Merge pull request #29 from ncihtan/specific_assay_files

Modifications to Data Model, Data Submission sections

data_model/data_levels.md

@@ -0,0 +1,20 @@
+---
+order: 997
+---
+
+# Data Levels and Clinical Data Tiers
+
+The [Data Standards](https://humantumoratlas.org/standards) pages of the HTAN Data Portal provide a detailed overview of the HTAN Data Model. A general overview of how the HTAN Data Model is organized is provided in the next sections.
+
+## Assay Data Levels
+The HTAN Data Model divides assay data into levels. Each assay type has levels progressing from raw data to more processed data.  This is illustrated in the following figure for sequencing data.  Please see each assay's page within [Data Standards](https://humantumoratlas.org/standards) for more information.
+
+![HTAN Sequencing Data levels](../img/sequencing_data_levels.svg)
+
+For Sequencing data, the HTAN Model Data levels help distinguish data as Open Access versus Controlled Access.  For example, level 1 and 2 sequencing data are Controlled Access data.     
+
+## Clinical Data Tiers
+Clinical data is organized into three tiers.  Tier one is based on the NCI's Genomic Data Commons (GDC) clinical data model.  Tiers two and three are disease-agnostic (tier 2) and disease-specific (tier 3) extensions to the GDC model. These tiers are described more on the [Clinical Data Page](https://humantumoratlas.org/standard/clinical). 
+
+## Specific Details
+Please see [Data Standards](https://humantumoratlas.org/standards) for up-to-date details regarding the HTAN Data Model, including attribute descriptions and requirements. For additional notes regarding how to submit data for each data type, please see the [Specific Assay/Data Element Details](../data_submission/specific_details.md) page of this manual. 

data_submission/dates.md

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 # What is the index date?
 
-HTAN cannot accept dates because they are considered Protect Health Information (PHI). In order to obfuscate dates, they should be converted
-to days from an index date.  In this case, the index date is the participant's date of birth.  For example, a participant's therapy start date 
-would be recorded as 365 days if the therapy took place 365 days after a participant's date of birth.
+HTAN cannot accept dates because they are considered Protect Health Information (PHI). In order to obfuscate dates, they should be converted to days from an index date.  For most data case, the index date is the participant's date of birth.  For example, a participant's therapy start date would be recorded as 365 days if the therapy took place 365 days after a participant's date of birth. 
+
+!!!
+:warning: If your center has data indexed to enrollment date, the data needs to be converted to days from birth. 
+!!!
+
+## "Index" exceptions
+For sequencing data, there are four attributes with 'index' in their names for which 'index' is not the date of birth.  These include:
+
+- Single Cell Dissociation Days from Index;
+- Library Preparation Days from Index;
+- Sequencing Library Construction Days from Index; and
+- Nucleic Acid Capture Days from Index.
+
+Please note the descriptions for these fields in the data model.
+
+## Time intervals
+The 'Diagnosis' manifest includes two attributes which are not indexed:
+
+- Days to Last Follow up; and
+- Days to Last Known Disease Status.
+
+Please provide these time intervals for these attributes as described in the data model.

data_submission/specific_details.md

@@ -7,7 +7,7 @@ order: 993
 Please see [Data Standards](https://data.humantumoratlas.org/standards) for an overview of HTAN Data Levels and Metadata Attributes for each data type. The following links provide specific submission details for each data type.  
 
 !!! under development.  
-:construction: Currently this page contains additional information for Imaging data.  The Data Coordinating Center (DCC) plans to develop additional documents which will be linked from this page at a later time.
+:construction: Documents for some assays are still in development.  Links will be added soon!
 !!!
 
 [Accessory Files](https://docs.google.com/document/d/1c7WPfgOpjd8B44LDccuR4quwrVXg3yhGQlbQ6Bp4p7Q/edit?usp=sharing)