From 3a18fddc3071d30974965be24ef5ff7082de3d46 Mon Sep 17 00:00:00 2001 From: Retype GitHub Action Date: Fri, 2 Aug 2024 19:47:23 +0000 Subject: [PATCH] Refreshes Retype-generated documentation. Process triggered by jen-dfci. --- 404.html | 8 +- access_controlled/cds_access/index.html | 8 +- access_controlled/db_gap/index.html | 8 +- access_controlled/introduction/index.html | 8 +- addtnl_info/data_release/index.html | 8 +- addtnl_info/publications/index.html | 8 +- addtnl_info/rfc/index.html | 8 +- addtnl_info/tnps/index.html | 8 +- addtnl_info/tool_protocol/index.html | 8 +- addtnl_info/wg_internal/index.html | 8 +- .../index.html | 79 +++++++++--------- data_model/identifiers/index.html | 8 +- data_model/overview/index.html | 8 +- data_model/relationships/index.html | 12 +-- data_submission/checklist/index.html | 8 +- data_submission/clin_biospec_assay/index.html | 8 +- .../data_deidentification/index.html | 8 +- data_submission/data_liaisons/index.html | 8 +- data_submission/dates/index.html | 61 +++++++++++--- .../information_new_centers/index.html | 8 +- data_submission/metadata/index.html | 8 +- data_submission/overview/index.html | 8 +- data_submission/specific_details/index.html | 10 +-- img/sequencing_data_levels.svg | 2 +- index.html | 8 +- open_access/biq_query/index.html | 8 +- open_access/cds_imaging/index.html | 8 +- open_access/cell_by_gene/index.html | 8 +- open_access/introduction/index.html | 12 +-- open_access/minerva/index.html | 8 +- open_access/portal/index.html | 8 +- overview/centers/index.html | 8 +- overview/data_levels/index.html | 8 +- overview/introduction/index.html | 8 +- overview/tool_catalog/index.html | 8 +- resources/js/config.js | 2 +- resources/js/search.json | 2 +- sitemap.xml.gz | Bin 678 -> 672 bytes 38 files changed, 228 insertions(+), 184 deletions(-) rename data_model/{data_standards => data_levels}/index.html (83%) diff --git a/404.html b/404.html index ecb59921..21657e99 100644 --- a/404.html +++ b/404.html @@ -4,7 +4,7 @@ - + @@ -28,11 +28,11 @@ - + - + - +
diff --git a/access_controlled/cds_access/index.html b/access_controlled/cds_access/index.html index 601cc6d4..0035e1fa 100644 --- a/access_controlled/cds_access/index.html +++ b/access_controlled/cds_access/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/access_controlled/db_gap/index.html b/access_controlled/db_gap/index.html index 0d8ffd84..82b1932e 100644 --- a/access_controlled/db_gap/index.html +++ b/access_controlled/db_gap/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/access_controlled/introduction/index.html b/access_controlled/introduction/index.html index 83f16b17..2f3c1e21 100644 --- a/access_controlled/introduction/index.html +++ b/access_controlled/introduction/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/addtnl_info/data_release/index.html b/addtnl_info/data_release/index.html index d05ee46d..592d0dc6 100644 --- a/addtnl_info/data_release/index.html +++ b/addtnl_info/data_release/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/addtnl_info/publications/index.html b/addtnl_info/publications/index.html index df13fcbc..edff517f 100644 --- a/addtnl_info/publications/index.html +++ b/addtnl_info/publications/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/addtnl_info/rfc/index.html b/addtnl_info/rfc/index.html index 61b5554a..8d0f0dc1 100644 --- a/addtnl_info/rfc/index.html +++ b/addtnl_info/rfc/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/addtnl_info/tnps/index.html b/addtnl_info/tnps/index.html index 7f914edf..ec64b5ba 100644 --- a/addtnl_info/tnps/index.html +++ b/addtnl_info/tnps/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/addtnl_info/tool_protocol/index.html b/addtnl_info/tool_protocol/index.html index 06b89373..f92226f1 100644 --- a/addtnl_info/tool_protocol/index.html +++ b/addtnl_info/tool_protocol/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/addtnl_info/wg_internal/index.html b/addtnl_info/wg_internal/index.html index e11495d4..3eb115e7 100644 --- a/addtnl_info/wg_internal/index.html +++ b/addtnl_info/wg_internal/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/data_model/data_standards/index.html b/data_model/data_levels/index.html similarity index 83% rename from data_model/data_standards/index.html rename to data_model/data_levels/index.html index 94f4c27d..98fa13f9 100644 --- a/data_model/data_standards/index.html +++ b/data_model/data_levels/index.html @@ -4,40 +4,40 @@ - + - Data Standards - - + Data Levels and Clinical Data Tiers + + - + - - - + + + - - - + + + - + - + - +
@@ -166,37 +166,40 @@
- +

- # - Data Standards + # + Data Levels and Clinical Data Tiers

-

This page is a place holder for a data standards page/set of data standards pages similar to MC2 Center Data Model. The HTAN version of the MC2 tables will include additional columns such as "required_if_component" and "required_if_value". Until the new pages are constructed, please see the information on the Data Standards page of the HTAN Data Portal.

-

The HTAN data model includes data 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 the Data Standards page of the HTAN Data Portal for more information.

+

The Data 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 for more information.

HTAN Sequencing Data levels
HTAN Sequencing Data levels

-
-
- -
+

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.

+ +

+ # + Specific Details +

+ +

Please see Data 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 page of this manual.

@@ -263,6 +266,6 @@
Note
- + diff --git a/data_model/identifiers/index.html b/data_model/identifiers/index.html index 42bb9f1f..c0ef231a 100644 --- a/data_model/identifiers/index.html +++ b/data_model/identifiers/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/data_model/overview/index.html b/data_model/overview/index.html index 99b4d220..9df21288 100644 --- a/data_model/overview/index.html +++ b/data_model/overview/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/data_model/relationships/index.html b/data_model/relationships/index.html index 0970b8f2..c5ae303f 100644 --- a/data_model/relationships/index.html +++ b/data_model/relationships/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
@@ -247,10 +247,10 @@

- + Next - Data Standards + Data Levels and Clinical Data Tiers diff --git a/data_submission/checklist/index.html b/data_submission/checklist/index.html index 4d9de088..c4a0983c 100644 --- a/data_submission/checklist/index.html +++ b/data_submission/checklist/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/data_submission/clin_biospec_assay/index.html b/data_submission/clin_biospec_assay/index.html index 831a0ef6..8c60e84d 100644 --- a/data_submission/clin_biospec_assay/index.html +++ b/data_submission/clin_biospec_assay/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/data_submission/data_deidentification/index.html b/data_submission/data_deidentification/index.html index 5970f799..05765a3a 100644 --- a/data_submission/data_deidentification/index.html +++ b/data_submission/data_deidentification/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/data_submission/data_liaisons/index.html b/data_submission/data_liaisons/index.html index 20b10886..03352001 100644 --- a/data_submission/data_liaisons/index.html +++ b/data_submission/data_liaisons/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/data_submission/dates/index.html b/data_submission/dates/index.html index 8884a0c7..6237dcd2 100644 --- a/data_submission/dates/index.html +++ b/data_submission/dates/index.html @@ -4,7 +4,7 @@ - + @@ -12,7 +12,7 @@ What is the index date? - + @@ -21,21 +21,21 @@ - + - + - + - + - +
@@ -170,9 +170,50 @@

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.

+
+
+ +
+ +

+ # + "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.

diff --git a/data_submission/information_new_centers/index.html b/data_submission/information_new_centers/index.html index 58c02c82..068f1e50 100644 --- a/data_submission/information_new_centers/index.html +++ b/data_submission/information_new_centers/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/data_submission/metadata/index.html b/data_submission/metadata/index.html index b81c938c..805084ba 100644 --- a/data_submission/metadata/index.html +++ b/data_submission/metadata/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/data_submission/overview/index.html b/data_submission/overview/index.html index 16157af9..e458a4c9 100644 --- a/data_submission/overview/index.html +++ b/data_submission/overview/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/data_submission/specific_details/index.html b/data_submission/specific_details/index.html index 707a37c0..68b08b33 100644 --- a/data_submission/specific_details/index.html +++ b/data_submission/specific_details/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
@@ -185,7 +185,7 @@

under development.
-

🚧 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.

+

🚧 Documents for some assays are still in development. Links will be added soon!

diff --git a/img/sequencing_data_levels.svg b/img/sequencing_data_levels.svg index 16cc6ae1..bcd75c1d 100644 --- a/img/sequencing_data_levels.svg +++ b/img/sequencing_data_levels.svg @@ -1 +1 @@ - \ No newline at end of file + \ No newline at end of file diff --git a/index.html b/index.html index 28cfe863..f799f140 100644 --- a/index.html +++ b/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
diff --git a/open_access/biq_query/index.html b/open_access/biq_query/index.html index 73dd72b8..8d1eb5da 100644 --- a/open_access/biq_query/index.html +++ b/open_access/biq_query/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/open_access/cds_imaging/index.html b/open_access/cds_imaging/index.html index c5a31172..b4724907 100644 --- a/open_access/cds_imaging/index.html +++ b/open_access/cds_imaging/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/open_access/cell_by_gene/index.html b/open_access/cell_by_gene/index.html index 7030cb8f..9a29ee69 100644 --- a/open_access/cell_by_gene/index.html +++ b/open_access/cell_by_gene/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/open_access/introduction/index.html b/open_access/introduction/index.html index 90f117be..6344dfa1 100644 --- a/open_access/introduction/index.html +++ b/open_access/introduction/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
@@ -205,11 +205,11 @@
For more detailed information about the HTAN Portal, CellxGene, Minerva-rend