Skip to content

Branch improve missing values #200

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Woolly-at-EBI wants to merge 8 commits into
base: master
Choose a base branch
from
Open

Branch improve missing values #200

Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
81 changes: 43 additions & 38 deletions submit/samples/missing-values.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
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* |
+---------------------------+----------------------------------------------+-----------------------------------------------+