attribute type isotope value

dustymc commented 1 year ago

Initial Request

Goal: Describe what you're trying to accomplish. This is the only necessary step to start this process. The Committee is available to assist with all other steps. Please clearly indicate any uncertainty or desired guidance if you proceed beyond this step.

I don't know what this means. Perhaps it's better as a 'detected' attribute?? Maybe it's fine?? ???

isotope value [ link ]

The abundance of certain stable isotopes and chemical elements within organic and inorganic compounds.

Discussion: Please reach out to anyone who might be affected by this change. Leave a comment or add this to the Committee agenda if you believe more focused conversation is necessary.


 guid_prefix | count 
-------------+-------
 UAM:Mamm    |    30

@amgunderson

@ArctosDB/arctos-code-table-administrators

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ewommack commented 1 year ago

with isobank now active this could be switch over to there? https://isobank.tacc.utexas.edu/

jldunnum commented 1 year ago

Agreed, developing reciprocal linkouts to Isobank (like we do to GenBank) has been on the to-develop list for a while I think. Joe Cook will be meeting with the Isobank group in the next couple weeks and could revive this discussion.

Jonathan L. Dunnum Ph.D. (he, him, his) Senior Collection Manager Division of Mammals, Museum of Southwestern Biology University of New Mexico Albuquerque, NM 87131 (505) 277-9262 Fax (505) 277-1351

Chair, Systematic Collections Committee, American Society of Mammalogists Latin American Fellowship Committee, ASM

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: Elizabeth Wommack @.> Sent: Tuesday, May 23, 2023 12:30 PM To: ArctosDB/arctos @.> Cc: Jonathan Dunnum @.>; Team mention @.> Subject: Re: [ArctosDB/arctos] Code Table Request - QUESTION - isotope value (Issue #6330)

[EXTERNAL]

with isobank now active this could be switch over to there? https://isobank.tacc.utexas.edu/

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campmlc commented 1 year ago

We have isotope as a proposed examined_detected code table value. With an IsoBank reciprocal link and the examined for: isotope attribute, that should get folks to where they need? Or they could put the value in detected: isotopes remarks. The alternative is to put this as a part attribute - which is where it really belongs.

On Tue, May 23, 2023 at 12:30 PM Elizabeth Wommack @.***> wrote:

[EXTERNAL]*

with isobank now active this could be switch over to there? https://isobank.tacc.utexas.edu/

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/6330#issuecomment-1559945546, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADQ7JBB6SEDWQU54TVDHRXTXHT63HANCNFSM6AAAAAAYMH7KTM . You are receiving this because you are on a team that was mentioned.Message ID: @.***>

jldunnum commented 1 year ago

[like] Jonathan Dunnum reacted to your message:

From: Mariel Campbell @.> Sent: Tuesday, May 23, 2023 7:07:02 PM To: ArctosDB/arctos @.> Cc: Jonathan Dunnum @.>; Team mention @.> Subject: Re: [ArctosDB/arctos] Code Table Request - QUESTION - isotope value (Issue #6330)

[EXTERNAL]

We have isotope as a proposed examined_detected code table value. With an IsoBank reciprocal link and the examined for: isotope attribute, that should get folks to where they need? Or they could put the value in detected: isotopes remarks. The alternative is to put this as a part attribute - which is where it really belongs.

On Tue, May 23, 2023 at 12:30 PM Elizabeth Wommack @.***> wrote:

[EXTERNAL]*

with isobank now active this could be switch over to there? https://isobank.tacc.utexas.edu/

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/6330#issuecomment-1559945546, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADQ7JBB6SEDWQU54TVDHRXTXHT63HANCNFSM6AAAAAAYMH7KTM . You are receiving this because you are on a team that was mentioned.Message ID: @.***>

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mkoo commented 1 year ago

Just to sort through this, I think this is what this issue is really about:

Creating a new external link to isoBank if you want it to function like Genbank-- @jldunnum @campmlc Honestly this seems like the easy-to-do, proper, doesnt-break-Arctos response and best parallels Genbank links. We have been chatting about this for a while so let's

eg https://arctos.database.museum/guid/MVZ:Bird:4381 has a link to: https://isobank.tacc.utexas.edu/analyses/analysis_detail/1463/

The question becomes then do we treat as Identifiers or an Attribute? Is Arctos/collections really storing the isotopic values? There seems to be a LOT of relevant metadata for isotope analysis that is better handled in a Isotope database so a link as an Identifier seems more sustainable, useful and 'honest' than trying to replicate IsoBank metadata. Maybe we need to remove as 'isotope value' and instead use the proposed relationship 'examined for' (https://arctos.database.museum/info/ctDocumentation.cfm?table=ctid_references)

I dont think you are suggesting we create parts even if the collections are not housing/ did not do the isotopes/ isotopic analysis, right?!! I think that's not so workable but I think that's what you're implying. Is there an example of an record like that or is it still 'theoretical'?

If I am interpreting this correctly then let's close this issue and file a new one. If not, let's put this on the next AWG /Issues meeting so we can discuss and rope in Joe Cook too

campmlc commented 1 year ago

My understanding from many previous discussions and from Carla's participation in the planning process is that we had planned all along for this to be modeled after GenBank, using identifiers with reciprocal links. I support this approach. The only other modification that we've discussed to this model is to make it possible to link these identifiers to the parts that were examined to generate sequences and isotope values. I don't know if we can do that through the interface, or if we need to add GenBank and IsoBank IDs as part attributes as well - or if there is some other means of creating those linkages. That way we'd have the ability to link loans of a specific tissue type to a specific researcher to the sequence and isotopic results, which would be very useful when we have dozens of GenBank IDs that currently are attached only at the record level.

On Mon, Jun 5, 2023 at 11:39 AM Michelle Koo @.***> wrote:

[EXTERNAL]*

Just to sort through this, I think this is what this issue is really about:

Creating a new external link to isoBank if you want it to function like Genbank-- @jldunnum https://github.com/jldunnum @campmlc https://github.com/campmlc Honestly this seems like the easy-to-do, proper, doesnt-break-Arctos response and best parallels Genbank links. We have been chatting about this for a while so let's

eg https://arctos.database.museum/guid/MVZ:Bird:4381 has a link to: https://isobank.tacc.utexas.edu/analyses/analysis_detail/1463/

The question becomes then do we treat as Identifiers or an Attribute? Is Arctos/collections really storing the isotopic values? There seems to be a LOT of relevant metadata for isotope analysis that is better handled in a Isotope database so a link as an Identifier seems more sustainable, useful and 'honest' than trying to replicate IsoBank metadata. Maybe we need to remove as 'isotope value' and instead use the proposed relationship 'examined for' ( https://arctos.database.museum/info/ctDocumentation.cfm?table=ctid_references )

I dont think you are suggesting we create parts even if the collections are not housing/ did not do the isotopes/ isotopic analysis, right?!! I think that's not so workable but I think that's what you're implying. Is there an example of an record like that or is it still 'theoretical'?

If I am interpreting this correctly then let's close this issue and file a new one. If not, let's put this on the next AWG /Issues meeting so we can discuss and rope in Joe Cook too

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/6330#issuecomment-1577207015, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADQ7JBELEDIYKLYNWCECILTXJYKT5ANCNFSM6AAAAAAYMH7KTM . You are receiving this because you were mentioned.Message ID: @.***>

dustymc commented 1 year ago

Is Arctos/collections really storing the isotopic values?

Beats me, data below, didn't help me much...

If that's what this is, can it be moved to isobank? (I think these data pre-date the project.)

suggesting we create parts

That would only be appropriate if there's something to which a barcode might be stuck.

example of an record

https://arctos.database.museum/search.cfm?attribute_type_1=isotope%20value

rope in

These all all @amgunderson data.

reciprocal links

That's a question for isobank.

link loans of a specific tissue type to a specific researcher

That's a matter of loan agreements. (Get good partIDs, add them to https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecpart_attribute_type#part_identifier, require them to be used. https://github.com/ArctosDB/arctos/discussions/5231 might streamline something but it can't really change any of that.)


arctosprod@arctos>> select attribute_value,attribute_units  from attributes where attribute_type ='isotope value';
 attribute_value | attribute_units 
-----------------+-----------------
 -17.84          | 
 11.118          | 
 -18.41          | 
 -16.7           | 
 11.345          | 
 -16.28          | 
 11.87           | 
 11.627          | 
 -16.7           | 
 11.335          | 
 -17.41          | 
 -17.59          | 
 11.349          | 
 11.87           | 
 -16.43          | 
 -20             | 
 -15.96          | 
 11.944          | 
 11.768          | 
 -16.91          | 
 -16.41          | 
 12.289          | 
 -17.05          | 
 13.316          | 
 -16.83          | 
 11.692          | 
 12.026          | 
 -18.87          | 
 12.37           | 
 11.464          | 
(30 rows)

campmlc commented 1 year ago

So if I understand the UAM situation correctly - for these 30 records, these would have to be converted to "examined for: isotope" and "detected: isotope" attributes, with the value in methods or remarks? And the proposal is to delete the isotope value attribute? I assume these are legacy records that are very unlikely to have an IsoBank submission. I am not sure the attribute is really hurting anything at the moment, but if we do need to get rid of it, then does @amgunderson support this approach?

Jegelewicz commented 1 year ago

That would only be appropriate if there's something to which a barcode might be stuck.

Or could have been stuck to - not all parts are around forever and some get lost...

ewommack commented 1 year ago

Is Arctos/collections really storing the isotopic values?

I'd really suggest we try not to in the future. That metadata really influences how you can use the isotopic values you get from a sample. What machine you ran on, what your standard was, where the lab was situated, what prep they did of the sample, what conversion you used, etc. That will really affect your isotopic results, and the value can look the same but actually be telling you something really different with the metadata. I liked the Isobank reporting set-up from a researcher side of things, because they have the metadata collection set-up. Then I could go to the lab that completed the analysis and say - hey I need these values too to report the data correctly.

mkoo commented 1 year ago

@ewommack yes that was a rhetorical question!-- agreed best to handle like a Genbank link and record

thx @campmlc for highlighting the issue here with the 30 UAM records with legacy data-- does Isobank have a mechanism for dealing with legacy data? (just wondering, like maybe they could have a record even with missing fields?) -- which may be what Beth was suggesting.... we would have to create 30 isobank records probably without the all the fields if they are not known, then link to UAM records

I still fear losing data however since the raw values would likely be relegated to remarks, so going to tentatively agree with @campmlc that we consider leaving this one. CT committee could change the description with best practise of using and linking to Isobank. Data could still be useful if only as guidance/ benchmark for future isotopic work.

dustymc commented 1 year ago

losing data

See initial comment, my goal is to understand these data, I don't think we can tell if we're losing anything or not without that. I do not understand where the other comment came from, I think my goals were spelled out pretty clearly and they do not involve jumping to deleting!

raw values would likely be relegated to remarks,

They already are! These data are not understandable without delving into remarks, and I'm not sure they are after either but hopefully that's just my ignorance showing.

consider leaving this one

The big lump under the rug is a serious trip hazard; these things are piling up into cumulatively-blocking messes. If this is doing something that can be defined (or restructured to do something or whatever) and I'm just not getting it then clarifying the definition is a satisfactory solution. If this is the unstable mess it looks like from here, then let's PLEASE not just sweep it under the proverbial rug, at least not before exhausting all other options.

Jegelewicz commented 1 year ago

fear losing data

There isn't much to lose? What do those numbers even mean? From digital data today:

"data linkages and relationships are indicators of digital provenance and quality"

Even with a date and determiner - those numbers are completely useless in Arctos. If there is no metadata in a usable format, the numbers are just numbers lacking any context and we are saving them for why?

Sorry for the rant, but we do need to start considering what data is important for managing a collection and what we should feel responsible for managing. We cannot be the repository for EVERYTHING. YES, we should pursue the path of getting these into isobank and setting up links to that data - that is the dream of the digitally extended specimen. Just tell me who I need to call...

ewommack commented 1 year ago

Chris Jordan at TACC was my main contact for getting the MVZ data into Isobank.

campmlc commented 1 year ago

They have divine guidance? 😏

On Tue, Jun 6, 2023, 8:05 PM Elizabeth Wommack @.***> wrote:

[EXTERNAL]*

Christ at TACC was my main contact for getting the MVZ data into Isobank.

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