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Rebuild ER diagrams #99

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Mar 16, 2023
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Rebuild ER diagrams #99

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d613dbd
Rebuild ER diagrams
lkuchenb Mar 16, 2023
14ad60b
Regenerate linkml docs
lkuchenb Mar 16, 2023
c0263cd
Fix missing removal of extraneous files
lkuchenb Mar 16, 2023
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684 changes: 12 additions & 672 deletions docs/entity_relations.md
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3 changes: 1 addition & 2 deletions docs/schema_markdown/Analysis.md
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Expand Up @@ -7,7 +7,7 @@ An Analysis is a data transformation that transforms input data to output data.
URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Analysis](https://w3id.org/GHGA-Submission-Metadata-Schema/Analysis)


[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[File],[EgaAccessionMixin],[Dataset],[DataTransformation],[File]<has%20output%201..*-++[Analysis&#124;type:string%20%3F;reference_genome:string;reference_chromosome:string;description:string%20%3F;alias:string%20%3F;accession:string;ega_accession:string;title(i):string%20%3F;id(i):string;xref(i):string%20*],[Study]<has%20study%201..1-++[Analysis],[File]<has%20input%201..*-++[Analysis],[Dataset]++-%20has%20analysis%200..*>[Analysis],[Dataset]-%20has%20analysis(i)%200..1>[Analysis],[Submission]-%20has%20analysis(i)%200..1>[Analysis],[Submission]++-%20has%20analysis%200..*>[Analysis],[Analysis]uses%20-.->[AccessionMixin],[Analysis]uses%20-.->[EgaAccessionMixin],[DataTransformation]^-[Analysis],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[File],[EgaAccessionMixin],[Dataset],[DataTransformation],[File]<has%20output%201..*-++[Analysis&#124;type:string%20%3F;reference_genome:string;reference_chromosome:string;description:string%20%3F;alias:string%20%3F;accession:string;ega_accession:string;title(i):string%20%3F;id(i):string;xref(i):string%20*],[Study]<has%20study%201..1-++[Analysis],[File]<has%20input%201..*-++[Analysis],[Dataset]++-%20has%20analysis%200..*>[Analysis],[Dataset]-%20has%20analysis(i)%200..1>[Analysis],[Submission]-%20has%20analysis(i)%200..1>[Analysis],[Submission]++-%20has%20analysis%200..*>[Analysis],[Analysis]uses%20-.->[AccessionMixin],[Analysis]uses%20-.->[EgaAccessionMixin],[DataTransformation]^-[Analysis],[AccessionMixin])
[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[File],[EgaAccessionMixin],[DataTransformation],[File]<has%20output%201..*-++[Analysis&#124;type:string%20%3F;reference_genome:string;reference_chromosome:string;description:string%20%3F;alias:string%20%3F;accession:string;ega_accession:string;title(i):string%20%3F;id(i):string;xref(i):string%20*],[Study]<has%20study%201..1-++[Analysis],[File]<has%20input%201..*-++[Analysis],[Submission]-%20has%20analysis(i)%200..1>[Analysis],[Submission]++-%20has%20analysis%200..*>[Analysis],[Analysis]uses%20-.->[AccessionMixin],[Analysis]uses%20-.->[EgaAccessionMixin],[DataTransformation]^-[Analysis],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[File],[EgaAccessionMixin],[DataTransformation],[File]<has%20output%201..*-++[Analysis&#124;type:string%20%3F;reference_genome:string;reference_chromosome:string;description:string%20%3F;alias:string%20%3F;accession:string;ega_accession:string;title(i):string%20%3F;id(i):string;xref(i):string%20*],[Study]<has%20study%201..1-++[Analysis],[File]<has%20input%201..*-++[Analysis],[Submission]-%20has%20analysis(i)%200..1>[Analysis],[Submission]++-%20has%20analysis%200..*>[Analysis],[Analysis]uses%20-.->[AccessionMixin],[Analysis]uses%20-.->[EgaAccessionMixin],[DataTransformation]^-[Analysis],[AccessionMixin])

## Parents

Expand All @@ -20,7 +20,6 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Analysis](https://w3id.or

## Referenced by Class

* **[Dataset](Dataset.md)** *[dataset➞has analysis](dataset_has_analysis.md)* <sub>0..\*</sub> **[Analysis](Analysis.md)**
* **None** *[has analysis](has_analysis.md)* <sub>0..1</sub> **[Analysis](Analysis.md)**
* **[Submission](Submission.md)** *[submission➞has analysis](submission_has_analysis.md)* <sub>0..\*</sub> **[Analysis](Analysis.md)**

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21 changes: 3 additions & 18 deletions docs/schema_markdown/Dataset.md
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Expand Up @@ -7,7 +7,7 @@ A Dataset is a collection of Files that is prepared for distribution and is tied
URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Dataset](https://w3id.org/GHGA-Submission-Metadata-Schema/Dataset)


[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[Sample],[Publication],[InformationContentEntity],[File],[Experiment],[EgaAccessionMixin],[DataAccessPolicy]<has%20data%20access%20policy%201..1-++[Dataset&#124;title:string;description:string;type:string%20%2B;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[Publication]<has%20publication%200..*-++[Dataset],[File]<has%20file%201..*-++[Dataset],[Analysis]<has%20analysis%200..*-++[Dataset],[Sample]<has%20sample%201..*-++[Dataset],[Experiment]<has%20experiment%201..*-++[Dataset],[Study]<has%20study%201..*-++[Dataset],[Submission]-%20has%20dataset(i)%200..1>[Dataset],[Submission]++-%20has%20dataset%201..*>[Dataset],[Dataset]uses%20-.->[AccessionMixin],[Dataset]uses%20-.->[EgaAccessionMixin],[Dataset]uses%20-.->[AttributeMixin],[InformationContentEntity]^-[Dataset],[DataAccessPolicy],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[Sample],[Publication],[InformationContentEntity],[File],[Experiment],[EgaAccessionMixin],[DataAccessPolicy]<has%20data%20access%20policy%201..1-++[Dataset&#124;title:string;description:string;type:string%20%2B;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[Publication]<has%20publication%200..*-++[Dataset],[File]<has%20file%201..*-++[Dataset],[Analysis]<has%20analysis%200..*-++[Dataset],[Sample]<has%20sample%201..*-++[Dataset],[Experiment]<has%20experiment%201..*-++[Dataset],[Study]<has%20study%201..*-++[Dataset],[Submission]-%20has%20dataset(i)%200..1>[Dataset],[Submission]++-%20has%20dataset%201..*>[Dataset],[Dataset]uses%20-.->[AccessionMixin],[Dataset]uses%20-.->[EgaAccessionMixin],[Dataset]uses%20-.->[AttributeMixin],[InformationContentEntity]^-[Dataset],[DataAccessPolicy],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin])
[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Publication],[InformationContentEntity],[File],[EgaAccessionMixin],[DataAccessPolicy]<has%20data%20access%20policy%201..1-++[Dataset&#124;title:string;description:string;type:string%20%2B;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[Publication]<has%20publication%200..1-%20[Dataset],[File]<has%20file%201..*-++[Dataset],[Submission]-%20has%20dataset(i)%200..1>[Dataset],[Submission]++-%20has%20dataset%201..*>[Dataset],[Dataset]uses%20-.->[AccessionMixin],[Dataset]uses%20-.->[EgaAccessionMixin],[Dataset]uses%20-.->[AttributeMixin],[InformationContentEntity]^-[Dataset],[DataAccessPolicy],[AttributeMixin],[Attribute],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Publication],[InformationContentEntity],[File],[EgaAccessionMixin],[DataAccessPolicy]<has%20data%20access%20policy%201..1-++[Dataset&#124;title:string;description:string;type:string%20%2B;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[Publication]<has%20publication%200..1-%20[Dataset],[File]<has%20file%201..*-++[Dataset],[Submission]-%20has%20dataset(i)%200..1>[Dataset],[Submission]++-%20has%20dataset%201..*>[Dataset],[Dataset]uses%20-.->[AccessionMixin],[Dataset]uses%20-.->[EgaAccessionMixin],[Dataset]uses%20-.->[AttributeMixin],[InformationContentEntity]^-[Dataset],[DataAccessPolicy],[AttributeMixin],[Attribute],[AccessionMixin])

## Parents

Expand Down Expand Up @@ -38,27 +38,12 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Dataset](https://w3id.org
* [dataset➞type](dataset_type.md) <sub>1..\*</sub>
* Description: The type of a dataset.
* Range: [String](types/String.md)
* [dataset➞has study](dataset_has_study.md) <sub>1..\*</sub>
* Description: One or more Study entities that are referenced by this Dataset.
* Range: [Study](Study.md)
* [dataset➞has experiment](dataset_has_experiment.md) <sub>1..\*</sub>
* Description: One or more Experiment entities that are referenced by this Dataset.
* Range: [Experiment](Experiment.md)
* in subsets: (restricted)
* [dataset➞has sample](dataset_has_sample.md) <sub>1..\*</sub>
* Description: One or more Sample entities that are referenced by this Dataset.
* Range: [Sample](Sample.md)
* in subsets: (restricted)
* [dataset➞has analysis](dataset_has_analysis.md) <sub>0..\*</sub>
* Description: One or more Analysis entities that are referenced by this Dataset.
* Range: [Analysis](Analysis.md)
* in subsets: (restricted)
* [dataset➞has file](dataset_has_file.md) <sub>1..\*</sub>
* Description: One or more File entities that collectively are part of this Dataset.
* Range: [File](File.md)
* in subsets: (restricted)
* [dataset➞has publication](dataset_has_publication.md) <sub>0..\*</sub>
* Description: One or more Publication entities associated with this Dataset.
* [has publication](has_publication.md) <sub>0..1</sub>
* Description: The Publication associated with an entity.
* Range: [Publication](Publication.md)
* [dataset➞has data access policy](dataset_has_data_access_policy.md) <sub>1..1</sub>
* Description: The Data Access Policy that applies to this Dataset.
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3 changes: 1 addition & 2 deletions docs/schema_markdown/Experiment.md
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Expand Up @@ -7,7 +7,7 @@ An experiment is an investigation that consists of a coordinated set of actions
URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Experiment](https://w3id.org/GHGA-Submission-Metadata-Schema/Experiment)


[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[Sample],[Protocol],[Investigation],[File],[Protocol]<has%20protocol%201..*-++[Experiment&#124;type:string%20%3F;biological_replicates:string%20%3F;technical_replicates:string%20%3F;title:string%20%3F;description:string;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[File]<has%20file%201..*-++[Experiment],[Sample]<has%20sample%201..*-++[Experiment],[Study]<has%20study%201..1-++[Experiment],[Dataset]++-%20has%20experiment%201..*>[Experiment],[Dataset]-%20has%20experiment(i)%200..1>[Experiment],[Submission]-%20has%20experiment(i)%200..1>[Experiment],[Submission]++-%20has%20experiment%200..*>[Experiment],[Experiment]uses%20-.->[AttributeMixin],[Experiment]uses%20-.->[AccessionMixin],[Experiment]uses%20-.->[EgaAccessionMixin],[Investigation]^-[Experiment],[EgaAccessionMixin],[Dataset],[AttributeMixin],[Attribute],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[Sample],[Protocol],[Investigation],[File],[Protocol]<has%20protocol%201..*-++[Experiment&#124;type:string%20%3F;biological_replicates:string%20%3F;technical_replicates:string%20%3F;title:string%20%3F;description:string;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[File]<has%20file%201..*-++[Experiment],[Sample]<has%20sample%201..*-++[Experiment],[Study]<has%20study%201..1-++[Experiment],[Dataset]++-%20has%20experiment%201..*>[Experiment],[Dataset]-%20has%20experiment(i)%200..1>[Experiment],[Submission]-%20has%20experiment(i)%200..1>[Experiment],[Submission]++-%20has%20experiment%200..*>[Experiment],[Experiment]uses%20-.->[AttributeMixin],[Experiment]uses%20-.->[AccessionMixin],[Experiment]uses%20-.->[EgaAccessionMixin],[Investigation]^-[Experiment],[EgaAccessionMixin],[Dataset],[AttributeMixin],[Attribute],[AccessionMixin])
[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[Sample],[Protocol],[Investigation],[File],[Protocol]<has%20protocol%201..*-++[Experiment&#124;type:string%20%3F;biological_replicates:string%20%3F;technical_replicates:string%20%3F;title:string%20%3F;description:string;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[File]<has%20file%201..*-++[Experiment],[Sample]<has%20sample%201..*-++[Experiment],[Study]<has%20study%201..1-++[Experiment],[Submission]-%20has%20experiment(i)%200..1>[Experiment],[Submission]++-%20has%20experiment%200..*>[Experiment],[Experiment]uses%20-.->[AttributeMixin],[Experiment]uses%20-.->[AccessionMixin],[Experiment]uses%20-.->[EgaAccessionMixin],[Investigation]^-[Experiment],[EgaAccessionMixin],[AttributeMixin],[Attribute],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[Sample],[Protocol],[Investigation],[File],[Protocol]<has%20protocol%201..*-++[Experiment&#124;type:string%20%3F;biological_replicates:string%20%3F;technical_replicates:string%20%3F;title:string%20%3F;description:string;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[File]<has%20file%201..*-++[Experiment],[Sample]<has%20sample%201..*-++[Experiment],[Study]<has%20study%201..1-++[Experiment],[Submission]-%20has%20experiment(i)%200..1>[Experiment],[Submission]++-%20has%20experiment%200..*>[Experiment],[Experiment]uses%20-.->[AttributeMixin],[Experiment]uses%20-.->[AccessionMixin],[Experiment]uses%20-.->[EgaAccessionMixin],[Investigation]^-[Experiment],[EgaAccessionMixin],[AttributeMixin],[Attribute],[AccessionMixin])

## Parents

Expand All @@ -21,7 +21,6 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Experiment](https://w3id.

## Referenced by Class

* **[Dataset](Dataset.md)** *[dataset➞has experiment](dataset_has_experiment.md)* <sub>1..\*</sub> **[Experiment](Experiment.md)**
* **None** *[has experiment](has_experiment.md)* <sub>0..1</sub> **[Experiment](Experiment.md)**
* **[Submission](Submission.md)** *[submission➞has experiment](submission_has_experiment.md)* <sub>0..\*</sub> **[Experiment](Experiment.md)**

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3 changes: 1 addition & 2 deletions docs/schema_markdown/File.md
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Expand Up @@ -7,7 +7,7 @@ A file is an object that contains information generated from a process, either a
URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/File](https://w3id.org/GHGA-Submission-Metadata-Schema/File)


[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[InformationContentEntity],[Individual],[Analysis]++-%20has%20input%201..*>[File&#124;name:string;format:file_format_enum;size:integer;checksum:string;checksum_type:string;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[Analysis]++-%20has%20output%201..*>[File],[Dataset]++-%20has%20file%201..*>[File],[Experiment]++-%20has%20file%201..*>[File],[Study]-%20has%20file(i)%200..1>[File],[Experiment]-%20has%20file(i)%200..1>[File],[Individual]-%20has%20file(i)%200..1>[File],[Dataset]-%20has%20file(i)%200..1>[File],[Submission]-%20has%20file(i)%200..1>[File],[Analysis]-%20has%20input(i)%200..1>[File],[Analysis]-%20has%20output(i)%200..1>[File],[Individual]++-%20has%20file%200..*>[File],[Study]++-%20has%20file%200..*>[File],[Submission]++-%20has%20file%201..*>[File],[File]uses%20-.->[AccessionMixin],[File]uses%20-.->[EgaAccessionMixin],[File]uses%20-.->[AttributeMixin],[InformationContentEntity]^-[File],[Experiment],[EgaAccessionMixin],[Dataset],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[InformationContentEntity],[Individual],[Analysis]++-%20has%20input%201..*>[File&#124;name:string;format:file_format_enum;size:integer;checksum:string;checksum_type:string;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[Analysis]++-%20has%20output%201..*>[File],[Dataset]++-%20has%20file%201..*>[File],[Experiment]++-%20has%20file%201..*>[File],[Study]-%20has%20file(i)%200..1>[File],[Experiment]-%20has%20file(i)%200..1>[File],[Individual]-%20has%20file(i)%200..1>[File],[Dataset]-%20has%20file(i)%200..1>[File],[Submission]-%20has%20file(i)%200..1>[File],[Analysis]-%20has%20input(i)%200..1>[File],[Analysis]-%20has%20output(i)%200..1>[File],[Individual]++-%20has%20file%200..*>[File],[Study]++-%20has%20file%200..*>[File],[Submission]++-%20has%20file%201..*>[File],[File]uses%20-.->[AccessionMixin],[File]uses%20-.->[EgaAccessionMixin],[File]uses%20-.->[AttributeMixin],[InformationContentEntity]^-[File],[Experiment],[EgaAccessionMixin],[Dataset],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin])
[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[InformationContentEntity],[Individual],[Analysis]++-%20has%20input%201..*>[File&#124;name:string;format:file_format_enum;size:integer;checksum:string;checksum_type:string;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[Analysis]++-%20has%20output%201..*>[File],[Dataset]++-%20has%20file%201..*>[File],[Experiment]++-%20has%20file%201..*>[File],[Experiment]-%20has%20file(i)%200..1>[File],[Individual]-%20has%20file(i)%200..1>[File],[Dataset]-%20has%20file(i)%200..1>[File],[Submission]-%20has%20file(i)%200..1>[File],[Analysis]-%20has%20input(i)%200..1>[File],[Analysis]-%20has%20output(i)%200..1>[File],[Individual]++-%20has%20file%200..*>[File],[Submission]++-%20has%20file%201..*>[File],[File]uses%20-.->[AccessionMixin],[File]uses%20-.->[EgaAccessionMixin],[File]uses%20-.->[AttributeMixin],[InformationContentEntity]^-[File],[Experiment],[EgaAccessionMixin],[Dataset],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[InformationContentEntity],[Individual],[Analysis]++-%20has%20input%201..*>[File&#124;name:string;format:file_format_enum;size:integer;checksum:string;checksum_type:string;accession:string;ega_accession:string;id(i):string;alias(i):string;xref(i):string%20*],[Analysis]++-%20has%20output%201..*>[File],[Dataset]++-%20has%20file%201..*>[File],[Experiment]++-%20has%20file%201..*>[File],[Experiment]-%20has%20file(i)%200..1>[File],[Individual]-%20has%20file(i)%200..1>[File],[Dataset]-%20has%20file(i)%200..1>[File],[Submission]-%20has%20file(i)%200..1>[File],[Analysis]-%20has%20input(i)%200..1>[File],[Analysis]-%20has%20output(i)%200..1>[File],[Individual]++-%20has%20file%200..*>[File],[Submission]++-%20has%20file%201..*>[File],[File]uses%20-.->[AccessionMixin],[File]uses%20-.->[EgaAccessionMixin],[File]uses%20-.->[AttributeMixin],[InformationContentEntity]^-[File],[Experiment],[EgaAccessionMixin],[Dataset],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin])

## Parents

Expand All @@ -29,7 +29,6 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/File](https://w3id.org/GH
* **None** *[has input](has_input.md)* <sub>0..1</sub> **[File](File.md)**
* **None** *[has output](has_output.md)* <sub>0..1</sub> **[File](File.md)**
* **[Individual](Individual.md)** *[individual➞has file](individual_has_file.md)* <sub>0..\*</sub> **[File](File.md)**
* **[Study](Study.md)** *[study➞has file](study_has_file.md)* <sub>0..\*</sub> **[File](File.md)**
* **[Submission](Submission.md)** *[submission➞has file](submission_has_file.md)* <sub>1..\*</sub> **[File](File.md)**

## Attributes
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