New term - organismStatus

[sophiathirza]

This proposal is under active development in the 'OSR - How Did It Die?' Task Group.

• Submitter: Sophia Ratcliffe - NBN Trust (https://nbnatlas.org/)
• Proponents (at least two independent parties who need this term): I have had requests from several of our data providers asking for the ability to supply and filter records by alive/dead status
• Justification (why is this term necessary?): We receive many records where the occurrence was of a dead animal and at the moment there is no way store the status of the organism in a DwC term with a controlled vocabulary. It is really important in marine records, which often contain stranding information, and for road kill records.

Proposed definition of the new term:

• Term name (in lowerCamelCase): organismStatus
• Class (e.g. Location, Taxon): organism
• Definition of the term: A description of the status of the organism (alive or dead)
• Comment (examples, recommendations regarding content, etc.): Recommended best practice is to use a controlled vocabulary, with the terms alive, dead, unknown
• Refines (identifier of the broader term this term refines, if applicable): Currently we've been using occurrenceRemarks, but it is not easily searchable.
• Replaces (identifier of the existing term that would be deprecated and replaced by this term, if applicable): N/A
• ABCD 2.06 (XPATH of the equivalent term in ABCD, if applicable): N/A

[qgroom]

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.

[sophiathirza]

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).

[MattBlissett]

A possible name could use vitality.

Or viability, which is already used for seed collections (values might be viable, dormant, inviable, dead)

[qgroom]

I like vitality.

[as6699]

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 <notifications@github.com> 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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#228?email_source=notifications&email_token=AELXSJLSBECTAETW7V32U6TPX2I7NA5CNFSM4HQLPV62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWPR3PQ#issuecomment-496967102>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AELXSJKNXNV3GUF5XZIMXNTPX2I7NANCNFSM4HQLPV6Q>.

[qgroom]

Would reproducing or fertile be appropriate values for this term in that case?

dwc:reproductiveCondition and dwc:lifeStage cover this

[sophiathirza]

I like vitality

[qgroom]

Could the definition be changed to

An indication of whether the organism was alive or dead at the time of collection or observation.

Comment: Generally Intended to be used with a dwc:basisOfRecord of PreservedSpecimen, MaterialSample, or HumanObservation.

[qgroom]

A further thought

If this field is added to Darwin Core then next obvious need would be causeOfDeath.

Rather than just having a flag to say if something is dead, why not jump straight to a causeOfDeath field with a vocabulary?

[sophiathirza]

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.

[qgroom]

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 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?

[stanblum]

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.

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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? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#228?email_source=notifications&email_token=ACKZUDLS645A42HIJ2EWT43PYAAU7A5CNFSM4HQLPV62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWS3RVY#issuecomment-497400023>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACKZUDNM76ZYRUNX5NLL5E3PYAAU7ANCNFSM4HQLPV6Q> .

[MathildeMousset]

Potential user here: we work on wild ungulates, and would be interested in vitality and causeOfDeath terms.

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).