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Arctos is a museum collections management system
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Need mapping of GeologicalContext from Arctos to other publishers #2094

Closed dperriguey closed 5 years ago

dperriguey commented 5 years ago

I was made aware that our mapping was not done correctly for basis of record and missing for geological context in iDigBio. The basis of record was Preserved Specimen when it should have been Fossil Specimen. This was taken care of, just wanted to make the note for other earth science/paleo/archaeo collections.

The problem that needs work is mapping our geological attributes to iDigBio/GBIF geological context. Our method for mapping looks correct, but it is not showing up on the other end correctly.

Let me know if I need to give more information or if I even posted this in the correct place.

Jegelewicz commented 5 years ago

The basis of record was Preserved Specimen when it should have been Fossil Specimen.

Also see https://github.com/ArctosDB/arctos/issues/2075#issuecomment-491976353

dustymc commented 5 years ago

It's not that our mapping is incorrect, it's that it does not exist.

DWC fields are this:

https://terms.tdwg.org/wiki/Darwin_Core_GeologicalContext

By concept name: dwc:bed • dwc:earliestAgeOrLowestStage • dwc:earliestEonOrLowestEonothem • dwc:earliestEpochOrLowestSeries • dwc:earliestEraOrLowestErathem • dwc:earliestPeriodOrLowestSystem • dwc:formation • dwc:geologicalContextID • dwc:group • dwc:highestBiostratigraphicZone • dwc:latestAgeOrHighestStage • dwc:latestEonOrHighestEonothem • dwc:latestEpochOrHighestSeries • dwc:latestEraOrHighestErathem • dwc:latestPeriodOrHighestSystem • dwc:lithostratigraphicTerms • dwc:lowestBiostratigraphicZone • dwc:member

Arctos "fields" are

UAM@ARCTOS> select distinct GEOLOGY_ATTRIBUTE from CTGEOLOGY_ATTRIBUTE order by GEOLOGY_ATTRIBUTE;

GEOLOGY_ATTRIBUTE
------------------------------------------------------------------------------------------------------------------------
Eon/Eonothem
Erathem/Era
Series/Epoch
Stage/Age
System/Period
bed
block
field
formation
group
member
suite
unspecified

13 rows selected.

The authority is hierarchical, so we can also pull "parentage" for terms which are in a hierarchy - https://arctos.database.museum/info/ctDocumentation.cfm?table=CTGEOLOGY_ATTRIBUTE

Any locality can carry any number of geology attributes.

How should I transform Arctos data into something suitable for DWC?

http://arctos.database.museum/guid/UAM:ES:38746 is an example of a specimen with geology.

And can we get rid of "unspecified"?!

dperriguey commented 5 years ago

I'm not sure what unspecified is. It's not useful. If you don't specify (i.e. don't assign a geology attribute to it) then it is unspecified.

It seems that the structure is to bracket for level of uncertainties. Looks like there are two methods: default for using dwc:earliest(chronoterm), or putting both in e.g. dwc:earliestEraOrLowestErathem=Mesozoic dwc:latestEraOrHighestErathem=Mesozoic.

less redundant method: https://www.idigbio.org/portal/records/5c2dffb0-f6e4-4b9e-b4ab-1f14ad84c449 image

more redundant method: https://www.idigbio.org/portal/records/66487417-aff4-4bc3-9527-507329c17652 image

I'm comfortable with the less redundant method. All our lithostratigraphy should be easy. All the group, formation, member, bed terms are the same. Call everything else might fit into dwc:lithostratigraphicTerms. Probably a good thing that we control the vocabulary to have the lithostratigraphic term along side the attribute (e.g. Kakertok Suite).

Our group will have biostratigraphic terms that would be great to have in our hierarchy (dwc:lowest/highestBiostratigraphicZone) too.

dustymc commented 5 years ago

https://arctos.database.museum/guid/UNM:ES:10288

How would that map? I don't see anything in our data that would lead me to eg, Albian being either earliestAgeOrLowestStage or latestAgeOrHighestStage and Cenomanian being presumably the other - they are at the same relative position in the hierarchy. (I think it's in the parent term, but I'm not sure how I could write code to that??)

What if there were 30 more Stage/Age determinations? https://arctos.database.museum/guid/UAM:ES:38714 has multiple formation data - can I concatenate them using some separator, or ???

What if they were all the same - eg, 30 people looked at the specimen and all agree "X"? Should I somehow repeat X 30 times in a probably-futile attempt to express certainty in a model which doesn't allow for uncertainty, of can I just deal with DISTINCT(term, value) for this?

I need answers that I can write code to using only the data I can access from Arctos. Hopefully this is all blindingly obvious to ya'll, but it's not for me so maybe type slowly and use small words....

@dbloom assuming we eventually figure out the details, how should this be structured - more columns in the flattened view, another 'table' with OccurrenceID as fkey, ???

dustymc commented 5 years ago

"unspecified" is used for https://arctos.database.museum/guid/UNM:ES:5884

unspecified Main Street Limestone https://macrostrat.org/sift/#/strat_name_concept/9156 5340202 1 unspecified Main Street Limestone https://macrostrat.org/sift/#/strat_name_concept/9156   1 JEGELEWICZ 2019-02-04 07:14:17.0

@Jegelewicz ??

dperriguey commented 5 years ago

I say we just keep it simple. Make our own protocol for dealing with the weirdness of Darwin Core. That's why I'm saying use the less redundant method and just use earliest.

I don't know what to do with the multiple formations. If the data are that uncertain (that someone pulled a fossil out and just said, "well maybe it came from one of these two formations"...the Poul Creek Formation is about 1600m thick the Yakataga Formation is at least 4000m thick. It's pretty hard to mess that up unless you're at a boundary between formations, but even then you have to make a decision and then make the notes. Boundaries are not always easy to find, so especially if its found somewhere in between it needs to be noted as such) then that needs to go into notes and not hard data like our hierarchy. That record even says "Sample collected from Yakataga Reef. Exact locality not recorded. Note: Additional information in museum files." Really there is no ambiguity in that. If it came from the Yakataga Reef, it came from the Yakataga Formation as per multiple, good resources (https://ngmdb.usgs.gov/Geolex/UnitRefs/YakatagaRefs_12311.html).

"unspecified" That record should be Main Street Limestone Formation (child) of the Washita Group (parent)

dustymc commented 5 years ago

multiple formations

I don't think that can come only from uncertainty - maybe the name changed, a feature was split or adjusted, there are 20 specimens and 20 sources of data all sharing an identifier, ... We (and DWC) have invested a lot of unnecessary work if this is really all unambiguous and static. If we truly don't need that complexity then let's get rid of it.

just use earliest.

Given Albian and Cenomanian on a locality, send out earliestAgeOrLowestStage="Albian; Cenomanian" ??

dperriguey commented 5 years ago

multiple formations Don't need the complexity.

just use earliest good point, maybe we can still use both but default to earliest if simple. I have no idea how you map that. We would have to designate what is earliest or latest on our collections end right or can that be in the code? If we can easily search for multiple designations (two chronostratigraphic attributes), then we could clean that up in a sort of less time consuming way. If DWC had earliest and latest formation, we could do the same with the lithostratigraphy. If you have the lithostratigraphy in chronological order we could map that, or can you have multiple dwc:formation?

dustymc commented 5 years ago

Don't need the complexity.

@tucotuco do you happen to know the history leading to DWC having the earliest/latest thing? I think I'm hearing that that doesn't make sense.

If you have the lithostratigraphy in chronological order

That is explicitly what we removed when the chrono and litho data were separated!?

earliest or latest on our collections end right or can that be in the code

Well I'm less and less certain that I understand these particular data, but if "Mesozoic" means something in one collection (or when attached to one specimen, or as asserted by some agent, or...) and something else in some other context then the only place to express that is in the data itself (and we probably need to stop pretending that ambiguous terms can be authoritative), and if it means something that can be universally defined then good database design demands we do so in the authority.

dperriguey commented 5 years ago

Don't need the complexity. It makes sense in the context of uncertainty. You gave a perfect example. Our data associated with a particular formation without someone being specific about the chronostratigraphy gives us the ability to say, "because this formation spans the Albian to the Cenomanian, we can say this fossil specimen can be narrowed down to have come from this same age interval". We may just need to throw out that method but as you mentioned there are data that span multiple formations. All meaning the complexity may be necessary.

If you have the lithostratigraphy in chronological order They can be separated but also put into some chronological order. My thought was that it would help with the mapping. If formation B is older and formation A is younger, can your code distinguish between those. Older and younger being actual time (e.g. 83.6+/-0.2 - 72.1+/-0.2; all available through Macrostrat and the International Chronostratigraphic Chart.

we probably need to stop pretending that ambiguous terms can be authoritative If someone says Mesozoic, it means Mesozoic. If someone says Mesozoic through the Cenozoic, it means Mesozoic through the Cenozoic. I just wish DWC had earliest/latest/exactly. My point was again just about uncertainty you pointed out with our lithostratigraphy. Some rock spans the Albian through the Cenomainian. If we have a better way to deal with the uncertainty, I'm all for it. That is, if a record is specific about Chronostratigraphy to the level of e.g. Late Cretaceous, then it should only be recorded as such in Arctos. In this scenario: https://arctos.database.museum/guid/UAM:ES:38714 should only be Cenozoic. In this scenario: http://arctos.database.museum/guid/UNM:ES:15572 should only be Upper Cretaceous. Add notes if whoever is putting in the data really wants to get specific about uncertainties.
If the data was originally recorded with the uncertainties, the person putting in the data can reduce to the least ambiguous chronostratigraphic term. The Chronostratigraphy is not ambiguous (however, it changes every new release of the Chronostratigraphic chart=less uncertainty), but lithostratigraphy is very ambiguous. Lithostratigraphy spans different time depending on where you are in geographic space.

dustymc commented 5 years ago

Thanks, I think that helps. We (and DWC) do need the uncertainty - correct?

I just wish DWC had....

There is, or was, a process for that.

can your code distinguish between...all available through Macrostrat and the International Chronostratigraphic Chart.

If I can get those data from an external source, there's no need to replicate that. That comes back to https://github.com/ArctosDB/arctos/issues/1642 - I'm still not sure what you're trying to DO, what data we read directly from stuff in the collection and what's just derived from that, etc.

I threw something together that might satisfy our immediate needs.

https://github.com/ArctosDB/DDL/blob/master/functions/getGeologyForDWC.sql

create table temp_g_d as
select
  concatGeologyAttribute(collection_object_id) concatsrt,
  guid,
  getGeologyForDWC(collection_object_id,'Erathem/Era') as earliestEraOrLowestErathem,
  getGeologyForDWC(collection_object_id,'Eon/Eonothem') as earliestEonOrLowestEonothem,
  getGeologyForDWC(collection_object_id,'Series/Epoch') as earliestEpochOrLowestSeries,
  getGeologyForDWC(collection_object_id,'Stage/Age') as earliestAgeOrLowestStage,
  getGeologyForDWC(collection_object_id,'System/Period') as earliestPeriodOrLowestSystem,
  getGeologyForDWC(collection_object_id,'formation') as formation,
  getGeologyForDWC(collection_object_id,'group') as geo_group,
  getGeologyForDWC(collection_object_id,'member') as member
from
  flat 
where 
  guid in (
    'UAM:ES:38714',
    'UNM:ES:15572',
    'UAM:ES:38746',
    'UNM:ES:10288',
    'UNM:ES:5884'
  )
;

temp_g_d.csv.zip

dperriguey commented 5 years ago

We (and DWC) do need the uncertainty. How to relate those to our unspecified uncertainties, I don't know. If we had them specified, I think we could use the DWC more efficiently.

I'm guessing the Macrostrat API will be able to help us with the lithostratigraphy (but we had problems with that before and I don't know what to do). I'll go back and comment at #1642 later to be more specific about my ideas.

threw something together That LOOKS fine to me. But will it break when we have multiple formations and chronostrat stuff when it gets pulled into iDigBio? I would really prefer it if the code is set up to be less specific (i.e. not earliest or latest). What is or was the DWC process? For immediate needs, it looks fine to me. It's not as correct as I/someone downloading from iDigPaleo wants it, but if it gets the data in great.

Jegelewicz commented 5 years ago

Main Street Limestone should be a formation, not sure what happened there...I can't change it because it is being used - guessing @dustymc can. Should be:

Main Street Limestone Formation (formation)

Jegelewicz commented 5 years ago

If you have the lithostratigraphy in chronological order

That is explicitly what we removed when the chrono and litho data were separated!?

Because litho ARE NOT chronological.

The Chronostratigraphy is not ambiguous (however, it changes every new release of the Chronostratigraphic chart=less uncertainty), but lithostratigraphy is very ambiguous. Lithostratigraphy spans different time depending on where you are in geographic space.

Jegelewicz commented 5 years ago

See also https://github.com/tdwg/dwc-qa/issues/136 ?

dperriguey commented 5 years ago

Lithostratigraphy Each lithological unit spans some amount of time see macrostrat.org and search any name (say Main Street https://macrostrat.org/sift/#/strat_name_concept/9156). image

Litho, chrono, chemo, and biostratigraphy (as well as others) all have a primary focus in geochronology. As geologists, we are usually concerned with when something happened. You cannot mix your different stratigraphies in a weird hierarchy saying the rock unit spans exactly all of the Albian and all through the Cenomanian (you only can in a relative sense). Lets discus this more in #1642.

My idea was to help Dusty with the code for determining earliest and latest in a litho sense but that's not even available in DWC. It seems to complicated to explain my idea in Github though. Maybe a Skypeing might help. Regardless, I think what Dusty's come up with might work for now. I just need to see how it looks on the other end in iDigBio. Will it look just like your zip file @dustymc?

dustymc commented 5 years ago

IDK that (and if it'll melt DWC) is a question for @dbloom. I think it will be more columns on the big flat view.

dustymc commented 5 years ago

Main Street Limestone Formation (formation) should be happy now - thanks!

dperriguey commented 5 years ago

Does it take a while for it to show up in the geology attribute code table? Because I don't see it in either the code table or the data entry screen.

Jegelewicz commented 5 years ago

It's in there: image

dperriguey commented 5 years ago

I just noticed that it wasn't in there verbatim as Dusty stated in the comment above.

@dbloom How is it looking for this? Do you know if Dusty's basic format above will look the same in iDigBio or if it will "melt" DWC?

dustymc commented 5 years ago

verbatim

I know this has come up before, but can we standardize on either always including the "rank" ("Main Street Limestone Formation") or never doing so ("Main Street Limestone")? Along with being less confusing locally, I think that's going to be absolutely necessary if we ever want to plug in to a service.

We have no control over iDigBio. "Is this suitable for DWC?" is really as far as we can go with that.

dperriguey commented 5 years ago

I understand the point of standardizing. At least there is perhaps a reason of distinguishing between Main Street Formation and Main Street Limestone formation given their geography and named history: https://ngmdb.usgs.gov/Geolex/Units/MainStreet_9156.html https://macrostrat.org/sift/#/strat_name/71995 image

If we standardize it makes it clean. However, all the old data is not clean like this and we are then renaming the data. And honestly it's not wrong. The Main Street Limestone is a formation. It's not in the literature with the name "Formation" https://ngmdb.usgs.gov/Geolex/UnitRefs/MainStreetRefs_9156.html But I'm totally ok with standardizing. What is the advantage of standardizing by rank? By plug into a service do you mean like Macrostrat?

no control

So do we just wait and see after the next pull of data from iDigBio and GBIF?

dustymc commented 5 years ago

I need to hear back from @dbloom before I can send geology data out with the DWC.

Jegelewicz commented 5 years ago

He was traveling today - it might be next week before he gets to this....

dperriguey commented 5 years ago

Ok, thanks, good to know

dustymc commented 5 years ago

From tuco:

Future consideration: Should we do something different for collections that don't have geology data?

dustymc commented 5 years ago

New IPT view with live geology data:


UAM@ARCTOS> desc digir_query.ipt_view;
 Name                                  Null?    Type
 ----------------------------------------------------------------- -------- --------------------------------------------
 COLLECTION_ID                             NOT NULL NUMBER
 LANGUAGE                                   CHAR(2)
 RIGHTS                                     VARCHAR2(4000)
 TYPE                                       VARCHAR2(20)
 BASISOFRECORD                                  VARCHAR2(20)
 COLLECTIONCODE                                 VARCHAR2(5)
 RECORDEDBY                                 VARCHAR2(4000)
 INFORMATIONWITHHELD                                VARCHAR2(4000)
 INDIVIDUALCOUNT                                NUMBER
 INSTITUTIONCODE                                VARCHAR2(20)
 MODIFIED                                   DATE
 ASSOCIATEDOCCURRENCES                              VARCHAR2(4000)
 REFERENCES                                 VARCHAR2(102)
 OCCURRENCEREMARKS                              VARCHAR2(4000)
 TYPESTATUS                                 VARCHAR2(4000)
 ASSOCIATEDTAXA                                 VARCHAR2(4000)
 OTHERCATALOGNUMBERS                                VARCHAR2(4000)
 INDIVIDUALID                                   VARCHAR2(102)
 CATALOGNUMBER                                  VARCHAR2(67)
 ASSOCIATEDSEQUENCES                                VARCHAR2(4000)
 RECORDNUMBER                                   VARCHAR2(4000)
 FIELDNUMBER                                    VARCHAR2(4000)
 SEX                                        VARCHAR2(4000)
 LIFESTAGE                                  VARCHAR2(4000)
 DYNAMICPROPERTIES                              VARCHAR2(4000)
 IDENTIFICATIONREMARKS                              VARCHAR2(4000)
 FAMILY                                     VARCHAR2(4000)
 HIGHERCLASSIFICATION                               VARCHAR2(4000)
 GENUS                                      VARCHAR2(4000)
 IDENTIFICATIONREFERENCES                           VARCHAR2(255)
 IDENTIFICATIONQUALIFIER                            VARCHAR2(25)
 IDENTIFIEDBY                                   VARCHAR2(4000)
 TAXONRANK                                  VARCHAR2(255)
 KINGDOM                                    VARCHAR2(4000)
 DATEIDENTIFIED                                 VARCHAR2(22)
 IDVERIFICATIONSTATUS                               VARCHAR2(255)
 NOMENCLATURALCODE                              VARCHAR2(4000)
 PREPARATIONS                                   VARCHAR2(4000)
 PCLASS                                     VARCHAR2(4000)
 PORDER                                     VARCHAR2(4000)
 PHYLUM                                     VARCHAR2(4000)
 SCIENTIFICNAME                                 VARCHAR2(255)
 SPECIFICEPITHET                                VARCHAR2(4000)
 INFRASPECIFICEPITHET                               VARCHAR2(4000)
 PREVIOUSIDENTIFICATIONS                            VARCHAR2(4000)
 ASSOCIATEDMEDIA                                VARCHAR2(121)
 OCCURRENCEID                                   VARCHAR2(130)
 SPECIMENEVENTTYPE                              VARCHAR2(60)
 SAMPLINGPROTOCOL                               VARCHAR2(4000)
 ESTABLISHMENTMEANS                             VARCHAR2(60)
 LOCATIONACCORDINGTO                                VARCHAR2(4000)
 GEOREFERENCEDBY                                VARCHAR2(4000)
 GEOREFERENCEDDATE                              DATE
 HABITAT                                    VARCHAR2(4000)
 GEOREFERENCEVERIFICATIONSTATUS                         VARCHAR2(60)
 EVENTREMARKS                                   VARCHAR2(4000)
 GEODETICDATUM                                  VARCHAR2(55)
 VERBATIMEVENTDATE                              VARCHAR2(60)
 VERBATIMLOCALITY                               VARCHAR2(4000)
 VERBATIMCOORDINATESYSTEM                           VARCHAR2(20)
 EVENTDATE                                  VARCHAR2(88)
 EVENTTIME                                  VARCHAR2(45)
 DAY                                        VARCHAR2(8)
 MONTH                                      VARCHAR2(8)
 YEAR                                       VARCHAR2(16)
 ENDDAYOFYEAR                                   NUMBER
 VERBATIMCOORDINATES                                VARCHAR2(255)
 COORDINATEUNCERTAINTYINMETERS                          NUMBER
 DECIMALLATITUDE                                NUMBER
 DECIMALLONGITUDE                               NUMBER
 LOCALITY                                   VARCHAR2(255)
 GEOREFERENCEPROTOCOL                               VARCHAR2(255)
 GEOREFERENCESOURCES                                VARCHAR2(4000)
 MINIMUMDEPTHINMETERS                               NUMBER
 MAXIMUMDEPTHINMETERS                               NUMBER
 MINIMUMELEVATIONINMETERS                           NUMBER
 MAXIMUMELEVATIONINMETERS                           NUMBER
 LOCATIONREMARKS                                VARCHAR2(4000)
 CONTINENT                                  VARCHAR2(50)
 COUNTRY                                    VARCHAR2(50)
 COUNTY                                     VARCHAR2(50)
 ISLAND                                     VARCHAR2(50)
 ISLANDGROUP                                    VARCHAR2(50)
 QUAD                                       VARCHAR2(30)
 WATERBODY                                  VARCHAR2(50)
 FEATURE                                    VARCHAR2(50)
 STATEPROVINCE                                  VARCHAR2(75)
 HIGHERGEOGRAPHY                                VARCHAR2(255)
 INSTITUTION                                    VARCHAR2(60)
 COLLECTION                                 VARCHAR2(50)
 EARLIESTERAORLOWESTERATHEM                         VARCHAR2(4000)
 EARLIESTEONORLOWESTEONOTHEM                            VARCHAR2(4000)
 EARLIESTEPOCHORLOWESTSERIES                            VARCHAR2(4000)
 EARLIESTAGEORLOWESTSTAGE                           VARCHAR2(4000)
 EARLIESTPERIODORLOWESTSYSTEM                           VARCHAR2(4000)
 FORMATION                                  VARCHAR2(4000)
 GEO_GROUP                                  VARCHAR2(4000)
 MEMBER                                     VARCHAR2(4000)
 OCCURRENCEID2                                  VARCHAR2(148)
dperriguey commented 5 years ago

Update

Things look like they mapped correctly! Thank you Dusty for getting mapping things out! Thanks everyone for their input. I'm really stoked about how good things look so far. Really appreciate the help!

Examples: Below are a couple records. I noticed an error with one of these.

Regular/less weird record: Looks great, but the Cretaceous is System/Period not Erathem/Era http://arctos.database.museum/guid/UNM:ES:15635 https://www.idigbio.org/portal/records/a13c1d88-730b-4245-ac96-767b98aed48c image

Irregular record: Looks great. The poorly determined formation seemed to map correctly with the appropriate Event Remark at the bottom clarifying the determination. http://arctos.database.museum/guid/UNM:ES:15633 https://www.idigbio.org/portal/records/0ec77035-6b3a-4561-9933-906f70c07b89 image

I should probably make sure that there are not more issues. I'm currently hard copying our data and refining localities. Whenever I encounter a strange record or one with geological information I haven't seen in iDigBio yet, I'll make note of it here.

dustymc commented 5 years ago

Cretaceous is System/Period not Erathem/Era

Here's what we're sending out.


select
  'earliestEraOrLowestErathem: ' || earliestEraOrLowestErathem,
  'earliestPeriodOrLowestSystem: ' || earliestPeriodOrLowestSystem
from
digir_query.ipt_view_too
where
"dcterms:references"='http://arctos.database.museum/guid/UNM:ES:15635'
  8  ;

'EARLIESTERAORLOWESTERATHEM:'||EARLIESTERAORLOWESTERATHEM
------------------------------------------------------------------------------------------------------------------------
'EARLIESTPERIODORLOWESTSYSTEM:'||EARLIESTPERIODORLOWESTSYSTEM
------------------------------------------------------------------------------------------------------------------------
earliestEraOrLowestErathem:
earliestPeriodOrLowestSystem: Cretaceous

1 row selected.
dperriguey commented 5 years ago

Is that the fix? Or is that what you've mapped and its not being ingested by iDigBio correctly?

dustymc commented 5 years ago

That's what's in Arctos right now. I suppose there's some chance I fixed something since the last export, but I don't think so. VertNet is the next logical place to check. http://ipt.vertnet.org:8080/ipt/resource?r=unm_es

So this is either something I've recently fixed or the fault of @tucotuco.

tucotuco commented 5 years ago

I don't understand. Can you give me an example of what you see versus what you expect, then I can track it down. To me everything looks as it should following the last publication a couple of weeks ago.

dperriguey commented 5 years ago

Regular/less weird record: Looks great, but the Cretaceous is System/Period not Erathem/Era http://arctos.database.museum/guid/UNM:ES:15635 https://www.idigbio.org/portal/records/a13c1d88-730b-4245-ac96-767b98aed48c image

Irregular record: Looks great. The poorly determined formation seemed to map correctly with the appropriate Event Remark at the bottom clarifying the determination. http://arctos.database.museum/guid/UNM:ES:15633 https://www.idigbio.org/portal/records/0ec77035-6b3a-4561-9933-906f70c07b89 image

Both of these say Earliest Era or Lowest Erathem - Cretaceous They need to say Earliest Period or Lowest System - Cretaceous

Dusty's point above is that he has mapped them as Earliest Period or Lowest System, meaning the switch seems to have happened outside of Arctos.

tucotuco commented 5 years ago

OK, Perfect. Yes. There were three mis-mapped fields in the IPT. I have just corrected those and republished the resource. I don't know how long it will take for iDigBio to renew that. For GBIF it takes about 15 minutes usually.

Good eye.

On Fri, Jul 19, 2019 at 7:01 PM dperriguey notifications@github.com wrote:

Regular/less weird record: Looks great, but the Cretaceous is System/Period not Erathem/Era http://arctos.database.museum/guid/UNM:ES:15635 https://www.idigbio.org/portal/records/a13c1d88-730b-4245-ac96-767b98aed48c image

Irregular record: Looks great. The poorly determined formation seemed to map correctly with the appropriate Event Remark at the bottom clarifying the determination. http://arctos.database.museum/guid/UNM:ES:15633 https://www.idigbio.org/portal/records/0ec77035-6b3a-4561-9933-906f70c07b89 image

Both of these say Earliest Era or Lowest Erathem - Cretaceous They need to say Earliest Period or Lowest System - Cretaceous

Dusty's point above is that he has mapped them as Earliest Period or Lowest System, meaning the switch seems to have happened outside of Arctos.

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dperriguey commented 5 years ago

@tucotuco It looks like they mapped correctly in GBIF. Just one point of nuance I guess; Earliest period or lowest system should be above Earliest epoch or lowest series, and Group should be above Formation when displayed. This is hierarchical, just like Linnaean hierarchy.

tucotuco commented 5 years ago

The sensible ordering would be a nice improvement. It is curious that no one has told GBIF this before. I recommend sending them feedback from the GBIF portal on a page where the issue is apparent.

On Tue, Aug 6, 2019 at 1:36 PM dperriguey notifications@github.com wrote:

@tucotuco https://github.com/tucotuco It looks like they mapped correctly in GBIF. Just one point of nuance I guess; Earliest period or lowest system should be above Earliest epoch or lowest series, and Group should be above Formation when displayed. This is hierarchical, just like Linnaean hierarchy.

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dperriguey commented 5 years ago

Ok, great! Thanks @tucotuco