[tdwg-content] terms for sample data in DwC

Fri Dec 12 16:58:31 CET 2014

Yes, thank you, that would work well!  --Gail

________________________________
From: Éamonn Ó Tuama [GBIF] [eotuama at gbif.org]
Sent: Friday, December 12, 2014 03:28
To: Kampmeier, Gail E; tdwg-content at lists.tdwg.org
Subject: RE: [tdwg-content] terms for sample data in DwC

Thanks for feedback, Gail.
We propose to change the definition of “quantity” from this (which you find too vague) -

quantity: the quantity, per sampling event, given as a number or enumeration value for the quantityType.

to this –
quantity: a number or enumeration value for the quantityType (e.g., individuals, %biomass, %biovolume, BraunBlanquetScale) per sampling event.

I trust by including examples of quantityType in the definition, the examples given (“12.5”, “r”) have the context you felt was missing.

Best regards,
Éamonn

From: Kampmeier, Gail E [mailto:gkamp at illinois.edu]
Sent: 13 November 2014 16:55
To: Éamonn Ó Tuama [GBIF]; tdwg-content at lists.tdwg.org
Subject: RE: [tdwg-content] terms for sample data in DwC

The term "quantity" seems to beg a qualifier (i.e., "sampleQuantity"), and perhaps this is because the definition of "quantity" seems insufficient/vague. I was wondering why the definition in an earlier email (19 Aug. 2014) from Eammon, "quantity: the number or enumeration value of the quantityType (e.g., individuals, biomass, biovolume, BraunBlanquetScale) per samplingUnit or a percentage measure recorded for the sample." was not used The examples given ("12.5, r") are not very helpful, as a decimal quantity is not immediately what comes to mind without context (I know, that's in quantityType). What is used for quantityType is actually more relatable, or enumeration of what is in the sample data primer.

Sorry if I have missed other emails discussing this, but I am very glad to see the doors opening to the huge volume of experimental data from agriculture as well as other fields.

Cheers!

Gail

Gail E. Kampmeier
Illinois Natural History Survey
Prairie Research Institute
University of Illinois
1816 So. Oak St.
Champaign, IL 61820
www.inhs.illinois.edu/~gkamp<http://www.inhs.illinois.edu/~gkamp>
________________________________
From: tdwg-content-bounces at lists.tdwg.org<mailto:tdwg-content-bounces at lists.tdwg.org> [tdwg-content-bounces at lists.tdwg.org] on behalf of Éamonn Ó Tuama [GBIF] [eotuama at gbif.org]
Sent: Friday, November 07, 2014 08:21
To: tdwg-content at lists.tdwg.org<mailto:tdwg-content at lists.tdwg.org>
Subject: [tdwg-content] terms for sample data in DwC
In compliance with the directions for requesting changes to the Darwin Core (DwC) vocabulary, we hereby submit to the TDWG Content list a proposal for five new terms to express information on sample-based data.

Sample-based data is a type of data available from thousands of environmental, ecological, and natural resource investigations. These can be one-off studies or monitoring programmes. Such data are usually quantitative, calibrated, and follow certain protocols so that changes and trends of populations can be detected. This is in contrast to opportunistic observation and collection data which today form a significant proportion of openly accessible biodiversity data.  Sample-based data are often not shared because the underlying protocols have been hard to encode in a standardised way. For further background information and examples, please consult the sample data primer document [1].

We cannot emphasise enough that our intention here is not to establish how data should be captured or modelled but rather demonstrate one way data can be exposed to maximize discoverability and reuse. In particular, GBIF, in association with EU BON [2] project partners, is exploring how the IPT and Darwin Core Archives can enable the flow of sample based data in support of GEO BON Essential Biodiversity Variables (EBVs) [3].

While DwC already provides many terms that are relevant for describing sample-based data, based on several inputs (GBIF organised workshop on sample data, May 2013 ; previous discussions on the TDWG mailing list; discussions on the EU BON mailing list), we have identified a need for five new terms. These are:

sampleSize
https://github.com/tdwg/dwc/issues/10
#Justification
Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e., sampling events). For an introduction to the sampling proposal please see http://links.gbif.org/ipt-sample-data-primer.
#Definition
A numeric value for the time duration, length, area or volume involved in the sampling event.
#Comment
The terms sampleSize and sampleSizeUnit are required to be used as a pair. The value of sampleSize is a number. Example: “5” for the value part of 5m.
#Term group
Event

sampleSizeUnit
https://github.com/tdwg/dwc/issues/11
#Justification
Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e., sampling events). For an introduction to the sampling proposal please see http://links.gbif.org/ipt-sample-data-primer.
#Definition
The unit of measurement used in the sampling event.
#Comment
The terms sampleSize and sampleSizeUnit are required to be used as a pair, e.g., “5 metre”. Example values of sampleSizeUnit include “minute”, “hour”, “day, “metre”, “square metre”, “cubic metre”. Recommended best practice is to use a controlled vocabulary such as the Ontology of Units of Measure http://www.wurvoc.org/vocabularies/om-1.8/ of SI units, derived units or other non-SI units accepted for use within the SI (e.g. minute, hour, day, litre). Example: “metre” for the unit part of 5m.
#Term group
Event

quantity
https://github.com/tdwg/dwc/issues/12
#Justification
Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e. sampling events). For an introduction to the sampling proposal please see http://links.gbif.org/ipt-sample-data-primer.
#Definition
The quantity, per sampling event, given as a number or enumeration value for the quantityType.
#Comment
The terms quantity and quantityType are required to be used as a pair. The value of quantity is a number or enumeration. Examples: “12.5”, “r”
#Term group
Occurrence

quantityType
https://github.com/tdwg/dwc/issues/13
#Justification
Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e., sampling events). For an introduction to the sampling proposal please see http://links.gbif.org/ipt-sample-data-primer.
#Definition
The entity to which the number or enumeration reported in quantity refers.
#Comment
The terms quantity and quantityType are required to be used as a pair, e.g., “14 individuals”. The value of quantityType (i.e., the entity being measured) is expected to be drawn from a small controlled vocabulary. Examples: “Individuals”, “% Biomass”, “% Biovolume”, “% species”, “% coverage”, “BraunBlanquetScale”, “DominScale”.
#Term group
Occurrence

parentEventID
https://github.com/tdwg/dwc/issues/9
#Justification
Allows arbitrary linking of sub sampling events, e.g., for nested sampling plots. This was demanded by several people during the discussion of the TDWG sample based data session. For an introduction to the sampling proposal please see http://links.gbif.org/ipt-sample-data-primer.
#Definition
An event identifier for the super event which is composed of one or more sub-sampling events.
#Comment
The value must refer to an existing eventID. If the identifier is local it must exist within the given dataset. Example: “A1” identifying the main Whittaker Plot in nested samples, each with their own eventID (e.g., “A1:1”, “A1:2”).
#Term group
Event

None of the existing DwC terms is sufficient for any of the proposed terms although two are somewhat related: sampleEffort ("The amount of effort expended during an Event") and individualCount ("The number of individuals represented present at the time of the Occurrence"). Neither are adequate – sampleEffort just provides a free text statement so is hard to parse in comparison to sampleSize and sampleSizeUnit and individualCount refers exclusively to individuals and not percentages or entities like biomass, biovolume, etc.

[1] http://links.gbif.org/ipt-sample-data-primer
[2] http://eubon.eu<http://eubon.eu/>
[3] http://www.earthobservations.org/documents/cop/bi_geobon/ebvs/201301_ebv_paper_pereira_et_al.pdf

____________________________________________________
Éamonn Ó Tuama, Markus Döring, GBIF Secretariat

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