Arctos DB
Replies: 31 comments
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definitions please |
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I like the idea. We cannot proceed without definitions. There should be some indication of units - is that -20K (which would be an interesting state...)? "Ultralow" is ambiguous - could mean -40, -80, and probably some other stuff. Suggest sticking to numbers. Maybe for LN2 as well, that's consistent and an easy way to separate liquid vs vapor. |
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I think we can put rough numbers, but there is implicit variability in all
of these. Ultralow freezers sometimes lose cooling capacity and can't go
below -50C, but usually they are between -70 and -80C. We can't put too
much detail in here - we need a real environmental module to do that.
Really these should be three separate attributes - but we will never get
community buy in for that.
frozen, -20C: frozen in a standard freezer at -20 degrees Celsius..
frozen, ultralow: frozen in an ultralow freezer at temperatures typically
-50 to -80 degrees Celsius. Specify exact temperature outside of this range
in remarks.
frozen, nitrogen: frozen in liquid or vapor phase nitrogen at -150 to -194
degrees Celsius.
…On Mon, Jun 7, 2021 at 6:59 PM dustymc ***@***.***> wrote:
* [EXTERNAL]*
I like the idea.
We cannot proceed without definitions.
There should be some indication of units - is that -20K (which would be an
interesting state...)?
"Ultralow" is ambiguous - could mean -40, -80, and probably some other
stuff. Suggest sticking to numbers.
Maybe for LN2 as well, that's consistent and an easy way to separate
liquid vs vapor.
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We should add:
frozen, dry ice: frozen on dry ice at -70 to -80 Celsius for temporary
storage/shipping.
frozen, ice: stored on ice at 0 degrees C for temporary storage/shipping.
On Mon, Jun 7, 2021 at 10:33 PM Mariel Campbell ***@***.***>
wrote:
… I think we can put rough numbers, but there is implicit variability in all
of these. Ultralow freezers sometimes lose cooling capacity and can't go
below -50C, but usually they are between -70 and -80C. We can't put too
much detail in here - we need a real environmental module to do that.
Really these should be three separate attributes - but we will never get
community buy in for that.
frozen, -20C: frozen in a standard freezer at -20 degrees Celsius..
frozen, ultralow: frozen in an ultralow freezer at temperatures typically
-50 to -80 degrees Celsius. Specify exact temperature outside of this range
in remarks.
frozen, nitrogen: frozen in liquid or vapor phase nitrogen at -150 to -194
degrees Celsius.
On Mon, Jun 7, 2021 at 6:59 PM dustymc ***@***.***> wrote:
> * [EXTERNAL]*
>
> I like the idea.
>
> We cannot proceed without definitions.
>
> There should be some indication of units - is that -20K (which would be
> an interesting state...)?
>
> "Ultralow" is ambiguous - could mean -40, -80, and probably some other
> stuff. Suggest sticking to numbers.
>
> Maybe for LN2 as well, that's consistent and an easy way to separate
> liquid vs vapor.
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#3649 (comment)>,
> or unsubscribe
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We have one. I argued for using it instead of doing this. |
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@dustymc please explain re: environmental module. Arctos screenshot? |
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I WISH SOMEONE would DO this consistently. It would make a great publication. |
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How about these terms? frozen, -20: frozen in a standard freezer at -20 degrees Celsius. |
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@ArctosDB/arctos-code-table-administrators suggest that we add container types to address this issue. @ebraker to write a How To for using containers without barcodes (or record a video tutorial, or both?) :-) Suggested additions to the container type code table: freezer -20: frozen in a standard freezer at -20 degrees Celsius. We already have cryotank to cover the frozen, LN2 instance. |
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Sorry I missed the meeting - Is the proposal to make the different types of
frozen a container type or a preservation type? Because we use the same
container type (cryovial) at different temperatures.
…On Thu, Jul 15, 2021 at 3:38 PM Teresa Mayfield-Meyer < ***@***.***> wrote:
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@ArctosDB/arctos-code-table-administrators
<https://github.com/orgs/ArctosDB/teams/arctos-code-table-administrators>
suggest that we add container types to address this issue. @ebraker
<https://github.com/ebraker> to write a How To for using containers
without barcodes (or record a video tutorial, or both?) :-)
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Container type.
The containers will be the freezers, so the fact that the cryovial is in an ultralow freezer would tell you how it is frozen and if it moves to cryo, that history would go with it. |
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We did discuss that container info is not public - that will need to be worked out. Probably a new issue if anyone feels strongly about it and assuming this solution works... |
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Adding to AWG Issues Meeting Agenda |
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That sounds reasonable. Even better if we could somehow integrate container
environment with preservation history - but that is a different issue.
Freezer temps go up and down - we should be able to record this, at least
extreme events such as freezer failures.
…On Thu, Jul 15, 2021 at 4:20 PM Teresa Mayfield-Meyer < ***@***.***> wrote:
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Container type.
Because we use the same container type (cryovial) at different
temperatures.
The containers will be the freezers, so the fact that the cryovial is in
an ultralow freezer would tell you how it is frozen and if it moves to
cryo, that history would go with it.
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We need a protocol for how to integrate these two data streams, then. Right now, container history is only visible through object tracking. If a freezer fails and I record a high temp value as a container check - does that history propagate to the history of all containers within the freezer? |
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Also, container history should be integrated with part Condition history for this approach to work, e.g. in catalog record -> Edit Parts |
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Where did these get added? |
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There's no direction, no use case, no recent activity, this isn't actionable and I see little indication that it will become so. I can transfer to discussions, but making a habit of that will probably lead to everything over there becoming inaccessible behind all the clutter. I really think that at some point we need to just close issues that don't seem to be getting closer to a resolution so that we can keep track of the things that are active and/or actionable. |
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@RJSS8 the frozen discussion is above, feel free to chime in. Note that there are two discussions here - one for those NOT using object tracking (the first comment and one for those who are using object tracking (all the stuff near the end). |
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Hi everyone. Regarding this discussion above I have interest in getting a new term in part preservation regarding cryopreserved samples. Referring mostly to the collections that don't use object tracking, could the term " cryopreservation " have its own definition so as to be something different than frozen? Since having something frozen and something cryopreserved involves different processes and has different intentions/outcomes in my view of things. |
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I agree something like this is needed as the current mix of object tracking, part attributes, and preservation terms is inadequate to track and discover samples preserved in liquid nitrogen. Frozen encompasses too many things, and flash frozen is not clear or generally used. Adding a storage temperature attribute is confusing - what is our standard for LN2? - 196C? This is also a separate attribute from preservation. |
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What I thought might be possible would be the introduction of the term "cryopreservation" Possible definition: " Process where biological samples are preserved through cooling to very low temperatures stopping all biological activity, including processes related to cell death allowing for the preservation of the sample for future use. This process can be used to preserve a wide range of biological samples." Maybe the specific process/cryoprotective agents used should be then explained in methods/remarks? Have no defined units for this and utilize storage temperature as the way of describing the specific temperature at which it is preserved maybe? |
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I agree with adopting the term, but the definition should be broader (see below), as cryopreservation can be very effective across a wide range of temperatures (-20 °C to -196 °C) while “stopping biological activity” occurs only at the coldest temperatures.
" Process where biological samples are preserved through cooling to very low temperatures, stopping all slowing biological and chemical activity, including processes related to cell death, allowing for the preservation of the sample for future use. This process can be used to preserve a wide range of biological samples."
The specific process/cryoprotective agents used should be explained in methods/remarks.
There should be no defined temperature units for this term. Storage temperature can describe the specific temperature at which it is preserved.
Daniel L. Distel, PhD
(He, Him, His)
Director
Ocean Genome Legacy
Northeastern University Marine Science Center
430 Nahant Rd Nahant, MA 01908
(617) 373-2576
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From: Renato Soares ***@***.***>
Date: Tuesday, July 30, 2024 at 5:04 AM
To: ArctosDB/arctos ***@***.***>
Cc: Subscribed ***@***.***>
Subject: Re: [ArctosDB/arctos] Code Table Request - add preservation values for different types of 'frozen' (Discussion #5407)
What I thought might be possible would be the introduction of the term "cryopreservation"
Possible definition:
" Process where biological samples are preserved through cooling to very low temperatures stopping all biological activity, including processes related to cell death allowing for the preservation of the sample for future use. This process can be used to preserve a wide range of biological samples."
Maybe the specific process/cryoprotective agents used should be then explained in methods/remarks?
Have no defined units for this and utilize storage temperature as the way of describing the specific temperature at which it is preserved maybe?
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Yes, that is the critical attribute; terms should not be arbitrary, and we should not have multiple terms attempting to do the same thing. The current definition of frozen involves 'below 0C.' Updating that would mean updating any material using that definition to whatever becomes appropriate, as required. There are currently 1068883 parts using 'frozen.' I believe this would need a migration plan/pathway to proceed. |
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This is a problem we run into a lot, migrating less specific code table values to more specific code table values. It would be helpful if we had a protocol to cover all migrations like this. Clarifying type of frozen for a million+ records is an impossible task, so are there any alternatives to just adding the new more specific values and hope people start using them? Wild idea, is it within the realm of possibility to "lock" a code table value so that it cannot be used for new records? That way new, better values can be added while giving time to clean up the older values? |
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I'm not sure the details of any two would be the same, but some sort of mechanism to avoid getting stuck in between states would be amazing.
If anyone cares about discoverability (and we all clearly do, particularly regarding 'frozen'), avoiding any form of that situation should be a top priority. Can this be cast or clarified as a functional need? I don't think I adequately understand the use case (or ??) - surely if one can separate the various categories of 'frozen' that are being proposed, one could just use https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecpart_attribute_type#storage_temperature to record whatever information lead to such conclusions? Minimally, one 'frozen' and one "cryotemp" recording seems to accomplish @RJSS8 's request without adding any denormalizing or confusing terms. Such an approach also establishes a framework for recording a rough history I think better than any categorization could eg
and from that a researcher should be able to get a pretty decent idea of what uses the part might support. I think that would also allow some sort of UI-magic like we do for 'tissues' - eg those data could support a 'high-quality frozen tissues' flag/shortcut to find things which have always been below some temperature, if that's part of what's wanted. What am I not understanding? |
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The challenge is to record and discover samples collected into and kept below a certain temperature given the above structure, especially with the variability in different recorded temperatures. |
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Ok I understand the different uses of frozen with the support of the storage temperature to indicate that they're cryopreserved, but I think there should be a term that indicates it independently from that. Is there a way to search by what is cryopreserved like lets say through the storage temperature? |
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The goals needs functionally defined. (Are people asking for things that that might have been suitable for their use, but no longer are?! Is the use case not in support of discovering high-quality samples? ??)
I see three possibilities:
Where am I getting lost? |
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Currently CTPART_PRESERVATION has the following values for 'frozen'
frozen
frozen, flash
Suggestion is to add values for:
frozen, -20
frozen, ultralow
frozen, LN2
(or spell out liquid nitrogen?)
This will allow us to better distinguish how parts are frozen.
Given 'High Priority' since we're actively separating parts from preservation now. It would be good to do this before the change so that new parts can choose different frozen preservation methods.
Related issue: https://github.com/ArctosDB/arctos/issues/1460
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