From 4837bdc6af4bca12a258d6623ee684f36ad7ce28 Mon Sep 17 00:00:00 2001 From: Retype GitHub Action Date: Wed, 14 Aug 2024 19:40:04 +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 ++--- data_model/data_levels/index.html | 8 ++--- data_model/identifiers/index.html | 8 ++--- data_model/overview/index.html | 8 ++--- data_model/relationships/index.html | 8 ++--- data_submission/checklist/index.html | 8 ++--- data_submission/clin_biospec_assay.html | 4 ++- data_submission/clin_biospec_assay/index.html | 32 +++++++++++++++--- .../data_deidentification/index.html | 8 ++--- data_submission/data_liaisons/index.html | 8 ++--- data_submission/dates/index.html | 12 +++---- .../information_new_centers/index.html | 8 ++--- data_submission/metadata/index.html | 8 ++--- data_submission/overview/index.html | 8 ++--- data_submission/specific_details/index.html | 8 ++--- 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 | 8 ++--- 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 672 -> 672 bytes 38 files changed, 166 insertions(+), 142 deletions(-) diff --git a/404.html b/404.html index 21657e99..c8bef825 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 0035e1fa..cfc457bb 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 82b1932e..3db259df 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 2f3c1e21..1e4a671d 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 592d0dc6..13e79dfb 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 edff517f..bae02eb6 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 8d0f0dc1..7ab4275b 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 ec64b5ba..a58db376 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 f92226f1..de4b65f8 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 3eb115e7..3b86b191 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_levels/index.html b/data_model/data_levels/index.html index 98fa13f9..1acf3ef8 100644 --- a/data_model/data_levels/index.html +++ b/data_model/data_levels/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/data_model/identifiers/index.html b/data_model/identifiers/index.html index c0ef231a..eab072e5 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 9df21288..10f95f10 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 c5ae303f..44e710a6 100644 --- a/data_model/relationships/index.html +++ b/data_model/relationships/index.html @@ -4,7 +4,7 @@ - + @@ -33,11 +33,11 @@ - + - + - +
diff --git a/data_submission/checklist/index.html b/data_submission/checklist/index.html index c4a0983c..942adcf9 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.html b/data_submission/clin_biospec_assay.html index e4ab1b66..80b509c8 100644 --- a/data_submission/clin_biospec_assay.html +++ b/data_submission/clin_biospec_assay.html @@ -48,6 +48,7 @@

Submitting Assay Data and Metadata

As stated in Data Submission Overview, data submission involves two key steps: 1. Uploading assay data files to Synapse; and 2. Completing and validating metadata using the Data Curator App (DCA).

+

!!! Once assay data files are submitted to Synapse, the files will have entityIDs (e.g. syn12345670) assigned to them. These can then be prepopulated into the manifests on the DCA. For this reason, assay files should be submitted before generating the associated manifests. !!!

This page provides details regarding those steps.

@@ -97,7 +98,8 @@

Validate and submit metadata using Synapse’s Data Curator App (DCA).

-

The DCA contains HTAN-specific metadata templates which can be completed on the app or downloaded. Once these are completed by your center, they should then be validated and submitted via the DCA.

+

The DCA contains HTAN-specific manifests (metadata templates) which can be 1) completed on the app, or 2) downloaded, completed and uploaded back to the DCA. Manifests for assay data will be pre-populated with assay file entityIDs once they are associated with a particular dataset folder. Once the metadata templates are completed by your center, they should then be validated and submitted via the DCA.

+

!!! Please note: If you have added files where a pre-existing manifest exists, please add to data to the existing manifest on the DCA app or download the existing manifest from the DCA to make updates. Do not use a local copy of the manifest at your center. !!!

Please see Synapse’s Data Ingress Docs for more details regarding the web app.

diff --git a/data_submission/clin_biospec_assay/index.html b/data_submission/clin_biospec_assay/index.html index 8c60e84d..e19bc0a7 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 @@ - + - + - +
@@ -295,7 +295,29 @@

Validate and submit metadata using Synapse's Data Curator App (DCA).

-

The DCA contains HTAN-specific metadata templates which can be completed on the app or downloaded. Once these are completed by your center, they should then be validated and submitted via the DCA.

+

The DCA contains HTAN-specific manifests (metadata templates) which can be

+
    +
  1. completed on the app, or
    2. +
  2. downloaded, completed and uploaded back to the DCA.
    3. +
+

Manifests for assay data will be pre-populated with assay file entityIDs once they are associated with a particular Synapse dataset folder. Once the manifests are completed by your center, they should then be validated and submitted via the DCA. DCA validation checks for a subset of common errors. If any of these errors are found, you can edit the metadata and then revalidate and submit.

+
+
+ +

Please see Synapse's Data Ingress Docs for more details regarding the web app.

diff --git a/data_submission/data_deidentification/index.html b/data_submission/data_deidentification/index.html index 05765a3a..e9366729 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 03352001..7b13e9b8 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 6237dcd2..73d0e542 100644 --- a/data_submission/dates/index.html +++ b/data_submission/dates/index.html @@ -4,7 +4,7 @@ - + @@ -31,11 +31,11 @@ - + - + - +
@@ -170,7 +170,7 @@

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, 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.