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You can import this JSON and convert to LinkML: + +.. code-block:: + + schemauto import-cadsr "cdes/*.json" + + Packages ------- @@ -81,3 +96,5 @@ Packages .. autoclass:: DOSDPImportEngine :members: +.. autoclass:: CADSRImportEngine + :members: \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index ef48b44..dd714bc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -201,32 +201,32 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} [[package]] name = "attrs" -version = "23.2.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, - {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, + {file = "attrs-24.2.0-py3-none-any.whl", hash = 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b/schema_automator/importers/cadsr_import_engine.py @@ -68,7 +68,9 @@ class CADSRImportEngine(ImportEngine): Ingests the output of `caDSR API `_. - - Each CDE becomes a unique slot + Note that we include a LinkML schema for this in schema_automator.metamodels.cadsr + + - Each CDE (DataElement) becomes a unique slot - the CDE is added as a lot of a context-specific class - the context-specific class is a subclass of the CDE's DataElementConcept @@ -109,24 +111,32 @@ def convert(self, paths: Iterable[str], id: str=None, name: str=None, **kwargs) container = json_loader.load(file, target_class=cadsr.DataElementContainer) cde = container.DataElement ctxt = cde.context + ln = cde.longName source = urllib.parse.quote(ctxt) source = f"cadsr:{source}" + # Each DataElement becomes one slot; + # we make the name both unique and human readable + # TODO: check this; frequently reused, e.g. + # NCI Standards + Group ID slot = SlotDefinition( - name=urllib.parse.quote(underscore(f"{ctxt} {cde.preferredName}")), + name=urllib.parse.quote(underscore(f"{ctxt} {cde.preferredName} {ln}")), slot_uri=f"cadsr:{cde.publicId}", title=cde.preferredName, description=cde.preferredDefinition, - aliases=[cde.longName], + aliases=[ln], conforms_to=f"cadsr:DataElement", source=source, ) # each data element belongs to a concept # (may be reused across classes?) slots[slot.name] = slot - concept = cde.DataElementConcept + dec = cde.DataElementConcept + property = dec.Property + main_prop_concept, prop_mappings = extract_concepts(property.Concepts) # a concept is linked to a class - objectClass = concept.ObjectClass - # NCIT concepts describing the class + objectClass = dec.ObjectClass + # NCIT concepts describing the class; + # there will be one primary and possibly secondary concepts mainConcept, mappings = extract_concepts(objectClass.Concepts) class_name = objectClass.longName concept_name = urllib.parse.quote(camelcase(f"{ctxt} {class_name}")) @@ -146,10 +156,10 @@ def convert(self, paths: Iterable[str], id: str=None, name: str=None, **kwargs) if concept_name not in classes: cls = ClassDefinition( name=concept_name, - title=f"{concept.preferredName} ({ctxt})", - description=concept.preferredDefinition, - aliases=[concept.longName], - class_uri=f"cadsr:{concept.publicId}", + title=f"{dec.preferredName} ({ctxt})", + description=dec.preferredDefinition, + aliases=[dec.longName], + class_uri=f"cadsr:{dec.publicId}", is_a=parent_concept_name, conforms_to=f"cadsr:DataElementConcept", ) diff --git a/schema_automator/metamodels/cadsr.yaml b/schema_automator/metamodels/cadsr.yaml index a418b67..74b6241 100644 --- a/schema_automator/metamodels/cadsr.yaml +++ b/schema_automator/metamodels/cadsr.yaml @@ -11,6 +11,10 @@ slots: description: The unique identifier for an Administered Item within a Registration Authority. required: false + range: string ## usually a number encoded as string? + # identifier: true ## TODO - try this + comments: + - note this can appear at different levels version: description: The unique version identifier of the Administered Item. required: false @@ -453,6 +457,11 @@ classes: description: The text of the most desirable meaning for the Administered Item. longName: description: A 255 character limit name for an item in the registry. + examples: + - value: ASSESS + - value: TX + - value: ANAT_SITES + - value: AE_RESULTS context: description: An associated gov.nih.nci.cadsr.domain.Context object contextVersion: {} @@ -521,6 +530,10 @@ classes: range: DataElementQuery required: false DataElement: + description: An element representing a specific metadata element. + Corresponds to *slot* in LinkML + exact_mappings: + - linkml:SlotDefinition slots: - publicId - version @@ -560,16 +573,31 @@ classes: preferredName: description: A 30 character limit name by which an Administered Item is designated within a specific Context. + examples: + - value: Completion Status + - value: Specimen Type + - value: Date of Collection preferredDefinition: description: The text of the most desirable meaning for the Administered Item. longName: - description: A 255 character limit name for an item in the registry. + description: The long name of the data element. Maybe be a semi-human readable code, + may be a non-semantic number. Not guaranteed to be unique + examples: + - value: AE_OUTCOME_CD + - value: 2854464v1.0:2854442v1.0 context: description: An associated gov.nih.nci.cadsr.domain.Context object contextVersion: {} DataElementConcept: range: DataElementConcept required: false + description: The long name of the data element concept. Like the parent DataElement, + Maybe be a semi-human readable code, may be a non-semantic number. Not guaranteed to be unique, + in fact we should see reuse of the same DEC across DEs + examples: + - value: TX_COHORT_STDY + - value: 2867629v1.0:2423441v1.0 + - value: PERSON_ID ValueDomain: range: ValueDomain required: false @@ -748,6 +776,12 @@ classes: description: An indicator that characterizes the item as eliminated from the registry, thought the physical record still exists. ObjectClass: + aliases: + - OC + description: Class or class expression used to annotated a DataElementConcept (DEC). + OCs may correspond to a single NCIT concept, or they may be a composition. E.g. + DEC.OC.ln=C41136:C52673 (Dental Professional Practice) may correspond to + C52673 'Professional Practice' (primary) and C41136 'Dental' (secondary) slots: - publicId - version @@ -786,13 +820,22 @@ classes: preferredDefinition: description: The text of the most desirable meaning for the Administered Item. longName: - description: A 255 character limit name for an item in the registry. + description: The long name of the ObjectClass. This is typically the NCIT code, + or composition of codes + examples: + - value: C16960 + description: example value for DataElementConcept.ObjectClass + - value: C41136:C52673 + description: example value for DataElementConcept.ObjectClass + - value: Adverse Event + description: example value for DataElementConcept.ObjectClass context: description: An associated gov.nih.nci.cadsr.domain.Context object contextVersion: {} Concepts: multivalued: true range: Concept + description: Concepts from NCIT that annotate the ObjectClass origin: description: The source (document, project, discipline or model) for the Administered Item. @@ -850,8 +893,15 @@ classes: - displayOrder slot_usage: longName: - description: A 255 character limit name for an item in the registry. - conceptCode: {} + description: name of the concept. Note that in other contexts, longName may be an identifier, + but in Concepts it is the label (always from NCIT). + examples: + - value: "No" + - value: "Increase" + - value: "Nucleic Acid Amplification Test" + conceptCode: + examples: + - value: C20055 definition: {} evsSource: description: The name of the EVS concept code that was the source for the @@ -987,9 +1037,13 @@ classes: description: The unique version identifier of the Administered Item. required: false preferredName: - description: A 30 character limit name by which an Administered Item is designated - within a specific Context. + description: human-readable name of the PV required: false + examples: + - value: "No" + - value: "Not Applicable" + - value: "Absent" + - value: "Liver" longName: description: A 255 character limit name for an item in the registry. required: false