added the importance: required|recommended|optional to each of the fi…

docs/templates/.sheet_documentation_template.md.jinja

@@ -7,7 +7,13 @@
 {% for slot in slots %}
 ### ***{{ slot.name }}***
 **description** : {{ slot.description }}<br>
-**required** : {{ slot.required }}<br>
+{% if slot.requirement == "required" %}
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
+{% elif slot.requirement == "recommended" %}
+**requirement**:  $\color{blue}{\textbf{recommended}}$<br>
+{% else %}
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
+{% endif %}
 {% if 'Enum' in slot.data_type.range  %}
 **data type** : Controlled Vocabulary <br>
 {% else %}

scripts/update_metadata_docs.py

@@ -142,7 +142,8 @@ def extract_slots_from(
         [SchemaView, Union[str, None]], Union[dict, None]
     ] = extract_permissible_values,
 ) -> list[dict]:
-    """Extracts slot information of a given class"""
+    """Extract slot information of a given class. Additionally add the slot significance which takes one the 3 values: required, recommended and optional.
+    """
 
     return [
         {
@@ -152,12 +153,11 @@ def extract_slots_from(
                 "range": slot.range,
                 "enum": add_enum(schema, slot.range),
             },
-            "required": slot.required,
+            "requirement": "required" if slot.required else "recommended" if slot.recommended else "optional"
         }
         for slot in schema.class_induced_slots(sheet_name)
     ]
 
-
 def generate_workbook(
     schema: SchemaView,
     sheets: list[str],

user_docs/metadata/data_dictionary/Analysis.md

@@ -6,29 +6,29 @@ An Analysis is a data transformation that transforms input data to output data.
 ## Fields
 ### ***analysis_method***
 **description** : The alias of the Analysis Method that is associated with this Analysis.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : AnalysisMethod <br>
 ### ***title***
 **description** : The title that describes an entity.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<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>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : string <br>
 ### ***type***
 **description** : The type of this Analysis.<br>
-**required** : False<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : string <br>
 ### ***ega_accession***
 **description** : The EGA accession of the 'Analysis' entity (EGAZ).<br>
-**required** : False<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<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>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : ResearchDataFile <br>
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>

user_docs/metadata/data_dictionary/AnalysisMethod.md

@@ -6,45 +6,49 @@ An Analysis Method captures the workflow steps that were performed to analyze da
 ## Fields
 ### ***name***
 **description** : A name identifying this Analysis Method.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***description***
 **description** : Description of an entity.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***type***
 **description** : The type of an entity. Note: Not to be confused with rdf:type.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***workflow_name***
 **description** : The workflow name.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***workflow_version***
 **description** : The workflow version.<br>
-**required** : False<br>
+**requirement**:  $\color{blue}{\textbf{recommended}}$<br>
 **data type** : string <br>
 ### ***workflow_repository***
 **description** : The workflow repository (e.g., the URL).<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<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>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***workflow_tasks***
 **description** : Tasks performed by the workflow<br>
-**required** : False<br>
+**requirement**:  $\color{blue}{\textbf{recommended}}$<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>
+**requirement**:  $\color{blue}{\textbf{recommended}}$<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>
+**requirement**:  $\color{blue}{\textbf{recommended}}$<br>
+**data type** : Attribute <br>
+### ***attributes***
+**description** : One or more attributes that further characterize this Analysis Method.<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : Attribute <br>
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>

user_docs/metadata/data_dictionary/AnalysisMethodSupportingFile.md

@@ -6,7 +6,7 @@ An Analysis Method Supporting File is a File that contains additional informatio
 ## Fields
 ### ***format***
 **description** : The file format of the Supporting File (e.g., TXT, JSON).<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : Controlled Vocabulary <br>
 
 /// details | Permissible Values
@@ -23,25 +23,25 @@ An Analysis Method Supporting File is a File that contains additional informatio
 
 ### ***analysis_method***
 **description** : The Analysis Process associated with an entity.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : AnalysisMethod <br>
 ### ***name***
 **description** : The given filename.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***dataset***
 **description** : The Dataset alias associated with this File.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : Dataset <br>
 ### ***ega_accession***
 **description** : The EGA accession ID of an entity.<br>
-**required** : False<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : string <br>
 ### ***included_in_submission***
 **description** : Whether a File is included in the Submission or not.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : boolean <br>
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>

user_docs/metadata/data_dictionary/DataAccessCommittee.md

@@ -6,17 +6,17 @@ A group of members that are delegated to grant access to one or more datasets af
 ## Fields
 ### ***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>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***institute***
 **description** : The Institute a person is affiliated with.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***ega_accession***
 **description** : The EGA accession ID of an entity.<br>
-**required** : False<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : string <br>
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>

user_docs/metadata/data_dictionary/DataAccessPolicy.md

@@ -6,23 +6,23 @@ A Data Access Policy specifies under which circumstances, legal or otherwise, a
 ## Fields
 ### ***name***
 **description** : A name for this Data Access Policy.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***description***
 **description** : A short description for this Data Access Policy.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***policy_text***
 **description** : The complete text for the Data Access Policy.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<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>
+**requirement**:  $\color{blue}{\textbf{recommended}}$<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>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : Controlled Vocabulary <br>
 
 /// details | Permissible Values
@@ -37,11 +37,11 @@ A Data Access Policy specifies under which circumstances, legal or otherwise, a
 
 ### ***data_use_permission_id***
 **description** : The DUO ID corresponding to the Data Use Permission term (e.g., DUO:0000004).<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<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>
+**requirement**:  $\color{blue}{\textbf{recommended}}$<br>
 **data type** : Controlled Vocabulary <br>
 
 /// details | Permissible Values
@@ -69,17 +69,17 @@ A Data Access Policy specifies under which circumstances, legal or otherwise, a
 
 ### ***data_use_modifier_ids***
 **description** : The DUO IDs corresponding to the Data Use Modifier terms (e.g., DUO:0000043).<br>
-**required** : False<br>
+**requirement**:  $\color{blue}{\textbf{recommended}}$<br>
 **data type** : string <br>
 ### ***ega_accession***
 **description** : The EGA accession ID of an entity.<br>
-**required** : False<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : string <br>
 ### ***data_access_committee***
 **description** : The Data Access Committee linked to this Data Use Policy.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : DataAccessCommittee <br>
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>

user_docs/metadata/data_dictionary/Dataset.md

@@ -6,29 +6,29 @@ A Dataset is a collection of Files that is prepared for distribution and is tied
 ## Fields
 ### ***title***
 **description** : A title for this Dataset.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***description***
 **description** : A description summarizing this Dataset.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***types***
 **description** : The type of this Dataset.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***ega_accession***
 **description** : The EGA accession ID of an entity.<br>
-**required** : False<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : string <br>
 ### ***data_access_policy***
 **description** : The Data Access Policy that applies to this Dataset.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : DataAccessPolicy <br>
 ### ***study***
 **description** : The Study associated with this Dataset.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : Study <br>
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>

user_docs/metadata/data_dictionary/Experiment.md

@@ -6,33 +6,33 @@ An Experiment is an investigation that consists of a coordinated set of actions
 ## Fields
 ### ***experiment_method***
 **description** : The alias of one or more Experiment Methods that are associated with this Experiment.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : ExperimentMethod <br>
 ### ***title***
 **description** : The title for this Experiment (e.g., GHGAE_PBMC_RNAseq).<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***description***
 **description** : A detailed description of this Experiment.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>
 ### ***type***
 **description** : The type of this Experiment.<br>
-**required** : False<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : string <br>
 ### ***ega_accession***
 **description** : The EGA accession of the 'Run' entity (EGAR).<br>
-**required** : False<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : string <br>
 ### ***sample***
 **description** : The alias of one or more Samples that are associated with this Experiment.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : Sample <br>
 ### ***attributes***
 **description** : Key/value pairs corresponding to an entity.<br>
-**required** : False<br>
+**requirement**:  $\color{green}{\textbf{optional}}$<br>
 **data type** : Attribute <br>
 ### ***alias***
 **description** : The alias for an entity at the time of submission.<br>
-**required** : True<br>
+**requirement**:  $\color{red}{\textbf{required}}$<br> 
 **data type** : string <br>