Scoping checklists and packages

[ramonawalls]

Discussed at the TWG meeting on Oct. 4.

Our understanding is that checklists are for different sequence types and packages are for different source materials or environments. With the advent of new sequencing types stable isotope fractioning of samples before sequencing, those distinctions may blur.

Can the CIG help us with defining some public guidance on when to add a new checklist vs. a package and how to handle gray areas?

[turbomam]

This was in response to @mslarae13's suggestion for a SIP stable isotope profiling checklist or package, right?

[ramonawalls]

Discussed at the CIG call on 24 Jan 2023.

Definitions and decisions:

• “Checklists”
  • Sets of terms that describe a particular sequence type or method (genome, metagenome, mimag etc)
• “Extensions”
  • Additions terms to describe a specific environment or sample type that can be used in combination with any sequence type
• We also publish all possible combinations of checklists and extensions.
  • Currently call the CombinationClasses. We should name them “Packages”.
• Encode this information in LinkML
• Update website.
  • On the website, but we should have the links to checklists, extensions, and packages go to the automatically generated documentation from LinkML.
  • We need to either generate the website documentation automatically from the LinkML docs or have an SOP in place to make sure they stay in sync.
  • Need to update the figure that is under extensions on the website so that it reflects our current terminology and status of packages, etc.
• Need to search github repos to see if there is any out of date documentation there. If so, move it to LinkML docs.

[ramonawalls]

@lschriml @only1chunts @pbuttigieg @turbomam @mslarae13 Please review the comment above to make sure you agree. Once we have agreement, I will write definitions for checklist, extension, and package that can be added to the schema.

[lschriml]

A few edits below:

Definitions and decisions:

“Checklists” Defined sets of metadata terms that describe minimal information about a sequenced genome, marker gene or metagenome. “Extensions” Defined sets of environmental package “extensions” metadata terms that describe the specific environment of the collected sample, that can be combined with other Extensions and Checklists

Mix and Match combinations of checklists and extensions are available, to support broad utilization. In our LinkML schema, these are currently called the CombinationClasses. We will re-name them to “Packages”. And encode this information in LinkML Update website. On the website, but we should have the links to checklists, extensions, and packages go to the automatically generated documentation from LinkML. We need to either generate the website documentation automatically from the LinkML docs or have an SOP in place to make sure they stay in sync. [Lynn: I vote to maintain the some static webpages, that describe the scope and description of checklists and extensions]

Need to update the figure that is under extensions on the website so that it reflects our current terminology and status of packages, etc. Need to search github repos to see if there is any out of date documentation there. If so, move it to LinkML docs.

[only1chunts]

@lschriml , I think your definitions are a bit narrower than we want aren't they? Checklists aren't just for "sequenced genome, marker gene or metagenome" we also have microbiomes and want to include transcriptomes as well as single cell genomics, and possibly even synthetic sequences and who knows what else in the future. So can we use the more generic terminology from the meeting notes, maybe something like this: Checklists are; Defined sets of metadata terms that describe sequences from a particular experiment type or methodology. Extensions are; Defined sets of metadata terms that extend a given checklist to describe the specific environment and/or collection details of the collected sample(s). Packages are; The combination of a checklist with one or more extensions.

[lschriml]

yes, that sounds good Chris

On Wed, Jan 25, 2023 at 7:15 AM Chris Hunter @.***> wrote:

@lschriml https://github.com/lschriml , I think your definitions are a bit narrower than we want aren't they? Checklists aren't just for "sequenced genome, marker gene or metagenome" we also have microbiomes and want to include transcriptomes as well as single cell genomics, and possibly even synthetic sequences and who knows what else in the future. So can we use the more generic terminology from the meeting notes, maybe something like this: Checklists are; Defined sets of metadata terms that describe sequences from a particular experiment type or methodology. Extensions are; Defined sets of metadata terms that extend a given checklist to describe the specific environment and/or collection details of the collected sample(s). Packages are; The combination of a checklist with one or more extensions.

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[only1chunts]

@ramonawalls , you've closed this ticket, does that mean the definition have been added to the SoT somewhere? if so, please can you mention here, exactly where they have been put, and confirm that the definitions provided by me above are the ones used? I can them update the gensc.org website with the definitions to match.