Minor changes (#161)

* Move ega_accession to File base class

* Make ResearchDataFile.experiment plural

* Update artifacts

Author: lkuchenb

docs/entity_relations.md

@@ -94,7 +94,7 @@ ProcessDataFile ||--|| Analysis : "analysis"
 ProcessDataFile ||--|| Dataset : "dataset"
 Analysis ||--|| AnalysisMethod : "analysis_method"
 Analysis ||--}| ResearchDataFile : "research_data_files"
-ResearchDataFile ||--}| Experiment : "experiment"
+ResearchDataFile ||--}| Experiment : "experiments"
 ResearchDataFile ||--|| Dataset : "dataset"
 Experiment ||--|| ExperimentMethod : "experiment_method"
 Experiment ||--|| Sample : "sample"
@@ -152,7 +152,7 @@ Experiment {
 ExperimentMethodSupportingFile ||--|| ExperimentMethod : "experiment_method"
 ExperimentMethodSupportingFile ||--|| Dataset : "dataset"
 ExperimentMethod ||--}o Attribute : "attributes"
-ResearchDataFile ||--}| Experiment : "experiment"
+ResearchDataFile ||--}| Experiment : "experiments"
 ResearchDataFile ||--|| Dataset : "dataset"
 Sample ||--|| Individual : "individual"
 Sample ||--}o Attribute : "attributes"
@@ -220,6 +220,7 @@ erDiagram
 ExperimentMethodSupportingFile {
     SupportingFileFormatEnum format  
     string name  
+    string ega_accession  
     boolean included_in_submission  
     string alias  
 }
@@ -251,8 +252,8 @@ ResearchDataFile {
     ResearchDataFileFormatEnum format  
     integer technical_replicate  
     string sequencing_lane_id  
-    string ega_accession  
     string name  
+    string ega_accession  
     boolean included_in_submission  
     string alias  
 }
@@ -288,7 +289,7 @@ Experiment {
 ExperimentMethodSupportingFile ||--|| ExperimentMethod : "experiment_method"
 ExperimentMethodSupportingFile ||--|| Dataset : "dataset"
 ExperimentMethod ||--}o Attribute : "attributes"
-ResearchDataFile ||--}| Experiment : "experiment"
+ResearchDataFile ||--}| Experiment : "experiments"
 ResearchDataFile ||--|| Dataset : "dataset"
 Sample ||--|| Individual : "individual"
 Sample ||--}o Attribute : "attributes"

docs/schema_markdown/AnalysisMethodSupportingFile.md

@@ -7,7 +7,7 @@ An Analysis Method Supporting File is a File that contains additional informatio
 URI: [GHGA:AnalysisMethodSupportingFile](https://w3id.org/GHGA/AnalysisMethodSupportingFile)
 
 
-[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[File],[Dataset],[AnalysisMethod]<analysis_method%201..1-%20[AnalysisMethodSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20analysis_method_supporting_files%201..*>[AnalysisMethodSupportingFile],[Submission]-%20analysis_method_supporting_files(i)%200..*>[AnalysisMethodSupportingFile],[File]^-[AnalysisMethodSupportingFile],[AnalysisMethod])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[File],[Dataset],[AnalysisMethod]<analysis_method%201..1-%20[AnalysisMethodSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20analysis_method_supporting_files%201..*>[AnalysisMethodSupportingFile],[Submission]-%20analysis_method_supporting_files(i)%200..*>[AnalysisMethodSupportingFile],[File]^-[AnalysisMethodSupportingFile],[AnalysisMethod])
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[File],[Dataset],[AnalysisMethod]<analysis_method%201..1-%20[AnalysisMethodSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;ega_accession(i):string%20%3F;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20analysis_method_supporting_files%201..*>[AnalysisMethodSupportingFile],[Submission]-%20analysis_method_supporting_files(i)%200..*>[AnalysisMethodSupportingFile],[File]^-[AnalysisMethodSupportingFile],[AnalysisMethod])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[File],[Dataset],[AnalysisMethod]<analysis_method%201..1-%20[AnalysisMethodSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;ega_accession(i):string%20%3F;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20analysis_method_supporting_files%201..*>[AnalysisMethodSupportingFile],[Submission]-%20analysis_method_supporting_files(i)%200..*>[AnalysisMethodSupportingFile],[File]^-[AnalysisMethodSupportingFile],[AnalysisMethod])
 
 ## Parents
 
@@ -38,6 +38,9 @@ URI: [GHGA:AnalysisMethodSupportingFile](https://w3id.org/GHGA/AnalysisMethodSup
  * [File➞dataset](File_dataset.md)  <sub>1..1</sub>
      * Description: The Dataset alias associated with this File.
      * Range: [Dataset](Dataset.md)
+ * [File➞ega_accession](File_ega_accession.md)  <sub>0..1</sub>
+     * Description: The EGA accession ID of an entity.
+     * Range: [String](types/String.md)
  * [File➞included_in_submission](File_included_in_submission.md)  <sub>1..1</sub>
      * Description: Whether a File is included in the Submission or not.
      * Range: [Boolean](types/Boolean.md)

docs/schema_markdown/Experiment.md

@@ -7,7 +7,7 @@ An Experiment is an investigation that consists of a coordinated set of actions
 URI: [GHGA:Experiment](https://w3id.org/GHGA/Experiment)
 
 
-[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Sample],[ResearchDataFile],[IdentifiedByAliasMixin],[ExperimentMethod],[Sample]<sample%201..1-%20[Experiment&#124;title:string;description:string;type:string%20%3F;ega_accession:string%20%3F;alias:string],[ExperimentMethod]<experiment_method%201..1-%20[Experiment],[ResearchDataFile]-%20experiment%201..*>[Experiment],[Submission]++-%20experiments%201..*>[Experiment],[ResearchDataFile]-%20experiment(i)%200..1>[Experiment],[Submission]-%20experiments(i)%200..*>[Experiment],[Experiment]uses%20-.->[IdentifiedByAliasMixin],[Experiment]uses%20-.->[AttributeMixin],[AttributeMixin],[Attribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Sample],[ResearchDataFile],[IdentifiedByAliasMixin],[ExperimentMethod],[Sample]<sample%201..1-%20[Experiment&#124;title:string;description:string;type:string%20%3F;ega_accession:string%20%3F;alias:string],[ExperimentMethod]<experiment_method%201..1-%20[Experiment],[ResearchDataFile]-%20experiment%201..*>[Experiment],[Submission]++-%20experiments%201..*>[Experiment],[ResearchDataFile]-%20experiment(i)%200..1>[Experiment],[Submission]-%20experiments(i)%200..*>[Experiment],[Experiment]uses%20-.->[IdentifiedByAliasMixin],[Experiment]uses%20-.->[AttributeMixin],[AttributeMixin],[Attribute])
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Sample],[ResearchDataFile],[IdentifiedByAliasMixin],[ExperimentMethod],[Sample]<sample%201..1-%20[Experiment&#124;title:string;description:string;type:string%20%3F;ega_accession:string%20%3F;alias:string],[ExperimentMethod]<experiment_method%201..1-%20[Experiment],[ResearchDataFile]-%20experiments%201..*>[Experiment],[Submission]++-%20experiments%201..*>[Experiment],[ResearchDataFile]-%20experiments(i)%200..*>[Experiment],[Submission]-%20experiments(i)%200..*>[Experiment],[Experiment]uses%20-.->[IdentifiedByAliasMixin],[Experiment]uses%20-.->[AttributeMixin],[AttributeMixin],[Attribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Sample],[ResearchDataFile],[IdentifiedByAliasMixin],[ExperimentMethod],[Sample]<sample%201..1-%20[Experiment&#124;title:string;description:string;type:string%20%3F;ega_accession:string%20%3F;alias:string],[ExperimentMethod]<experiment_method%201..1-%20[Experiment],[ResearchDataFile]-%20experiments%201..*>[Experiment],[Submission]++-%20experiments%201..*>[Experiment],[ResearchDataFile]-%20experiments(i)%200..*>[Experiment],[Submission]-%20experiments(i)%200..*>[Experiment],[Experiment]uses%20-.->[IdentifiedByAliasMixin],[Experiment]uses%20-.->[AttributeMixin],[AttributeMixin],[Attribute])
 
 ## Uses Mixin
 
@@ -16,9 +16,8 @@ URI: [GHGA:Experiment](https://w3id.org/GHGA/Experiment)
 
 ## Referenced by Class
 
- *  **[ResearchDataFile](ResearchDataFile.md)** *[ResearchDataFile➞experiment](ResearchDataFile_experiment.md)*  <sub>1..\*</sub>  **[Experiment](Experiment.md)**
+ *  **[ResearchDataFile](ResearchDataFile.md)** *[ResearchDataFile➞experiments](ResearchDataFile_experiments.md)*  <sub>1..\*</sub>  **[Experiment](Experiment.md)**
  *  **[Submission](Submission.md)** *[Submission➞experiments](Submission_experiments.md)*  <sub>1..\*</sub>  **[Experiment](Experiment.md)**
- *  **None** *[experiment](experiment.md)*  <sub>0..1</sub>  **[Experiment](Experiment.md)**
  *  **None** *[experiments](experiments.md)*  <sub>0..\*</sub>  **[Experiment](Experiment.md)**
 
 ## Attributes

docs/schema_markdown/ExperimentMethodSupportingFile.md

@@ -7,7 +7,7 @@ An Experiment Method Supporting File is a File that contains additional informat
 URI: [GHGA:ExperimentMethodSupportingFile](https://w3id.org/GHGA/ExperimentMethodSupportingFile)
 
 
-[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[File],[ExperimentMethod]<experiment_method%201..1-%20[ExperimentMethodSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20experiment_method_supporting_files%201..*>[ExperimentMethodSupportingFile],[Submission]-%20experiment_method_supporting_files(i)%200..*>[ExperimentMethodSupportingFile],[File]^-[ExperimentMethodSupportingFile],[ExperimentMethod],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[File],[ExperimentMethod]<experiment_method%201..1-%20[ExperimentMethodSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20experiment_method_supporting_files%201..*>[ExperimentMethodSupportingFile],[Submission]-%20experiment_method_supporting_files(i)%200..*>[ExperimentMethodSupportingFile],[File]^-[ExperimentMethodSupportingFile],[ExperimentMethod],[Dataset])
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[File],[ExperimentMethod]<experiment_method%201..1-%20[ExperimentMethodSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;ega_accession(i):string%20%3F;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20experiment_method_supporting_files%201..*>[ExperimentMethodSupportingFile],[Submission]-%20experiment_method_supporting_files(i)%200..*>[ExperimentMethodSupportingFile],[File]^-[ExperimentMethodSupportingFile],[ExperimentMethod],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[File],[ExperimentMethod]<experiment_method%201..1-%20[ExperimentMethodSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;ega_accession(i):string%20%3F;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20experiment_method_supporting_files%201..*>[ExperimentMethodSupportingFile],[Submission]-%20experiment_method_supporting_files(i)%200..*>[ExperimentMethodSupportingFile],[File]^-[ExperimentMethodSupportingFile],[ExperimentMethod],[Dataset])
 
 ## Parents
 
@@ -38,6 +38,9 @@ URI: [GHGA:ExperimentMethodSupportingFile](https://w3id.org/GHGA/ExperimentMetho
  * [File➞dataset](File_dataset.md)  <sub>1..1</sub>
      * Description: The Dataset alias associated with this File.
      * Range: [Dataset](Dataset.md)
+ * [File➞ega_accession](File_ega_accession.md)  <sub>0..1</sub>
+     * Description: The EGA accession ID of an entity.
+     * Range: [String](types/String.md)
  * [File➞included_in_submission](File_included_in_submission.md)  <sub>1..1</sub>
      * Description: Whether a File is included in the Submission or not.
      * Range: [Boolean](types/Boolean.md)

docs/schema_markdown/File.md

@@ -7,7 +7,7 @@ A file is an object that contains information generated from a process, either a
 URI: [GHGA:File](https://w3id.org/GHGA/File)
 
 
-[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ResearchDataFile],[ProcessDataFile],[IndividualSupportingFile],[IdentifiedByAliasMixin],[Dataset]<dataset%201..1-%20[File&#124;name:string;included_in_submission:boolean;alias:string],[File]uses%20-.->[IdentifiedByAliasMixin],[File]^-[ResearchDataFile],[File]^-[ProcessDataFile],[File]^-[IndividualSupportingFile],[File]^-[ExperimentMethodSupportingFile],[File]^-[AnalysisMethodSupportingFile],[ExperimentMethodSupportingFile],[Dataset],[AnalysisMethodSupportingFile])](https://yuml.me/diagram/nofunky;dir:TB/class/[ResearchDataFile],[ProcessDataFile],[IndividualSupportingFile],[IdentifiedByAliasMixin],[Dataset]<dataset%201..1-%20[File&#124;name:string;included_in_submission:boolean;alias:string],[File]uses%20-.->[IdentifiedByAliasMixin],[File]^-[ResearchDataFile],[File]^-[ProcessDataFile],[File]^-[IndividualSupportingFile],[File]^-[ExperimentMethodSupportingFile],[File]^-[AnalysisMethodSupportingFile],[ExperimentMethodSupportingFile],[Dataset],[AnalysisMethodSupportingFile])
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ResearchDataFile],[ProcessDataFile],[IndividualSupportingFile],[IdentifiedByAliasMixin],[Dataset]<dataset%201..1-%20[File&#124;name:string;ega_accession:string%20%3F;included_in_submission:boolean;alias:string],[File]uses%20-.->[IdentifiedByAliasMixin],[File]^-[ResearchDataFile],[File]^-[ProcessDataFile],[File]^-[IndividualSupportingFile],[File]^-[ExperimentMethodSupportingFile],[File]^-[AnalysisMethodSupportingFile],[ExperimentMethodSupportingFile],[Dataset],[AnalysisMethodSupportingFile])](https://yuml.me/diagram/nofunky;dir:TB/class/[ResearchDataFile],[ProcessDataFile],[IndividualSupportingFile],[IdentifiedByAliasMixin],[Dataset]<dataset%201..1-%20[File&#124;name:string;ega_accession:string%20%3F;included_in_submission:boolean;alias:string],[File]uses%20-.->[IdentifiedByAliasMixin],[File]^-[ResearchDataFile],[File]^-[ProcessDataFile],[File]^-[IndividualSupportingFile],[File]^-[ExperimentMethodSupportingFile],[File]^-[AnalysisMethodSupportingFile],[ExperimentMethodSupportingFile],[Dataset],[AnalysisMethodSupportingFile])
 
 ## Uses Mixin
 
@@ -35,6 +35,9 @@ URI: [GHGA:File](https://w3id.org/GHGA/File)
  * [File➞dataset](File_dataset.md)  <sub>1..1</sub>
      * Description: The Dataset alias associated with this File.
      * Range: [Dataset](Dataset.md)
+ * [File➞ega_accession](File_ega_accession.md)  <sub>0..1</sub>
+     * Description: The EGA accession ID of an entity.
+     * Range: [String](types/String.md)
  * [File➞included_in_submission](File_included_in_submission.md)  <sub>1..1</sub>
      * Description: Whether a File is included in the Submission or not.
      * Range: [Boolean](types/Boolean.md)

docs/schema_markdown/File_ega_accession.md

@@ -0,0 +1,28 @@
+
+# Slot: ega_accession
+
+
+The EGA accession ID of an entity.
+
+URI: [GHGA:File_ega_accession](https://w3id.org/GHGA/File_ega_accession)
+
+
+## Domain and Range
+
+[File](File.md) &#8594;  <sub>0..1</sub> [String](types/String.md)
+
+## Parents
+
+ *  is_a: [ega_accession](ega_accession.md)
+
+## Children
+
+
+## Used by
+
+ * [AnalysisMethodSupportingFile](AnalysisMethodSupportingFile.md)
+ * [ExperimentMethodSupportingFile](ExperimentMethodSupportingFile.md)
+ * [File](File.md)
+ * [IndividualSupportingFile](IndividualSupportingFile.md)
+ * [ProcessDataFile](ProcessDataFile.md)
+ * [ResearchDataFile](ResearchDataFile.md)

docs/schema_markdown/IndividualSupportingFile.md

@@ -7,7 +7,7 @@ An Individual Supporting File is a File that contains additional information rel
 URI: [GHGA:IndividualSupportingFile](https://w3id.org/GHGA/IndividualSupportingFile)
 
 
-[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Individual]<individual%201..1-%20[IndividualSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20individual_supporting_files%201..*>[IndividualSupportingFile],[Submission]-%20individual_supporting_files(i)%200..*>[IndividualSupportingFile],[File]^-[IndividualSupportingFile],[Individual],[File],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Individual]<individual%201..1-%20[IndividualSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20individual_supporting_files%201..*>[IndividualSupportingFile],[Submission]-%20individual_supporting_files(i)%200..*>[IndividualSupportingFile],[File]^-[IndividualSupportingFile],[Individual],[File],[Dataset])
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Individual]<individual%201..1-%20[IndividualSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;ega_accession(i):string%20%3F;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20individual_supporting_files%201..*>[IndividualSupportingFile],[Submission]-%20individual_supporting_files(i)%200..*>[IndividualSupportingFile],[File]^-[IndividualSupportingFile],[Individual],[File],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Individual]<individual%201..1-%20[IndividualSupportingFile&#124;format:SupportingFileFormatEnum;name(i):string;ega_accession(i):string%20%3F;included_in_submission(i):boolean;alias(i):string],[Submission]++-%20individual_supporting_files%201..*>[IndividualSupportingFile],[Submission]-%20individual_supporting_files(i)%200..*>[IndividualSupportingFile],[File]^-[IndividualSupportingFile],[Individual],[File],[Dataset])
 
 ## Parents
 
@@ -38,6 +38,9 @@ URI: [GHGA:IndividualSupportingFile](https://w3id.org/GHGA/IndividualSupportingF
  * [File➞dataset](File_dataset.md)  <sub>1..1</sub>
      * Description: The Dataset alias associated with this File.
      * Range: [Dataset](Dataset.md)
+ * [File➞ega_accession](File_ega_accession.md)  <sub>0..1</sub>
+     * Description: The EGA accession ID of an entity.
+     * Range: [String](types/String.md)
  * [File➞included_in_submission](File_included_in_submission.md)  <sub>1..1</sub>
      * Description: Whether a File is included in the Submission or not.
      * Range: [Boolean](types/Boolean.md)