what is a "tissue"? #1084
Comments
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Changes to tissue flag made 4 April 2017 - see attached spreadsheet. Proposed change of "1" means add flag. Proposed change of "-1" means remove flag. |
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I'm pretty sure the "vial (70% ethanol) whole organism" are 'collected with the intent of genetic sampling'." ( @DerekSikes ) Can we firm up our definition? Here are the de-tissued ("-1") specimens. |
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Yes, we need to firm up the definition. I think this requires broader community input. What if we put the list of distinct parts into a google doc and sent that to everyone, asked them to put a "1" if they consider it a 'tissue' for purposes of Arctos querying. The important thing is that we don't get false positives where researchers are asking for tissues of things that aren't really 'tissue' in the sense of subsampling for loans. The person's name should be the column heading so we know who is scoring these. |
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We have been getting a huge number of requests lately from researchers that flagged "tissue" on VertNet and GBIF which returns specimens with prep types of 'whole organism (70% ethanol)' (I'm not sure about local searches on Arctos). In our case, these specimens are not suitable for genetic sampling. I like Carla's idea for community input on whether collections consider these preps as tissues. Though for UCM I'd rather just do a global update replacing all parts = 'whole organism (70% ethanol)' with 'whole organism (formalin-fixed, 70% ethanol)' to avoid any confusion for Mamm, Bird, Herp, and Fish collections. |
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https://docs.google.com/spreadsheets/d/1b9_JAx0LobFarYN-LYHVtvrZWi5o_p9T62qjrOwOwZo/edit?usp=sharing is all distinct part/tissue, and should be editable by anyone. DO NOT EDIT PART_NAME or IS_TISSUE COLUMNS!! They are the path back to the original data. I copied the is_tissue column, pasted it back in, changed the heading, and cast my "vote" there. |
It is critical that definitions are global. As a researcher, I should NOT have to guess at the history of an item to know what it is. That is, "some part" should mean one thing wherever it's used, and nothing else which means "some part" should be used anywhere.
Results of attached - confirm that's what needs updated and I'll change them. |
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Confirmed. I see no Fish collection specimens on the report. Looking at our data they are all recorded as ‘whole organism (ethanol)’ with 70% noted in part_remarks and can also be globally updated to ‘whole organism (70% ethanol)’ as we don’t have any specimens in 95%. THANK YOU.
From: dustymc [mailto:[email protected]]
Sent: Tuesday, May 09, 2017 10:29 AM
To: ArctosDB/arctos <[email protected]>
Cc: Emily M. Braker <[email protected]>; Comment <[email protected]>
Subject: Re: [ArctosDB/arctos] what is a "tissue"? (#1084)
whether collections consider
It is critical that definitions are global. As a researcher, I should NOT have to guess at the history of an item to know what it is. That is, "some part" should mean one thing wherever it's used, and nothing else which means "some part" should be used anywhere.
global update replacing all parts = 'whole organism (70% ethanol)' with 'whole organism (formalin-fixed, 70% ethanol)' to avoid any confusion for Mamm, Bird, Herp, and Fish collections.
Results of
create table temp_ucm_p1 as select
flat.guid,
flat.parts
from
flat,
specimen_part
where
flat.collection_object_id=specimen_part.derived_from_cat_item and
flat.guid like 'UCM:%' and
specimen_part.part_name='whole organism (70% ethanol)'
;
attached - confirm that's what needs updated and I'll change them.
temp_ucm_p1.csv.zip<https://github.com/ArctosDB/arctos/files/987303/temp_ucm_p1.csv.zip>
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done
Attached for confirmation. |
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Thanks Dusty! Yup, fish can be updated. |
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done |
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Mammals preserved in ethanol are not intended to be used as sources of DNA and when extracted they often yield no or very poor quality and quantity DNA. That is why we sample tissue from these and put it in the freezer. If we call these tissue we will be getting requests for tissues from ethanol preserved specimens when fresh frozen tissue is available from other suitable specimens. We will be wading through every tissue request to weed out the ethanol specimens and have to correct every request with suitable alternatives. Researchers who want to attempt DNA extraction from ethanol preserved specimens should do so as a last resort so we should make that an exception, not a default option. I say NO to calling mammals in ethanol tissue. |
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On Tue, May 9, 2017 at 9:22 AM, dustymc ***@***.***> wrote:
https://docs.google.com/spreadsheets/d/1b9_JAx0LobFarYN-LYHVtvrZWi5o_
p9T62qjrOwOwZo/edit?usp=sharing
is all distinct part/tissue, and should be editable by anyone.
DO NOT EDIT *PART_NAME* or *IS_TISSUE* COLUMNS!! They are the path back
to the original data.
I just 'locked' these columns so no one should be able to edit (I don't
think) - except maybe Dusty who created the sheet. Someone else should try
and let me know if they can.
… I copied the is_tissue column, pasted it back in, changed the heading, and
cast my "vote" there.
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Hi Emily - The VertNet issue is a separate one from the Arctos issue. I chatted with John W this morning and we have a new issue re: false positives in VN searches - will require re-indexing to use the tissue tokens that we use to filter on tissues in VN. Here's the related VN issue: VertNet/post-harvest-processor#8 |
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Carol and Michelle - Following on Emily's suggestion, I think we should do the same for MVZ: anything that is 'whole organism (ethanol)' should be changed to 'whole organism (formalin-fixed, 70% ethanol)' which is what is intended by that preservation type for our collections. Our practice has been to be more specific - e.g., 'whole organism (95% ethanol)' if it wasn't preserved in the standard way. Do you both agree with this? @mkoo @atrox10 |
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Thanks Carla, I’ve been meaning to email those guys. Our part names needed to be updated anyhow for clarity, but glad that the tissue query issue is on the radar.
From: Carla Cicero [mailto:[email protected]]
Sent: Tuesday, May 09, 2017 11:35 AM
To: ArctosDB/arctos <[email protected]>
Cc: Emily M. Braker <[email protected]>; Comment <[email protected]>
Subject: Re: [ArctosDB/arctos] what is a "tissue"? (#1084)
Hi Emily - The VertNet issue is a separate one from the Arctos issue. I chatted with John W this morning and we have a new issue re: false positives in VN searches - will require re-indexing to use the tissue tokens that we use to filter on tissues in VN.
Here's the related VN issue: VertNet/post-harvest-processor#8<VertNet/post-harvest-processor#8>
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Should we go ahead and send an email to the whole Arctos group asking for input on this? I'm happy to do that. |
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I think it would be a good idea. A lot of us migrated when the ‘whole organism (formalin-fixed, 70% ethanol)’ was not an option in the part_name code table, and I would imagine that many collections may want to do global replacements pertaining to these records.
From: Carla Cicero [mailto:[email protected]]
Sent: Tuesday, May 09, 2017 11:39 AM
To: ArctosDB/arctos <[email protected]>
Cc: Emily M. Braker <[email protected]>; Comment <[email protected]>
Subject: Re: [ArctosDB/arctos] what is a "tissue"? (#1084)
Should we go ahead and send an email to the whole Arctos group asking for input on this? I'm happy to do that.
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Sorry, I meant input on the tissue issue, but can also ask for input on that. I'm also curious on the difference between 'whole organism (alcohol)' and 'whole organism (ethanol)' - is there any? Likewise, we use(d) 'whole organism (ethanol-fixed)' to really mean 'whole organism (95% ethanol)' and I'm wondering who else does/did. |
Thanks! (And my "vote" on the spreadsheet was more of an experiment than a vote - I really don't want a say in this!) And just to say it again, "when mammals...." is just going to make sure that users cannot get what they want (eg there are lots of mammals and mammal-bits cataloged in not-Mamm collections). If a "whatever (ethanol)" from a mammal collection is not a tissue and and a "whatever (ethanol)" from a clam (ethnology, paleontology, bird, "host", WHATEVER) collection is a tissue, then one (or all) collection types will need to revise their vocabulary.
Could you also clarify that everyone who receives that email should also be getting GitHub notifications, and that http://dx.doi.org/10.7299/X75B02M5 has instructions for doing so?
Please make those requests here https://docs.google.com/spreadsheets/d/10mprhlOFP_qyiTH0d6WVfRHuJvoGtC5z4BoY_sS_rHY/edit?usp=sharing (or I'll get lost and miss something)
I believe "ethanol" is ethanol and "alcohol" is "ethanol or isopropanol" - let me know if that seems right and I'll update the code table definition. |
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Yes, I think it is worth soliciting feedback from users on the tissue issue and fluid collection part name usage. |
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I do not want to do this for MVZ Herps because for many animals, it was not
recorded anywhere that they were prepped in formalin, and it's possible for
older things from collectors I don't personally know, that they did not use
formalin. So I would rather leave it whole organism (ethanol) for the 70%
stuff that was probably formalin fixed, and only those in 95% ethanol are
different for our collection. We always get folks asking about our
collections and requesting things are tissues, it happens constantly, but
as long as the ones that are not obviously tissues (obvious tissue have a
tissue part or are the whole animals (95% ethanol)" of which there aren't
many) don't come up in tissue searches on Arctos, VN or GBIF, I would
rather leave my MVZ collections as is. I have been using the whole
organisms (ethanol) on purpose for that reason.
…On Tue, May 9, 2017 at 10:38 AM, Carla Cicero ***@***.***> wrote:
Carol and Michelle - Following on Emily's suggestion, I think we should do
the same for MVZ: anything that is 'whole organism (ethanol)' should be
changed to 'whole organism (formalin-fixed, 70% ethanol)' which is what is
intended by that preservation type for our collections. Our practice has
been to be more specific - e.g., 'whole organism (95% ethanol)' if it
wasn't preserved in the standard way. Do you both agree with this? @mkoo
<https://github.com/mkoo> @atrox10 <https://github.com/atrox10>
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"ikewise, we use(d) 'whole organism (ethanol-fixed)' to really mean 'whole organism (95% ethanol)' and I'm wondering who else does/did."
We have many thousands of mammals which are ethanol fixed (95% ETOH) and archived in 70% ETOH.
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Jonathan L. Dunnum Ph.D.
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Division of Mammals, Museum of Southwestern Biology
University of New Mexico
Albuquerque, NM 87131
(505) 277-9262
Fax (505) 277-1351
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________________________________
From: Carla Cicero <[email protected]>
Sent: Tuesday, May 9, 2017 11:49:21 AM
To: ArctosDB/arctos
Cc: Subscribed
Subject: Re: [ArctosDB/arctos] what is a "tissue"? (#1084)
Sorry, I meant input on the tissue issue, but can also ask for input on that. I'm also curious on the difference between 'whole organism (alcohol)' and 'whole organism (ethanol)' - is there any? Likewise, we use(d) 'whole organism (ethanol-fixed)' to really mean 'whole organism (95% ethanol)' and I'm wondering who else does/did.
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This is a good case to emphasize the need to have "part" name separated
from fixation and preservation. Whole organism should be a separate field,
with part preservation history being first 95% ethanol and then 70%
ethanol. We need a way to standardize preservation methods across
collections, instead of the current ad hoc interpretations.
…On Tue, May 9, 2017 at 2:36 PM, jldunnum ***@***.***> wrote:
"ikewise, we use(d) 'whole organism (ethanol-fixed)' to really mean 'whole
organism (95% ethanol)' and I'm wondering who else does/did."
We have many thousands of mammals which are ethanol fixed (95% ETOH) and
archived in 70% ETOH.
______________________________________________________________
Jonathan L. Dunnum Ph.D.
Senior Collection Manager
Division of Mammals, Museum of Southwestern Biology
University of New Mexico
Albuquerque, NM 87131
(505) 277-9262
Fax (505) 277-1351
MSB Mammals website: http://www.msb.unm.edu/mammals/index.html
Facebook: http://www.facebook.com/MSBDivisionofMammals
Shipping Address:
Museum of Southwestern Biology
Division of Mammals
University of New Mexico
CERIA Bldg 83, Room 204
Albuquerque, NM 87131
________________________________
From: Carla Cicero ***@***.***>
Sent: Tuesday, May 9, 2017 11:49:21 AM
To: ArctosDB/arctos
Cc: Subscribed
Subject: Re: [ArctosDB/arctos] what is a "tissue"? (#1084)
Sorry, I meant input on the tissue issue, but can also ask for input on
that. I'm also curious on the difference between 'whole organism (alcohol)'
and 'whole organism (ethanol)' - is there any? Likewise, we use(d) 'whole
organism (ethanol-fixed)' to really mean 'whole organism (95% ethanol)' and
I'm wondering who else does/did.
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agreed
On Tue, May 9, 2017 at 1:19 PM, Mariel Campbell <[email protected]>
wrote:
… This is a good case to emphasize the need to have "part" name separated
from fixation and preservation. Whole organism should be a separate field,
with part preservation history being first 95% ethanol and then 70%
ethanol. We need a way to standardize preservation methods across
collections, instead of the current ad hoc interpretations.
On Tue, May 9, 2017 at 2:36 PM, jldunnum ***@***.***> wrote:
> "ikewise, we use(d) 'whole organism (ethanol-fixed)' to really mean
'whole
> organism (95% ethanol)' and I'm wondering who else does/did."
>
> We have many thousands of mammals which are ethanol fixed (95% ETOH) and
> archived in 70% ETOH.
>
>
> ______________________________________________________________
>
> Jonathan L. Dunnum Ph.D.
> Senior Collection Manager
> Division of Mammals, Museum of Southwestern Biology
> University of New Mexico
> Albuquerque, NM 87131
> (505) 277-9262
> Fax (505) 277-1351
>
> MSB Mammals website: http://www.msb.unm.edu/mammals/index.html
> Facebook: http://www.facebook.com/MSBDivisionofMammals
>
> Shipping Address:
> Museum of Southwestern Biology
> Division of Mammals
> University of New Mexico
> CERIA Bldg 83, Room 204
> Albuquerque, NM 87131
> ________________________________
> From: Carla Cicero ***@***.***>
> Sent: Tuesday, May 9, 2017 11:49:21 AM
> To: ArctosDB/arctos
> Cc: Subscribed
> Subject: Re: [ArctosDB/arctos] what is a "tissue"? (#1084)
>
>
> Sorry, I meant input on the tissue issue, but can also ask for input on
> that. I'm also curious on the difference between 'whole organism
(alcohol)'
> and 'whole organism (ethanol)' - is there any? Likewise, we use(d) 'whole
> organism (ethanol-fixed)' to really mean 'whole organism (95% ethanol)'
and
> I'm wondering who else does/did.
>
> —
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Here are the parts which have been used in loans that resulted in GenBank numbers. It's not perfect - there's no direct part-->loan-->otherID pathway, so two parts from a specimen might have been loaned and only one produced a GenBank number or the GenBank number came from undocumented usage or etc. |
Here's what's in freezers: |
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I'm pretty sure the "media" or "observation" in the freezer is not intended for genetic usage. In my ideal world, I would like a direct part-->loan-->otherID pathway. I want to know exactly which part resulted in a Genbank number. |
I suppose that depends on what was observed in the freezer.... PART_NAMEGUIDmedia observation 2 rows selected.
Yea, me too, but I'm not sure how it lines up with reality. A GenBank sequence magically appears, now what? All too often we don't have that middle step in the happy pathway because of incomplete loan data or something done before we got the specimen or because some grad student dug something out of a freezer and didn't tell anyone or ... I still like the idea. |
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FYI My lab tech made this:
http://arctos.database.museum/guid/UAM:Ento:312087
accidentally - barcodes & UAM:Ento are for specimens we own (or once owned)
but something that we never owned should be in the UAMObs:ento and not have
a barcode.
…-D
On Mon, Jul 24, 2017 at 3:32 PM, dustymc ***@***.***> wrote:
"media" or "observation" in the freezer is not intended for genetic usage
I suppose that depends on what was observed in the freezer....
PART_NAME GUID
media
UAM:Ento:66331
observation
UAM:Ento:312087
2 rows selected.
direct part-->loan-->otherID
Yea, me too, but I'm not sure how it lines up with reality. A GenBank
sequence magically appears, now what? All too often we don't have that
middle step in the happy pathway because of incomplete loan data or
something done before we got the specimen or because some grad student dug
something out of a freezer and didn't tell anyone or ...
I still like the idea.
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Associate Professor of Entomology
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[email protected]
phone: 907-474-6278
FAX: 907-474-5469
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http://arctos.database.museum/uam_ento_all
<http://www.uaf.edu/museum/collections/ento/>
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I also like the idea of part -->loan-->otherID to attach Genbank sequences to loans/parts. Could we use a part attribute= relationship? |
I'm splitting that conversation off to #1257 and reserving this one for discussing how we might be able to usefully define "tissues." |
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From recent MSB visit: DGR (=most of MSB's tissues) was NOT 'collected with the intent of genetic sampling.' |
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Definition (from @jtgiermakowski ): institution is willing to subsample |
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Discussed at AWG meeting:
Closing |
Ref: email "Arctos tissue growth" (w/ @campmlc @ccicero @KyndallH )
We need to come up with documentation for the "is tissues?" flag in http://arctos.database.museum/info/ctDocumentation.cfm?table=CTSPECIMEN_PART_NAME.
Random list of things which may influence tissue-ness:
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