Primary Deliverable - FossilSpecimen definition

Jegelewicz commented 3 years ago

Current Definition

http://rs.tdwg.org/dwc/terms/FossilSpecimen

A preserved specimen that is a fossil.

Please suggest changes/improvements in this issue.

FossilSpecimen (http://resource.isamples.org/vocabulary/specimentype/fossil): the remains of one or more organisms preserved in rock; includes whole body, body parts (usually bone or shell), and trace fossils. An organism or organism part becomes a fossil when it has undergone some fossilization process that generally entails physical and chemical changes akin to diagenesis in a sedimentary rock. Trace fossils are manifestations of biologic activity preserved in a rock body (typically sedimentary), without included preserved body parts. There are many processes that lead to fossilization, including permineralization, casts and molds, authigenic mineralization, replacement and recrystallization, adpression, carbonization, and bioimmuration (https://en.wikipedia.org/wiki/Fossil).

tucotuco commented 3 years ago

@smrgeoinfo This seems very clear for what a fossil is. Accepting it would "only" leave us with figuring out what a specimen is for a FossilSpecimen definition upgrade.

Should that first URL resolve to something other than a 404?

smrgeoinfo commented 3 years ago

Oops, thought we had set up the URIs to resolve. They don't yet. Stay tuned. The vocab is at https://github.com/isamplesorg/metadata/blob/main/vocabulary/iSample-SpecimenType.ttl

Jegelewicz commented 3 years ago

FossilSpecimen (http://resource.isamples.org/vocabulary/specimentype/fossil): the remains of one or more organisms preserved in rock; includes whole body, body parts (usually bone or shell), and trace fossils. An organism or organism part becomes a fossil when it has undergone some fossilization process that generally entails physical and chemical changes akin to diagenesis in a sedimentary rock. Trace fossils are manifestations of biologic activity preserved in a rock body (typically sedimentary), without included preserved body parts. There are many processes that lead to fossilization, including permineralization, casts and molds, authigenic mineralization, replacement and recrystallization, adpression, carbonization, and bioimmuration (https://en.wikipedia.org/wiki/Fossil).

I am not sure that everyone would agree with that definition. I think it would exclude UTEP:ES:22-1609

would that then become PreservedSpecimen?

How about things that are "in process" like what I am looking at here?

I think it is the first sentence of the definition that bothers me. Also, I am still thinking that "fossil" is relative and that modifiers to MaterialSample would let everyone use their preferred definition of "fossil" to find what they want: Things with an associated stratigraphy, things with an associated deposit date in MYA, things with "permineralizied" in preservation, etc.

RogerBurkhalter commented 3 years ago

Member My take is the @smrgeoinfo FossilSpecimen definition is too complex. Long ago I learned fossils were the "Remains of past life", a simple and inclusive definition. Some would say that is too inclusive and would include all of the biological collections in a museum but exclude most objects from a zoo. You could add "was deceased when collected" but that has issues as well. As a CM I have 70 million-year-old mollusks that are virtually unaltered and look as if they died yesterday. Marine and terrestrial palynomorphs are perhaps numerically the most common fossils in earth's entire history, but typically have minimal alteration after 100's of millions of years. @Jegelewicz is correct that the term "fossil" is relative and I think complicated definitions become exclusive. I know some archaeologists that consider excavated floral and faunal remains as fossils even if only a few hundred years old.

I don't think an alignment of FossilSpecimen with PreservedSpecimen is useful. Fossils are not typically something anthropogenically preserved, that is how that class is used, but are instead naturally preserved.

As far as "in process", I avoid the use of "sub-fossil". I do have many kg of material that are unprocessed, containing fossil specimens, that I record on my CMS as a "Sample" in much the same way as we are discussing MaterialSample. These "Sample", mainly from former curators or students, have a UUID and may become processed into specimens at some point.

Jegelewicz commented 3 years ago

I don't think an alignment of FossilSpecimen with PreservedSpecimen is useful. Fossils are not typically something anthropogenically preserved, that is how that class is used, but are instead naturally preserved.

Does it really matter who preserved it? Does preservation imply that a human did it?

I think there may also be "naturally" preserved non-fossil specimens. How about a mummified animal found in the desert?

https://arctos.database.museum/guid/UTEP:Mamm:1750

Nobody "preserved" it, but it certainly is preserved and may or may not be a fossil depending on your definition.

RogerBurkhalter commented 3 years ago

I see your point, however, PreservedSpecimen is typically used for anthropogenic preservation as given in the DwC examples "A plant on an herbarium sheet. A cataloged lot of fish in a jar". Because these terms are usually aligned (best practice) with basisOfRecord (Other Deliverable - BasisOfRecord review #11) where, as a practical matter, FossilSpecimen is used by collections and researchers to include or exclude within data searches. A search for "Canidae" AND "FossilSpecimen" yields a manageable dataset of only fossilized Canidae. The same is true for a search at the genus level where genera include both extant and fossil organisms. This efficiency is of huge importance in making paleontological specimens more accessible. Lumping FossilSpecimen with PreservedSpecimen makes the data more cumbersome and inefficient for both biologists and paleontologists. It is quite easy to include All by searching at whatever level you want and not filtering basisOfRecord.

deepreef commented 3 years ago

Certainly the fact that a physical MaterialSample item represents a fossilized impression of an organism (as opposed to directly preserved tissue from a recently living organism, or a still-living organism) is critical information that should be included within the spectrum of data exchanged using DwC terms. But the question is: is basisOfRecord really the best way to capture this?

Put another way, is the distinction between MaterialSample, PreservedSpecimen, FossilSpecimen, and LivingSpecimen more or less the same kind of distinction as that which divides Location from Event from Taxon from Identification, etc.? The latter examples seem to me to be fundamentally different classes of things with very few (if any) shared properties; whereas the former examples seem to me to be slightly different kinds of things, which otherwise share largely the same set of properties.

In other words, I think we all feel that it's important to distinguish instances of MaterialSample that are fossils from those that are living or recently dead & preserved. But it seems (to me at least) that treating them as different classes of things distinguished at the level of basisOfRecord is out of place.

Jegelewicz commented 3 years ago

In other words, I think we all feel that it's important to distinguish instances of MaterialSample that are fossils from those that are living or recently dead & preserved. But it seems (to me at least) that treating them as different classes of things distinguished at the level of basisOfRecord is out of place.

Thank you - that is exactly what I have been trying to get at!

Jegelewicz commented 2 years ago

The Task Group has decided to deprecate this term and perhaps integrate it into controlled vocabulary for materialSampleType. This is a draft of the dwc issue to submit.

Term change

Submitter: TDWG MaterialSample Task Group
Efficacy Justification (why is this change necessary?): Deprecate this term for consolidation of physical objects into the class MaterialSample rather than including specific classes for different kinds of physical objects which can be covered under materialSamplType
Demand Justification (if the change is semantic in nature, name at least two organizations that independently need this term):
Stability Justification (what concerns are there that this might affect existing implementations?):
Implications for dwciri: namespace (does this change affect a dwciri term version)?: Yes

Current Term definition: https://dwc.tdwg.org/list/#dwc_FossilSpecimen

Proposed attributes of the new term version (Please put actual changes to be implemented in bold and ~strikethrough~):

Term name (in lowerCamelCase for properties, UpperCamelCase for classes): ~FossilSpecimen~
Organized in Class (e.g., Occurrence, Event, Location, Taxon):
Definition of the term (normative): ~A preserved specimen that is a fossil.~
Usage comments (recommendations regarding content, etc., not normative):
Examples (not normative): ~A body fossil. A coprolite. A gastrolith. An ichnofossil. A piece of a petrified tree.~
Refines (identifier of the broader term this term refines; normative):
Replaces (identifier of the existing term that would be deprecated and replaced by this term; normative):
ABCD 2.06 (XPATH of the equivalent term in ABCD or EFG; not normative):

dagendresen commented 2 years ago

Is there a way to say "replaced by" (on deprecated term level) -- pointing to the new controlled vocabulary term we plan to propose?

baskaufs commented 2 years ago

@dagendresen Yes, dcterms:isReplacedBy. See http://rs.tdwg.org/dwc/terms/individualID.rdf for an existing example, which also includes deprecation.

Jegelewicz commented 1 year ago

Based upon requested change in the MaterialSample definition change and taking the opportunity to make this definition more than an extended version of the term. I will add a revised definition for this term to the review package.

Current Definition

FossilSpecimen - A preserved specimen that is a fossil.

Proposed Definition

FossilSpecimen - A material entity that represents an entity of interest in whole or in part that is the preserved remains, impression, or trace of any once-living thing from a past geological age.

Jegelewicz commented 1 year ago

BUT

Should this really be MaterialEntity instead of None?

Refines (identifier of the broader term this term refines; normative): None

baskaufs commented 1 year ago

See my comments here and here with a description of the problem I have with these new specimen definitions.

Jegelewicz commented 1 year ago

The Task Group participants today decided that changing this definition will raise issues that are beyond the scope of the Task Group. Ideally, the next step will be a Task Group to more fully develop Material terms with an extension.

Suggest removing this from the review package.

tdwg / material-sample