include-dcc · lopierra · Oct 24, 2022 · Oct 18, 2022 · Oct 18, 2022 · Oct 18, 2022
diff --git a/about.yaml b/about.yaml
@@ -1,3 +1,3 @@
 name: include_linkml
 description: my awesome datamodel is for awesome things
-source_schema_path: src/linkml/include_linkml.yaml
+source_schema_path: src/linkml/include_core.yaml
diff --git a/docs/Thing.md b/docs/Thing.md
@@ -5,38 +5,21 @@ _Highest Level Class_
 
 
 
-URI: [include:Thing](https://w3id.org/include/Thing)
+URI: [https://w3id.org/include/core/:Thing](https://w3id.org/include/core/:Thing)
 
 
 
 
 ```mermaid
  classDiagram
-      Thing <|-- Biospecimen
-      Thing <|-- DataFile
-      Thing <|-- Participant
-      Thing <|-- Study
-      Thing <|-- FamilyGroup
-      Thing <|-- Aliquot
-      Thing <|-- Assay
-
+    class Thing
 
 ```
 
 
 
 
-
-## Inheritance
-* **Thing**
-    * [Biospecimen](Biospecimen.md)
-    * [DataFile](DataFile.md)
-    * [Participant](Participant.md)
-    * [Study](Study.md)
-    * [FamilyGroup](FamilyGroup.md)
-    * [Aliquot](Aliquot.md)
-    * [Assay](Assay.md)
-
+<!-- no inheritance hierarchy -->
 
 
 ## Slots
@@ -60,7 +43,7 @@ URI: [include:Thing](https://w3id.org/include/Thing)
 ### Schema Source
 
 
-* from schema: https://w3id.org/include
+* from schema: https://w3id.org/include/core
 
 
 
@@ -72,8 +55,8 @@ URI: [include:Thing](https://w3id.org/include/Thing)
 
 | Mapping Type | Mapped Value |
 | ---  | ---  |
-| self | ['include:Thing'] |
-| native | ['include:Thing'] |
+| self | ['https://w3id.org/include/core/:Thing'] |
+| native | ['https://w3id.org/include/core/:Thing'] |
 
 
 ## LinkML Specification
@@ -88,7 +71,7 @@ name: Thing
 definition_uri: schema:Thing
 description: Highest Level Class
 title: Thing
-from_schema: https://w3id.org/include
+from_schema: https://w3id.org/include/core
 rank: 1000
 
 ```
@@ -102,7 +85,7 @@ name: Thing
 definition_uri: schema:Thing
 description: Highest Level Class
 title: Thing
-from_schema: https://w3id.org/include
+from_schema: https://w3id.org/include/core
 rank: 1000
 
 ```

diff --git a/docs/include-assay-schema.md b/docs/include-assay-schema.md
@@ -0,0 +1,6 @@
+# include-assay-schema
+
+None
+
+URI: https://w3id.org/include/assay
+
diff --git a/docs/include-core-schema.md b/docs/include-core-schema.md
@@ -0,0 +1,6 @@
+# include-core-schema
+
+None
+
+URI: https://w3id.org/include/core
+
diff --git a/docs/include-enums.md b/docs/include-enums.md
@@ -0,0 +1,6 @@
+# include-enums
+
+None
+
+URI: https://w3id.org/include/enums
+
diff --git a/docs/include-participant-schema.md b/docs/include-participant-schema.md
@@ -0,0 +1,6 @@
+# include-participant-schema
+
+None
+
+URI: https://w3id.org/include/participant
+
diff --git a/docs/include-study-schema.md b/docs/include-study-schema.md
@@ -0,0 +1,6 @@
+# include-study-schema
+
+None
+
+URI: https://w3id.org/include/study
+
diff --git a/docs/index.md b/docs/index.md
@@ -1,130 +1,33 @@
-# IncludeV2DataModel
+# include-core-schema
 
-Initial Include Schema
+None
 
-URI: https://w3id.org/include
-Name: IncludeV2DataModel
+URI: https://w3id.org/include/core
+Name: include-core-schema
 
 ## Classes
 
 | Class | Description |
 | --- | --- |
-| [Aliquot](Aliquot.md) | An aliquot of a sample |
-| [Assay](Assay.md) | An assay |
-| [Biospecimen](Biospecimen.md) | A Biospecimen Collected from A Participant |
-| [Condition](Condition.md) |  |
-| [DataFile](DataFile.md) | A DataFile Associated with a Participant or Study or Biospecimen |
-| [FamilyGroup](FamilyGroup.md) | A group of Participants in the same Study |
-| [Participant](Participant.md) | A Participant in a Study |
-| [Study](Study.md) | A Study |
 | [Thing](Thing.md) | Highest Level Class |
 
 
 ## Slots
 
 | Slot | Description |
 | --- | --- |
-| [access_url](access_url.md) | Storage location for this file |
-| [age_at_biospecimen_collection](age_at_biospecimen_collection.md) | Age in days of participant at time of biospecimen collection |
-| [age_at_condition_observation](age_at_condition_observation.md) | Age in days at which condition was observed, recorded, or diagnosed |
-| [age_at_last_vital_status](age_at_last_vital_status.md) | Age in days when participant's vital status was last recorded |
-| [biospecimen_storage](biospecimen_storage.md) | Method by which Container is stored (e |
-| [collection_id](collection_id.md) | Identifier for the eldest sample in a lineage of processed, pooled, or aliquo... |
-| [collection_sample_type](collection_sample_type.md) | Type of biological material comprising the collected sample (e |
-| [condition_data_source](condition_data_source.md) | Whether condition information was obtained from medical records (Clinical) or... |
-| [condition_description](condition_description.md) | Condition as worded by data contributor - this will be displayed in the porta... |
-| [condition_interpretation](condition_interpretation.md) | Whether condition was observed or not |
-| [container_id](container_id.md) | Identifier for specific container/aliquot of sample, if applicable |
-| [data_access](data_access.md) | Type of access control on this file, determined by DCC |
-| [data_category](data_category.md) | General category of data in file (e |
-| [data_type](data_type.md) | Specific type of data contained in file (e |
-| [dbgap](dbgap.md) | dbGaP study accession code |
-| [down_syndrome_status](down_syndrome_status.md) | Down Syndrome status of participant (T21 = Trisomy 21; D21 = Disomy 21, euplo... |
-| [ethnicity](ethnicity.md) | Ethnicity of participant |
-| [experimental_strategy](experimental_strategy.md) | Experimental method used to obtain data in file (e |
-| [external_id](external_id.md) | Unique identifier for the participant, assigned by data contributor |
-| [family_id](family_id.md) | Unique identifer for family to which Participant belongs |
-| [family_relationship](family_relationship.md) | Relationship of Participant to other family members |
-| [family_type](family_type.md) | Structure of family members participating in the study (proband-only = no fam... |
-| [father_id](father_id.md) | Participant ID for Participant's father |
-| [file_id](file_id.md) | File identifier, assigned by DCC |
-| [file_name](file_name.md) | Synapse ID for file |
-| [format](format.md) | Format of file (e |
-| [has_aliquot](has_aliquot.md) | An aliquot of a sample |
-| [has_biospecimen](has_biospecimen.md) | Link to a Biospecimen |
-| [has_datafile](has_datafile.md) | Link to a DataFile |
-| [has_output](has_output.md) | The DataFile Output of an Assay |
-| [has_parent_sample](has_parent_sample.md) | Link from a sample to its parent Sample |
-| [has_participant](has_participant.md) | Link to a Participant |
-| [has_study](has_study.md) | Link to a Study |
-| [has_subject](has_subject.md) | Link from Data File to a Participant |
-| [hpo_code](hpo_code.md) | Code for condition in the Human Phenotype Ontology (HPO) |
-| [hpo_label](hpo_label.md) | Label for condition in the Human Phenotype Ontology (HPO) |
-| [laboratory_procedure](laboratory_procedure.md) | Procedure by which Sample was derived from Parent Sample (e |
-| [maxo_code](maxo_code.md) | Code for condition in the Medical Action Ontology (MAXO) |
-| [maxo_label](maxo_label.md) | Label for condition in the Medical Action Ontology (MAXO) |
-| [mondo_code](mondo_code.md) | Code for condition in the Mondo Disease Ontology (MONDO) |
-| [mondo_label](mondo_label.md) | Label for condition in the Mondo Disease Ontology (MONDO) |
-| [mother_id](mother_id.md) | Participant ID for Participant's mother |
-| [original_file_name](original_file_name.md) | Name of file, assigned by data contributor |
-| [other_code](other_code.md) | Code for condition in another ontology (if no match in HPO, MONDO, or MAXO) |
-| [other_label](other_label.md) | Label for condition in another ontology (if no match in HPO, MONDO, or MAXO) |
-| [outcomes_vital_status](outcomes_vital_status.md) | Whether participant is alive or dead |
-| [parent_sample_id](parent_sample_id.md) | Identifier for the direct parent from which Sample was derived, processed, po... |
-| [parent_sample_type](parent_sample_type.md) | Type of biological material comprising the parent sample (e |
-| [participant_id](participant_id.md) | Unique identifier for the participant, assigned by DCC |
-| [program](program.md) | Funding source for the study |
-| [race](race.md) | Race of participant |
-| [sample_availability](sample_availability.md) | Whether or not the sample is potentially available for sharing through the Vi... |
-| [sample_id](sample_id.md) | Identifier for sample |
-| [sample_type](sample_type.md) | Type of biological material comprising the sample (e |
-| [sex](sex.md) | Sex of participant |
-| [size](size.md) | Size of file |
-| [study_code](study_code.md) | Unique identifer for the study, assigned by DCC |
-| [study_name](study_name.md) | Name of the study, chosen by data contributor |
-| [uses_biospecimen](uses_biospecimen.md) | The Biospecimen an Assay is performed on |
-| [validation_rules](validation_rules.md) | Rules for Validation of Property Constraints and Values |
-| [volume](volume.md) | Amount of sample in container |
-| [volume_unit](volume_unit.md) | Unit of sample volume |
 
 
 ## Enumerations
 
 | Enumeration | Description |
 | --- | --- |
-| [EnumConditionDataSource](EnumConditionDataSource.md) |  |
-| [EnumConditionInterpretation](EnumConditionInterpretation.md) |  |
-| [EnumDataAccess](EnumDataAccess.md) |  |
-| [EnumDownSyndromeStatus](EnumDownSyndromeStatus.md) |  |
-| [EnumEthnicity](EnumEthnicity.md) |  |
-| [EnumFamilyType](EnumFamilyType.md) |  |
-| [EnumPhenotypeInterpretation](EnumPhenotypeInterpretation.md) |  |
-| [EnumProgram](EnumProgram.md) |  |
-| [EnumRace](EnumRace.md) |  |
-| [EnumSampleAvailability](EnumSampleAvailability.md) |  |
-| [EnumSex](EnumSex.md) |  |
-| [EnumStudyCode](EnumStudyCode.md) |  |
 
 
 ## Types
 
 | Type | Description |
 | --- | --- |
-| [xsd:boolean](xsd:boolean) | A binary (true or false) value |
-| [xsd:date](xsd:date) | a date (year, month and day) in an idealized calendar |
-| [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) | Either a date or a datetime |
-| [xsd:dateTime](xsd:dateTime) | The combination of a date and time |
-| [xsd:decimal](xsd:decimal) | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
-| [xsd:double](xsd:double) | A real number that conforms to the xsd:double specification |
-| [xsd:float](xsd:float) | A real number that conforms to the xsd:float specification |
-| [xsd:integer](xsd:integer) | An integer |
-| [xsd:string](xsd:string) | Prefix part of CURIE |
-| [shex:nonLiteral](shex:nonLiteral) | A URI, CURIE or BNODE that represents a node in a model |
-| [shex:iri](shex:iri) | A URI or CURIE that represents an object in the model |
-| [xsd:string](xsd:string) | A character string |
-| [xsd:dateTime](xsd:dateTime) | A time object represents a (local) time of day, independent of any particular... |
-| [xsd:anyURI](xsd:anyURI) | a complete URI |
-| [xsd:anyURI](xsd:anyURI) | a URI or a CURIE |
 
 
 ## Subsets

diff --git a/project/docs/Thing.md b/project/docs/Thing.md
@@ -4,23 +4,10 @@
 
 Highest Level Class
 
-URI: [include:Thing](https://w3id.org/include/Thing)
+URI: [https://w3id.org/include/core/Thing](https://w3id.org/include/core/Thing)
 
 
-[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Thing]^-[Study],[Thing]^-[Participant],[Thing]^-[FamilyGroup],[Thing]^-[DataFile],[Thing]^-[Biospecimen],[Thing]^-[Assay],[Thing]^-[Aliquot],[Study],[Participant],[FamilyGroup],[DataFile],[Biospecimen],[Assay],[Aliquot])](https://yuml.me/diagram/nofunky;dir:TB/class/[Thing]^-[Study],[Thing]^-[Participant],[Thing]^-[FamilyGroup],[Thing]^-[DataFile],[Thing]^-[Biospecimen],[Thing]^-[Assay],[Thing]^-[Aliquot],[Study],[Participant],[FamilyGroup],[DataFile],[Biospecimen],[Assay],[Aliquot])
-
-## Children
-
- * [Aliquot](Aliquot.md) - An aliquot of a sample
- * [Assay](Assay.md) - An assay
- * [Biospecimen](Biospecimen.md) - A Biospecimen Collected from A Participant
- * [DataFile](DataFile.md) - A DataFile Associated with a Participant or Study or Biospecimen
- * [FamilyGroup](FamilyGroup.md) - A group of Participants in the same Study
- * [Participant](Participant.md) - A Participant in a Study
- * [Study](Study.md) - A Study
-
-## Referenced by Class
-
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Thing])](https://yuml.me/diagram/nofunky;dir:TB/class/[Thing])
 
 ## Attributes
 
diff --git a/project/docs/include_core.md b/project/docs/include_core.md
@@ -0,0 +1,36 @@
+
+# include-core-schema
+
+
+**metamodel version:** 1.7.0
+
+**version:** None
+
+
+
+
+
+### Classes
+
+ * [Thing](Thing.md) - Highest Level Class
+
+### Mixins
+
+
+### Slots
+
+
+### Enums
+
+
+### Subsets
+
+
+### Types
+
+
+#### Built in
+
+
+#### Defined
+