[tdwg-content] Darwin Core terms sex and lifeStage with mixed content

John Wieczorek tuco at berkeley.edu
Thu Feb 5 20:41:28 CET 2015


Right. Should the range of the sex field be a valid sex or, should the sex
field be a term in which to say whatever you want related to sex. Right now
it is the former and "mixed" and "multiple" are not valid sexes.

On Thu, Feb 5, 2015 at 4:26 PM, Robert Guralnick <
Robert.Guralnick at colorado.edu> wrote:

>
>   I am against trying to use values that mix concepts - in this case
> conflating the definition of "sex" with definitions of multiple objects
> bearing different sexes.  Such an approach is only going to make it more
> difficult for end users to understand what they are getting.
>
> Best, Rob
>
> On Thu, Feb 5, 2015 at 12:18 PM, Chuck Miller <Chuck.Miller at mobot.org>
> wrote:
>
>> Another term instead of “mixed”, could be “multi”.
>>
>>
>>
>> Chuck
>>
>>
>>
>> *From:* tdwg-content-bounces at lists.tdwg.org [mailto:
>> tdwg-content-bounces at lists.tdwg.org] *On Behalf Of *Bryan
>> *Sent:* Thursday, February 05, 2015 1:13 PM
>> *To:* John Wieczorek
>> *Cc:* TDWG Content Mailing List
>> *Subject:* Re: [tdwg-content] Darwin Core terms sex and lifeStage with
>> mixed content
>>
>>
>>
>> I have one suggestion for conversation because the idea is incomplete.
>> "Sex: null" might not reflect the current knowledge about multiple sex
>> identified specimen individuals. Null seems to connote that the sex is
>> unknown or just not filled in. An option might be to add an item to the
>> controlled vocabulary such as "mixed" as in a mixture of sexes. Such a
>> designation could be a signal to look in dynamicProperties for additional
>> information on counts. I am not happy with the word "mixed" since it might
>> be read in rare cases to be a gender chimera but not hermaphrodite.
>>
>>
>>
>> --bryan
>>
>>
>>
>> On Thu, Feb 5, 2015 at 8:09 AM, John Wieczorek <tuco at berkeley.edu> wrote:
>>
>> Dear all,
>>
>>
>>
>> There is a body of topics surrounding Darwin Core terms for which it is
>> tempting to overload the content in an effort to provide richer data than
>> the standard would seem to support. We have a pair of older open issues on
>> this general topic in the Darwin Core issue tracker.
>>
>>
>>
>> https://github.com/tdwg/dwc/issues/35
>>
>> https://github.com/tdwg/dwc/issues/36
>>
>>
>>
>> You can see in the discussions on those issues that there is some
>> consensus that the content of Darwin Core terms should remain consistent
>> with the definitions and not mix concepts.
>>
>>
>>
>> I've had recent questions in particular about the fields 'sex' and
>> 'individualCount'. Here is an example. How should one populate Darwin Core
>> terms for a record of 2 males and 5 females in a single lot?
>>
>>
>>
>> I propose that part of this is easy - the individualCount should be 7.
>>
>>
>>
>> The definition of the sex term (without looking for clues in the
>> Comments) might be seen as a little ambiguous, "The sex of the
>> biological individual(s) represented in the Occurrence. Recommended best
>> practice is to use a controlled vocabulary."
>>
>> Strictly speaking, there is no single sex that matches the biological
>> individuals in this example lot Occurrence record, and so the sex fields
>> should be left blank.
>>
>>
>>
>> There are a number of terms in Darwin Core whose definitions suggest that
>> a list (formatted with ' | ' as a separator) be used to match multiple
>> values. Though it might seem that sex could be one of these terms, it isn't
>> currently. Again this argues for a single value for sex from a controlled
>> vocabulary.
>>
>>
>>
>> The biggest problem is with the Comment on the sex term, which gives an
>> example with different semantics from what the definition says - namely "8
>> males, 4 females". I pose that this is an error and must be corrected.
>>
>>
>>
>> Yet, all hope of retaining information in the Occurrence record is not
>> lost. To capture the richness of the information in the multi-sex lot
>> example, I would recommend the use of dynamicProperties.
>>
>>
>>
>> How should one populate Darwin Core terms for a record of 2 males and 5
>> females in a single lot? I would do this:
>>
>>
>>
>> sex = null
>>
>> individualCount = 7
>>
>> dynamicProperties= { "count of males":2, "count of females":5 }
>>
>>
>>
>> Hope that makes sense.
>>
>>
>>
>> Since this topic has arisen from multiple independent sources, I would
>> like to formally propose changes to the sex and lifeStage terms to remove
>> the spurious examples. Today begins a minimum 30-day public commentary
>> period to close on 5 March 2015 if no dissenting opinions are made in this
>> public forum.
>>
>>
>>
>> Here is how the new terms would appear if the changes are accepted:
>>
>>
>>
>> Identifier: http://rs.tdwg.org/dwc/terms/sex
>>
>> Namespace: http://rs.tdwg.org/dwc/terms/
>>
>> Label: Sex
>>
>> Definition: The sex of the biological individual(s) represented in the
>> Occurrence. Recommended best practice is to use a controlled vocabulary.
>>
>> Comment: Examples: "female", "hermaphrodite", "male". For discussion see
>> http://terms.tdwg.org/wiki/dwc:sex
>>
>> Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
>>
>> Refines:
>>
>> Status: recommended
>>
>> Date Issued: 2008-11-19
>>
>> Date Modified: 2015-02-05
>>
>> Has Domain:
>>
>> Has Range:
>>
>> Version: sex-2015-02-05
>>
>> Replaces: Sex-2009-04-24
>>
>> Is Replaced By:
>>
>> Class: http://rs.tdwg.org/dwc/terms/Occurrence
>>
>> ABCD 2.06: DataSets/DataSet/Units/Unit/Sex
>>
>>
>>
>> Identifier: http://rs.tdwg.org/dwc/terms/lifeStage
>>
>> Namespace: http://rs.tdwg.org/dwc/terms/
>>
>> Label: Life Stage
>>
>> Definition: The age class or life stage of the biological individual(s)
>> at the time the Occurrence was recorded. Recommended best practice is to
>> use a controlled vocabulary.
>>
>> Comment: Examples: "egg", "eft", "juvenile", "adult". For discussion see
>> http://terms.tdwg.org/wiki/dwc:lifeStage
>>
>> Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
>>
>> Refines:
>>
>> Status: recommended
>>
>> Date Issued: 2008-11-19
>>
>> Date Modified: 2015-02-05
>>
>> Has Domain:
>>
>> Has Range:
>>
>> Version: lifeStage-2015-02-05
>>
>> Replaces: LifeStage-2009-04-24
>>
>> Is Replaced By:
>>
>> Class: http://rs.tdwg.org/dwc/terms/Occurrence
>>
>> ABCD 2.06:
>> DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalSexualStage or
>> DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalLiveStages/MycologicalLiveStage
>> (Note DwC spec uses ”MycologicalLifeStage” or
>> DataSets/DataSet/Units/Unit/ZoologicalUnit/PhasesOrStages/PhaseOrStage
>>
>>
>>
>>
>>
>> Cheers,
>>
>>
>>
>> John
>>
>>
>> _______________________________________________
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>
>>
>>
>>
>>
>> --
>>
>> Bryan Heidorn
>> University of Arizona
>> http://www.sirls.arizona.edu/heidorn
>>
>> _______________________________________________
>> tdwg-content mailing list
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>>
>>
>
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