Code Table Request - Add environmental: eDNA to Examined_Detected code table

[campmlc]

Initial Request Add the term "environmental: DNA" to the Examined_Detected code table to aid in the migration of legacy data.

_Proposed Value: environmental: DNA - https://github.com/ArctosDB/arctos/issues/6263#issuecomment-1542299141

_Proposed Definition: environmental DNA (eDNA) is collected from a variety of environmental samples such as soil, seawater, snow or air, rather than directly sampled from an individual organism. Can be used to test for presence of organisms or pathogens through sampling the environment through the process of eDNA metabarcoding. https://en.wikipedia.org/wiki/Environmental_DNA

_Context: We are proposing migrating the attribute "tested for presence" to the examined/detected attribute system. This value is necessary to capture these legacy data.

_Table: https://arctos.database.museum/info/ctDocumentation.cfm?table=ctexamined_detected

_Priority: High

_Available for Public View: Yes

Project: Add the issue to the Code Table Management Project.

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.

@KyndallH @ArctosDB/arctos-code-table-administrators

Approval All of the following must be checked before this may proceed.

All of the following must be checked before this may proceed.

_The How-To Document should be followed. Pay particular attention to terminology (with emphasis on consistency) and documentation (with emphasis on functionality)._

• [x] Code Table Administrator[1] - check and initial, comment, or thumbs-up to indicate that the request complies with the how-to documentation and has your approval
• [ ] Code Table Administrator[2] - check and initial, comment, or thumbs-up to indicate that the request complies with the how-to documentation and has your approval
• [ ] DBA - The request is functionally acceptable. The term is not a functional duplicate, and is compatible with existing data and code.
• [ ] DBA - Appropriate code or handlers are in place as necessary. (ID_References, Media Relationships, Encumbrances, etc. require particular attention)

Rejection

If you believe this request should not proceed, explain why here. Suggest any changes that would make the change acceptable, alternate (usually existing) paths to the same goals, etc.

1. Can a suitable solution be found here? If not, proceed to (2)
2. Can a suitable solution be found by Code Table Committee discussion? If not, proceed to (3)
3. Take the discussion to a monthly Arctos Working Group meeting for final resolution.

Implementation

Once all of the Approval Checklist is appropriately checked and there are no Rejection comments, or in special circumstances by decree of the Arctos Working Group, the change may be made.

Review everything one last time. Ensure the How-To has been followed. Ensure all checks have been made by appropriate personnel.

Make changes as described above. Ensure the URL of this Issue is included in the definition.

Close this Issue.

DO NOT modify Arctos Authorities in any way before all points in this Issue have been fully addressed; data loss may result.

Special Exemptions

In very specific cases and by prior approval of The Committee, the approval process may be skipped, and implementation requirements may be slightly altered. Please note here if you are proceeding under one of these use cases.

1. Adding an existing term to additional collection types may proceed immediately and without discussion, but doing so may also subject users to future cleanup efforts. If time allows, please review the term and definition as part of this step.
2. The Committee may grant special access on particular tables to particular users. This should be exercised with great caution only after several smooth test cases, and generally limited to "taxonomy-like" data such as International Commission on Stratigraphy terminology.

[campmlc]

See #6228

[dustymc]

Is "environmental: e[nvironmental]" absolutely necessary?

I think "environmental" is a method - DNA is DNA and that's what's being tested for, no?

[Jegelewicz]

Agree with @dustymc and suggest changing the value to environmental: DNA.

[campmlc]

That works.

[dustymc]

I don't think that's an agreement!

I suggested that "environmental" is part of method.

The "thing" is just DNA.

The test will detect it whether it's in the environment or not.

Method should not be embedded in the terms.

[Jegelewicz]

Method should not be embedded in the terms.

then environmental: PFAS should cause issue too?

I guess I would argue that the "thing" is eDNA because I fear that using DNA on it's own will confuse users of the data.

[dustymc]

then https://github.com/ArctosDB/arctos/issues/6265 should cause issue too?

Probably? I'm sorta-sure throwing puddles at PCR is a way to detect https://github.com/ArctosDB/arctos/issues/6268, if we're going to have method embedded here then are we going to have a duplicate there? Surely there's something involving dirt and tapeworm eggs? Etc. etc.

There is of course an available solution, but I believe that's been summarily rejected.

[Jegelewicz]

That all makes sense and I would be fine with just DNA. I believe quite strongly that this SHOULD be a part attribute and I may be 100% crazy, but the detected things should totally be related records with their own identifications that would allow for metadata about the ID (including higher classification).

This really needs a development group (that includes potential users!) with time to think through the options and a test box to try them out. That group should also include a dedicated programmer who isn't trying to keep Arctos running for everyone, answer our daily questions and fix our UI issues on the side.

[campmlc]

Agree with @Jegelewicz . There are too many sources of DNA. We need this term to explicitly reference eDNA, to make it discoverable without confounding the attribute with other sources of DNA, such as a liver. Plus, it needs to be under the "environmental" category. You aren't testing an organism. You are testing a body of water, or soil. This term is widely used among researchers and the collections community. The point is to make the term discoverable to people who are looking for it, not to hide it under our own semantic labels.

[campmlc]

As we have said multiple times before, using these attributes this way is providing a place to put these data RIGHT NOW - because we have these data, they are on hold, this is delaying cataloging and delaying research by people who need to use them. These discussions have been going on since last year. If we can get SOMETHING online, we can get feedback from the user community and we are hoping this will lead to real funding for something better. Yes, there is always something better. I spent three years of my life developing something I thought would be a truly innovative and useable solution for this exact problem only to find out that was also supposedly merely temporary. So let's just create this solution, please, and re-evaluate once we have some data and some dedicated funding.

[campmlc]

Please move forward with "environmental: DNA" as modified. "DNA" by itself is not an acceptable option. @KyndallH

[Jegelewicz]

You aren't testing an organism. You are testing a body of water, or soil.

but I can see a time when you could also be testing an organism and find some other organism's DNA? Will we then need organism: DNA or some way to say "not environmental: DNA"? This also applies to PFAS and any other "environmental" things because you could certainly test a mouse for PFAS

Our other categories create a kind of hierarchy, but environmental doesn't. It just means we will end up with many ways to find "detected DNA" so that nobody can find all of the detected DNA. I suggest just DNA. But we really do need @KyndallH and/or @megulbranson to weigh in.

[campmlc]

eDNA is a thing, and part of an emerging paradigm in genomics research, only just starting to impact natural history collections. It needs it's own category, separate from everything else, otherwise researchers will be unable to discover we have these samples.

On Thu, Jul 20, 2023, 4:30 PM Teresa Mayfield-Meyer < @.***> wrote:

• [EXTERNAL]*

You aren't testing an organism. You are testing a body of water, or soil.

but I can see a time when you could also be testing an organism and find some other organism's DNA? Will we then need organism: DNA or some way to say "not environmental: DNA"? This also applies to PFAS and any other "environmental" things because you could certainly test a mouse for PFAS

Our other categories create a kind of hierarchy, but environmental doesn't. It just means we will end up with many ways to find "detected DNA" so that nobody can find all of the detected DNA. I suggest just DNA. But we really do need @KyndallH https://github.com/KyndallH and/or @megulbranson https://github.com/megulbranson to weigh in.

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/6263#issuecomment-1644703553, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADQ7JBDKDRGX2QESNV7NRMLXRGWPLANCNFSM6AAAAAAX3TPXFU . You are receiving this because you were assigned.Message ID: @.***>

[campmlc]

It needs its own category also because it is a radically different type of evidence for an occurrence, which will affect identifications and attributes. We will need to be able to find these records. https://www.nhm.ac.uk/discover/what-is-environmental-dna-edna.html

On Thu, Jul 20, 2023 at 4:39 PM Mariel Campbell @.***> wrote:

eDNA is a thing, and part of an emerging paradigm in genomics research, only just starting to impact natural history collections. It needs it's own category, separate from everything else, otherwise researchers will be unable to discover we have these samples.

On Thu, Jul 20, 2023, 4:30 PM Teresa Mayfield-Meyer < @.***> wrote:

• [EXTERNAL]*

You aren't testing an organism. You are testing a body of water, or soil.

but I can see a time when you could also be testing an organism and find some other organism's DNA? Will we then need organism: DNA or some way to say "not environmental: DNA"? This also applies to PFAS and any other "environmental" things because you could certainly test a mouse for PFAS

Our other categories create a kind of hierarchy, but environmental doesn't. It just means we will end up with many ways to find "detected DNA" so that nobody can find all of the detected DNA. I suggest just DNA. But we really do need @KyndallH https://github.com/KyndallH and/or @megulbranson https://github.com/megulbranson to weigh in.

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/6263#issuecomment-1644703553, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADQ7JBDKDRGX2QESNV7NRMLXRGWPLANCNFSM6AAAAAAX3TPXFU . You are receiving this because you were assigned.Message ID: @.***>

[Jegelewicz]

Found in GBIF slack

Just found out about a UN science summit that includes a session to discuss biodiversity and eDNA standards, with an emphasis on freshwater, September 12 - 29: https://sciencesummitunga78.sched.com/event/1NY6U The description emphasizes an interest in developing new ISO standards. It appears to be free and virtual, and many other sessions look interesting too.

sciencesummitunga78.sched.comsciencesummitunga78.sched.com Science Summit at United Nations General Assembly (UNGA78): [VIRTUAL] Towards inclusivity in interna... View more about this event at Science Summit at United Nations General Assembly (UNGA78)

[campmlc]

This really needs to be "eDNA". I can be "environmental: eDNA". https://static.sched.com/hosted_files/sciencesummitunga78/18/Hunter_UN%20Science%20Summit_eDNA%20best%20practices_standards_10Sept23.pptx?_gl=1*i7de5n*_ga*NzE4MDM4MDE2LjE2OTI3NDU2MTU.*_ga_XH5XM35VHB*MTY5NTMxNzU5Ny4yLjEuMTY5NTMxNzczMC4xMi4wLjA.

[happiah-madson]

The way that we handle this in our current database is to have a sample type = environmental sample and then the child extract is DNA. But I also agree with @campmlc that eDNA is a known entity in the research world and is highly sought so making it easier to find is useful.

but I can see a time when you could also be testing an organism and find some other organism's DNA?

@Jegelewicz this isn't the same thing. We already do this all the time (esp in our lab; Dan studies microbial endosymbionts). The environmental in eDNA is abiotic (soil, water, air) not any environment.

[happiah-madson]

Also, this may be helpful? (Via Abby Benson, who I work with at OBIS/USGS)

https://docs.gbif.org/publishing-dna-derived-data/en/#environmental-dna-as-a-source-for-dna-derived-occurrence-data

The Standardizing Marine Biological Data group has been grappling with eDNA and we could reach out to them as a resource, if that's useful?

[happiah-madson]

The environmental in eDNA is abiotic (soil, water, air) not any environment.

Okay, the link I just sent immediately refuted my point 😆: "eDNA is thus a sample type, not a method, including DNA derived from any environmental sample rather than from the capture and sequencing of a targeted individual. Such sample types includes water, soil, sediment and air, but also gut content samples and tissue (plant/animal) where the host DNA is not targeted (Taberlet et al. 2018)."

But also reiterates that eDNA is a sample type, not a method!

[campmlc]

Yes, I agree, that's why it needs to be "eDNA" as a value in the code table!

Mariel Campbell (she/her) Collection Manager, Division of Genomic Resources Museum of Southwestern Biology

Shipping Address: Museum of Southwestern Biology Division of Genomic Resources 1 University of New Mexico MSC03 2020 Albuquerque, NM 87131

(505) 277-7808 office email: @.***

---

From: Hannah Appiah-Madson @.> Sent: Thursday, September 21, 2023 12:19 PM To: ArctosDB/arctos @.> Cc: Mariel Campbell @.>; Mention @.> Subject: Re: [ArctosDB/arctos] Code Table Request - Add environmental: eDNA to Examined_Detected code table (Issue #6263)

[EXTERNAL]

The environmental in eDNA is abiotic (soil, water, air) not any environment.

Okay, the link I just sent immediately refuted my point 😆: eDNA is thus a sample type, not a method, including DNA derived from any environmental sample rather than from the capture and sequencing of a targeted individual. Such sample types includes water, soil, sediment and air, but also gut content samples and tissue (plant/animal) where the host DNA is not targeted (Taberlet et al. 2018https://doi.org/10.1093/oso/9780198767220.001.0001).

But also reiterates that eDNA is a sample type, not a method!

— Reply to this email directly, view it on GitHubhttps://github.com/ArctosDB/arctos/issues/6263#issuecomment-1730080155, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADQ7JBFZ3VT2WFWGKFTLQZ3X3SAJ5ANCNFSM6AAAAAAX3TPXFU. You are receiving this because you were mentioned.Message ID: @.***>

[dustymc]

eDNA is thus a sample type,

Exactly! This discussion can only pertain to "things which an be detected" - this code table provides value for eg https://arctos.database.museum/info/ctDocumentation.cfm?table=ctattribute_type#detected. If there's some way to detect (or fail to) environmental DNA while excluding - uhh, extra-environmental?!? - DNA then this could be useful, if not then this still looks like a square peg being hammered into a round hole.

[happiah-madson]

But you can collected an eDNA sample (ie, filter a ton of water from a place, or just collect a bunch of water from a place and freeze it) with the intention of it being used for eDNA work (ie, like how we can collect liver tissue for genomic work) and that's still functioning as a sample type?

[Jegelewicz]

I would think that water would be the identification. You could use geosample as the part, but the definition doesn't really fit. Maybe we would need some new part name for a jug of water - liquid sample?

[dustymc]

intention of it being used for eDNA work

YES!

cataloged item == water part == filter paper

this attribute== "we've [tested/detected/whatever] eDNA - not some specific primer or anything, definitely not nonenvironmental DNA, we've just [tested/detected/whatever] eDNA"

?????????

I can see how it's possible to test for DNA (not sure I'd understand why anyone would test for random DNA, but I guess I don't have to....) but - well, it gets really weird about there and I don't get it....

[happiah-madson]

sometimes you are looking for a specific species in an eDNA sample (ie, for invasive species monitoring) and sometimes you aren't and are looking for as much stuff as you can find (ie, for figuring whats in a place). So yes, people DO test for "random" DNA.

[mkoo]

Not to gum up the discussion but what collection type is using this? (I'm seeking some clarity with regard to Dusty's comment above). I am on board with the nice definition and schematic that Hannah provides-- eDNA is generally a environmental sample where DNA is detected so water, soil, air, etc is the actual part. So I can see a collection type of eDNA samples but I am struggling to see how this relates to a mammal specimen.

If you are using eDNA to create a species observation (we do this in the disease portal) this seems like it goes somewhere like part or method of identification or somewhere else...

or is the mammal fur or some part of it being subjected to the eDNA process to find its closest friends, etc?

[happiah-madson]

OGL has a small number materials with a of sample type of "environmental sample." They all have a 'scientific name' of not determined and are things like seawater filtrate, biofilm, water or sediment samples, a piece of a deep sea chimney...etc. And then a small number of them have child DNA extracts related to them.

[dustymc]

"environmental sample."

Record https://arctos.database.museum/guid/UAM:Env:65 is an environmental sample, the part ("thing to which one could stick a barcode") is https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecimen_part_name#filter_paper.

[campmlc]

Yes, this has been done at UAM as a separate environmental sample collection, and at MSB we have requested and MSB:Env for the same reason.. But this is an analogous situation to a host/parasite system, and that it causing the confusion. This issue is a request #6263 is a request to add "eDNA" to the examined detected code table which would be used for the Env collection type, for this particular term. It would not be used in a mammal collection. But essentially this is the same usage as "examined for" and "detected" records attribute in a host collection, but it is soil, water etc that is being examined.

We also need the part name, "eDNA", which could be added to the same record, in the same way we have part name "ectoparasite", which is added to a mammal host record.

Then ideally, in the best of all possible worlds, any taxonomic units which are identified in the DNA screening should be given their own records and linked via relationships. But that could be hundreds. Alternatively, we add multiple identifications to the Env record.

BTW I can't find any of the Alaska lake water samples that tested positive for frog DNA because logged in a public user, I can't access the Attributes view.

For @happiah-madson, since they have so few, can't they still use A string ID with eDNA as part, without setting up a separate collection?

[Jegelewicz]

There is no need for a separate collection. OGL can do exactly what UAM has done in their current collection.

We have geosample so a request to add the part environmental sample seems fair to use when the sample isn't something more specific like biofilm, filter paper, or sediment (geosample). But we can request that later if needed. As it is right now, I don't think that OGL would have use for the examined/detected attribute requested here.

[campmlc]

I see, "OGL:Genomic" works like "Env". So if the identification is "water" or "soil", then "examined/detected attributes would be appropriate.