updated request for changes; updated artifacts

ghga-de · mauerk · Dec 7, 2023 · Aug 1, 2023 · Aug 1, 2023 · Aug 1, 2023
commit de2adcc726d8f69440173b6be2975c9741cd5676
diff --git a/docs/schema_markdown/Analysis.md b/docs/schema_markdown/Analysis.md
@@ -29,13 +29,13 @@ URI: [GHGA:Analysis](https://w3id.org/GHGA/Analysis)
  * Description: The title that describes an entity.
  * Range: [String](types/String.md)
  * [Analysis➞description](Analysis_description.md) <sub>0..1</sub>
- * Description: A description summarizing how an Analysis was carried out, e.g.: computational tools, pipelines, workflows.
+ * Description: A description summarizing how this Analysis was carried out (e.g., computational tools, pipelines, workflows).
  * Range: [String](types/String.md)
  * [Analysis➞type](Analysis_type.md) <sub>0..1</sub>
- * Description: The type of the Analysis. Can be either Reference Alignment (BAM) or Sequence Variation (VCF).
+ * Description: The type of this Analysis.
  * Range: [String](types/String.md)
  * [Analysis➞reference_genome](Analysis_reference_genome.md) <sub>1..1</sub>
- * Description: A published genetic sequence that is used as a reference sequence against which other sequences are compared. Reference genome(s) or annotation(s) used for prior analyses, e.g. GRCh38.p13.
+ * Description: The reference genome or annotation used for prior analyses (e.g., GRCh38.p13).
  * Range: [String](types/String.md)
  * [Analysis➞reference_chromosome](Analysis_reference_chromosome.md) <sub>1..1</sub>
  * Description: The reference chromosome used for this Analysis.

diff --git a/docs/schema_markdown/AnalysisProcess.md b/docs/schema_markdown/AnalysisProcess.md
@@ -2,7 +2,7 @@
 # Class: AnalysisProcess
 
 
-An analysis process captures the workflow steps that were performed to analyze data obtained from sequencing experiments.
+An Analysis Process captures the workflow steps that were performed to analyze data obtained from a Sequencing Experiment.
 
 URI: [GHGA:AnalysisProcess](https://w3id.org/GHGA/AnalysisProcess)
 
@@ -29,7 +29,7 @@ URI: [GHGA:AnalysisProcess](https://w3id.org/GHGA/AnalysisProcess)
  * Description: The name for an entity.
  * Range: [String](types/String.md)
  * [AnalysisProcess➞analysis](AnalysisProcess_analysis.md) <sub>1..1</sub>
- * Description: The Analysis the Analysis Process is part of.
+ * Description: The Analysis that this Analysis Process is part of.
  * Range: [Analysis](Analysis.md)
  * [AnalysisProcess➞study_input_files](AnalysisProcess_study_input_files.md) <sub>0..\*</sub>
  * Description: The associated Study File used as an input for this Analysis Process.

diff --git a/docs/schema_markdown/AnalysisProcessOutputFile.md b/docs/schema_markdown/AnalysisProcessOutputFile.md
@@ -2,7 +2,7 @@
 # Class: AnalysisProcessOutputFile
 
 
-A AnalysisProcessOutputFile is a File that is associated as an output file with an AnalysisProcess.
+A Analysis Process OutputFile is a File that is associated as an output file with an Analysis Process.
 
 URI: [GHGA:AnalysisProcessOutputFile](https://w3id.org/GHGA/AnalysisProcessOutputFile)
 
@@ -33,16 +33,16 @@ URI: [GHGA:AnalysisProcessOutputFile](https://w3id.org/GHGA/AnalysisProcessOutpu
  * Description: The given filename.
  * Range: [String](types/String.md)
  * [File➞format](File_format.md) <sub>1..1</sub>
- * Description: The format of the file, e.g. BAM, SAM, CRAM, BAI.
+ * Description: The format of the File (e.g., BAM, SAM, CRAM, BAI).
  * Range: [FileFormatEnum](FileFormatEnum.md)
  * [File➞size](File_size.md) <sub>1..1</sub>
- * Description: The size of a file in bytes.
+ * Description: The size of the File in bytes.
  * Range: [Integer](types/Integer.md)
  * [File➞checksum](File_checksum.md) <sub>1..1</sub>
- * Description: A computed value which depends on the contents of a block of data and which is transmitted or stored along with the data in order to detect corruption of the data. The receiving system recomputes the checksum based upon the received data and compares this value with the one sent with the data. If the two values are the same, the receiver has some confidence that the data was received correctly.
+ * Description: The checksum of the File.
  * Range: [String](types/String.md)
  * [File➞checksum_type](File_checksum_type.md) <sub>1..1</sub>
- * Description: The type of algorithm used to generate the checksum of a file.
+ * Description: The type of algorithm used to generate the checksum of the File.
  * Range: [String](types/String.md)
  * [File➞forward_or_reverse](File_forward_or_reverse.md) <sub>0..1</sub>
  * Description: Denotes whether a submitted FASTQ file contains forward (R1) or reverse (R2) reads for paired-end sequencing.

diff --git a/docs/schema_markdown/AnalysisProcess_analysis.md b/docs/schema_markdown/AnalysisProcess_analysis.md
@@ -2,7 +2,7 @@
 # Slot: analysis
 
 
-The Analysis the Analysis Process is part of.
+The Analysis that this Analysis Process is part of.
 
 URI: [GHGA:AnalysisProcess_analysis](https://w3id.org/GHGA/AnalysisProcess_analysis)
 

diff --git a/docs/schema_markdown/Analysis_description.md b/docs/schema_markdown/Analysis_description.md
@@ -2,7 +2,7 @@
 # Slot: description
 
 
-A description summarizing how an Analysis was carried out, e.g.: computational tools, pipelines, workflows.
+A description summarizing how this Analysis was carried out (e.g., computational tools, pipelines, workflows).
 
 URI: [GHGA:Analysis_description](https://w3id.org/GHGA/Analysis_description)
 

diff --git a/docs/schema_markdown/Analysis_reference_genome.md b/docs/schema_markdown/Analysis_reference_genome.md
@@ -2,7 +2,7 @@
 # Slot: reference_genome
 
 
-A published genetic sequence that is used as a reference sequence against which other sequences are compared. Reference genome(s) or annotation(s) used for prior analyses, e.g. GRCh38.p13.
+The reference genome or annotation used for prior analyses (e.g., GRCh38.p13).
 
 URI: [GHGA:Analysis_reference_genome](https://w3id.org/GHGA/Analysis_reference_genome)
 

diff --git a/docs/schema_markdown/Analysis_type.md b/docs/schema_markdown/Analysis_type.md
@@ -2,7 +2,7 @@
 # Slot: type
 
 
-The type of the Analysis. Can be either Reference Alignment (BAM) or Sequence Variation (VCF).
+The type of this Analysis.
 
 URI: [GHGA:Analysis_type](https://w3id.org/GHGA/Analysis_type)
 

diff --git a/docs/schema_markdown/Attribute.md b/docs/schema_markdown/Attribute.md
@@ -26,13 +26,13 @@ URI: [GHGA:Attribute](https://w3id.org/GHGA/Attribute)
  * Description: The key of an attribute.
  * Range: [String](types/String.md)
  * [Attribute➞key_type](Attribute_key_type.md) <sub>0..1</sub>
- * Description: A semantic type that characterizes the attribute key. Usually this is a term from an ontology, e.g. 'MAXO:0000616' indicates that the attribute is a measurement of oxygen saturation in the blood.
+ * Description: A semantic type that characterizes the attribute key (e.g., oxygen saturation measurement (MAXO:0000616)).
  * Range: [String](types/String.md)
  * [Attribute➞value](Attribute_value.md) <sub>1..1</sub>
- * Description: The value for an attribute. Usually this is a numerical value (without the units).
+ * Description: The value for an attribute (e.g., a numerical value without the units).
  * Range: [String](types/String.md)
  * [Attribute➞value_type](Attribute_value_type.md) <sub>0..1</sub>
- * Description: The value_type that characterizes the attribute value. Usually this is a term from an ontology that describes how to interpret the value, e.g. 'SIO:001413' indicates that the value is to be interpreted as a percentage.
+ * Description: The value_type that characterizes the attribute value (e.g., percentage (SIO:001413)).
  * Range: [String](types/String.md)
 
 ## Other properties

diff --git a/docs/schema_markdown/AttributeMixin.md b/docs/schema_markdown/AttributeMixin.md
@@ -11,11 +11,11 @@ URI: [GHGA:AttributeMixin](https://w3id.org/GHGA/AttributeMixin)
 
 ## Mixin for
 
- * [Condition](Condition.md) (mixin) - The Condition specifies which special characteristics and treatments apply to a Sample. It is used to link comparable Samples.
- * [LibraryPreparationProtocol](LibraryPreparationProtocol.md) (mixin) - The Library Preparation Protocol captures information about the Library Preparation of an Sequencing Experiment.
- * [Sample](Sample.md) (mixin) - A sample is a limited quantity of something to be used for testing, analysis, inspection, investigation, demonstration, or trial use. A sample is prepared from a Biospecimen (isolate or tissue).
- * [SequencingExperiment](SequencingExperiment.md) (mixin) - An sequencing experiment is an investigation that consists of a coordinated set of actions and observations designed to generate data with the goal of verifying, falsifying, or establishing the validity of a hypothesis.
- * [SequencingProcess](SequencingProcess.md) (mixin) - The Sequencing Process captures the technical parameters that were used to produce sequencing output from a Sample. It links a Sample to sequencing output.
+ * [Condition](Condition.md) (mixin) - A Condition specifies which special characteristics and treatments apply to a Sample. It is used to link comparable Samples (e.g., healthy Samples, wildtype Samples).
+ * [LibraryPreparationProtocol](LibraryPreparationProtocol.md) (mixin) - The Library Preparation Protocol captures information about the library preparation of a Sequencing Experiment.
+ * [Sample](Sample.md) (mixin) - A Sample is a limited quantity of something to be used for testing, analysis, inspection, investigation, demonstration, or trial use. It is prepared from a Biospecimen.
+ * [SequencingExperiment](SequencingExperiment.md) (mixin) - A Sequencing Experiment is an investigation that consists of a coordinated set of actions and observations designed to generate data with the goal of verifying, falsifying, or establishing the validity of a hypothesis.
+ * [SequencingProcess](SequencingProcess.md) (mixin) - The Sequencing Process captures the technical parameters that were used to produce sequencing output from the Sample. It links the Sample to sequencing output.
  * [SequencingProtocol](SequencingProtocol.md) (mixin) - The Sequencing Protocol captures information about parameters and metadata associated with a Sequencing Experiment.
  * [Study](Study.md) (mixin) - A Study is an experimental investigation of a particular phenomenon. It involves a detailed examination and analysis of a subject to learn more about the phenomenon being studied.
 

diff --git a/docs/schema_markdown/Attribute_key_type.md b/docs/schema_markdown/Attribute_key_type.md
@@ -2,7 +2,7 @@
 # Slot: key_type
 
 
-A semantic type that characterizes the attribute key. Usually this is a term from an ontology, e.g. 'MAXO:0000616' indicates that the attribute is a measurement of oxygen saturation in the blood.
+A semantic type that characterizes the attribute key (e.g., oxygen saturation measurement (MAXO:0000616)).
 
 URI: [GHGA:Attribute_key_type](https://w3id.org/GHGA/Attribute_key_type)
 

diff --git a/docs/schema_markdown/Attribute_value.md b/docs/schema_markdown/Attribute_value.md
@@ -2,7 +2,7 @@
 # Slot: value
 
 
-The value for an attribute. Usually this is a numerical value (without the units).
+The value for an attribute (e.g., a numerical value without the units).
 
 URI: [GHGA:Attribute_value](https://w3id.org/GHGA/Attribute_value)
 

diff --git a/docs/schema_markdown/Attribute_value_type.md b/docs/schema_markdown/Attribute_value_type.md
@@ -2,7 +2,7 @@
 # Slot: value_type
 
 
-The value_type that characterizes the attribute value. Usually this is a term from an ontology that describes how to interpret the value, e.g. 'SIO:001413' indicates that the value is to be interpreted as a percentage.
+The value_type that characterizes the attribute value (e.g., percentage (SIO:001413)).
 
 URI: [GHGA:Attribute_value_type](https://w3id.org/GHGA/Attribute_value_type)
 

diff --git a/docs/schema_markdown/Biospecimen.md b/docs/schema_markdown/Biospecimen.md
@@ -2,7 +2,7 @@
 # Class: Biospecimen
 
 
-A Biospecimen is any natural material taken from a biological entity (usually a human) for testing, diagnostics, treatment, or research purposes. The Biospecimen is linked to the Individual from which the Biospecimen is derived.
+A Biospecimen is any natural material taken from a biological entity for testing, diagnostics, treatment, or research purposes. It is linked to the Individual from which the Biospecimen is derived.
 
 URI: [GHGA:Biospecimen](https://w3id.org/GHGA/Biospecimen)
 
@@ -26,30 +26,30 @@ URI: [GHGA:Biospecimen](https://w3id.org/GHGA/Biospecimen)
 ### Own
 
  * [Biospecimen➞name](Biospecimen_name.md) <sub>0..1</sub>
- * Description: A descriptive name of the Biospecimen (e.g. GHGAB_caudate_nucleus_biospecimen). Please do not enter any personally identifiable data!
+ * Description: A descriptive name of this Biospecimen (e.g., GHGAB_caudate_nucleus_biospecimen). This property must not include any personally identifiable data.
  * Range: [String](types/String.md)
  * [Biospecimen➞type](Biospecimen_type.md) <sub>0..1</sub>
  * Description: The type of Biospecimen.
  * Range: [String](types/String.md)
  * [Biospecimen➞description](Biospecimen_description.md) <sub>0..1</sub>
- * Description: A concise description about the Biospecimen source, the collection method, and the protocol which was followed to process the Biospecimen.
+ * Description: A concise description about the Biospecimen source, the collection method, and the protocol which was followed to process this Biospecimen.
  * Range: [String](types/String.md)
  * [Biospecimen➞age_at_sampling](Biospecimen_age_at_sampling.md) <sub>1..1</sub>
- * Description: Age of an individual.
+ * Description: The age of the Individual.
  * Range: [AgeRangeEnum](AgeRangeEnum.md)
  * [Biospecimen➞vital_status_at_sampling](Biospecimen_vital_status_at_sampling.md) <sub>0..1</sub>
- * Description: Vital Status of an Individual at the point of sampling, e.g. 'Alive' or 'Deceased'.
+ * Description: Vital Status of the Individual at the point of sampling (e.g., alive).
  * Range: [VitalStatusEnum](VitalStatusEnum.md)
  * [Biospecimen➞tissue](Biospecimen_tissue.md) <sub>1..1</sub>
  * Description: The tissue this Biospecimen originated from.
  * Range: [String](types/String.md)
  * in subsets: (ontology)
  * [Biospecimen➞isolation](Biospecimen_isolation.md) <sub>0..1</sub>
- * Description: Method or device employed for collecting/isolating the Sample.
+ * Description: Method or device employed for collecting/isolating this Biospecimen.
  * Range: [String](types/String.md)
  * in subsets: (ontology)
  * [Biospecimen➞storage](Biospecimen_storage.md) <sub>0..1</sub>
- * Description: Methods by which the Sample is stored (e.g. frozen in liquid nitrogen).
+ * Description: Methods by which this Biospecimen is stored.
  * Range: [StorageEnum](StorageEnum.md)
  * [Biospecimen➞individual](Biospecimen_individual.md) <sub>1..1</sub>
  * Description: The Individual entity from which this Biospecimen was derived.

diff --git a/docs/schema_markdown/Biospecimen_age_at_sampling.md b/docs/schema_markdown/Biospecimen_age_at_sampling.md
@@ -2,7 +2,7 @@
 # Slot: age_at_sampling
 
 
-Age of an individual.
+The age of the Individual.
 
 URI: [GHGA:Biospecimen_age_at_sampling](https://w3id.org/GHGA/Biospecimen_age_at_sampling)
 

diff --git a/docs/schema_markdown/Biospecimen_description.md b/docs/schema_markdown/Biospecimen_description.md
@@ -2,7 +2,7 @@
 # Slot: description
 
 
-A concise description about the Biospecimen source, the collection method, and the protocol which was followed to process the Biospecimen.
+A concise description about the Biospecimen source, the collection method, and the protocol which was followed to process this Biospecimen.
 
 URI: [GHGA:Biospecimen_description](https://w3id.org/GHGA/Biospecimen_description)
 

diff --git a/docs/schema_markdown/Biospecimen_isolation.md b/docs/schema_markdown/Biospecimen_isolation.md
@@ -2,7 +2,7 @@
 # Slot: isolation
 
 
-Method or device employed for collecting/isolating the Sample.
+Method or device employed for collecting/isolating this Biospecimen.
 
 URI: [GHGA:Biospecimen_isolation](https://w3id.org/GHGA/Biospecimen_isolation)
 

diff --git a/docs/schema_markdown/Biospecimen_name.md b/docs/schema_markdown/Biospecimen_name.md
@@ -2,7 +2,7 @@
 # Slot: name
 
 
-A descriptive name of the Biospecimen (e.g. GHGAB_caudate_nucleus_biospecimen). Please do not enter any personally identifiable data!
+A descriptive name of this Biospecimen (e.g., GHGAB_caudate_nucleus_biospecimen). This property must not include any personally identifiable data.
 
 URI: [GHGA:Biospecimen_name](https://w3id.org/GHGA/Biospecimen_name)
 

diff --git a/docs/schema_markdown/Biospecimen_storage.md b/docs/schema_markdown/Biospecimen_storage.md
@@ -2,7 +2,7 @@
 # Slot: storage
 
 
-Methods by which the Sample is stored (e.g. frozen in liquid nitrogen).
+Methods by which this Biospecimen is stored.
 
 URI: [GHGA:Biospecimen_storage](https://w3id.org/GHGA/Biospecimen_storage)
 

diff --git a/docs/schema_markdown/Biospecimen_vital_status_at_sampling.md b/docs/schema_markdown/Biospecimen_vital_status_at_sampling.md
@@ -2,7 +2,7 @@
 # Slot: vital_status_at_sampling
 
 
-Vital Status of an Individual at the point of sampling, e.g. 'Alive' or 'Deceased'.
+Vital Status of the Individual at the point of sampling (e.g., alive).
 
 URI: [GHGA:Biospecimen_vital_status_at_sampling](https://w3id.org/GHGA/Biospecimen_vital_status_at_sampling)
 

diff --git a/docs/schema_markdown/Condition.md b/docs/schema_markdown/Condition.md
@@ -2,7 +2,7 @@
 # Class: Condition
 
 
-The Condition specifies which special characteristics and treatments apply to a Sample. It is used to link comparable Samples.
+A Condition specifies which special characteristics and treatments apply to a Sample. It is used to link comparable Samples (e.g., healthy Samples, wildtype Samples).
 
 URI: [GHGA:Condition](https://w3id.org/GHGA/Condition)
 
@@ -27,19 +27,19 @@ URI: [GHGA:Condition](https://w3id.org/GHGA/Condition)
 ### Own
 
  * [Condition➞name](Condition_name.md) <sub>1..1</sub>
- * Description: The name of the Condition.
+ * Description: The name of this Condition.
  * Range: [String](types/String.md)
  * [Condition➞description](Condition_description.md) <sub>1..1</sub>
  * Description: A concise description of the applied Condition.
  * Range: [String](types/String.md)
  * [Condition➞disease_or_healthy](Condition_disease_or_healthy.md) <sub>1..1</sub>
- * Description: Whether a condition corresponds to a disease or a healthy state.
+ * Description: Whether a Condition corresponds to a disease or a healthy state.
  * Range: [DiseaseOrHealthyEnum](DiseaseOrHealthyEnum.md)
  * [Condition➞case_control_status](Condition_case_control_status.md) <sub>1..1</sub>
- * Description: Whether a condition corresponds to a treatment or a control.
+ * Description: Whether a Condition corresponds to a treatment or a control.
  * Range: [CaseControlStatusEnum](CaseControlStatusEnum.md)
  * [Condition➞mutant_or_wildtype](Condition_mutant_or_wildtype.md) <sub>1..1</sub>
- * Description: Whether a condition corresponds to a mutant or a wildtype.
+ * Description: Whether a Condition corresponds to a mutant or a wildtype.
  * Range: [MutantOrWildtypeEnum](MutantOrWildtypeEnum.md)
  * [Condition➞study](Condition_study.md) <sub>1..1</sub>
  * Description: The Study associated with this Condition.

diff --git a/docs/schema_markdown/Condition_case_control_status.md b/docs/schema_markdown/Condition_case_control_status.md
@@ -2,7 +2,7 @@
 # Slot: case_control_status
 
 
-Whether a condition corresponds to a treatment or a control.
+Whether a Condition corresponds to a treatment or a control.
 
 URI: [GHGA:Condition_case_control_status](https://w3id.org/GHGA/Condition_case_control_status)
 

diff --git a/docs/schema_markdown/Condition_disease_or_healthy.md b/docs/schema_markdown/Condition_disease_or_healthy.md
@@ -2,7 +2,7 @@
 # Slot: disease_or_healthy
 
 
-Whether a condition corresponds to a disease or a healthy state.
+Whether a Condition corresponds to a disease or a healthy state.
 
 URI: [GHGA:Condition_disease_or_healthy](https://w3id.org/GHGA/Condition_disease_or_healthy)
 

diff --git a/docs/schema_markdown/Condition_mutant_or_wildtype.md b/docs/schema_markdown/Condition_mutant_or_wildtype.md
@@ -2,7 +2,7 @@
 # Slot: mutant_or_wildtype
 
 
-Whether a condition corresponds to a mutant or a wildtype.
+Whether a Condition corresponds to a mutant or a wildtype.
 
 URI: [GHGA:Condition_mutant_or_wildtype](https://w3id.org/GHGA/Condition_mutant_or_wildtype)
 

diff --git a/docs/schema_markdown/Condition_name.md b/docs/schema_markdown/Condition_name.md
@@ -2,7 +2,7 @@
 # Slot: name
 
 
-The name of the Condition.
+The name of this Condition.
 
 URI: [GHGA:Condition_name](https://w3id.org/GHGA/Condition_name)
 

diff --git a/docs/schema_markdown/DataAccessCommittee.md b/docs/schema_markdown/DataAccessCommittee.md
@@ -2,7 +2,7 @@
 # Class: DataAccessCommittee
 
 
-A group of members that are delegated to grant access to one or more datasets after ensuring the minimum criteria for data sharing has been met, and request for data use does not raise ethical and/or legal concerns.
+A group of members that are delegated to grant access to one or more datasets after ensuring the criteria for data sharing has been met, and request for data use does not raise ethical and/or legal concerns.
 
 URI: [GHGA:DataAccessCommittee](https://w3id.org/GHGA/DataAccessCommittee)
 
@@ -26,10 +26,10 @@ URI: [GHGA:DataAccessCommittee](https://w3id.org/GHGA/DataAccessCommittee)
 ### Own
 
  * [DataAccessCommittee➞email](DataAccessCommittee_email.md) <sub>1..1</sub>
- * Description: The email of the Data Access Committee. Please do not enter personal email addresses!
+ * Description: The email of the Data Access Committee (e.g., DAC[at]email.com). This property must not include any personally identifiable data.
  * Range: [String](types/String.md)
  * [DataAccessCommittee➞institute](DataAccessCommittee_institute.md) <sub>1..1</sub>
- * Description: The institute a person is affiliated with.
+ * Description: The Institute a person is affiliated with.
  * Range: [String](types/String.md)
 
 ### Mixed in from IdentifiedByAliasMixin:

diff --git a/docs/schema_markdown/DataAccessCommittee_email.md b/docs/schema_markdown/DataAccessCommittee_email.md
@@ -2,7 +2,7 @@
 # Slot: email
 
 
-The email of the Data Access Committee. Please do not enter personal email addresses!
+The email of the Data Access Committee (e.g., DAC[at]email.com). This property must not include any personally identifiable data.
 
 URI: [GHGA:DataAccessCommittee_email](https://w3id.org/GHGA/DataAccessCommittee_email)