indendation fix

user_docs/metadata/entities.md

@@ -8,95 +8,95 @@ A breakdown of each metadata element described in the different entities will pr
 
 The Research Metadata focuses on the reusability and FAIRness of the data. The Research Metadata encapsulates a set of classes that shape the model in accordance to the performed experiment ensuring reproducibility and scalability. The classes include *Individual*, *Biospecimen/Sample*, *Experiment*, *Experiment Method*, *Analysis* and *Analysis Method*.
 
-## **Individual**
+### **Individual**
 
 The *Individual* entity collects non-personal metadata about the *Individual* from which the samples were collected. The content of the *Individual* entity is crucial to identify cohorts of interest and gives valuable insight on the target group of an experiment. 
 
-### **Individual metadata properties**
+#### **Individual metadata properties**
 
 In order to describe an *Individual*, data submitters are required to provide information about sex and are recommended to provide information about phenotypic features and diagnoses. Additional information about the geographical region and ancestries can also be provided.
 
 The Individual entity is linked to the *Sample* entity.
 
-## **Individual Supporting File**
+### **Individual Supporting File**
 
 If the data submitters have additional information to provide about the individual, then they can make use of the Individual supporting file class which requires the following information -  file format, file name, dataset associated with this file as well as if the file is included as part of the submission. 
 
-## **Biospecimen/Sample**
+### **Biospecimen/Sample**
 
 The *Biospecimen/Sample* describes the extracted sample and tissue for an experimental process. Furthermore, a *Sample* is defined as 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).
 
 A *Biospecimen* is defined in GHGAs metadata as any natural material taken from a biological entity for testing, diagnostics, treatment or research purposes. The *Biospecimen* is linked to the *Individual* entity from which the biospecimen itself has been derived.
 
 The *Biospecimen/Sample* is linked to the *Individual* entity describing the collection of biological material. Further, it is linked to the *Experiment*.```
 
-### **Biospecimen/Sample metadata properties**
+#### **Biospecimen/Sample metadata properties**
 
 The *Sample* entity requires data submitters to provide the name, description, whether the sample is case or control, as well as the alias to the *Individual* from which the *Sample* was derived. In addition to the mandatory information, the data submitter is recommended to provide information about the storage, whether the sample can be classified as  diseased or healthy, and biological replicate information. Other optional fields include the type of the sample and an EGA accession ID. 
 
 The *Biospecimen* entity requires data submitters to provide information about the age of the individual at the time of sampling and the biospecimen tissue. The recommended properties include a name for the biospecimen, its type, the vital status of the individual at the time of sampling, and the biospecimen isolation and storage.
 
-## **Experiment**
+### **Experiment**
 
 An *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. The *Experiment* enttity describes the experimental setup or a protocol used for performing an omics experiment. 
 
 The *Experiment* entity is linked to the *Sample* which implies one or more samples associated with this Experiment and the *Experimental Method* which implies one or more Experimental methods associated with this Experiment. The outcome of an *Experiment* results in *Research Data File*.
 
-### **Experiment metadata properties**
+#### **Experiment metadata properties**
 
 The *Experiment* entity requires the data submitters to provide information about experiment method, title, description and sample information.
 
-## **Experiment Methods**
+### **Experiment Methods**
 
 The *Experiment Method* entity captures information about the protocol that was followed to perform the omics experiment.
 
-### **Experiment Method metadata properties**
+#### **Experiment Method metadata properties**
 
 The data submitter is required to provide information about the name, description, library type, selection methods, preparation, the instrument model and sequencing layout to fulfil the *Experiment Method* pertaining to an omics experiment. Furthermore, it is recommended to provide information about the library preparation kit name and manufacturer, the primer, end bias, flow cell ID and type, rna seq strandedness, sample barcode read and sequencing center. The optional properties include target region, target coverage and EGA accession ID.
 
-## **Experiment Method Supporting File**
+### **Experiment Method Supporting File**
 
 Any additional information pertaining to the *Experiment Method* can be provided here. The submitter is required to provide information about the file format, the *Experiment Method* this file supports, the file name, the *Dataset* associated with this file and whether this file is included as part of the submission.
 
-## **Research Data File**
+### **Research Data File**
 
 The *Research Data File* entity is generated as a result of a direct measurement or sequencing of a sample. They are the raw files that were generated while carrying out an *Experiment*. This entity is linked to the *Experiment* that produced this file as well as the *Dataset* that is associated with this file. The GHGA metadata model emphasizes on the submission of a *Research Data File* alone or accompanied by *Process Data Files* for enabling reconstruction of the analytical process representing a submission.
 
-### **Research Data File metadata properties**
+#### **Research Data File metadata properties**
 
 The *Research Data File* entity requires a data submitter to provide information about the file format, technical replicate, the *Experiment* that generated this *Research Data File*, the file name, the *Dataset* and whether the file is included in the submission. It is also recommended to provide information about the sequencing lane. The EGA accession ID is an optional property.
 
-## **Analysis**
+### **Analysis**
 
 The *Analysis* entity permutates a *Research Data File* into a *Process Data File* through a computational workflow. 
 
 The *Analysis* entity is linked to *Experiment* via *Research Data File* and also linked to *Analysis Method*.
 
-### **Analysis metadata properties**
+#### **Analysis metadata properties**
 
 The data submitter is required to provide information about the *Analysis* title, the *Analysis Method* that is associated with this *Analysis* and the *Research Data Files* that this *Analysis* used as input to generate *Process Data Files*.
 
-## **Analysis Methods**
+### **Analysis Methods**
 
 The *Analysis Method* entity describes the computational workflow that created *Process Data Files* in more detail. 
 
-### **Analysis Methods metadata properties**
+#### **Analysis Methods metadata properties**
 
 For this submission, the data submitter is required to provide information about the *Analysis Method* name, a description, type, the workflow name, workflow repository and workflow DOI. Furthermore, it is also recommended to provide information about the workflow version, workflow tasks, parameters and software versions.
 
-## **Analysis Method Supporting File**
+### **Analysis Method Supporting File**
 
 For any additional information pertaining to the *Analysis Methods* entity, the data submitter can use the *Analysis Method Supporting File*.
 
-### **Analysis Method Supporting File properties**
+#### **Analysis Method Supporting File properties**
 
 For supporting information about the *Analysis Method*, the data submitter is required to provide information about the file format, the *Analysis Method* this file supports, the file name, and the *Dataset* associated with this file.
 
-## **Process Data File**
+### **Process Data File**
 
 The *Process Data File* entity is a generated outcome of an analysis, alignment or  processing of a *Research Data File*. The *Process Data File* entity is linked to the *Dataset* that is associated with the file and the *Analysis* that produced this *Process Data File*.
 
-### **Process Data File metadata properties**
+#### **Process Data File metadata properties**
 
 The *Process Data File* entity requires the data submitter to provide information about the file format, the *Analysis* from which this file originated, the file name, and the *Dataset*. Additionally, it is also possible to submit an optional EGA accession ID.
 
@@ -106,39 +106,39 @@ The submission process allows submission of processed data file alone but this i
 
 The administrative metadata focusses on managing the resources such as creation or acquisition of the data, rights management, and disposition. 
 
-## **Dataset**
+### **Dataset**
 
 GHGA presents its content to potential data requesters and submitters with the *Dataset* entity, which focuses on sharing functionality by describing the contents at a high level. Each dataset is linked to a *Data Access Policy*, which builds the legal basis for the sharing of data. One dataset has links to *Experiment* via *Research Data File*, and to  *Analysis* entities via *Process Data File*. The dataset is also linked to *Analysis Methods* and *Experiment methods* via *Analysis Methods Supporing Files* and *Experiment Methods Supporing Files* respectively. The *Dataset* entity is also linked to *Study*.
 
-### **Dataset metadata properties**
+#### **Dataset metadata properties**
 
 The *Dataset* entity is aimed at capturing relevant information about a dataset itself. The mandatory information required for *Dataset* entity includes title, description, type, data access policy and Study. Optionally, the data submitter could also provide information about the ega accession.
 
-## **Data Access Policy and Committee**
+### **Data Access Policy and Committee**
 
 Depositing data at GHGA requires a data submitter to provide a *Data Access Committee (DAC)* and *Data Access Policy (DAP)*. This ensures controlled access to their deposited data and a clear guideline for data requesters to access the data. This includes a defined contact person and a consent-based legal basis for getting access to a dataset. The *DAP* entity is linked to *Dataset* and *DAC*.
 
-### **DAP and DAC metadata properties**
+#### **DAP and DAC metadata properties**
 
 A *DAP* is directly linked to the *DAC* and *Dataset* entity, thus providing  the condition under which the data deposited at GHGA can be re-used by a data requester. The submitter must provide an alias, name, description and either the policy text for the *DAP* or the URL where the *DAP* is stored, data use permission term and id, data use modifier term and id and DAC.
 
 A *DAC* is linked directly to *DAP* and requires information about email and institute and optionally about ega accession.
 
-## **Study**
+### **Study**
 
 All data deposited at GHGA is subject to a specific study, under which relevant data has been aggregated. A *Study* is an experimental investigation of a particular phenomenon and involves a detailed examination and analysis of a subject to learn more about the phenomenon being studied. A detailed description of a study can guide data requesters to identify the most relevant datasets for their own research.  The *Study* entity is linked to *Dataset*.
 
-### **Study metadata properties**
+#### **Study metadata properties**
 
 In order to describe a *Study*, data submitters are required to provide information about the study affiliation(s), the title, a description and the study type. Optionally, they can provide an EGA accession ID.
 
-## **Publication**
+### **Publication**
 
 The *Publication* entity refers to a journal article, book, or conference paper that presents original research or scholarly findings in a specific field of study, contributing to the collective knowledge and understanding of that discipline. 
 
 The *Publication* entity is linked to *Study*.
 
-### **Publication metadata properties**
+#### **Publication metadata properties**
 
 The data submitter is required to provide information about the *Study* associated with this publication. Optionally, the data submitter can also provide information about the publication title, abstract, author, year, journal and DOI.