ghga-de · virag-compbio · Dec 9, 2024 · Dec 17, 2024 · Dec 17, 2024 · Dec 17, 2024
diff --git a/user_docs/metadata/data_dictionary/Analysis.md b/user_docs/metadata/data_dictionary/Analysis.md
@@ -7,28 +7,42 @@ An Analysis is a data transformation that transforms input data to output data.
 ### ***analysis_method***
 **description** : The alias of the Analysis Method that is associated with this Analysis.<br>
 **required** : True<br>
-**data type** : AnalysisMethod <br>
+**importance** : required<br>
+**data_type** : AnalysisMethod<br>
+
 ### ***title***
 **description** : The title that describes an entity.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***description***
 **description** : A description summarizing how this Analysis was carried out (e.g., description of computational tools, pipelines, workflows).<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : optional<br>
+**data_type** : string<br>
+
 ### ***type***
 **description** : The type of this Analysis.<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : optional<br>
+**data_type** : string<br>
+
 ### ***ega_accession***
 **description** : The EGA accession of the 'Analysis' entity (EGAZ).<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : optional<br>
+**data_type** : string<br>
+
 ### ***research_data_files***
 **description** : One or more aliases of the Research Data Files that this Analysis used as input to create Process Data Files.<br>
 **required** : True<br>
-**data type** : ResearchDataFile <br>
+**importance** : required<br>
+**data_type** : ResearchDataFile<br>
+
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
diff --git a/user_docs/metadata/data_dictionary/AnalysisMethod.md b/user_docs/metadata/data_dictionary/AnalysisMethod.md
@@ -7,44 +7,66 @@ An Analysis Method captures the workflow steps that were performed to analyze da
 ### ***name***
 **description** : A name identifying this Analysis Method.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***description***
 **description** : Description of an entity.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***type***
 **description** : The type of an entity. Note: Not to be confused with rdf:type.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***workflow_name***
 **description** : The workflow name.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***workflow_version***
 **description** : The workflow version.<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : recommended<br>
+**data_type** : string<br>
+
 ### ***workflow_repository***
 **description** : The workflow repository (e.g., the URL).<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***workflow_doi***
 **description** : A digital object identifier for the workflow. Can be a publication or the workflow commit that was used for the Analysis.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***workflow_tasks***
 **description** : Tasks performed by the workflow<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : recommended<br>
+**data_type** : string<br>
+
 ### ***parameters***
 **description** : Key/value pairs where key corresponds to a parameter name and value corresponds to a parameter value (e.g., 'aligner' = 'star_salmon',  'hisat2_build_memory' = '200.GB', 'split_fastq' = 50000000).<br>
 **required** : False<br>
-**data type** : Attribute <br>
+**importance** : recommended<br>
+**data_type** : Attribute<br>
+
 ### ***software_versions***
 **description** : key/value pairs where key corresponds to a software name and value corresponds to a version descriptor (e.g., `salmon` = '1.3.0', `trim-galore` = '0.6.6', `bedtools` = '2.29.2').<br>
 **required** : False<br>
-**data type** : Attribute <br>
+**importance** : recommended<br>
+**data_type** : Attribute<br>
+
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
diff --git a/user_docs/metadata/data_dictionary/AnalysisMethodSupportingFile.md b/user_docs/metadata/data_dictionary/AnalysisMethodSupportingFile.md
@@ -7,7 +7,8 @@ An Analysis Method Supporting File is a File that contains additional informatio
 ### ***format***
 **description** : The file format of the Supporting File (e.g., TXT, JSON).<br>
 **required** : True<br>
-**data type** : Controlled Vocabulary <br>
+**importance** : required<br>
+**data_type** : Controlled Vocabulary<br>
 
 /// details | Permissible Values
 | Permissible Values | Description |
@@ -21,27 +22,40 @@ An Analysis Method Supporting File is a File that contains additional informatio
 | `OTHER` | `A file format not captured by the controlled vocabulary.` |
 ///
 
+
 ### ***analysis_method***
 **description** : The Analysis Process associated with an entity.<br>
 **required** : True<br>
-**data type** : AnalysisMethod <br>
+**importance** : required<br>
+**data_type** : AnalysisMethod<br>
+
 ### ***name***
 **description** : The given filename.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***dataset***
 **description** : The Dataset alias associated with this File.<br>
 **required** : True<br>
-**data type** : Dataset <br>
+**importance** : required<br>
+**data_type** : Dataset<br>
+
 ### ***ega_accession***
 **description** : The EGA accession ID of an entity.<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : optional<br>
+**data_type** : string<br>
+
 ### ***included_in_submission***
 **description** : Whether a File is included in the Submission or not.<br>
 **required** : True<br>
-**data type** : boolean <br>
+**importance** : required<br>
+**data_type** : boolean<br>
+
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
diff --git a/user_docs/metadata/data_dictionary/DataAccessCommittee.md b/user_docs/metadata/data_dictionary/DataAccessCommittee.md
@@ -7,16 +7,24 @@ A group of members that are delegated to grant access to one or more datasets af
 ### ***email***
 **description** : The email of the Data Access Committee (e.g., DAC[at]email.com). This property must not include any personally identifiable data.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***institute***
 **description** : The Institute a person is affiliated with.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***ega_accession***
 **description** : The EGA accession ID of an entity.<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : optional<br>
+**data_type** : string<br>
+
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
diff --git a/user_docs/metadata/data_dictionary/DataAccessPolicy.md b/user_docs/metadata/data_dictionary/DataAccessPolicy.md
@@ -7,23 +7,32 @@ A Data Access Policy specifies under which circumstances, legal or otherwise, a
 ### ***name***
 **description** : A name for this Data Access Policy.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***description***
 **description** : A short description for this Data Access Policy.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***policy_text***
 **description** : The complete text for the Data Access Policy.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***policy_url***
 **description** : An alternative to the Data Access Policy text is to provide the URL for the policy. This is useful if the terms of the policy are available online at a resolvable URL.<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : recommended<br>
+**data_type** : string<br>
+
 ### ***data_use_permission_term***
 **description** : The Data Use Permission associated with this Data Use Policy. The used term should be a descendant of 'DUO:0000001: data use permission' (e.g., no restriction).<br>
 **required** : True<br>
-**data type** : Controlled Vocabulary <br>
+**importance** : required<br>
+**data_type** : Controlled Vocabulary<br>
 
 /// details | Permissible Values
 | Permissible Values | Description |
@@ -35,14 +44,18 @@ A Data Access Policy specifies under which circumstances, legal or otherwise, a
 | `POPULATION_ORIGINS_OR_ANCESTRY_RESEARCH_ONLY` | `This data use permission indicates that use of the data is limited to the study of population origins or ancestry.` |
 ///
 
+
 ### ***data_use_permission_id***
 **description** : The DUO ID corresponding to the Data Use Permission term (e.g., DUO:0000004).<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***data_use_modifier_terms***
 **description** : One or more Data Use Modifiers for the Data Use Permission associated with this Data Use Policy. The used terms should be descendants of 'DUO:0000017: data use modifier' (e.g., clinical care use). Please use 'USER_SPECIFIC_RESTRICTION' if no other modifier applies.<br>
 **required** : False<br>
-**data type** : Controlled Vocabulary <br>
+**importance** : recommended<br>
+**data_type** : Controlled Vocabulary<br>
 
 /// details | Permissible Values
 | Permissible Values | Description |
@@ -67,19 +80,28 @@ A Data Access Policy specifies under which circumstances, legal or otherwise, a
 | `POPULATION_ORIGINS_OR_ANCESTRY_RESEARCH_PROHIBITED` | `This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited.` |
 ///
 
+
 ### ***data_use_modifier_ids***
 **description** : The DUO IDs corresponding to the Data Use Modifier terms (e.g., DUO:0000043).<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : recommended<br>
+**data_type** : string<br>
+
 ### ***ega_accession***
 **description** : The EGA accession ID of an entity.<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : optional<br>
+**data_type** : string<br>
+
 ### ***data_access_committee***
 **description** : The Data Access Committee linked to this Data Use Policy.<br>
 **required** : True<br>
-**data type** : DataAccessCommittee <br>
+**importance** : required<br>
+**data_type** : DataAccessCommittee<br>
+
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
diff --git a/user_docs/metadata/data_dictionary/Dataset.md b/user_docs/metadata/data_dictionary/Dataset.md
@@ -7,28 +7,42 @@ A Dataset is a collection of Files that is prepared for distribution and is tied
 ### ***title***
 **description** : A title for this Dataset.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***description***
 **description** : A description summarizing this Dataset.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***types***
 **description** : The type of this Dataset.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+
 ### ***ega_accession***
 **description** : The EGA accession ID of an entity.<br>
 **required** : False<br>
-**data type** : string <br>
+**importance** : optional<br>
+**data_type** : string<br>
+
 ### ***data_access_policy***
 **description** : The Data Access Policy that applies to this Dataset.<br>
 **required** : True<br>
-**data type** : DataAccessPolicy <br>
+**importance** : required<br>
+**data_type** : DataAccessPolicy<br>
+
 ### ***study***
 **description** : The Study associated with this Dataset.<br>
 **required** : True<br>
-**data type** : Study <br>
+**importance** : required<br>
+**data_type** : Study<br>
+
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
 **required** : True<br>
-**data type** : string <br>
+**importance** : required<br>
+**data_type** : string<br>
+