: <= MAT
determinerCode*: <= KIND
code*: CE CWE [1..1] < EntityCode
name: BAG<TN> [0..*]
1..1 generalizedMaterialKind *
SpecializedKind
Substance
EquivalentSubstance
classCode*: <= EQUIV (EQUIV)
quantity: RTO<PQ,PQ> [0..1]
(qty of ingredient over that of
0..* asEquivalentSubstance reference substance)
classCode*: <= GEN
code: CE CWE [0..1] <
MedicationGeneralizationRoleType
Note:
ChemicalStructure - SMILES, MolFile, InChi - ED
MolecularFormula - CV “structured” code system
- SumFormula, e.g. “C2H5OH”
- NucleicAcidCode, e.g. “GTAATCTGTATGTA...”
- AminoAcidCode, e.g., “MPATCHLLIAT…"
Stereochemistry - CV - racemic, meso, mixed, axial, absolute
OpticalActivity - CV - +, -, +/MolecularMass - PQ ~ 1 g/mol
pH - PQ ~ 1 [pH]
viscosity - PQ
enzymatic activity - PQ ~ 1 mol/s
R_Substance
(UUDD_RMnnnnnn)
Description: The IDMP
Substances model.
0..* asSpecializedKind1
Substance
classCode*: <= MMAT
determinerCode*: <= KIND
code*: CV CNE [1..1] < EntityCode
name*: BAG<TN> [1..*] (established name)
desc: ED [0..1]
1..1 ingredientSubstance *
Characteristic
SubstanceRole
Ingredient
classCode*: <= INGR
id: II [0..1]
confidentialityCode: SET<CE> CWE [0..*] < Confidentiality
(B - trade secret)
quantity*: RTO<PQ,PQ> [0..1]
(strength, qty of ingredient in medicine)
subjectOf2
classCode*: <= OBS
0..* scopedRoleName
typeCode*: <= SBJ
moodCode*: <= EVN
0..* characteristic code: CD CWE [0..1] < ActCode
value: ANY CWE [0..1] < ObservationValue
IdentifiedSubstance
subjectOf1
0..1 scopingEntityName
1..* identifiedSubstance
*
Interaction
typeCode*: <= SBJ
classCode*: <= ACT
functionCode: CD CWE [0..1]
moodCode*: <= DEF
<= MolecularInteractionFunction
code*: CD CNE [1..1] <= MolecularInteractionType
0..* interaction
1..1 identifiedSubstance *
IdentifiedSubstance
classCode*: <= IDENT
productOf
subject
typeCode*: <= SBJ
functionCode: CD CWE [0..1]
<= MolecularInteractionFunction
1..* identifiedSubstance *
Transcription
classCode*: <= ACT
typeCode*: <= PRD
moodCode*: <= DEF
functionCode: CD CWE [0..1]
code*: CD CNE [1..1] <= MolecularTranscriptionType
<= MolecularInteractionFunction
0..* identifiedSubstance
0..* transcription
subject
typeCode*: <= SBJ
functionCode: CD CWE [0..1]
0..1 playingEntityName
<= MolecularInteractionFunction
NamedEntity
classCode*: <= IDENT
0..* asNamedEntity name: BAG<EN> [0..*]
1..1 assigningTerritory *
Territory
0..1 territory *
classCode*: <= STATE
determinerCode*: <= INSTANCE
code*: CE CWE [1..1] <= CountryEntityType
name: TN [0..1] (country name if not coded)
0..1 governingAgency
TerritorialAuthority
classCode*: <= TERR
Agency
classCode*: <= PUB
determinerCode*: <= INSTANCE
id*: II [0..1]
name*: ON [0..1] (e.g., the FDA for the USA)
Moiety
1..1 partMoietyEntity *
Moiety
classCode*: <= PART
code: CE CWE [0..1] <= MoleculePartRoleType
quantity: RTO<INT,INT> [0..1] "1:1"
0..* moiety positionNumber: LIST<INT> [0..*]
0..* activeMoiety
ActiveMoiety
1..1 partMoietyEntity *
MoietyEntity
classCode*: <= MAT
determinerCode*: <= KIND
id: II [0..1]
code: CD CWE [0..1]
SpecializedKind
<= MoleculeEntityType
Modification
classCode*: <= PART
code: CE CWE [0..1] <=
MoleculeBondRoleType
0..* asSpecializedKind
0..* modification positionNumber: LIST<INT> [0..*]
classCode*: <= ACTM
quantity: RTO<PQ,PQ> [0..1]
(amount of active moiety in ingredient)
ActiveMoietyEntity
E_SubstanceChemical
(PORR_MT320025)
Description
SpecializedKind
1..1 activeMoiety * classCode*: <= MMAT
determinerCode*: <= KIND
code*: CE CWE [0..1] < EntityCode (Active moiety code)
name*: BAG<TN> [1..*]
0..* asSpecializedKind
Recommendation for HL7 RIM Change (continued)
E_Substance
R_SubstancePresence
(PORR_MT620023)
(PORR_MT620026)
Description
Description
Substance
1..1 *
CMET: (MAT)
E_SubstanceClinical
[universal]
SubstancePresence
0..* substancePresence
classCode*: <= SubstancePresence
(PORR_MT620024UV)
CMET: (MAT)
E_SubstanceChemical
[universal]
(PORR_MT620025UV)
Entity
classCode*: <= SubstancePresenceEntityClass(MAT,LIV,PLC)
determinerCode*: <= KIND
code: CD CWE [0..1] <= SubstancePresenceEntityType
ACTION ITEMS:
M&M to implement recommendation
RESOLUTION:
<< REQUIRED before recommendation can be closed. Indicates how recommendation was
brought to closure. Can include notes on further study or networking required, and by whom.>>
Vocabulary Submission Checklist:
The following identifies the pieces of information that must be included or identified for the
different types of vocabulary harmonization actions. It is included here for convenience in order
to make certain the proposal is complete; this is not intended to be ‘filled in’, but are things that
must be checked and/or considered when making the proposals. Any of these that are not
included or done must be done during the application of the harmonization proposals after the
meeting, and thus may not be deduced correctly if not explicit. Each of these needed pieces of
information is REQUIRED for that particular operation.
New Concept Domain:
Parent Domain if the new Domain is not at the root
Definition, plus three examples of concepts which would be in the same semantic category
labeled by the Domain OR an Example binding. NOTE: these are not coded concepts, ie
codes from a codeSystem
The name of the new Domain should follow the current practice pattern for naming
Modify Concept Domain:
New Parent if hierarchy change
Evaluation or Disposition of existing bindings
Impact on any models if name is to be changed
Remove Concept Domain:
Disposition of existing bindings
Removal comment
New Code Systems
Whether they are HL7-maintained or External, OID if one exists
Description
Full name (title) and short name (with no spaces or punctuation)
Modify Code System:
Only descriptions or full names may be modified; for content see Concept Codes
Deprecate/Delete Code System:
Disposition of existing value sets built on it, along with their existing bindings
Identification of what it is being superceded by
Recommendation for HL7 RIM Change (continued)
Deprecation comment
New Concept Codes:
The code system they are to be added to
The extensional value set(s) they are to be added to, if any
Their parent, if they are not at the root of the code system
Whether or not they are abstract (selectable)
Mnemonic, or code value (try to follow any pre-existing practice pattern)
Description
Print Name (try to follow any pre-existing practice pattern)
Deprecation/Deletion of Concept Codes:
The code system they are to be removed from
The new parent for any child concepts they may have had
The extensional value set(s) that they should also be removed from, if any
Deprecation comment
Modify Concept Codes:
The code system it is in
Modified description (if that is the modification)
Change to/from abstract (if that is the modification)
Change position of code in hierarchy – identify old/new parent, and any impacts on child
codes
New Value Set:
Name (without spaces); must fit the current practice pattern of naming style
Name (Title)
Optional Description
Code System it is based on (primary)
Extensional vs. Intensional
Definition expression/contents list
Deprecate/Delete Value Set:
Disposition of existing bindings, both Model and Context
Identification of other value sets that include the one to be deleted
Modify Value Set
Updated Print Name, with identification of Model bindings affected
Updated defining expression/contents list
New Context Binding
Name of Domain plus Name of Value Set plus OID of Value Set (if present) plus Context
Modify Context Binding
Name of Domain plus Name of Value Set plus OID of Value Set (if present) plus New
Context
Removal of Existing Context Binding
Name of Domain plus Name of Value Set plus OID of Value Set (if present) plus Context
Note that you must follow up name changes to Concept Domains or Value Sets that are
done during the harmonization meeting are applied to any bindings that have been
specified in the Static Model (using the RMIM designer tool) so that the binding will
point to the new name of the object.
Recommendation for HL7 RIM Change (continued)
Recommendation Details: Template for Vocabulary Proposal
EXISTING CONTEXT: positions the proposal within the HL7 vocabulary, and provides related
descriptions necessary for understanding and evaluating the proposal. Use as many levels as
necessary in each hierarchy illustrated.
RIM_nnnn
Concept Code (conceptID = xxxxxx)
Concept Code (conceptID = xxxxxx)
Concept Code (conceptID = xxxxxx)
Description [optional]: provide existing description for any concept for which description
is to be changed, or where specifics in the description are critical to understanding the
proposed change. Descriptions may occur at multiple levels, but are illustrated in this
template only once.
Parent (RoleClass / ActClass / EntityClass  choose one) [required for roleCode,
actCode, and entityCode concepts]: give the full hierarchy for the classCode to which the
code belongs.
Concept Code for classCode (conceptID = xxxxxx)
Concept Code for classCode (conceptID = xxxxxx)
Concept Code for classCode (conceptID = xxxxxx)
Description of classCode: provide existing description only for the classCode to
which the code belongs
Value Set [optional]: for any concept for which a valueSet change is proposed, list (or
describe) existing value sets of interest in evaluating the proposal.
RECOMMENDATION: freeform description of the recommended changes, making reference to
the Existing Context as appropriate.
Always provide conceptID when mentioning any existing concept.
For all new concepts and values, provide:
Concept Code
Concept Name (print name)
Concept Description