From 0376464e4c1405a2a08b69a551269f9dad47f23e Mon Sep 17 00:00:00 2001 From: Jennifer Altreuter Date: Fri, 2 Aug 2024 09:05:14 -0400 Subject: [PATCH 1/5] Clarifications for index dates. --- data_submission/dates.md | 24 ++++++++++++++++++++++-- 1 file changed, 22 insertions(+), 2 deletions(-) diff --git a/data_submission/dates.md b/data_submission/dates.md index 5c3c2277..5b960f62 100644 --- a/data_submission/dates.md +++ b/data_submission/dates.md @@ -5,5 +5,25 @@ order: 995 # 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. \ No newline at end of file +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. +!!! + +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 addition, 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 as described for these attributes. \ No newline at end of file From 17f864a5c1582e39e35601ea65af30477f0f1ddb Mon Sep 17 00:00:00 2001 From: Jennifer Altreuter Date: Fri, 2 Aug 2024 09:06:59 -0400 Subject: [PATCH 2/5] minot edit to under construction box for specific details. --- data_submission/specific_details.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data_submission/specific_details.md b/data_submission/specific_details.md index 034b8eae..4fa23cc5 100644 --- a/data_submission/specific_details.md +++ b/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) From f9e4bcda9abc5794174b384ad936c883158d0eb7 Mon Sep 17 00:00:00 2001 From: Jennifer Altreuter Date: Fri, 2 Aug 2024 09:53:41 -0400 Subject: [PATCH 3/5] Make data_standards page into explanation of data levels. Make seq levels svg dark mode compatible. --- .DS_Store | Bin 10244 -> 10244 bytes data_model/data_levels.md | 13 +++++++++++++ data_model/data_standards.md | 15 --------------- img/sequencing_data_levels.svg | 2 +- 4 files changed, 14 insertions(+), 16 deletions(-) create mode 100644 data_model/data_levels.md delete mode 100644 data_model/data_standards.md diff --git a/.DS_Store b/.DS_Store index 7b5ddc54e16f9acce774dd5599ce018614899b7d..49102f563157ae505b2652b6bccf9fddfe3616c8 100644 GIT binary patch delta 78 zcmZn(XbG6$&&aniU^hP_-)0^Gc1Bq)h7^WGh7ur-XUJv92l7%Ga#D(ubCUA&b2jq} f3NSJ \ No newline at end of file + \ No newline at end of file From 90b9b577e3396b9864a3e0b07644b107214e0327 Mon Sep 17 00:00:00 2001 From: Jennifer Altreuter Date: Fri, 2 Aug 2024 10:39:24 -0400 Subject: [PATCH 4/5] minor edits for data_levels section. --- data_model/data_levels.md | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/data_model/data_levels.md b/data_model/data_levels.md index 478641c1..77178e4d 100644 --- a/data_model/data_levels.md +++ b/data_model/data_levels.md @@ -2,12 +2,19 @@ order: 997 --- -# Data Standard Levels +# Data Levels and Clinical Data Tiers -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. +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) -Clinical data is organized into tiers. These tiers are described more on the [Clinical Data Page](https://humantumoratlas.org/standard/clinical). +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). -The [Data Standards](https://humantumoratlas.org/standards) provides up-to-date details regarding the HTAN Data Model. 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. \ No newline at end of file +## 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. \ No newline at end of file From ac217009e413c1170eb995c151f3fb5d8b742a46 Mon Sep 17 00:00:00 2001 From: Jennifer Altreuter Date: Fri, 2 Aug 2024 10:48:50 -0400 Subject: [PATCH 5/5] minor edits to dates.md text. --- data_submission/dates.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/data_submission/dates.md b/data_submission/dates.md index 5b960f62..9a938512 100644 --- a/data_submission/dates.md +++ b/data_submission/dates.md @@ -4,14 +4,13 @@ order: 995 # 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. 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. +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; @@ -19,11 +18,12 @@ For sequencing data, there are four attributes with 'index' in their names for w - Sequencing Library Construction Days from Index; and - Nucleic Acid Capture Days from Index. -Please note the descriptions for these fields. +Please note the descriptions for these fields in the data model. -In addition, the 'Diagnosis' manifest includes two attributes which are not indexed: +## 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 as described for these attributes. \ No newline at end of file +Please provide these time intervals for these attributes as described in the data model. \ No newline at end of file