New Term - vitality #363
Comments
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We will submit a proposal for a causeOfDeath extension in due course. |
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Because shells persist for thousands to millions of years after the death of the animal who formed it, whether the specimen was collected alive can be important to understand the distribution in time and space of LIVING individuals of species. |
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I'd reiterate TimAPearce: if we know whether the specimen was collected alive or dead and can add that information to the specimen record, that can help researchers using the data understand more about the biology of the organism. |
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I support this in the strongest possible way. Because of the long-term persistence of calcareous skeletal material (e.g., molluscan shells) these may have been dead for decades or even centuries when collected. Such data are obviously suspect when used in discussions/maps of recent changes in faunal distributions. We need to find a meaningful way to flag live/dead-collected specimens and have that distinction readily piped to relevant data aggregators. |
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Plus one here, others have already made the case well enough. |
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@sophiathirza - thanks for proposing this term. I've seen a similar term described at "physiological state", with terms from ontologies like PATO:
Examples in GloBI would be something like: Jane saw a cat eating a dead mouse. How did you come to the name |
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thanks @jhpoelen, physiological state might be a name than vitality. We will do a poll at the working session to see what everyone thinks. Is physiological state in PATO? do you have an example where physiological state has been used? |
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@sophiathirza "physiological state" is defined via: http://purl.obolibrary.org/obo/PATO_0001912 Also, it looks like the term is re-used in various other ontologies like: Ontology listed in Ontobee Ontology OWL file View class in context Project home page
(see screenshots) |
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Note however that PATO is using viability (http://purl.obolibrary.org/obo/PATO_0000169) as a "parent" term for dead/alive etc. I would assume the viability is the state of a physiology of an organism (e.g., http://purl.obolibrary.org/obo/PATO_0001912), but perhaps specialized ontologists like @cmungall can chime on on this. See attached screenshot. |
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Thanks to everyone for their work on this- I support it |
peterdesmet
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the
Task Group - How Did It Die?
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Other organizations that need this term include iNaturalist, which has an attribute of "Alive" or "Dead" and the Academy of Natural Sciences of Philadelphia (ANSP). Currently more than 3.5 million observations in iNaturalist are annotated for this attribute, including 125,000 for mollusks. The malacology database as ANSP also supports the live dead distinction, which has been made for 56,000 samples. |
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The distinction between live/dead is a key problem for the entire molluscan community because it affects the usability/fidelity of mollusk-based biodiversity records. Dead-collected shells can be hundreds of years old; therefore, their records |
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@gparosenberg wrote:
I note that iNaturalist also has "evidence of recent life" to convey something was alive not too long ago (as opposed to a shell that's been there for who knows how long which could be more of a "relict" idea). |
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@rbieler @fmrdelapena what other collections (outside mollusks) would / could use this term meaningfully? As you put it so nicely in a use case Robin, knowing it is/was recently alive (until collected anyway) then the data is fit for use in addressing range extension assessment (for example). Are there other collections, that could use this similarly? (Doesn't really seem to work for herbarium specimens -- they are all (I think?) alive at time of collection by default). But would this distinction work for other collection types that can then support a research purpose? |
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@debpaul This would apply to many of the calcareous skeletons in our (proverbial) closets of "dry" collections -- corals, bryozoans, brachiopods, foraminiferans, etc. |
I do wonder about the use of this term. It seems like unknown would cover this, and adding it in will lead to confusion between when a collection chooses to use one or the other term. |
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Since the vitality field (or fields) can often be determined after collection, I would add another term: "not yet determined." It seems to me, because this is a new field (or fields), the first entry for all existing dry preserved records would be "not yet determined". In practice, I don't see that every specimen within a lot will be evaluated. In my mind, the question is, Is there at least one specimen in the lot that was collected live? Conceivably a specimen lot could have specimens that were live collected, dead collected, "not recorded" and "unable to determine" I'm having a hard time seeing what the fields will be here. Is there one Vitality field with the above terms and they are check boxes? I don't think that is very informative for Queries/Searches. Are the fields dead, alive and not recorded? And the alive and dead fields have values of True, False and unable to determine and not yet determined? I think that is a lot of checkboxes. Or, because the primary question is whether or not there is at least one live specimen, there are two fields only: Alive and Not recorded. Where the alive field is T, F, not yet determined or unable to determine. That seems simplest of all. A field that indicates at least one specimen was collected live. My apologies if this is dealing too specific for this thread. I'm just trying to see how this is going to look in practice. |
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@ekools For our Thematic Collections Network project (Eastern Seaboard mollusks), we have agreed - at the collections end - to record the following for each lot:
Because of the wide variety of database systems involved in our project (EMu, Specify, Arctos, Filemaker, etc.) we are still working on the collections-level implementation of the above. We understand that our desired collection-level distinction might be too detailed to pass on to aggregators, so we could readily combine them into a smaller number of items (e.g., live [including mixed lots] / dead [only] / unknown -- or live / dead/ unable to determine / unknown) once such an option exists |
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@debpaul: I agree - not sure this term would find much use in the herbarium community. |
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I'm fascinated and also a little worried if I come across a vertebrate object that would use either of the:
I'm sure IACUC would have words with me... |
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Thank you, @rbieler I think in practice we would focus on whether or not there is a live collected specimen, eliminating the need to evaluate each specimen. So, would lean towards your last example and eliminate the live + dead field as this could be indicated by a True Value in both the live and dead collected fields. The field Not Recorded is interesting because it indicates the evaluation was made after collection. Fun stuff. Thanks! |
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I support the use of this term as currently defined. It would be useful in the entomological collections community, as we mostly collected specimens alive and kill them, but occasionally find "preservable" specimens that died recently, but it would be useful to have this term in order to indicate that it was not alive at time of collection, and therefore should not have bearing on things like phenology, etc ... |
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@debpaul -- In some cases entomological collections could use this term. I myself have collected quite a bit of material where the specimen was found dead. Currently, we use "hand collected" as the collection method and "found dead" as the detail. Since many arthropod life cycles are annual, it would be easier to assume a specimen's "age". On the other hand, if a season or two has passed, a dead insect specimen would most likely have deteriorated from the elements and wouldn't be worth collecting anyway. |
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For vertebrate collections you may want to talk to eBird, iNaturalist, and the Zoo community. They will have the largest sample sets currently that may get listed as Live. The majority of vertebrate museum specimens currently are going to be dead. This may change as we work with more behavioral researchers, but the full vouchered specimens are still going to come into our collections already expired. |
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I don't really see anything in the comments that is a real block to this in the comments, or anyone suggesting concrete changes. |
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I thought the same thing as Quentin. |
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In re-reading the thread, I still wonder why we're not re-using the physiological state from PATO (see #363 (comment)). Especially after reading the examples described in: https://github.com/tdwg/rs.tdwg.org/blob/vitality/process/page_build_scripts/vitality.md
To me, vitality seems to suggest some kind of quantitative score between alive (e.g., 10) and dead (e.g., 1). and I think describing a physiological state may be a little more nuanced than that. Inventing new terms is easy, but keeping them is . . . time intensive! (e.g., oborel/obo-relations#368 - a new term request is still ongoing after first being proposed in 2020). So, I favor re-use of existing terms. my 2 cents. |
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I realize that the public review is for the proposal as it currently stands, and that there were no explicit objections during the public commentary period. However, there are comments from prior to the public review for which it is not apparent that they were ever addressed, and the outcomes if they were is not in evidence. Here are the specific comments in question: #363 (comment) Others were discussions about vocabulary values (whose final proposed values can be seen at https://github.com/tdwg/rs.tdwg.org/blob/vitality/process/page_build_scripts/vitality.md. Many of the comments about the proposed vocabulary seem to have been addressed, but not all, at least in this issue. For example, It would be good to know if these comments were addressed anywhere, and what the outcome was. |
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All of these fields pertain to data from the observer/collector. Why not include the Inferred Data in the same Vitality Scheme ? |
The PATO definitions of dead and alive are quite similar, though they are under PATO viability which is different from the definition of
I'm not sure the difference in definition of the parent matters, but other siblings of
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I don't follow, can you explain further? |
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@qgroom Yes. It is clear from the discussions that data pertaining to the vitality of organisms at the time of collection or observation is needed. However, the definitions developed for the Vitality Scheme appear to rely solely on data recorded at the time the observation or collection was made. The vast majority of dry preserved material held in museums does not have this data recorded by the collectors. This does not mean that this data cannot be inferred. I think the scheme (or individual databases) can take this into account by indicating the "source" of the data. It is either the collector, or another "Agent". For the definition of "uncertain" "The functional metabolism of the organism was not possible to determine at the time that the observation or collection was made" would be changed to read "The functional metabolism of the organism (at the time of observation or collection) is not possible to determine." The term "not assessed", defined as "The functional metabolism of the organism was not recorded at the time that the observation or collection was made" would be changed to "The functional metabolism of the organism has not yet been determined or assessed." I think it is the order of the wording that is throwing me off. For alive, it is easier for me if "The state where the organism has functional metabolism at the time that the observation or collection was made" reads "The state where the organism (at the time of observation or collection) had functional metabolism. I also think that persons using data available in the aggregators are going to find "Evidence of Recent Life" and/or "Recently Alive" (=fresh dead) of immense value and we want to include them in the definitions. The term aestivating may also be included too. I'm not sure. Hope that is clear. |
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In the Eastern Seaboard TCN, we have recommended adding fields to record means of inference of the vitality status. Also, because mollusk collections usually catalogue by lots rather than individual specimens, we've found that it might speed assessment to allow additional values beyond "live" dead" and"uncertain". Ech of the items below can be mapped to one of the three main values .
Live and dead: Both live and dead collected specimens are in the lot. Maps to "live"
Possibly live: at least one specimen might have been live collected. Indicates that the specimen is in good enough condition that it might have been alive when collected. Maps to "Can't be determined"
Fresh dead: no specimen in the lot was live collected, but at least one is known to have been fresh dead (e.g., valves of bivalves still attached by ligament). Maps to "Dead".
Best wishes,
Gary
From: ekools ***@***.***>
Sent: Friday, March 31, 2023 12:44 PM
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Subject: Re: [tdwg/dwc] New Term - vitality (#363)
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@qgroom<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fqgroom&data=05%7C01%7Crosenberg.ansp%40drexel.edu%7C90cad11cb7844548bc0f08db32071b50%7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C638158778376605406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xVkM2r5ZmN0gNPNNdnvf%2BIYzVjz0DaVC1LrCXN%2FG6xI%3D&reserved=0> Yes. It is clear from the discussions that data pertaining to the vitality of organisms at the time of collection or observation is needed. However, the definitions developed for the Vitality Scheme appear to rely solely on data recorded at the time the observation or collection was made. The vast majority of dry preserved material held in museums does not have this data recorded by the collectors. This does not mean that this data cannot be inferred. I think the scheme (or individual databases) can take this into account by indicating the "source" of the data. It is either the collector, or another "Agent".
For the definition of "uncertain" "The functional metabolism of the organism was not possible to determine at the time that the observation or collection was made" would be changed to read "The functional metabolism of the organism (at the time of observation or collection) is not possible to determine."
The term "not assessed", defined as "The functional metabolism of the organism was not recorded at the time that the observation or collection was made" would be changed to "The functional metabolism of the organism has not yet been determined or assessed."
I think it is the order of the wording that is throwing me off. For alive, it is easier for me if "The state where the organism has functional metabolism at the time that the observation or collection was made" reads "The state where the organism (at the time of observation or collection) had functional metabolism.
I also think that persons using data available in the aggregators are going to find "Evidence of Recent Life" and/or "Recently Alive" (=fresh dead) of immense value and we want to include them in the definitions. The term aestivating may also be included too. I'm not sure.
Hope that is clear.
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I don't think anyone would have a problem with those amendments. The vocabulary is only a recommendation and non-normative, which is why I can't really understand why this causes a block to vitality be accepted, particularly when there is such obvious and immediate demand. |
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The issue is not blocked. It just requires consensus. Consensus has not been achieved for the reasons described here. Examples of vocabulary terms would be non-normative, but given this comment, a formal vocabulary (normative) is also being proposed. Consensus has not been demonstrated on the controlled vocabulary. |
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But a consensus was formed by the task group. You will understand my frustration when we could have dispensed with a whole bunch of task group meetings if the consensus we built there doesn't really count for anything. The comments by @gparosenberg, @jhpoelen and @ekools don't even seem to conflict with the suggested controlled vocabulary. |
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I agree with Quentin. There are 24 thumbs up and many people saying they would use this term once available. I guess I'm confused how three mild suggestions that are not even outright disagreements means there is not consensus. How long do we have available to provide responses from the task group to what's been outlined here to still get this term approved during this public commentary period? I have a dataset that cannot be shared until this term is available and I would really like to move that one forward if I can. |
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I think a bit of explanation would help this issue. The goal of the task group is to define terms for the question "How did it die?" We are discussing many other terms with their own vocabularies to expand this set of terms. The goal with the term Vitality is to expedite the acceptance of a single term the for which the community has expressed an immediate need. Once we have the basic question of if an organism was dead or live at the time of observation/collection, we can expand the terms for use by, among others GGBN. Physiological State is a much broader term then what we are hoping to achieve with Vitality. |
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If the problem is only with the controlled vocabulary itself, it seems to me that the It is frustrating to me when the perfect becomes the enemy of the good. That seems to be a common problem with Darwin Core proposals. It leads to frustration and cynicism on the part of people who put in a lot of work on a proposal and we risk losing the participation of those people in future efforts if they feel the time they've expended doesn't pay off. This proposed term has been languishing for a long time and there's huge demand for it. If there is a way to cut out or fix the aspects of the propose that lack consensus, we should do it and get at least the term itself adopted. |
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I am sorry - I realised that I didn't add the notes from the TDWG 2021 working session, where we had a poll on the name of the term. I've uploaded the group chat and meeting notes here: https://github.com/tdwg/how-did-it-die/tree/main/meetings/TDWG%202021%20WG%20session The options for the poll were: 1. vitality, 2. viability and 3. physiological state. Nine people voted (there were only 12 in the session), results: vitality 5 It was agreed to continue with vitality as the term name and to add the term 'mixed' to indicate collection lots of both live and dead organisms. |
I am happy for the definitions to change, as described above.
We did discuss including dormant in the vocabulary, but the organism is alive - and we wanted to keep the term as simple as possible for the most practical use. The date of death is going to be covered in the cause of death extension proposal and the group agreed that 'recently alive' or 'freshly dead' could be covered by the date of death. If there is a use case of including it in the vocabulary then we can consider it again, but we should be clear what recent or fresh means. |
tucotuco
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Thanks @sophiathirza for the Task Group background information. Looking through the thread it seems that the justification for the choice of term name has been met. All other open discussion is about the controlled vocabulary. It also seems there is clear and immediate use for the term even without the associated formal controlled vocabulary. I'll change the status of this issue to "Ready for Executive Review" and start to prepare the entire package. A new issue should be created to move forward with the controlled vocabulary, and should reference this issue as background and the source for remaining issues that need to be resolved. Thank you everyone for your efforts and patience. Progress! |
tucotuco
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Huzzah! |
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For those of you interested in a causeOfDeath term I have added a specific term request here #521 |
and others
New term
Submitter: Sophia Ratcliffe
Efficacy Justification (why is this term necessary?): There is a requirement that species records express whether the organism was dead or alive at the time of the observation or collection. Currently no such explicit term exists in Darwin Core.
Demand Justification (name at least two organizations that independently need this term):
Stability Justification (what concerns are there that this might affect existing implementations?): None
Implications for dwciri: namespace (does this change affect a dwciri term version)?: The term
dwciri:vitalitywill be created simultaneously with the term in the main DwC namespace:dwc:vitality.Proposed attributes of the new term:
vitalityOccurrencePreservedSpecimen,MaterialSample, orHumanObservation.dwc:namespace term only):alive,dead,mixedLot,uncertain,notAssessedNOTE:
The Darwin Core Maintenance Group has assessed that more work is required to have a consensus on a controlled vocabulary, so that part of this proposal did not pass the 2023-02-12 public review cycle. Because of this, and in an effort to make the term available as soon as possible, the following originally proposed Comments section has be replaced by what is seen in the final proposal, above:
dwc:basisOfRecordofPreservedSpecimen,MaterialSample, orHumanObservation.The Vitality Controlled Vocabulary to be used as values for this term can be viewed here (note: the URL listed in the comments will not dereference until after ratification).
dwc:vitalitywill use the controlled value string for the appropriate concept in this vocabulary as its value.dwciri:vitalitywill use the unabbreviated term IRI as its value.The text was updated successfully, but these errors were encountered: