New Term - causeOfDeath

[qgroom]

New term

• Submitter: Quentin Groom, Toke Thomas Høye (@tokehoye), Lien Reyserhove (@LienReyserhove)
• Efficacy Justification (why is this term necessary?): The term dwc:vitality allows users to indicate whether an organism was dead when it was observed. Although the cause of death may often be unknown, in cases when it is identifiable, this information is invaluable for a wide range of studies. These include assessing the impact of invasive species, monitoring the spread of wildlife diseases, evaluating human activities' effects on wildlife, and more.
• Demand Justification (name at least two organisations that independently need this term): From the dwc:vitality term proposal the following organisations were mentioned, NBN Trust, Ocean Biodiversity Information System (OBIS), The Field Museum, Global Genome Biodiversity Network (GGBN), to those I add Meise Botanic Garden, The Research Institute for Nature and Forest (INBO) and Aarhus University.
  The need for a causeOfDeath term has been thoroughly discussed by the "How did it die?" task group, as documented in issues #228 and #363.
  The issue 228 was closed when the term dwc:vitality was accepted into Darwin Core, yet the need for a causeOfDeath term persists. In my specific case, this term is crucial for a project that aims to identify roadkill animals using AI, but there are many other documented use cases. While there were discussions about creating an associated vocabulary, it was recognized that this would be an enormous task, and potentially overly restrictive for the term. Therefore, like many other terms in Darwin Core, it is likely more effective to recommend the use of a vocabulary without mandating it.
• 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)?: no

Proposed attributes of the new term:

• Term name (in lowerCamelCase for properties, UpperCamelCase for classes): causeOfDeath
• Term label (English, not normative): Cause of death
• Organized in Class (e.g., Occurrence, Event, Location, Taxon): Occurrence
• Definition of the term (normative): An indication of the known or suspected cause of an organism's death at the time of observation. This may include natural causes (e.g., disease, predation), human-related activities (e.g., roadkill, pollution), or other environmental factors (e.g., extreme weather events). Intended to be used only when dwc:vitality indicates that the organism was dead at the moment of observation.
• Usage comments (recommendations regarding content, etc., not normative):
• Examples (not normative): trapped, poisoned, starved, drowned, shot, of old age, roadkill, disease, herbicide, burned
• Refines (identifier of the broader term this term refines; normative): vitality
• Replaces (identifier of the existing term that would be deprecated and replaced by this term; normative): none
• ABCD 2.06 (XPATH of the equivalent term in ABCD or EFG; not normative): none

[qgroom]

Although the "How Did it Die" task group is not active there are some relevant notes on the webpage https://www.tdwg.org/community/osr/how-did-it-die/

[tokehoye]

Camera traps fitted to cars are beginning to emerge (e.g. https://doi.org/10.3390/s21186126) and pilot testing suggest that they can facilitate the observation of road kill animals. We are making such trials in EU-wide projects. To be able to make such data FAIR, it will be important to adapt metadata standards to these new sensor-based observations. Thanks to @qgroom for proposing this new term!

[gparosenberg]

I favor adding this term to the Darwin Core. I think we would need to distinguish observation from inference. Mollusk collections sometimes have clams killed by seagulls, by dropping them on rocks or roads. Sometimes death of the organism is directly observed, but more often it is inferred from the condition of the specimen.

[tmcelrath]

I favor this term as well. Would allow entomological collections to add things like "dead in a spider web" or "killed by a specific organism".

[gparosenberg]

I've added this term to our database and started trying to populate it. There's a lot of inference involved: for example, "ex pisces" is sometime stated in a record, so I've added for cause of death "eaten by fish". That's a proximal reason; also mollusks are known to occasionally pass alive through the digestive tracts of fish and birds, so it's an inference that might at times be wrong. (The specimen might have been alive at the time it was collected.)

In the Eastern Seaboard TCN, we've added the vitality field and we also require a basis of inference of vitality status. The later can be reported as an "occurrenceRemark," which shows up a note in Invertebase (e.g,, https://invertebase.org/portal/collections/individual/index.php?occid=9197331&clid=0). It turns out that when cause of death is known or inferred, that would also serve as the basis of inference of vitality.

[tucotuco]

I think this term should be proposed to be organized in the Organism class rather than the Occurrence class. It is an Organism that dies, not an Occurrence of an Organism.

[qgroom]

I think this term should be proposed to be organized in the Organism class rather than the Occurrence class. It is an Organism that dies, not an Occurrence of an Organism.

I don't really understand the distinction. I think I was following the same logic as these terms - individualID, lifeStage, reproductiveCondition, sex and vitality

[tucotuco]

The terms lifeStage, reproductiveCondition, and vitality are all attributes of an organism at a place and time - things that can change from one Event (Occurrence) to another. The causeOfDeath term would be singularly tied to the Organism - it is not something that can change from one Event (Occurrence) to another.

The term individualID no longer exists in Darwin Core.

[qgroom]

That makes sense, thanks for the explanation.

BTW: individualID is still mentioned here https://dwc.tdwg.org/list/ I guess it needs correcting.

[tucotuco]

BTW: individualID is still mentioned here https://dwc.tdwg.org/list/ I guess it needs correcting.

Good catch. @baskaufs Something must be wrong with the maintenance scripts that produce the term list document. Thanks!

[baskaufs]

No this is not an error. The list of terms document contains every term that has ever been minted in the dwc: and dwciri: namespaces, including deprecated ones. See https://dwc.tdwg.org/list/#dwc_individualID, which contains the note "This term is deprecated and should no longer be used."

All of the terms ever minted need to be included in the list of terms, since when terms in those namespaces are dereferenced, they redirect to fragment identifiers in the list of terms document. If they were not included in the list of terms document, there would effectively be no way for someone to discover the meaning of the term by dereferencing its IRI: http://rs.tdwg.org/dwc/terms/individualID

[LienReyserhove]

Thank you @qgroom for proposing this term. I believe it will be a valuable addition to the DwC standard!

[tucotuco]

Thanks @baskaufs . Of course. And a relief.

[vijaybarve]

I favor the addition of this term, would be particularly useful for roadkill datasets and undesirable reasons like electrocution and wind mills etc.

[dbloom]

I agree that this would make a good addition. It will be of relevance to the recently funded ZooMu RCN - https://www.nsf.gov/awardsearch/showAward?AWD_ID=2403654&HistoricalAwards=false

[gparosenberg]

The terms lifeStage, reproductiveCondition, and vitality are all attributes of an organism at a place and time - things that can change from one Event (Occurrence) to another. The causeOfDeath term would be singularly tied to the Organism - it is not something that can change from one Event (Occurrence) to another.

The term individualID no longer exists in Darwin Core.

If we are talking about things that are observed only once, then it is true that it is tied to the organism. But supposed there multiple observations of the same individual. It might be alive on the first observation and dead on the second one. Or there can be multiple observations post mortem, for example, of the time course of decay. If there is no individualID in the Darwin core does that mean that each observation stands on its own?

[tucotuco]

dwc:individualID was deprecated in favor or dwc:orgnismID, when the dwc:Organism class came into being, so the concept still exists.