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futres / template

user template for FuTRES data import
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John changes #3

Closed jdeck88 closed 5 years ago

jdeck88 commented 5 years ago

I made a few changes to the template (beyond just formatting).
Basically, the changes were meant to align organismID,specimenType, and dataAggregate to DwC terms. I think the terms i provided map OK but we can talk about it if you want. I also filled out the entity_alias column for all fields.

jdeck88 commented 5 years ago

I think we should give precedence to DwC for the organismID... has a longer history of use. And, no, the GUID is not typically the same as the catalog number for a specimen

jdeck88 commented 5 years ago

If the goal is to make a unique reference only within the FUTRES universe we can do that easily with a UUID. Creating a persistent GUID is much harder.

John

On Tue, Jun 18, 2019 at 7:04 PM Meghan Balk notifications@github.com wrote:

@megbalk commented on this pull request.

Is it easy to generate a GUID for a specimen?

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jdeck88 commented 5 years ago

we should add a field called catalogNumber ( http://rs.tdwg.org/dwc/terms/catalogNumber)

On Wed, Jun 19, 2019 at 10:32 AM Meghan Balk notifications@github.com wrote:

@megbalk commented on this pull request.

Got it. Where can users report the catalog number?

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ramonawalls commented 5 years ago

Actually, I think organismID is the wrong DwC field to use. Organisms in Darwin Core has a specific meaning that is not tied to specimens, but rather the individuals or collections of organisms (see http://purl.obolibrary.org/obo/PCO_0000031). Instead, I suggest we use http://rs.tdwg.org/dwc/terms/materialSampleID. @jdeck88 I am kind of shocked that you did not suggest using that in the first place, after the years of effort that went into it.

Very few specimens coming in to FuTRES will have GUIDs already, so, as John indicated, we will need to make internal IDs for those. If they do have one, great. We should use it.

I'm not sure about the entity alias -- I am going to give this some deep thought.

jdeck88 commented 5 years ago

I saw dwc:organismID in the URI field and i was thinking that we wanted to track a particular bone coming from the same organism. So, what about materialSampleID for the particular sample and organismID in cases where we know it is from the same individual?

On Wed, Jun 19, 2019 at 12:29 PM Ramona Walls notifications@github.com wrote:

Actually, I think organismID is the wrong DwC field to use. Organisms in Darwin Core has a specific meaning that is not tied to specimens, but rather the individuals or collections of organisms (see http://purl.obolibrary.org/obo/PCO_0000031). Instead, I suggest we usehttp://rs.tdwg.org/dwc/terms/materialSampleID. @jdeck88 https://github.com/jdeck88 I am kind of shocked that you did not suggest using that in the first place, after the years of effort that went into it.

Very few specimens coming in to FuTRES will have GUIDs already, so, as John indicated, we will need to make internal IDs for those. If they do have one, great. We should use it.

I'm not sure about the entity alias -- I am going to give this some deep thought.

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meghalithic commented 5 years ago

So we need a few extra fields:

  1. spot for a catalog number using dwc: catalogNumber
  2. way to say if something is a fossil or not using organismID
  3. a way to say if something is part of a lot or an individual materialSampleID
jdeck88 commented 5 years ago

i just committed an update adding dwc:catalogNumber and dwc:materialSampleID. Left organismID in there which people can use to designate a particular organism. We can leave out the naval-gazing which will ultimately ensue when we start talking individuals and populations.

John

On Wed, Jun 19, 2019 at 12:49 PM Meghan Balk notifications@github.com wrote:

So we need a few extra fields:

  1. spot for a catalog number using dwc: catalogNumber
  2. way to say if something is a fossil or not using organismID
  3. a way to say if something is part of a lot or an individual materialSampleID

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