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Checklist updates refactor #202

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6badd1f
added the missing explicitly in the first column
Woolly-at-EBI Jul 9, 2024
20ba68a
doc: multiple updates to this missing-values.rst file. The table need…
Woolly-at-EBI Oct 17, 2024
7c2409b
doc: reformat table
Woolly-at-EBI Oct 17, 2024
b9fd468
doc: reformat table yet again
Woolly-at-EBI Oct 17, 2024
fbd665c
doc: fixed rst emphasis formatting issue
Woolly-at-EBI Oct 17, 2024
2262f1f
doc: tidied the formatting and language syntax
Woolly-at-EBI Oct 17, 2024
ec0f509
doc: re-removing the excess hyphen...
Woolly-at-EBI Oct 21, 2024
c10b48c
doc: tabulated the Example usage with short and long names, so works …
Woolly-at-EBI Oct 21, 2024
99e9908
Initial: converted md to rst
Woolly-at-EBI Dec 2, 2024
b5900ba
Initial: converted md to rst
Woolly-at-EBI Dec 2, 2024
3ec058e
removed: md files
Woolly-at-EBI Dec 2, 2024
5adde2d
docs: added path to sample_checklist.rst to samples.rst
Woolly-at-EBI Dec 2, 2024
26652d0
docs: added path to updates/2024-02-29_Incorporating_MIxS_V6.2.rs to …
Woolly-at-EBI Dec 2, 2024
0a380bb
initial: samples/sample_checklist.rst
Woolly-at-EBI Dec 2, 2024
b1e1888
doc: initial rough notes for sample_checklist_infrastructure.rst
Woolly-at-EBI Feb 28, 2025
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1 change: 1 addition & 0 deletions submit/samples.rst
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Expand Up @@ -88,3 +88,4 @@ Find specific advice on registering studies using your preferred method below:

samples/interactive
samples/programmatic
samples/sample_checklist
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81 changes: 43 additions & 38 deletions submit/samples/missing-values.rst
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Expand Up @@ -20,52 +20,57 @@ INSDC Missing Value Reporting Terms

+----------------------------+------------------------------+-----------------------------------------------+----------------------------------+---------------------------------------------------+
| **INSDC term (top level)** | **INSDC term (lower level)** | **Definition** | **INSDC term (reporting level)** | **Definition** |
+============================+==============================+===============================================+==================================+===================================================+
| not applicable | | information is inappropriate to report, can | control sample | Information is not applicable as the sample |
| | | indicate that the standard itself fails to | | represents a negative control sample |
| | | model or represent the information | | collected in a lab |
| | | appropriately +----------------------------------+---------------------------------------------------+
| | | | sample group | Information is not applicable as the sample |
| | | | | represents a group of samples that do not |
| | | | | have a single origin. E.g. for co-assembly or |
| | | | | transcriptome assembly. |
+----------------------------+------------------------------+-----------------------------------------------+----------------------------------+---------------------------------------------------+
| not applicable | | | information is inappropriate to report, can | control sample | | Information is not applicable as the sample |
| | | | indicate that the standard itself fails to | | | represents a negative control sample |
| | | | model or represent the information | | | collected in a lab |
| | | | appropriately +----------------------------------+---------------------------------------------------+
| | | | | sample group | | Information is not applicable as the sample |
| | | | | | | represents a group of samples that do not |
| | | | | | | have a single origin. E.g. for co-assembly or |
| | | | | | | transcriptome assembly. |
| missing | not collected | information of an expected format was not | synthetic construct | Information does not exist as the sample |
| | | given because it has not been collected | | represents an ab-initio synthetic construct. |
| | | +----------------------------------+---------------------------------------------------+
| | | | lab stock | Information was not collected as the sample |
| | | | | represents a cultured cell line or model |
| | | | | organism under long-term lab control. |
| | | +----------------------------------+---------------------------------------------------+
| | | | third party data | Information does not exist as the metadata |
| | | | | was not collected or reported in records |
| | | | | predating the 2023 agreement. For use in |
| | | | | Third Party data submissions. |
+----------------------------+------------------------------+-----------------------------------------------+----------------------------------+---------------------------------------------------+
| missing | not collected | | information of an expected format was not | synthetic construct | | Information does not exist as the sample |
| | | | given because it has not been collected | | | represents an ab-initio synthetic construct. |
| | | | +----------------------------------+---------------------------------------------------+
| | | | | lab stock | | Information was not collected as the sample |
| | | | | | | represents a cultured cell line or model |
| | | | | | | organism under long-term lab control. |
| | | | +----------------------------------+---------------------------------------------------+
| | | | | third party data | | Information does not exist as the metadata |
| | | | | | | was not collected or reported in records |
| | | | | | | predating the 2023 agreement. For use in |
| | | | | | | Third Party data submissions. |
| +------------------------------+-----------------------------------------------+----------------------------------+---------------------------------------------------+
| | not provided | | information of an expected format was not | data agreement established | | Data agreements were established before the |
| | | | given, a value may be given at the later | pre-2023 | | 2023 INSDC standard and metadata can not be |
| | | | stage | | | provided. A value may be given at a later stage |
| +------------------------------+-----------------------------------------------+----------------------------------+---------------------------------------------------+
| | restricted access | | information exists but can not be released | endangered species | | Information can not be reported as the target |
| | | | openly because of privacy concerns | | | organism is endangered e.g. on the IUCN red- |
| | | | | | | list |
| | | | +----------------------------------+---------------------------------------------------+
| | | | | human-identifiable | | Information can not be reported as the |
| | | | | | | metadata would make the sample human- |
| | | | | | | identifiable. |
| missing | not provided | information of an expected format was not | data agreement established | Data agreements were established before the |
| | | given, a value may be given at the later | pre-2023 | 2023 INSDC standard and metadata can not be |
| | | stage | | provided. A value may be given at a later stage |
+----------------------------+------------------------------+-----------------------------------------------+----------------------------------+---------------------------------------------------+
| missing | restricted access | information exists but can not be released | endangered species | Information can not be reported as the target |
| | | openly because of privacy concerns | | organism is endangered e.g. on the IUCN red- |
| | | | | list |
| | | +----------------------------------+---------------------------------------------------+
| | | | human-identifiable | Information can not be reported as the |
| | | | | metadata would make the sample human- |
| | | | | identifiable. |
+----------------------------+------------------------------+-----------------------------------------------+----------------------------------+---------------------------------------------------+


Usage of INSDC Missing Value Reporting Terms
============================================

Please use the above standardised missing value vocabulary **only if a true value of an expected format for a mandatory field is missing**. If a true value is missing for a **recommended** or an **optional** field, then these fields should not be used for reporting at all. When reporting a missing mandatory field, the eight granular **‘reporting level’** terms need to be preceded with the term *missing:* to declare both the absence of a true value as well as the reason.
*not applicable* is only ever used as a top level term, its reporting level terms ought to be prefixed by *missing:*

Example of usage:
-----------------

**geographic location (country and/or sea)**: *missing: data agreement-established pre-2023*

**collection date**: *missing: control sample*
Examples of Usage:
------------------

**geographic location (country and/or sea)**: *missing: human-identifiable*
+---------------------------+----------------------------------------------+-----------------------------------------------+
| **Short Field Name** | **Long Field Name** | **Missing Value** Example |
+===========================+==============+===============================+===============================================+
| **geo_loc_name** | **geographic location (country and/or sea)** |*missing: data agreement established pre-2023* |
+---------------------------+----------------------------------------------+-----------------------------------------------+
| **collection_date** | **collection date** | *missing: control sample* |
+---------------------------+----------------------------------------------+-----------------------------------------------+
| **geo_loc_name** | **geographic location (country and/or sea)** + *missing: human-identifiable* |
+---------------------------+----------------------------------------------+-----------------------------------------------+
10 changes: 10 additions & 0 deletions submit/samples/sample_checklist.rst
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@@ -0,0 +1,10 @@
========================
Sample Checklist Related
========================

Various sample related information

.. toctree:
:maxdepth: 1
sample_checklist/sample_checklist_introduction.rst
sample_checklist/updates.rst
36 changes: 36 additions & 0 deletions submit/samples/sample_checklist/sample_checklist_infrastructure.rst
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@@ -0,0 +1,36 @@
===============================
Sample Checklist Infrastructure
===============================


DRAFT!

------------
Introduction
------------


In late 2024/early 2025 ENA implementing modernisation of the underlying ENA checklist systems architecture.

---------------------------------------------------
Why we moved to using Versioning Sample Checklists?
---------------------------------------------------
It will allow ENA to more rapidly update checklists (e.g. when new GSC MIxS releases) and also use ontologies for terms.

What it has meant is that checklists will all have versions and you will need to pull down the latest one after submission.
Changes that need a new version could be as simple as the required pattern changing.

------
High Level Infrastructural Changes
It makes the system more maintenance friendly.

--------------------------------------------------------
Technical Endpoints to Computationally Access Checklists
--------------------------------------------------------

Endpoints, you can use here, (TO BE UPDATED TO PROD instances)
Paginate over all versioned schemas.
Schema and metadata (JSON Schema is embedded here)
Just a summary of schema
Paginate over latest schemas (same as above 'a', with latest=true query param)
Get JSON Schema of the latest version of a given checklist (eg. ERC000022)
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