diff --git a/docs/entity_relations.md b/docs/entity_relations.md index cbe9645e..499eca8e 100644 --- a/docs/entity_relations.md +++ b/docs/entity_relations.md @@ -99,6 +99,7 @@ DataAccessPolicy ||--|| DataUsePermission : "has data use permission" DataAccessPolicy ||--}o DataUseModifier : "has data use modifier" DataAccessPolicy ||--}o Attribute : "has attribute" Dataset ||--}| File : "has file" +Dataset ||--|o Publication : "has publication" Dataset ||--|| DataAccessPolicy : "has data access policy" Dataset ||--}o Attribute : "has attribute" File ||--}o Attribute : "has attribute" @@ -133,304 +134,27 @@ Focusses on the relation between Sample, Biospecimen, and Individual. ```mermaid erDiagram -Submission { - string id - string affiliation - string submission_date - string submission_status -} -Publication { - string title - string abstract - string author - integer year - string journal - string doi - string id - string alias - stringList xref -} -Study { - string study_type - stringList affiliation - string accession - string ega_accession - string title - string description - string id - string alias - stringList xref -} -Attribute { - string key - string key_type - string value - string value_type -} -Project { - string accession - string title - string description - string id - string alias - stringList xref -} -Member { - string email - string telephone - string organization - string given_name - string family_name - string additional_name - string id - string alias - stringList xref -} -DataAccessCommittee { - string name - string description - string accession - string ega_accession - string id - string alias - stringList xref -} -DataAccessPolicy { - string name - string description - string policy_text - string policy_url - string data_request_form - string accession - string ega_accession - string id - string alias - stringList xref -} -DataUseModifier { - string id - string concept_identifier - string concept_name - string description - string ontology_name - string ontology_version - string alias - stringList xref -} -DataUsePermission { - string id - string concept_identifier - string concept_name - string description - string ontology_name - string ontology_version - string alias - stringList xref -} -Dataset { - string title - string description - stringList type - string accession - string ega_accession - string id - string alias - stringList xref -} -File { - string name - string file_format - integer size - string checksum - string checksum_type - string accession - string ega_accession - string id - string alias - stringList xref -} -Analysis { - string type - string reference_genome - string reference_chromosome - string description - string accession - string ega_accession - string title - string id - string alias - stringList xref -} -Protocol { - string name - string type - string description - string url - string id - string alias - stringList xref -} -Experiment { - string type - string biological_replicates - string technical_replicates - string accession - string ega_accession - string title - string description - string id - string alias - stringList xref -} -Sample { - string name - string type - string description - string case_control_status - string vital_status - string isolation - string storage - string accession - string ega_accession - string id - string alias - stringList xref +Individual { + } Biospecimen { - string name - string type - string description - string isolation - string storage - string accession - string id - string alias - stringList xref + } -Individual { +Sample { } -Submission ||--|| Study : "has study" -Submission ||--|o Project : "has project" -Submission ||--}o Sample : "has sample" -Submission ||--}o Biospecimen : "has biospecimen" -Submission ||--}o Individual : "has individual" -Submission ||--}o Experiment : "has experiment" -Submission ||--}o Protocol : "has protocol" -Submission ||--}o Analysis : "has analysis" -Submission ||--}| File : "has file" -Submission ||--}| Dataset : "has dataset" -Submission ||--}| DataAccessPolicy : "has data access policy" -Submission ||--}| DataAccessCommittee : "has data access committee" -Submission ||--}| Member : "has member" -Submission ||--}o Publication : "has publication" -Publication ||--|| Study : "has study" -Study ||--|o Project : "has project" -Study ||--}o Attribute : "has attribute" -Project ||--}o Attribute : "has attribute" -DataAccessCommittee ||--|| Member : "main contact" -DataAccessCommittee ||--}o Member : "has member" -DataAccessCommittee ||--}o Attribute : "has attribute" -DataAccessPolicy ||--|| DataAccessCommittee : "has data access committee" -DataAccessPolicy ||--|| DataUsePermission : "has data use permission" -DataAccessPolicy ||--}o DataUseModifier : "has data use modifier" -DataAccessPolicy ||--}o Attribute : "has attribute" -Dataset ||--}| File : "has file" -Dataset ||--}o Publication : "has publication" -Dataset ||--|| DataAccessPolicy : "has data access policy" -Dataset ||--}o Attribute : "has attribute" -File ||--}o Attribute : "has attribute" -Analysis ||--}| File : "has input" -Analysis ||--|| Study : "has study" -Analysis ||--}| File : "has output" -Protocol ||--}| Attribute : "has attribute" -Experiment ||--|| Study : "has study" -Experiment ||--}| Sample : "has sample" -Experiment ||--}| File : "has file" -Experiment ||--}| Protocol : "has protocol" -Experiment ||--}o Attribute : "has attribute" -Sample ||--|| Individual : "has individual" -Sample ||--}| AnatomicalEntity : "has anatomical entity" -Sample ||--|o Biospecimen : "has biospecimen" -Sample ||--}o Attribute : "has attribute" -Biospecimen ||--|| Individual : "has individual" Individual ||--}o Ancestry : "has ancestry" Individual ||--}o Individual : "has parent" Individual ||--}o Individual : "has children" Individual ||--}| Disease : "has disease" Individual ||--}o PhenotypicFeature : "has phenotypic feature" Individual ||--}o File : "has file" -``` - - -## GHGA-Base-Metadata-Schema - -### Basic Diagram: - -```mermaid -erDiagram -NamedThing { - -} -Person { - -} -Committee { - -} -MaterialEntity { - -} -BiologicalQuality { - -} -InformationContentEntity { - -} -PlannedProcess { - -} -Investigation { - -} -DataTransformation { - -} -ResearchActivity { - -} -Protocol { - -} -Population { - -} -DiseaseOrPhenotypicFeature { - -} -OntologyClassMixin { - -} -Attribute { - -} -AccessionMixin { - -} -EgaAccessionMixin { - -} -AttributeMixin { - -} -DeprecatedMixin { - -} - -Protocol ||--}| Attribute : "has attribute" -AttributeMixin ||--}o Attribute : "has attribute" -DeprecatedMixin ||--|| NamedThing : "replaced by" +Biospecimen ||--|| Individual : "has individual" +Sample ||--|| Individual : "has individual" +Sample ||--}| AnatomicalEntity : "has anatomical entity" +Sample ||--|o Biospecimen : "has biospecimen" +Sample ||--}o Attribute : "has attribute" ``` @@ -442,410 +166,26 @@ Focusses on the relation between Experiment, Sample, and File. ```mermaid erDiagram -Submission { - -} -Publication { - -} -Study { - -} -Attribute { - -} -Project { - -} -Member { - -} -DataAccessCommittee { - -} -DataAccessPolicy { - -} -DataUseModifier { - -} -DataUsePermission { - -} -Dataset { - -} File { -} -Analysis { - -} -Protocol { - -} -Experiment { - } Sample { } -Biospecimen { - -} -Individual { - -} -PhenotypicFeature { - -} -Disease { - -} -Ancestry { - -} -AnatomicalEntity { +Experiment { } -Submission ||--|| Study : "has study" -Submission ||--|o Project : "has project" -Submission ||--}o Sample : "has sample" -Submission ||--}o Biospecimen : "has biospecimen" -Submission ||--}o Individual : "has individual" -Submission ||--}o Experiment : "has experiment" -Submission ||--}o Protocol : "has protocol" -Submission ||--}o Analysis : "has analysis" -Submission ||--}| File : "has file" -Submission ||--}| Dataset : "has dataset" -Submission ||--}| DataAccessPolicy : "has data access policy" -Submission ||--}| DataAccessCommittee : "has data access committee" -Submission ||--}| Member : "has member" -Submission ||--}o Publication : "has publication" -Publication ||--|| Study : "has study" -Study ||--|o Project : "has project" -Study ||--}o Attribute : "has attribute" -Project ||--}o Attribute : "has attribute" -DataAccessCommittee ||--|| Member : "main contact" -DataAccessCommittee ||--}o Member : "has member" -DataAccessCommittee ||--}o Attribute : "has attribute" -DataAccessPolicy ||--|| DataAccessCommittee : "has data access committee" -DataAccessPolicy ||--|| DataUsePermission : "has data use permission" -DataAccessPolicy ||--}o DataUseModifier : "has data use modifier" -DataAccessPolicy ||--}o Attribute : "has attribute" -Dataset ||--}| File : "has file" -Dataset ||--|| DataAccessPolicy : "has data access policy" -Dataset ||--}o Attribute : "has attribute" File ||--}o Attribute : "has attribute" -Analysis ||--}| File : "has input" -Analysis ||--|| Study : "has study" -Analysis ||--}| File : "has output" -Protocol ||--}| Attribute : "has attribute" -Experiment ||--|| Study : "has study" -Experiment ||--}| Sample : "has sample" -Experiment ||--}| File : "has file" -Experiment ||--}| Protocol : "has protocol" -Experiment ||--}o Attribute : "has attribute" Sample ||--|| Individual : "has individual" Sample ||--}| AnatomicalEntity : "has anatomical entity" Sample ||--|o Biospecimen : "has biospecimen" Sample ||--}o Attribute : "has attribute" -Biospecimen ||--|| Individual : "has individual" -Individual ||--}o Ancestry : "has ancestry" -Individual ||--}o Individual : "has parent" -Individual ||--}o Individual : "has children" -Individual ||--}| Disease : "has disease" -Individual ||--}o PhenotypicFeature : "has phenotypic feature" -Individual ||--}o File : "has file" - -``` - - - -### Detailed Diagram: - -```mermaid -erDiagram -Submission { - string id - string affiliation - string submission_date - string submission_status -} -Publication { - string title - string abstract - string author - integer year - string journal - string doi - string id - string alias - stringList xref -} -Study { - string study_type - stringList affiliation - string accession - string ega_accession - string title - string description - string id - string alias - stringList xref -} -Attribute { - string key - string key_type - string value - string value_type -} -Project { - string accession - string title - string description - string id - string alias - stringList xref -} -Member { - string email - string telephone - string organization - string given_name - string family_name - string additional_name - string id - string alias - stringList xref -} -DataAccessCommittee { - string name - string description - string accession - string ega_accession - string id - string alias - stringList xref -} -DataAccessPolicy { - string name - string description - string policy_text - string policy_url - string data_request_form - string accession - string ega_accession - string id - string alias - stringList xref -} -DataUseModifier { - string id - string concept_identifier - string concept_name - string description - string ontology_name - string ontology_version - string alias - stringList xref -} -DataUsePermission { - string id - string concept_identifier - string concept_name - string description - string ontology_name - string ontology_version - string alias - stringList xref -} -Dataset { - string title - string description - stringList type - string accession - string ega_accession - string id - string alias - stringList xref -} -File { - string name - string file_format - integer size - string checksum - string checksum_type - string accession - string ega_accession - string id - string alias - stringList xref -} -Analysis { - string type - string reference_genome - string reference_chromosome - string description - string accession - string ega_accession - string title - string id - string alias - stringList xref -} -Protocol { - string name - string type - string description - string url - string id - string alias - stringList xref -} -Experiment { - string type - string biological_replicates - string technical_replicates - string accession - string ega_accession - string title - string description - string id - string alias - stringList xref -} -Sample { - string name - string type - string description - string case_control_status - string vital_status - string isolation - string storage - string accession - string ega_accession - string id - string alias - stringList xref -} -Biospecimen { - string name - string type - string description - string isolation - string storage - string accession - string id - string alias - stringList xref -} -Individual { - string biological_sex - string karyotype - string age_range - string vital_status - string geographical_region - string accession - string ega_accession - string given_name - string family_name - string additional_name - string id - string alias - stringList xref -} -PhenotypicFeature { - string id - string concept_identifier - string concept_name - string description - string ontology_name - string ontology_version - string alias - stringList xref -} -Disease { - string id - string concept_identifier - string concept_name - string description - string ontology_name - string ontology_version - string alias - stringList xref -} -Ancestry { - string id - string concept_identifier - string concept_name - string description - string ontology_name - string ontology_version - string name - string alias - stringList xref -} -AnatomicalEntity { - string id - string concept_identifier - string concept_name - string description - string ontology_name - string ontology_version - string alias - stringList xref -} - -Submission ||--|| Study : "has study" -Submission ||--|o Project : "has project" -Submission ||--}o Sample : "has sample" -Submission ||--}o Biospecimen : "has biospecimen" -Submission ||--}o Individual : "has individual" -Submission ||--}o Experiment : "has experiment" -Submission ||--}o Protocol : "has protocol" -Submission ||--}o Analysis : "has analysis" -Submission ||--}| File : "has file" -Submission ||--}| Dataset : "has dataset" -Submission ||--}| DataAccessPolicy : "has data access policy" -Submission ||--}| DataAccessCommittee : "has data access committee" -Submission ||--}| Member : "has member" -Submission ||--}o Publication : "has publication" -Publication ||--|| Study : "has study" -Study ||--|o Project : "has project" -Study ||--}o Attribute : "has attribute" -Project ||--}o Attribute : "has attribute" -DataAccessCommittee ||--|| Member : "main contact" -DataAccessCommittee ||--}o Member : "has member" -DataAccessCommittee ||--}o Attribute : "has attribute" -DataAccessPolicy ||--|| DataAccessCommittee : "has data access committee" -DataAccessPolicy ||--|| DataUsePermission : "has data use permission" -DataAccessPolicy ||--}o DataUseModifier : "has data use modifier" -DataAccessPolicy ||--}o Attribute : "has attribute" -Dataset ||--}| File : "has file" -Dataset ||--|| DataAccessPolicy : "has data access policy" -Dataset ||--}o Attribute : "has attribute" -File ||--}o Attribute : "has attribute" -Analysis ||--}| File : "has input" -Analysis ||--|| Study : "has study" -Analysis ||--}| File : "has output" -Protocol ||--}| Attribute : "has attribute" Experiment ||--|| Study : "has study" Experiment ||--}| Sample : "has sample" Experiment ||--}| File : "has file" Experiment ||--}| Protocol : "has protocol" Experiment ||--}o Attribute : "has attribute" -Sample ||--|| Individual : "has individual" -Sample ||--}| AnatomicalEntity : "has anatomical entity" -Sample ||--|o Biospecimen : "has biospecimen" -Sample ||--}o Attribute : "has attribute" -Biospecimen ||--|| Individual : "has individual" -Individual ||--}o Ancestry : "has ancestry" -Individual ||--}o Individual : "has parent" -Individual ||--}o Individual : "has children" -Individual ||--}| Disease : "has disease" -Individual ||--}o PhenotypicFeature : "has phenotypic feature" -Individual ||--}o File : "has file" ``` + diff --git a/docs/schema_markdown/Analysis.md b/docs/schema_markdown/Analysis.md index f90bc599..76e87a48 100644 --- a/docs/schema_markdown/Analysis.md +++ b/docs/schema_markdown/Analysis.md @@ -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][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][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][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][Analysis],[Submission]++-%20has%20analysis%200..*>[Analysis],[Analysis]uses%20-.->[AccessionMixin],[Analysis]uses%20-.->[EgaAccessionMixin],[DataTransformation]^-[Analysis],[AccessionMixin]) ## Parents @@ -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)* 0..\* **[Analysis](Analysis.md)** * **None** *[has analysis](has_analysis.md)* 0..1 **[Analysis](Analysis.md)** * **[Submission](Submission.md)** *[submission➞has analysis](submission_has_analysis.md)* 0..\* **[Analysis](Analysis.md)** diff --git a/docs/schema_markdown/Dataset.md b/docs/schema_markdown/Dataset.md index 8e9a7670..cc131790 100644 --- a/docs/schema_markdown/Dataset.md +++ b/docs/schema_markdown/Dataset.md @@ -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][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][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][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][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 @@ -38,27 +38,12 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Dataset](https://w3id.org * [dataset➞type](dataset_type.md) 1..\* * Description: The type of a dataset. * Range: [String](types/String.md) - * [dataset➞has study](dataset_has_study.md) 1..\* - * Description: One or more Study entities that are referenced by this Dataset. - * Range: [Study](Study.md) - * [dataset➞has experiment](dataset_has_experiment.md) 1..\* - * 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) 1..\* - * 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) 0..\* - * 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) 1..\* * 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) 0..\* - * Description: One or more Publication entities associated with this Dataset. + * [has publication](has_publication.md) 0..1 + * Description: The Publication associated with an entity. * Range: [Publication](Publication.md) * [dataset➞has data access policy](dataset_has_data_access_policy.md) 1..1 * Description: The Data Access Policy that applies to this Dataset. diff --git a/docs/schema_markdown/Experiment.md b/docs/schema_markdown/Experiment.md index a336fbcc..75a36d4e 100644 --- a/docs/schema_markdown/Experiment.md +++ b/docs/schema_markdown/Experiment.md @@ -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][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][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][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][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 @@ -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)* 1..\* **[Experiment](Experiment.md)** * **None** *[has experiment](has_experiment.md)* 0..1 **[Experiment](Experiment.md)** * **[Submission](Submission.md)** *[submission➞has experiment](submission_has_experiment.md)* 0..\* **[Experiment](Experiment.md)** diff --git a/docs/schema_markdown/File.md b/docs/schema_markdown/File.md index 9fef4275..291e1164 100644 --- a/docs/schema_markdown/File.md +++ b/docs/schema_markdown/File.md @@ -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|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|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|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|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 @@ -29,7 +29,6 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/File](https://w3id.org/GH * **None** *[has input](has_input.md)* 0..1 **[File](File.md)** * **None** *[has output](has_output.md)* 0..1 **[File](File.md)** * **[Individual](Individual.md)** *[individual➞has file](individual_has_file.md)* 0..\* **[File](File.md)** - * **[Study](Study.md)** *[study➞has file](study_has_file.md)* 0..\* **[File](File.md)** * **[Submission](Submission.md)** *[submission➞has file](submission_has_file.md)* 1..\* **[File](File.md)** ## Attributes diff --git a/docs/schema_markdown/Publication.md b/docs/schema_markdown/Publication.md index 3537d31e..365628bd 100644 --- a/docs/schema_markdown/Publication.md +++ b/docs/schema_markdown/Publication.md @@ -7,7 +7,7 @@ The Publication entity represents a publication. While a publication can be any URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Publication](https://w3id.org/GHGA-Submission-Metadata-Schema/Publication) -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[PublicationMixin],[Dataset]++-%20has%20publication%200..*>[Publication|title:string%20%3F;abstract:string%20%3F;author:string%20%3F;year:integer%20%3F;journal:string%20%3F;doi:string;xref:string%20*;id(i):string;alias(i):string],[Study]-%20has%20publication(i)%200..1>[Publication],[Dataset]-%20has%20publication(i)%200..1>[Publication],[Submission]-%20has%20publication(i)%200..1>[Publication],[PublicationMixin]-%20has%20publication(i)%200..1>[Publication],[PublicationMixin]-%20has%20publication%201..1>[Publication],[Study]++-%20has%20publication%200..*>[Publication],[Submission]++-%20has%20publication%200..*>[Publication],[InformationContentEntity]^-[Publication],[InformationContentEntity],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[PublicationMixin],[Dataset]++-%20has%20publication%200..*>[Publication|title:string%20%3F;abstract:string%20%3F;author:string%20%3F;year:integer%20%3F;journal:string%20%3F;doi:string;xref:string%20*;id(i):string;alias(i):string],[Study]-%20has%20publication(i)%200..1>[Publication],[Dataset]-%20has%20publication(i)%200..1>[Publication],[Submission]-%20has%20publication(i)%200..1>[Publication],[PublicationMixin]-%20has%20publication(i)%200..1>[Publication],[PublicationMixin]-%20has%20publication%201..1>[Publication],[Study]++-%20has%20publication%200..*>[Publication],[Submission]++-%20has%20publication%200..*>[Publication],[InformationContentEntity]^-[Publication],[InformationContentEntity],[Dataset]) +[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[PublicationMixin],[Study][Publication],[Submission]-%20has%20publication(i)%200..1>[Publication],[PublicationMixin]-%20has%20publication(i)%200..1>[Publication],[PublicationMixin]-%20has%20publication%201..1>[Publication],[Submission]++-%20has%20publication%200..*>[Publication],[InformationContentEntity]^-[Publication],[InformationContentEntity],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Study],[PublicationMixin],[Study][Publication],[Submission]-%20has%20publication(i)%200..1>[Publication],[PublicationMixin]-%20has%20publication(i)%200..1>[Publication],[PublicationMixin]-%20has%20publication%201..1>[Publication],[Submission]++-%20has%20publication%200..*>[Publication],[InformationContentEntity]^-[Publication],[InformationContentEntity],[Dataset]) ## Parents @@ -15,10 +15,8 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Publication](https://w3id ## Referenced by Class - * **[Dataset](Dataset.md)** *[dataset➞has publication](dataset_has_publication.md)* 0..\* **[Publication](Publication.md)** * **None** *[has publication](has_publication.md)* 0..1 **[Publication](Publication.md)** * **[PublicationMixin](PublicationMixin.md)** *[publication mixin➞has publication](publication_mixin_has_publication.md)* 1..1 **[Publication](Publication.md)** - * **[Study](Study.md)** *[study➞has publication](study_has_publication.md)* 0..\* **[Publication](Publication.md)** * **[Submission](Submission.md)** *[submission➞has publication](submission_has_publication.md)* 0..\* **[Publication](Publication.md)** ## Attributes @@ -44,6 +42,9 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Publication](https://w3id * [publication➞doi](publication_doi.md) 1..1 * Description: DOI identifier of the Publication. * Range: [String](types/String.md) + * [publication➞has study](publication_has_study.md) 1..1 + * Description: The Study entity associated with this Publication. + * Range: [Study](Study.md) * [publication➞xref](publication_xref.md) 0..\* * Description: One or more cross-references for this Publication. * Range: [String](types/String.md) diff --git a/docs/schema_markdown/Restricted.md b/docs/schema_markdown/Restricted.md index ef8d020d..166b2a79 100644 --- a/docs/schema_markdown/Restricted.md +++ b/docs/schema_markdown/Restricted.md @@ -29,11 +29,8 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/restricted](https://w3id. * [data access policy➞has data use permission](data_access_policy_has_data_use_permission.md) - Data use permission associated with a policy. Typically one or more terms from DUO and should be descendants of 'DUO:0000001 data use permission'. * [data access policy➞policy text](data_access_policy_policy_text.md) - The terms of data use and policy verbiage should be captured here. * [data access policy➞policy url](data_access_policy_policy_url.md) - URL for the policy, if available. This is useful if the terms of the policy is made available online at a resolvable URL. - * [dataset➞has analysis](dataset_has_analysis.md) - One or more Analysis entities that are referenced by this Dataset. * [dataset➞has data access policy](dataset_has_data_access_policy.md) - The Data Access Policy that applies to this Dataset. - * [dataset➞has experiment](dataset_has_experiment.md) - One or more Experiment entities that are referenced by this Dataset. * [dataset➞has file](dataset_has_file.md) - One or more File entities that collectively are part of this Dataset. - * [dataset➞has sample](dataset_has_sample.md) - One or more Sample entities that are referenced by this Dataset. * [experiment➞has file](experiment_has_file.md) - One or more Files entities that are generated as output of this Experiment. * [experiment➞has protocol](experiment_has_protocol.md) - One or more Protocol entities associated with this Experiment. * [experiment➞has sample](experiment_has_sample.md) - The Sample entity associated with this Experiment. @@ -91,7 +88,6 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/restricted](https://w3id. * [sequencing protocol➞has attribute](sequencing_protocol_has_attribute.md) - One or more attributes that further characterizes this Sequencing Protocol. * [sex](sex.md) - The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female. * [study➞has attribute](study_has_attribute.md) - Custom key/value pairs that further characterizes the Study. (e.g.: approaches - single-cell, bulk etc) - * [study➞has file](study_has_file.md) - Additional/supplementary files associated with a Study. * [submission➞has analysis](submission_has_analysis.md) - Information about one or more Analysis entities associated with this submission. * [submission➞has biospecimen](submission_has_biospecimen.md) - Information about one or more Biospecimen entities associated with this submission. * [submission➞has data access committee](submission_has_data_access_committee.md) - The Data Access Committee that applies to Dataset in this submission. diff --git a/docs/schema_markdown/Sample.md b/docs/schema_markdown/Sample.md index 13a5ec9c..1e184b7b 100644 --- a/docs/schema_markdown/Sample.md +++ b/docs/schema_markdown/Sample.md @@ -7,7 +7,7 @@ A sample is a limited quantity of something to be used for testing, analysis, in URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Sample](https://w3id.org/GHGA-Submission-Metadata-Schema/Sample) -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Biospecimen][Sample],[Experiment]++-%20has%20sample%201..*>[Sample],[Experiment]-%20has%20sample(i)%200..1>[Sample],[Dataset]-%20has%20sample(i)%200..1>[Sample],[Submission]-%20has%20sample(i)%200..1>[Sample],[Submission]++-%20has%20sample%200..*>[Sample],[Sample]uses%20-.->[AccessionMixin],[Sample]uses%20-.->[EgaAccessionMixin],[Sample]uses%20-.->[AttributeMixin],[MaterialEntity]^-[Sample],[MaterialEntity],[Individual],[Experiment],[EgaAccessionMixin],[Dataset],[Biospecimen],[AttributeMixin],[Attribute],[AnatomicalEntity],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Biospecimen][Sample],[Experiment]++-%20has%20sample%201..*>[Sample],[Experiment]-%20has%20sample(i)%200..1>[Sample],[Dataset]-%20has%20sample(i)%200..1>[Sample],[Submission]-%20has%20sample(i)%200..1>[Sample],[Submission]++-%20has%20sample%200..*>[Sample],[Sample]uses%20-.->[AccessionMixin],[Sample]uses%20-.->[EgaAccessionMixin],[Sample]uses%20-.->[AttributeMixin],[MaterialEntity]^-[Sample],[MaterialEntity],[Individual],[Experiment],[EgaAccessionMixin],[Dataset],[Biospecimen],[AttributeMixin],[Attribute],[AnatomicalEntity],[AccessionMixin]) +[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Biospecimen][Sample],[Experiment]-%20has%20sample(i)%200..1>[Sample],[Submission]-%20has%20sample(i)%200..1>[Sample],[Submission]++-%20has%20sample%200..*>[Sample],[Sample]uses%20-.->[AccessionMixin],[Sample]uses%20-.->[EgaAccessionMixin],[Sample]uses%20-.->[AttributeMixin],[MaterialEntity]^-[Sample],[MaterialEntity],[Individual],[Experiment],[EgaAccessionMixin],[Biospecimen],[AttributeMixin],[Attribute],[AnatomicalEntity],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Biospecimen][Sample],[Experiment]-%20has%20sample(i)%200..1>[Sample],[Submission]-%20has%20sample(i)%200..1>[Sample],[Submission]++-%20has%20sample%200..*>[Sample],[Sample]uses%20-.->[AccessionMixin],[Sample]uses%20-.->[EgaAccessionMixin],[Sample]uses%20-.->[AttributeMixin],[MaterialEntity]^-[Sample],[MaterialEntity],[Individual],[Experiment],[EgaAccessionMixin],[Biospecimen],[AttributeMixin],[Attribute],[AnatomicalEntity],[AccessionMixin]) ## Parents @@ -21,7 +21,6 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Sample](https://w3id.org/ ## Referenced by Class - * **[Dataset](Dataset.md)** *[dataset➞has sample](dataset_has_sample.md)* 1..\* **[Sample](Sample.md)** * **[Experiment](Experiment.md)** *[experiment➞has sample](experiment_has_sample.md)* 1..\* **[Sample](Sample.md)** * **None** *[has sample](has_sample.md)* 0..1 **[Sample](Sample.md)** * **[Submission](Submission.md)** *[submission➞has sample](submission_has_sample.md)* 0..\* **[Sample](Sample.md)** diff --git a/docs/schema_markdown/Study.md b/docs/schema_markdown/Study.md index d550ed10..f4357f9d 100644 --- a/docs/schema_markdown/Study.md +++ b/docs/schema_markdown/Study.md @@ -7,7 +7,7 @@ Studies are experimental investigations of a particular phenomenon. It involves URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Study](https://w3id.org/GHGA-Submission-Metadata-Schema/Study) -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Attribute][Study],[Dataset]++-%20has%20study%201..*>[Study],[Experiment]++-%20has%20study%201..1>[Study],[Experiment]-%20has%20study(i)%200..1>[Study],[Analysis]-%20has%20study(i)%200..1>[Study],[Dataset]-%20has%20study(i)%200..1>[Study],[Submission]-%20has%20study(i)%200..1>[Study],[Submission]++-%20has%20study%201..1>[Study],[Study]uses%20-.->[AccessionMixin],[Study]uses%20-.->[EgaAccessionMixin],[Study]uses%20-.->[AttributeMixin],[Investigation]^-[Study],[Publication],[Project],[Investigation],[File],[Experiment],[EgaAccessionMixin],[Dataset],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Attribute][Study],[Dataset]++-%20has%20study%201..*>[Study],[Experiment]++-%20has%20study%201..1>[Study],[Experiment]-%20has%20study(i)%200..1>[Study],[Analysis]-%20has%20study(i)%200..1>[Study],[Dataset]-%20has%20study(i)%200..1>[Study],[Submission]-%20has%20study(i)%200..1>[Study],[Submission]++-%20has%20study%201..1>[Study],[Study]uses%20-.->[AccessionMixin],[Study]uses%20-.->[EgaAccessionMixin],[Study]uses%20-.->[AttributeMixin],[Investigation]^-[Study],[Publication],[Project],[Investigation],[File],[Experiment],[EgaAccessionMixin],[Dataset],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin]) +[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Attribute][Study],[Experiment]++-%20has%20study%201..1>[Study],[Experiment]-%20has%20study(i)%200..1>[Study],[Analysis]-%20has%20study(i)%200..1>[Study],[Publication]-%20has%20study(i)%200..1>[Study],[Submission]-%20has%20study(i)%200..1>[Study],[Publication]++-%20has%20study%201..1>[Study],[Submission]++-%20has%20study%201..1>[Study],[Study]uses%20-.->[AccessionMixin],[Study]uses%20-.->[EgaAccessionMixin],[Study]uses%20-.->[AttributeMixin],[Investigation]^-[Study],[Publication],[Project],[Investigation],[Experiment],[EgaAccessionMixin],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Attribute][Study],[Experiment]++-%20has%20study%201..1>[Study],[Experiment]-%20has%20study(i)%200..1>[Study],[Analysis]-%20has%20study(i)%200..1>[Study],[Publication]-%20has%20study(i)%200..1>[Study],[Submission]-%20has%20study(i)%200..1>[Study],[Publication]++-%20has%20study%201..1>[Study],[Submission]++-%20has%20study%201..1>[Study],[Study]uses%20-.->[AccessionMixin],[Study]uses%20-.->[EgaAccessionMixin],[Study]uses%20-.->[AttributeMixin],[Investigation]^-[Study],[Publication],[Project],[Investigation],[Experiment],[EgaAccessionMixin],[AttributeMixin],[Attribute],[Analysis],[AccessionMixin]) ## Parents @@ -22,9 +22,9 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Study](https://w3id.org/G ## Referenced by Class * **[Analysis](Analysis.md)** *[analysis➞has study](analysis_has_study.md)* 1..1 **[Study](Study.md)** - * **[Dataset](Dataset.md)** *[dataset➞has study](dataset_has_study.md)* 1..\* **[Study](Study.md)** * **[Experiment](Experiment.md)** *[experiment➞has study](experiment_has_study.md)* 1..1 **[Study](Study.md)** * **None** *[has study](has_study.md)* 0..1 **[Study](Study.md)** + * **[Publication](Publication.md)** *[publication➞has study](publication_has_study.md)* 1..1 **[Study](Study.md)** * **[Submission](Submission.md)** *[submission➞has study](submission_has_study.md)* 1..1 **[Study](Study.md)** ## Attributes @@ -41,13 +41,6 @@ URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/Study](https://w3id.org/G * [study➞has project](study_has_project.md) 0..1 * Description: The project associated with this Study. * Range: [Project](Project.md) - * [study➞has file](study_has_file.md) 0..\* - * Description: Additional/supplementary files associated with a Study. - * Range: [File](File.md) - * in subsets: (restricted) - * [study➞has publication](study_has_publication.md) 0..\* - * Description: One or more Publication entities associated with this Study. - * Range: [Publication](Publication.md) * [study➞title](study_title.md) 1..1 * Description: A comprehensive title for the study. * Range: [String](types/String.md) diff --git a/docs/schema_markdown/dataset_has_analysis.md b/docs/schema_markdown/dataset_has_analysis.md deleted file mode 100644 index a89e3ce5..00000000 --- a/docs/schema_markdown/dataset_has_analysis.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: has analysis - - -One or more Analysis entities that are referenced by this Dataset. - -URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_analysis](https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_analysis) - - -## Domain and Range - -[Dataset](Dataset.md) → 0..\* [Analysis](Analysis.md) - -## Parents - - * is_a: [has analysis](has_analysis.md) - -## Children - - -## Used by - - * [Dataset](Dataset.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **In Subsets:** | | restricted | - diff --git a/docs/schema_markdown/dataset_has_experiment.md b/docs/schema_markdown/dataset_has_experiment.md deleted file mode 100644 index 43ba8591..00000000 --- a/docs/schema_markdown/dataset_has_experiment.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: has experiment - - -One or more Experiment entities that are referenced by this Dataset. - -URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_experiment](https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_experiment) - - -## Domain and Range - -[Dataset](Dataset.md) → 1..\* [Experiment](Experiment.md) - -## Parents - - * is_a: [has experiment](has_experiment.md) - -## Children - - -## Used by - - * [Dataset](Dataset.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **In Subsets:** | | restricted | - diff --git a/docs/schema_markdown/dataset_has_publication.md b/docs/schema_markdown/dataset_has_publication.md deleted file mode 100644 index e024d707..00000000 --- a/docs/schema_markdown/dataset_has_publication.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: has publication - - -One or more Publication entities associated with this Dataset. - -URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_publication](https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_publication) - - -## Domain and Range - -[Dataset](Dataset.md) → 0..\* [Publication](Publication.md) - -## Parents - - * is_a: [has publication](has_publication.md) - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/docs/schema_markdown/dataset_has_sample.md b/docs/schema_markdown/dataset_has_sample.md deleted file mode 100644 index 09c96af0..00000000 --- a/docs/schema_markdown/dataset_has_sample.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: has sample - - -One or more Sample entities that are referenced by this Dataset. - -URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_sample](https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_sample) - - -## Domain and Range - -[Dataset](Dataset.md) → 1..\* [Sample](Sample.md) - -## Parents - - * is_a: [has sample](has_sample.md) - -## Children - - -## Used by - - * [Dataset](Dataset.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **In Subsets:** | | restricted | - diff --git a/docs/schema_markdown/dataset_has_study.md b/docs/schema_markdown/dataset_has_study.md deleted file mode 100644 index ddd374cf..00000000 --- a/docs/schema_markdown/dataset_has_study.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: has study - - -One or more Study entities that are referenced by this Dataset. - -URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_study](https://w3id.org/GHGA-Submission-Metadata-Schema/dataset_has_study) - - -## Domain and Range - -[Dataset](Dataset.md) → 1..\* [Study](Study.md) - -## Parents - - * is_a: [has study](has_study.md) - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/docs/schema_markdown/has_analysis.md b/docs/schema_markdown/has_analysis.md index ab112a37..1b563b2d 100644 --- a/docs/schema_markdown/has_analysis.md +++ b/docs/schema_markdown/has_analysis.md @@ -16,7 +16,6 @@ None → 0..1 [Analysis](Analysis.md) ## Children - * [dataset➞has analysis](dataset_has_analysis.md) * [submission➞has analysis](submission_has_analysis.md) ## Used by diff --git a/docs/schema_markdown/has_experiment.md b/docs/schema_markdown/has_experiment.md index 425432ce..d08447a2 100644 --- a/docs/schema_markdown/has_experiment.md +++ b/docs/schema_markdown/has_experiment.md @@ -16,7 +16,6 @@ None → 0..1 [Experiment](Experiment.md) ## Children - * [dataset➞has experiment](dataset_has_experiment.md) * [submission➞has experiment](submission_has_experiment.md) ## Used by diff --git a/docs/schema_markdown/has_file.md b/docs/schema_markdown/has_file.md index 74c12aa9..dd714138 100644 --- a/docs/schema_markdown/has_file.md +++ b/docs/schema_markdown/has_file.md @@ -19,7 +19,6 @@ None → 0..1 [File](File.md) * [dataset➞has file](dataset_has_file.md) * [experiment➞has file](experiment_has_file.md) * [individual➞has file](individual_has_file.md) - * [study➞has file](study_has_file.md) * [submission➞has file](submission_has_file.md) ## Used by diff --git a/docs/schema_markdown/has_publication.md b/docs/schema_markdown/has_publication.md index 821f5f74..c0ecc394 100644 --- a/docs/schema_markdown/has_publication.md +++ b/docs/schema_markdown/has_publication.md @@ -16,10 +16,9 @@ None → 0..1 [Publication](Publication.md) ## Children - * [dataset➞has publication](dataset_has_publication.md) * [publication mixin➞has publication](publication_mixin_has_publication.md) - * [study➞has publication](study_has_publication.md) * [submission➞has publication](submission_has_publication.md) ## Used by + * [Dataset](Dataset.md) diff --git a/docs/schema_markdown/has_sample.md b/docs/schema_markdown/has_sample.md index cdf03a5a..9e7689c4 100644 --- a/docs/schema_markdown/has_sample.md +++ b/docs/schema_markdown/has_sample.md @@ -16,7 +16,6 @@ None → 0..1 [Sample](Sample.md) ## Children - * [dataset➞has sample](dataset_has_sample.md) * [experiment➞has sample](experiment_has_sample.md) * [submission➞has sample](submission_has_sample.md) diff --git a/docs/schema_markdown/has_study.md b/docs/schema_markdown/has_study.md index 0e21aa12..cde31e6c 100644 --- a/docs/schema_markdown/has_study.md +++ b/docs/schema_markdown/has_study.md @@ -17,8 +17,8 @@ None → 0..1 [Study](Study.md) ## Children * [analysis➞has study](analysis_has_study.md) - * [dataset➞has study](dataset_has_study.md) * [experiment➞has study](experiment_has_study.md) + * [publication➞has study](publication_has_study.md) * [submission➞has study](submission_has_study.md) ## Used by diff --git a/docs/schema_markdown/index.md b/docs/schema_markdown/index.md index 8c447d47..7ed74cf5 100644 --- a/docs/schema_markdown/index.md +++ b/docs/schema_markdown/index.md @@ -140,7 +140,6 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi * [given name](given_name.md) - First name. * [person➞given name](person_given_name.md) * [has analysis](has_analysis.md) - The analysis associated with an entity. - * [dataset➞has analysis](dataset_has_analysis.md) - One or more Analysis entities that are referenced by this Dataset. * [submission➞has analysis](submission_has_analysis.md) - Information about one or more Analysis entities associated with this submission. * [has anatomical entity](has_anatomical_entity.md) - Anatomical site associated with an entity. * [sample➞has anatomical entity](sample_has_anatomical_entity.md) @@ -172,13 +171,11 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi * [has disease](has_disease.md) - Disease concept that the entity is associated with. * [individual➞has disease](individual_has_disease.md) - The Disease entity that is associated with this Biospecimen at the time of retrieval from the organism. Typically, a concept from Mondo Disease Ontology. For example, 'MONDO:0003742' indicates that the Individual - from which the Biospecimen was extracted from - suffers from 'Heart Fibrosarcoma'. * [has experiment](has_experiment.md) - The experiment associated with an entity. - * [dataset➞has experiment](dataset_has_experiment.md) - One or more Experiment entities that are referenced by this Dataset. * [submission➞has experiment](submission_has_experiment.md) - Information about one or more Experiment entities associated with this submission. * [has file](has_file.md) - The file associated with an entity. * [dataset➞has file](dataset_has_file.md) - One or more File entities that collectively are part of this Dataset. * [experiment➞has file](experiment_has_file.md) - One or more Files entities that are generated as output of this Experiment. * [individual➞has file](individual_has_file.md) - Additional/supplementary files associated with an Individual. Typically, a phenopacket or pedigree file. - * [study➞has file](study_has_file.md) - Additional/supplementary files associated with a Study. * [submission➞has file](submission_has_file.md) - Information about one or more File entities associated with this submission. * [has individual](has_individual.md) - The subject/individual associated with an entity. * [biospecimen➞has individual](biospecimen_has_individual.md) - The Individual entity from which this Biospecimen was derived. @@ -203,19 +200,16 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi * [experiment➞has protocol](experiment_has_protocol.md) - One or more Protocol entities associated with this Experiment. * [submission➞has protocol](submission_has_protocol.md) - One or more Protocol entities associated with this Submission. * [has publication](has_publication.md) - The Publication associated with an entity. - * [dataset➞has publication](dataset_has_publication.md) - One or more Publication entities associated with this Dataset. * [publication mixin➞has publication](publication_mixin_has_publication.md) - * [study➞has publication](study_has_publication.md) - One or more Publication entities associated with this Study. * [submission➞has publication](submission_has_publication.md) - One or more Publication entities associated with this Submission. * [has sample](has_sample.md) - The sample associated with an entity. - * [dataset➞has sample](dataset_has_sample.md) - One or more Sample entities that are referenced by this Dataset. * [experiment➞has sample](experiment_has_sample.md) - The Sample entity associated with this Experiment. * [submission➞has sample](submission_has_sample.md) - Information about one or more Sample entities associated with this submission. * [has sequencing protocol](has_sequencing_protocol.md) - The sequencing protocol associated with an entity. * [has study](has_study.md) - The study associated with an entity. * [analysis➞has study](analysis_has_study.md) - The Study entity associated with this Analysis. - * [dataset➞has study](dataset_has_study.md) - One or more Study entities that are referenced by this Dataset. * [experiment➞has study](experiment_has_study.md) - The Study entity associated with this Experiment. + * [publication➞has study](publication_has_study.md) - The Study entity associated with this Publication. * [submission➞has study](submission_has_study.md) - Information about a Study entities associated with this submission. * [id](id.md) - An identifier that uniquely represents an entity. * [named thing➞id](named_thing_id.md) - The internal unique identifier for an entity. diff --git a/docs/schema_markdown/publication_has_study.md b/docs/schema_markdown/publication_has_study.md new file mode 100644 index 00000000..fd752c7b --- /dev/null +++ b/docs/schema_markdown/publication_has_study.md @@ -0,0 +1,23 @@ + +# Slot: has study + + +The Study entity associated with this Publication. + +URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/publication_has_study](https://w3id.org/GHGA-Submission-Metadata-Schema/publication_has_study) + + +## Domain and Range + +[Publication](Publication.md) → 1..1 [Study](Study.md) + +## Parents + + * is_a: [has study](has_study.md) + +## Children + + +## Used by + + * [Publication](Publication.md) diff --git a/docs/schema_markdown/study_has_file.md b/docs/schema_markdown/study_has_file.md deleted file mode 100644 index a52b8c05..00000000 --- a/docs/schema_markdown/study_has_file.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: has file - - -Additional/supplementary files associated with a Study. - -URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/study_has_file](https://w3id.org/GHGA-Submission-Metadata-Schema/study_has_file) - - -## Domain and Range - -[Study](Study.md) → 0..\* [File](File.md) - -## Parents - - * is_a: [has file](has_file.md) - -## Children - - -## Used by - - * [Study](Study.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **In Subsets:** | | restricted | - diff --git a/docs/schema_markdown/study_has_publication.md b/docs/schema_markdown/study_has_publication.md deleted file mode 100644 index e77f1644..00000000 --- a/docs/schema_markdown/study_has_publication.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: has publication - - -One or more Publication entities associated with this Study. - -URI: [https://w3id.org/GHGA-Submission-Metadata-Schema/study_has_publication](https://w3id.org/GHGA-Submission-Metadata-Schema/study_has_publication) - - -## Domain and Range - -[Study](Study.md) → 0..\* [Publication](Publication.md) - -## Parents - - * is_a: [has publication](has_publication.md) - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/scripts/generate_linkml_docs.py b/scripts/generate_linkml_docs.py index 48f5520e..c5b7227c 100755 --- a/scripts/generate_linkml_docs.py +++ b/scripts/generate_linkml_docs.py @@ -2,7 +2,7 @@ """Script to generate linkml markdown documents""" from pathlib import Path from filecmp import dircmp -import subprocess +import shutil from tempfile import TemporaryDirectory from typer import run from linkml.generators.markdowngen import MarkdownGenerator @@ -15,6 +15,8 @@ def generate_linkml_markdown(docs_dir: Path): """Function to generate markdown documentations of a given schema""" + shutil.rmtree(docs_dir) + docs_dir.mkdir() return MarkdownGenerator(schema=str(LINKML_YAML), directory_output=True).serialize( directory=docs_dir )