Data Model

The model is written once, as a DCTAP table. The SHACL shapes and all diagrams below are generated from it, so they cannot drift apart. The same approach is used for the PubChemRDF schema, and other formats such as ShEx or LinkML can be derived from the same table.

File	Purpose
model_dctap.csv	The DCTAP profile, the source of the model
dctap.yaml	Prefixes, extra columns and aspects
rules.ttl	Rules that compare several nodes, which a DCTAP row cannot express
model_shacl.ttl	The generated SHACL shapes, including those rules
ciaaw.owl	OWL ontology generated via SPARQL CONSTRUCT

Validation

Checked against the shapes when this site was built:

ciaaw.ttl: conforms
example-output-next.ttl: conforms

Overview

The main classes and how they connect. Attributes, back-references and history links are in the diagrams for each aspect.

classDiagram
    direction TB
    class Element["chemrof:ChemicalElement"]
    class Isotope["chemrof:Isotope"]
    class StandardAtomicWeightDeclaration["ciaaw:StandardAtomicWeightDeclaration"]
    class ConventionalAtomicWeightDeclaration["ciaaw:ConventionalAtomicWeightDeclaration"]
    class IsotopicAbundanceDeclaration["ciaaw:IsotopicAbundanceDeclaration"]
    class AtomicMassDeclaration["ciaaw:AtomicMassDeclaration"]
    class Declaration["Declaration"] {
        <<abstract>>
    }
    class Footnote["ciaaw:Footnote"]
    class IntervalValue["Interval"]
    class ValueWithUncertainty["Value with uncertainty"]
    class SingleValue["Single value"]
    class MassValue["Mass with uncertainty"]
    Declaration <|-- StandardAtomicWeightDeclaration
    Declaration <|-- ConventionalAtomicWeightDeclaration
    Declaration <|-- IsotopicAbundanceDeclaration
    Declaration <|-- AtomicMassDeclaration
    Element --> "0..*" Isotope : ciaaw#58;hasIsotope
    Element --> "0..1" StandardAtomicWeightDeclaration : ciaaw#58;currentStandardAtomicWeight
    Element --> "0..1" ConventionalAtomicWeightDeclaration : ciaaw#58;currentConventionalAtomicWeight
    Isotope --> "1" IsotopicAbundanceDeclaration : ciaaw#58;currentAbundance
    Isotope --> "0..1" AtomicMassDeclaration : ciaaw#58;currentAtomicMass
    Declaration --> "0..*" Footnote : ciaaw#58;footnote
    StandardAtomicWeightDeclaration --> "1" IntervalValue : ciaaw#58;value (one of)
    StandardAtomicWeightDeclaration --> "1" ValueWithUncertainty : ciaaw#58;value (one of)
    StandardAtomicWeightDeclaration --> "1" SingleValue : ciaaw#58;value (one of)
    ConventionalAtomicWeightDeclaration --> "1" SingleValue : ciaaw#58;value
    IsotopicAbundanceDeclaration --> "1" IntervalValue : ciaaw#58;value (one of)
    IsotopicAbundanceDeclaration --> "1" ValueWithUncertainty : ciaaw#58;value (one of)
    IsotopicAbundanceDeclaration --> "1" SingleValue : ciaaw#58;value (one of)
    AtomicMassDeclaration --> "1" MassValue : ciaaw#58;value

Elements and isotopes

Elements and isotopes keep a stable IRI. They hold identifying facts and pointers, while every published value lives in a separate declaration.

classDiagram
    direction LR
    class Element["chemrof:ChemicalElement"] {
        rdfs:label : langString [1..*]
        chemrof:symbol : string [1]
        chemrof:atomic_number : integer [1]
        skos:closeMatch : IRI [0..*]
        ciaaw:longestLivedMassNumber : integer [0..1]
    }
    class Isotope["chemrof:Isotope"] {
        ciaaw:massNumber : integer [1]
        skos:closeMatch : IRI [0..*]
    }
    Element --> "0..*" Isotope : ciaaw#58;hasIsotope

Shape	Property	Count	Value	Note
Chemical element	`rdfs:label`	1..*	`rdf:langString`	Lower case as printed in the CIAAW tables. Further languages may be added.
Chemical element	`chemrof:symbol`	1	`xsd:string`
Chemical element	`chemrof:atomic_number`	1	`xsd:integer`
Chemical element	`skos:closeMatch`	0..*	`IRI`	Taken from the supplement. Never guessed.
Chemical element	`ciaaw:hasIsotope`	0..*	`shape:Isotope`
Chemical element	`ciaaw:longestLivedMassNumber`	0..1	`xsd:integer`	Elements without stable isotopes: the mass number bracketed in the table.
Isotope	`ciaaw:massNumber`	1	`xsd:integer`
Isotope	`skos:closeMatch`	0..*	`IRI`	Taken from the supplement. Never guessed.

Atomic weight declarations

A standard atomic weight is either an interval or a value with an uncertainty. The element points to the one current declaration and repeats its numbers as derived shortcuts.

classDiagram
    direction TB
    class Element["chemrof:ChemicalElement"] {
        ciaaw:standardAtomicWeightLower : decimal [0..1]
        ciaaw:standardAtomicWeightUpper : decimal [0..1]
        ciaaw:standardAtomicWeightValue : decimal [0..1]
        ciaaw:standardAtomicWeightUncertainty : decimal [0..1]
    }
    class StandardAtomicWeightDeclaration["ciaaw:StandardAtomicWeightDeclaration"]
    class ConventionalAtomicWeightDeclaration["ciaaw:ConventionalAtomicWeightDeclaration"]
    class IntervalValue["Interval"]
    class ValueWithUncertainty["Value with uncertainty"]
    class SingleValue["Single value"]
    Element --> "0..1" StandardAtomicWeightDeclaration : ciaaw#58;currentStandardAtomicWeight
    Element --> "0..1" ConventionalAtomicWeightDeclaration : ciaaw#58;currentConventionalAtomicWeight
    Element --> "0..*" StandardAtomicWeightDeclaration : ciaaw#58;hasDeclaration (one of)
    Element --> "0..*" ConventionalAtomicWeightDeclaration : ciaaw#58;hasDeclaration (one of)
    StandardAtomicWeightDeclaration --> "1" Element : ciaaw#58;ofElement
    StandardAtomicWeightDeclaration --> "1" IntervalValue : ciaaw#58;value (one of)
    StandardAtomicWeightDeclaration --> "1" ValueWithUncertainty : ciaaw#58;value (one of)
    StandardAtomicWeightDeclaration --> "1" SingleValue : ciaaw#58;value (one of)
    ConventionalAtomicWeightDeclaration --> "1" Element : ciaaw#58;ofElement
    ConventionalAtomicWeightDeclaration --> "1" SingleValue : ciaaw#58;value

Shape	Property	Count	Value	Note
Chemical element	`ciaaw:currentStandardAtomicWeight`	0..1	`shape:StandardAtomicWeightDeclaration`	Absent when the table gives no standard atomic weight.
Chemical element	`ciaaw:currentConventionalAtomicWeight`	0..1	`shape:ConventionalAtomicWeightDeclaration`
Chemical element	`ciaaw:hasDeclaration`	0..*	`shape:StandardAtomicWeightDeclaration` or `shape:ConventionalAtomicWeightDeclaration`	All declarations including deprecated ones.
Chemical element	`ciaaw:standardAtomicWeightLower`	0..1	`xsd:decimal`	Derived shortcut copied from the current declaration. Never edited by hand.
Chemical element	`ciaaw:standardAtomicWeightUpper`	0..1	`xsd:decimal`	Derived shortcut.
Chemical element	`ciaaw:standardAtomicWeightValue`	0..1	`xsd:decimal`	Derived shortcut.
Chemical element	`ciaaw:standardAtomicWeightUncertainty`	0..1	`xsd:decimal`	Derived shortcut.
Standard atomic weight declaration	`ciaaw:ofElement`	1	`shape:Element`
Standard atomic weight declaration	`ciaaw:value`	1	`shape:IntervalValue` or `shape:ValueWithUncertainty` or `shape:SingleValue`
Conventional atomic weight declaration	`ciaaw:ofElement`	1	`shape:Element`
Conventional atomic weight declaration	`ciaaw:value`	1	`shape:SingleValue`	Not generated yet. The two source tables do not contain abridged values.

Isotopic abundance declarations

The representative isotopic composition of one isotope. It can be an interval, a value with an uncertainty, or a single value such as 1 for monoisotopic elements.

classDiagram
    direction TB
    class Element["chemrof:ChemicalElement"]
    class Isotope["chemrof:Isotope"]
    class IsotopicAbundanceDeclaration["ciaaw:IsotopicAbundanceDeclaration"]
    class AtomicMassDeclaration["ciaaw:AtomicMassDeclaration"]
    class IntervalValue["Interval"]
    class ValueWithUncertainty["Value with uncertainty"]
    class SingleValue["Single value"]
    Element --> "0..*" Isotope : ciaaw#58;hasIsotope
    Isotope --> "1" IsotopicAbundanceDeclaration : ciaaw#58;currentAbundance
    Isotope --> "1..*" IsotopicAbundanceDeclaration : ciaaw#58;hasDeclaration (one of)
    Isotope --> "1..*" AtomicMassDeclaration : ciaaw#58;hasDeclaration (one of)
    IsotopicAbundanceDeclaration --> "1" Isotope : ciaaw#58;ofIsotope
    IsotopicAbundanceDeclaration --> "1" IntervalValue : ciaaw#58;value (one of)
    IsotopicAbundanceDeclaration --> "1" ValueWithUncertainty : ciaaw#58;value (one of)
    IsotopicAbundanceDeclaration --> "1" SingleValue : ciaaw#58;value (one of)

Shape	Property	Count	Value	Note
Chemical element	`ciaaw:hasIsotope`	0..*	`shape:Isotope`
Isotope	`ciaaw:currentAbundance`	1	`shape:IsotopicAbundanceDeclaration`
Isotope	`ciaaw:hasDeclaration`	1..*	`shape:IsotopicAbundanceDeclaration` or `shape:AtomicMassDeclaration`	All declarations including deprecated ones.
Isotopic abundance declaration	`ciaaw:ofIsotope`	1	`shape:Isotope`
Isotopic abundance declaration	`ciaaw:value`	1	`shape:IntervalValue` or `shape:ValueWithUncertainty` or `shape:SingleValue`	Amount fraction between 0 and 1.

Atomic masses (planned)

Part of the draft vocabulary, but not generated yet because the two source tables do not contain atomic masses.

classDiagram
    direction TB
    class Isotope["chemrof:Isotope"]
    class AtomicMassDeclaration["ciaaw:AtomicMassDeclaration"]
    class IsotopicAbundanceDeclaration["ciaaw:IsotopicAbundanceDeclaration"]
    class MassValue["Mass with uncertainty"]
    Isotope --> "0..1" AtomicMassDeclaration : ciaaw#58;currentAtomicMass
    Isotope --> "1..*" IsotopicAbundanceDeclaration : ciaaw#58;hasDeclaration (one of)
    Isotope --> "1..*" AtomicMassDeclaration : ciaaw#58;hasDeclaration (one of)
    AtomicMassDeclaration --> "1" Isotope : ciaaw#58;ofIsotope
    AtomicMassDeclaration --> "1" MassValue : ciaaw#58;value

Shape	Property	Count	Value	Note
Isotope	`ciaaw:currentAtomicMass`	0..1	`shape:AtomicMassDeclaration`
Isotope	`ciaaw:hasDeclaration`	1..*	`shape:IsotopicAbundanceDeclaration` or `shape:AtomicMassDeclaration`	All declarations including deprecated ones.
Atomic mass declaration	`ciaaw:ofIsotope`	1	`shape:Isotope`
Atomic mass declaration	`ciaaw:value`	1	`shape:MassValue`	Not generated yet. The two source tables do not contain atomic masses.

Quantity values

Numbers are qudt:QuantityValue nodes in one of a few closed forms. Significant figures are stored separately because xsd:decimal does not preserve trailing zeros.

classDiagram
    direction LR
    class StandardAtomicWeightDeclaration["ciaaw:StandardAtomicWeightDeclaration"]
    class IntervalValue["Interval"] {
        qudt:hasUnit : IRI [1]
        qudt:lowerBound : decimal [1]
        qudt:upperBound : decimal [1]
        ciaaw:significantFiguresLower : integer [0..1]
        ciaaw:significantFiguresUpper : integer [0..1]
    }
    class ValueWithUncertainty["Value with uncertainty"] {
        qudt:hasUnit : IRI [1]
        qudt:numericValue : decimal [1]
        qudt:standardUncertainty : decimal [1]
        ciaaw:significantFigures : integer [1]
        ciaaw:significantFiguresUncertainty : integer [1]
    }
    class SingleValue["Single value"] {
        qudt:hasUnit : IRI [1]
        qudt:numericValue : decimal [1]
        ciaaw:significantFigures : integer [0..1]
    }
    class ConventionalAtomicWeightDeclaration["ciaaw:ConventionalAtomicWeightDeclaration"]
    class IsotopicAbundanceDeclaration["ciaaw:IsotopicAbundanceDeclaration"]
    class AtomicMassDeclaration["ciaaw:AtomicMassDeclaration"]
    class MassValue["Mass with uncertainty"] {
        qudt:hasUnit : IRI [1]
        qudt:numericValue : decimal [1]
        qudt:standardUncertainty : decimal [1]
        ciaaw:significantFigures : integer [1]
        ciaaw:significantFiguresUncertainty : integer [1]
    }
    StandardAtomicWeightDeclaration --> "1" IntervalValue : ciaaw#58;value (one of)
    StandardAtomicWeightDeclaration --> "1" ValueWithUncertainty : ciaaw#58;value (one of)
    StandardAtomicWeightDeclaration --> "1" SingleValue : ciaaw#58;value (one of)
    ConventionalAtomicWeightDeclaration --> "1" SingleValue : ciaaw#58;value
    IsotopicAbundanceDeclaration --> "1" IntervalValue : ciaaw#58;value (one of)
    IsotopicAbundanceDeclaration --> "1" ValueWithUncertainty : ciaaw#58;value (one of)
    IsotopicAbundanceDeclaration --> "1" SingleValue : ciaaw#58;value (one of)
    AtomicMassDeclaration --> "1" MassValue : ciaaw#58;value

Shape	Property	Count	Value	Note
Standard atomic weight declaration	`ciaaw:value`	1	`shape:IntervalValue` or `shape:ValueWithUncertainty` or `shape:SingleValue`
Conventional atomic weight declaration	`ciaaw:value`	1	`shape:SingleValue`	Not generated yet. The two source tables do not contain abridged values.
Isotopic abundance declaration	`ciaaw:value`	1	`shape:IntervalValue` or `shape:ValueWithUncertainty` or `shape:SingleValue`	Amount fraction between 0 and 1.
Atomic mass declaration	`ciaaw:value`	1	`shape:MassValue`	Not generated yet. The two source tables do not contain atomic masses.
Interval	`qudt:hasUnit`	1	`IRI`
Interval	`qudt:lowerBound`	1	`xsd:decimal`
Interval	`qudt:upperBound`	1	`xsd:decimal`
Interval	`ciaaw:significantFiguresLower`	0..1	`xsd:integer`	Absent when the bound is zero.
Interval	`ciaaw:significantFiguresUpper`	0..1	`xsd:integer`
Value with uncertainty	`qudt:hasUnit`	1	`IRI`
Value with uncertainty	`qudt:numericValue`	1	`xsd:decimal`
Value with uncertainty	`qudt:standardUncertainty`	1	`xsd:decimal`	Scaled from the digits in brackets in the table.
Value with uncertainty	`ciaaw:significantFigures`	1	`xsd:integer`
Value with uncertainty	`ciaaw:significantFiguresUncertainty`	1	`xsd:integer`
Single value	`qudt:hasUnit`	1	`IRI`
Single value	`qudt:numericValue`	1	`xsd:decimal`	Stated without an uncertainty.
Single value	`ciaaw:significantFigures`	0..1	`xsd:integer`
Mass with uncertainty	`qudt:hasUnit`	1	`IRI`
Mass with uncertainty	`qudt:numericValue`	1	`xsd:decimal`
Mass with uncertainty	`qudt:standardUncertainty`	1	`xsd:decimal`
Mass with uncertainty	`ciaaw:significantFigures`	1	`xsd:integer`
Mass with uncertainty	`ciaaw:significantFiguresUncertainty`	1	`xsd:integer`

Footnotes

The g, m and r notes printed below the CIAAW tables are shared nodes that declarations refer to.

classDiagram
    direction LR
    class Declaration["Declaration"] {
        <<abstract>>
    }
    class Footnote["ciaaw:Footnote"] {
        skos:notation : string [1]
        skos:definition : langString [1]
    }
    Declaration --> "0..*" Footnote : ciaaw#58;footnote

Shape	Property	Count	Value	Note
Declaration	`ciaaw:footnote`	0..*	`shape:Footnote`
Footnote	`skos:notation`	1	`xsd:string`
Footnote	`skos:definition`	1	`rdf:langString`	As printed below the CIAAW tables.

History and provenance

Declarations are never edited. A new value creates a new declaration, and the old one is kept, flagged as deprecated, and linked to its replacement.

classDiagram
    direction LR
    class Element["chemrof:ChemicalElement"]
    class NotDeprecated["Not deprecated"] {
        owl:deprecated : boolean [0..1]
    }
    class StandardAtomicWeightDeclaration["ciaaw:StandardAtomicWeightDeclaration"]
    class ConventionalAtomicWeightDeclaration["ciaaw:ConventionalAtomicWeightDeclaration"]
    class Isotope["chemrof:Isotope"]
    class IsotopicAbundanceDeclaration["ciaaw:IsotopicAbundanceDeclaration"]
    class AtomicMassDeclaration["ciaaw:AtomicMassDeclaration"]
    class Declaration["Declaration"] {
        <<abstract>>
        dcterms:issued : gYear [0..1]
        dcterms:source : IRI [0..*]
        owl:deprecated : boolean [0..1]
        adms:status : IRI [0..1]
    }
    Declaration <|-- StandardAtomicWeightDeclaration
    Declaration <|-- ConventionalAtomicWeightDeclaration
    Declaration <|-- IsotopicAbundanceDeclaration
    Declaration <|-- AtomicMassDeclaration
    Element --> "0..1" NotDeprecated : ciaaw#58;currentStandardAtomicWeight
    Element --> "0..1" NotDeprecated : ciaaw#58;currentConventionalAtomicWeight
    Element --> "0..*" StandardAtomicWeightDeclaration : ciaaw#58;hasDeclaration (one of)
    Element --> "0..*" ConventionalAtomicWeightDeclaration : ciaaw#58;hasDeclaration (one of)
    Isotope --> "1" NotDeprecated : ciaaw#58;currentAbundance
    Isotope --> "0..1" NotDeprecated : ciaaw#58;currentAtomicMass
    Isotope --> "1..*" IsotopicAbundanceDeclaration : ciaaw#58;hasDeclaration (one of)
    Isotope --> "1..*" AtomicMassDeclaration : ciaaw#58;hasDeclaration (one of)
    Declaration --> "0..1" Declaration : dcterms#58;isReplacedBy
    Declaration --> "0..1" Declaration : dcterms#58;replaces

Shape	Property	Count	Value	Note
Chemical element	`ciaaw:currentStandardAtomicWeight`	0..1	`shape:NotDeprecated`	A current pointer may never lead to a deprecated declaration.
Chemical element	`ciaaw:currentConventionalAtomicWeight`	0..1	`shape:NotDeprecated`	A current pointer may never lead to a deprecated declaration.
Chemical element	`ciaaw:hasDeclaration`	0..*	`shape:StandardAtomicWeightDeclaration` or `shape:ConventionalAtomicWeightDeclaration`	All declarations including deprecated ones.
Isotope	`ciaaw:currentAbundance`	1	`shape:NotDeprecated`	A current pointer may never lead to a deprecated declaration.
Isotope	`ciaaw:currentAtomicMass`	0..1	`shape:NotDeprecated`	A current pointer may never lead to a deprecated declaration.
Isotope	`ciaaw:hasDeclaration`	1..*	`shape:IsotopicAbundanceDeclaration` or `shape:AtomicMassDeclaration`	All declarations including deprecated ones.
Declaration	`dcterms:issued`	0..1	`xsd:gYear`	Year of the assigning report.
Declaration	`dcterms:source`	0..*	`IRI`	DOI of the assigning report.
Declaration	`owl:deprecated`	0..1	`xsd:boolean`	True once a later declaration has replaced this one.
Declaration	`adms:status`	0..1	`IRI`	The ADMS status IRI still needs to be confirmed.
Declaration	`dcterms:isReplacedBy`	0..1	`shape:Declaration`
Declaration	`dcterms:replaces`	0..1	`shape:Declaration`
Not deprecated	`owl:deprecated`	0..1	`xsd:boolean`	Helper shape: owl:deprecated is absent or false.

Rules across nodes

These checks are defined in rules.ttl:

Abundance is a fraction
Abundances of an element sum to 1
Bounds are in order
Current declaration is part of the history
Declaration points back to its subject
Deprecation names a replacement and a status
Derived shortcuts match the current declaration
Isotope belongs to one element
Replacement links run both ways
Uncertainty is positive