New term - organismStatus #228
Comments
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I support the concept, but not so much the suggested name. Status can mean so many things. Can't think of a better one yet. Also, there is the issue of dead museum specimens and living culture collections. I'm not certain these matter if they are described as dead or alive, as long as it is appropriate, but it is worth considering. I think basisOfRecord is currently used for some of these distinctions. |
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Yes, I didn't like using status, but it felt consistent with other DwC terms. The new term would be used for field observations where the basisOfRecord is HumanObservation (or Occurrence, as some data providers use). |
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A possible name could use vitality. Or viability, which is already used for seed collections (values might be viable, dormant, inviable, dead) |
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I like |
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Would reproducing or fertile be appropriate values for this term in that case? It's important for determining if a non-native species is established. (Excuse and ignore if another term already takes this into account.)
Annie Simpson
…________________________________
From: Quentin Groom <[email protected]>
Sent: Wednesday, May 29, 2019 10:43 AM
To: tdwg/dwc
Cc: Subscribed
Subject: Re: [tdwg/dwc] organismStatus - proposal for new term (#228)
I like vitality.
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I like vitality |
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Could the definition be changed to
Comment: Generally Intended to be used with a |
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A further thought If this field is added to Darwin Core then next obvious need would be Rather than just having a flag to say if something is dead, why not jump straight to a |
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causeOfDeath would be really useful, then we can differentiate strandings, road kills etc. A single term for vitality, with @qgroom's suggestion for the definition and comment, would still be useful, so that we can easily select all 'dead' records, but if needs be, we can derive that from causeOfDeath. |
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I don't like boolean flag fields in the standard when they can be derived from other fields. This doesn't mean they can't be implemented in a database to make searching faster, but as long as they are always derived from one source field there is no danger of a mismatch, where for example one It is a good question for GBIF though. @MattBlissett was saying |
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I would like to urge some caution here. In other words, please be very
explicit about your needs or use-case(s) for a controlled vocabulary
describing whether an organism is/was dead or alive. In many 'collecting
events", whole organisms are encountered alive, but the process transforms
them to dead. Organisms can be observed dead or alive in the field. An
organism could have been collected alive (a long time ago), lived many
years in captivity, and be dead now. "causeOfDeath" could venture easily
into necropsy results. In the case of cetacean and pinniped "strandings"
(i.e., organisms encountered dead on the shoreline), the cause of death is
of great interest and represents a summary conclusion based evidence found
in necropsy, pathology, and/or toxicology.
…On Thu, May 30, 2019 at 9:50 AM Quentin Groom ***@***.***> wrote:
I don't like boolean flag fields in the standard when they can be derived
from other fields. This doesn't mean they can't be implemented in a
database to make searching faster, but as long as they are always derived
from one source field there is no danger of a mismatch, where for example
one vitality says living, but the cause of death is roadkill.
It is a good question for GBIF though. @MattBlissett
<https://github.com/MattBlissett> was saying dwc:year is derived from
dwc:eventdate if it is empty. How much is GBIF willing to add
non-standard fields for indexing if they are derived from standard fields?
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Potential user here: we work on wild ungulates, and would be interested in Some of our data is road kill data (individual observed dead, with an obvious cause), hunting data (dead animals, through various types of hunting methods), monitoring data (live animals / animals found dead). |
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The executive of TDWG thinks this is an important issue to consider. The first step would be to engage in discussion with the Darwin Core Maintenance Group to figure out the next steps. @tucotuco @peterdesmet @mdoering @timrobertson100 @baskaufs @pzermoglio @morr @chicoreus |
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Consideration by the Darwin Core Maintenance Group should include whether development of this term and a controlled vocabulary of values for it (including the development of user stories and competency questions) would fall within the scope of the maintenance group, or whether this work is of sufficient scope to merit a new task group. Consideration also needs to be paid to alignment with ABCD, including the PaleontologicalUnit/Preservation/Taphonomy and PaleontologicalUnit/Preservation/Completeness terms. |
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It seems to me that this term should be organized under the Occurrence class rather than Organism. In the thread, we've been talking about the status of the organism at the time when it was observed or collected. That makes it specific to a particular Occurrence of the organism, since an organism can be observed repeatedly and on some of those Occurrences it might have been alive, then dead on its last occurrence (perhaps being made to be dead by the collection). |
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@baskaufs Agree. Changed label. |
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I very much like the term Would you also use it for exuviae or shells?
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Notes from the Biodiversity Next Unconference 25 October 2019 Vitality & CauseOfDeath Introduction
Relates to dwc:basisOfRecord
Use Cases
Scope
Consider the public sensitivity towards death and killing animals. Team 1:
(Fossils: Location)
Team 2:
Direct cause of death linked to event in time, such as a volcano eruption Team 3:
Age at death? Team 4:
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Codes used to express plant losses at Meise Botanic Garden DIE_WHY_CODES DIE_WHY_CODES DESCRIPTION |
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Is it still possible to contribute to this conversation related to OccurrenceStatus. Currently there are 2 terms: present or absent. if an animal/plant is dead it is still present. I would like to propose the addition of a new term called 'trace'. This term could be assigned to observations of shells - these animals should not be flagged as present/dead if the shell is empty. a crab shell can be considered present/dead but an empty snail shell should be flagged as 'trace'. |
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Many different things are added to the Darwin Core field establishmentMeans and published on GBIF. |
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Causes of Death from the UK Predatory Bird Monitoring Scheme (PBMS)
Email from Lee states
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Curious if this has advanced since 2019? I have a dataset of dead marine mammals and seabirds that wash up on shore and I haven't heard a new term has been added. |
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It hasn't progressed further than agreeing to set up a task group to explain the rationale of adding new terms for vitality and cause of death and their vocabularies. I've started the charter and meant to send it round to very one for comment. Let me know if you're interested in being involved. Thanks. |
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@qgroom, sorry for my delay writing the charter. I'll finish it off this week and send it round. Thanks, Sophia |
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@sophiathirza that's fantastic! I guess it would be easiest to share it here, but at some point soon we should transition off this issue thread. |
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The Charter for the new Task Group is attached. Please send me any comments/additions and let me know whether you would like to be added to the list of core members. I will then submit the final version to TDWG. Thanks, Sophia |
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Dear Sophia
Thank you for sending this on. It looks great and fit for purpose.
The only minor observation is that I added my own affiliation (John Nicholls, OBIS, Ireland)
Best wishes
John
John Nicholls
Data Manager / Researcher
NorFish Project https://www.tcd.ie/history/research/centres/ceh/norfish/people.php
Centre for Environmental Humanities
6th floor, Arts and History Department
Trinity College Dublin
College Green, Dublin 2
Email: [email protected]<mailto:[email protected]>
Phone: +3531896-1663
[cid:39354813-2db9-4c62-bc6a-a2e9a259a6a8]
…________________________________
From: Sophia <[email protected]>
Sent: 15 June 2020 15:08
To: tdwg/dwc <[email protected]>
Cc: John Nicholls <[email protected]>; Comment <[email protected]>
Subject: Re: [tdwg/dwc] organismStatus - proposal for new term (#228)
The Charter for the new Task Group is attached. Please send me any comments/additions and let me know whether you would like to be added to the list of core members.
I will then submit the final version to TDWG.
Thanks, Sophia
How did it die - task_group_charter.docx<https://github.com/tdwg/dwc/files/4781129/How.did.it.die.-.task_group_charter.docx>
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Thanks for all the interest in these changes. I think the process is
correct, but I believe that the Task Group should be instantiated
under the Darwin
Core Maintenance Group <https://www.tdwg.org/community/dwc/> rather than
the Observations & Specimens Interest Group
<https://www.tdwg.org/community/osr/>. I guess the TDWG Executive needs to
decide that based on the scope of the tasks proposed, but the Darwin Core
Maintenance Group is an Interest Group, and seems to me to have the correct
scope based on the discussion so far.
…On Mon, Jun 15, 2020 at 1:00 PM JohnNichollsTCD ***@***.***> wrote:
Dear Sophia
Thank you for sending this on. It looks great and fit for purpose.
The only minor observation is that I added my own affiliation (John
Nicholls, OBIS, Ireland)
Best wishes
John
John Nicholls
Data Manager / Researcher
NorFish Project
https://www.tcd.ie/history/research/centres/ceh/norfish/people.php
Centre for Environmental Humanities
6th floor, Arts and History Department
Trinity College Dublin
College Green, Dublin 2
Email: ***@***.******@***.***>
Phone: +3531896-1663
[cid:39354813-2db9-4c62-bc6a-a2e9a259a6a8]
________________________________
From: Sophia ***@***.***>
Sent: 15 June 2020 15:08
To: tdwg/dwc ***@***.***>
Cc: John Nicholls ***@***.***>; Comment <
***@***.***>
Subject: Re: [tdwg/dwc] organismStatus - proposal for new term (#228)
The Charter for the new Task Group is attached. Please send me any
comments/additions and let me know whether you would like to be added to
the list of core members.
I will then submit the final version to TDWG.
Thanks, Sophia
How did it die - task_group_charter.docx<
https://github.com/tdwg/dwc/files/4781129/How.did.it.die.-.task_group_charter.docx
>
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@tucotuco I think it would be appropriate that the Task Group be under the Observations & Specimens Interest Group, as @qgroom suggests. I don't think the Darwin Core Maintenance group should be dealing with this. In cases where new terms (or changes to existing terms) are needed that deal with specific necessities of the community, task groups that are specific to those needs should be under interest groups that are also specific (although less so) to those needs. Maybe in this case is not so obvious, but suppose some other case where paleo terms were needed. One should not expect the DwC MG -or task group within it- to deal with building those terms, their definitions, etc., but rather have the expert groups do it, and come to the DwC MG with a solid, full proposal, for incorporation of new/changed terms. As for what the Vocabulary Maintenance Specification says, it could actually happen both ways:
@baskaufs Thoughts? |
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My initial thought was that @tucotuco was correct, particularly since the charter describes the creation of two new Darwin Core terms, and that would clearly be the responsibility of the DwC Maintenance Group to shepherd. However, upon further reflection, I was thinking about the spirit behind section 4 of the VMS. Section 4 describes the development of "vocabulary enhancements". Vocabulary enhancements are defined in section 1.4 and development of controlled vocabularies does not fall within their definition. But the rationale behind section 4 is that when a set of coordinated additions to a vocabulary become complex, it is best to consider them a package that has a higher standard for development and testing than would be necessary for the adoption of a single term. In that situation, the best practice is to document the rationale and implementation testing through the two types of user feedback reports described in section 4. In Audubon Core, we are currently working three coordinated sets of additions to the standard (a set of terms related to 3D, controlled vocabularies for ac:subjectPart and ac:subjectOrientation, and a set of terms related to sound). Two of these sets of additions have associated task groups chartered under the MG and one does not. But given that they are complex coordinated additions, as AC MG convener, I'm requesting a Feature Report and Implementation Experience Report for all three proposals. The point of those reports is to streamline the adoption process by making it clear during the public comment period and Executive Decision what the proposal is supposed to accomplish and that it actually can accomplish what was proposed. The last paragraph is somewhat tangential to the question at hand, but the point of section 4 of the VMS is about how to effectively implement changes to a standard that are more complicated than a single term addition. Section 4 specifically allows vocabulary enhancements to be proposed by groups that are NOT task groups chartered by the maintenance group in order to enable those who take initiative and do the work to succeed in improving TDWG vocabularies regardless of whether the maintenance group asked them to do it or not. Given that spirit, if chartering this proposed Task Group under an interest group other than the DwC Maintenance Group is the most effective way to get a good proposal, then I wouldn't oppose that. The one thing that concerns me a bit about not chartering the Task Group under the Darwin Core MG is wondering how the task group would relate to the Observations and Specimens Group and to the DwC Maintenance Group. The last paragraph of section 4.1 of the VMG describes a back and forth process between the vocabulary MG and the group developing the enhancement, where the MG evaluates how the proposal will fit in with the operation of the existing vocabulary and gives feedback to the TG if it does not think the proposal is ready. The MG essentially acts as the gatekeeper to determine when the proposal is mature enough to advance to public comment. (In this case, the MG is acting in the role that would be assumed by a Review Manager for a new standard.) I'm assuming that if the Observations and Specimens Group Interest group charters this task group, the DwC MG would still operate in this gatekeeper role and that the O&S group would just act in an advisory role for the development of a better proposal. But I think it would be good to be clear about this from the start since we would be potentially creating a gray area if the Task Group is not clear about what their relationship is with the O&S "parent" interest group. |
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Thanks @pzermoglio and @baskaufs. I see what Paula is saying and it makes sense to me, particularly if/since ABCD could benefit from the work as well, and the two standards intend to work toward each other. I had the same concern about interaction with the DwC MG and hoped that something concrete could be in the TG charter about that. I fully support what Steve mentions about how to accomplish that. |
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The Task Group has been approved: https://www.tdwg.org/community/osr/how-did-it-die/. Many thanks for your help preparing the charter. We will have a working session at the TDWG 2020 virtual conference next month to begin work on the terms. It would be great if as many of you as possible could join us. Thanks again, Sophie |
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Folks in this thread might want to know that the meeting for the working session for this new task group is on Tuesday Sept 22 0800 - 1000 UTC (https://www.tdwg.org/conferences/2020/working-sessions-schedule/). I can't make it at that time (it's 0200 my local time) but I hope others can and that there will be other ways to contribute to the conversation. |
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Thanks @albenson-usgs. I've started an agenda for the working session: https://docs.google.com/document/d/1jvO6yMg0_PZq0KVWTJpk-358UYKkGqkPB-lw80v-3Xc. Once we've agreed the Task Group name we will set up a GitHub repository and we can report back from the session and continue the conversations there. I'm really looking forward to the session. |
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Curious what the status of the task group is? I didn't see a Github repo for it. Would like to watch the repo once it's up. Will someone report here when it is up? |
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Hi Abby - I've not heard anything from the group. I was not included in the meeting(s) and I am not even sure if nay progress has been made. Any repo would be much appreciated. |
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Hi Abby, |
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The GitHub repo has been set up for the Task Group: https://github.com/tdwg/how-did-it-die. I will copy all the information we have and the feedback from the working session into repo. |
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I have put all the information into the GitHub repository (https://github.com/tdwg/how-did-it-die) and it is now open for your contributions and discussions. The repository is organised following the Collection Descriptions Interest Group (https://github.com/tdwg/cd) repository, hopefully it's clear but do suggest changes if you think something could be improved. The proposed new properties (one to the core standard and four in a new extension) have separate issues to comment on the name, definition etc: https://github.com/tdwg/how-did-it-die/issues and I've created an issue for each new controlled vocabulary: https://github.com/tdwg/how-did-it-die/issues?q=is%3Aissue+is%3Aopen+label%3Avocabulary linked to a google document to add suggestions. The idea was to keep the vocabulary discussion separate from more general details of the property. What we need now is:
Please add use cases as individual issues (https://github.com/tdwg/how-did-it-die/issues); I've added one for the roadkill term to get started: https://github.com/tdwg/how-did-it-die/labels/use%20case. I will move the use cases to the folder in the repository (https://github.com/tdwg/how-did-it-die/tree/main/use_cases) once we've agreed which use cases to include. There is some holding text in the folder for now. I will arrange a meeting for early May to review the feedback and suggestions and decide how we can start writing it all up. Please let me know if you would like to join the call and what time zone you are in. We may need two calls. I will write to all the attendees of the working session in TDWG 2020, apologies if you get this twice. |
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I added a use case. I would like to be on the call if we can make it work given different time zones. My time zone is Mountain Daylight Time (GMT -6). Thanks Sophia for all your efforts on this! |
tucotuco
changed the title
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We have a zoom call on 16th June at 18:00 CEST to discuss the feedback and suggestions from the GitHub repository (https://github.com/tdwg/how-did-it-die) and to decide how to proceed. Let me me know if you would like to join. Thanks. |
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Dear Sophia
Unfortunately, I will not be able to attend on that date. I am still very interested in the developments of this group and I would be very happy to receive any updates that may arise from the meeting.
Best wishes
John
John Nicholls
Data Manager / Researcher
NorFish Project https://www.tcd.ie/history/research/centres/ceh/norfish/people.php
Centre for Environmental Humanities
6th floor, Arts and History Department
Trinity College Dublin
College Green, Dublin 2
Email: ***@***.******@***.***>
Phone: +3531896-1663
[cid:6908ccc8-dd49-480e-a7a6-3f256bccb8a6]
…________________________________
From: Sophia ***@***.***>
Sent: 04 June 2021 17:24
To: tdwg/dwc ***@***.***>
Cc: John Nicholls ***@***.***>; Comment ***@***.***>
Subject: Re: [tdwg/dwc] New term - organismStatus (#228)
We have a zoom call on 16th June at 18:00 CEST to discuss the feedback and suggestions from the GitHub repository (https://github.com/tdwg/how-did-it-die) and to decide how to proceed.
Let me me know if you would like to join. Thanks.
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The new term dwc:vitality has been ratified and incorporated in the standard. Closing issue. |
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For those of you interested in a causeOfDeath term I have added a specific term request here #521 |
This proposal is under active development in the 'OSR - How Did It Die?' Task Group.
Proposed definition of the new term:
The text was updated successfully, but these errors were encountered: