Darwin Core terms sex and lifeStage with mixed content
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
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@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@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Another term instead of “mixed”, could be “multi”.
Chuck
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@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@berkeley.edumailto:tuco@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@lists.tdwg.orgmailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
-- Bryan Heidorn University of Arizona http://www.sirls.arizona.edu/heidorn
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@mobot.org wrote:
Another term instead of “mixed”, could be “multi”.
Chuck
*From:* tdwg-content-bounces@lists.tdwg.org [mailto: tdwg-content-bounces@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@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@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 tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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@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@mobot.org wrote:
Another term instead of “mixed”, could be “multi”.
Chuck
*From:* tdwg-content-bounces@lists.tdwg.org [mailto: tdwg-content-bounces@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@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@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 tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
The problem is occurring because the definition of the term “sex” includes “biological individual(s)” and the example being given is for the individuals part of that duality. Individuals means multiple objects.
What is meant by THE “sex” of multiple individuals in plain language? When the individuals have different sexes, it seems nonsensical. There is no one sex that applies to all in that case.
Does the term “sex” need to be constrained to the case of one individual only, and not include individuals?
Cheers, Chuck
From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Robert Guralnick Sent: Thursday, February 05, 2015 1:27 PM To: Chuck Miller Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] Darwin Core terms sex and lifeStage with mixed content
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@mobot.orgmailto:Chuck.Miller@mobot.org> wrote: Another term instead of “mixed”, could be “multi”.
Chuck
From: tdwg-content-bounces@lists.tdwg.orgmailto:tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.orgmailto:tdwg-content-bounces@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@berkeley.edumailto:tuco@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
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-- Bryan Heidorn University of Arizona http://www.sirls.arizona.edu/heidorn
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The use of NULL is misleading. Imagine you are standing outside of a bar and you friend comes out. Your friend says, "A group of people are at the bar that want to party!" You say, "Are they man or women?" Your friend relies, "NULL"
On Thu, Feb 5, 2015 at 2:02 PM, Chuck Miller Chuck.Miller@mobot.org wrote:
The problem is occurring because the definition of the term “sex” includes “biological individual(s)” and the example being given is for the individuals part of that duality. Individuals means multiple objects.
What is meant by THE “sex” of multiple individuals in plain language? When the individuals have different sexes, it seems nonsensical. There is no one sex that applies to all in that case.
Does the term “sex” need to be constrained to the case of one individual only, and not include individuals?
Cheers, Chuck
*From:* tdwg-content-bounces@lists.tdwg.org [mailto: tdwg-content-bounces@lists.tdwg.org] *On Behalf Of *Robert Guralnick *Sent:* Thursday, February 05, 2015 1:27 PM *To:* Chuck Miller
*Cc:* TDWG Content Mailing List *Subject:* Re: [tdwg-content] Darwin Core terms sex and lifeStage with mixed content
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@mobot.org wrote:
Another term instead of “mixed”, could be “multi”.
Chuck
*From:* tdwg-content-bounces@lists.tdwg.org [mailto: tdwg-content-bounces@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@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
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--
Bryan Heidorn University of Arizona http://www.sirls.arizona.edu/heidorn
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Does the term “sex” need to be constrained to the case of one individual only, and not include individuals?
One thing to keep in mind: sex is actually best not thought of as a property of an individual, but rather a property of an individual at a particular time (i.e., an Occurrence) (Note to Chuck: I know this isn't what you were suggesting, but your suggestion reminded me of it). This is because many organisms change sex throughout their lifetimes. So if pinning "sex" (and "lifestage") down to a particular individual (for which we have the new DwC class "Organism"), it should not be represented as a property of an individual/organism, but rather as a property of an individual/organism at a particular point in time (which we represent as Occurrences).
This seems like a nit-pick, but if this conversation leads to changes in DwC, I think it's important that we not allow it to lead to a step backwards.
Aloha, Rich
Right, Rich. And this is exactly the reason why they are grouped under Occurrence now.
To me the problem of having mixed values for sex and lifestage in a “lot” is pretty much the same as having different taxa in it. And to avoid that mess we defined Organism, on which an occurrence is based, to be taxonomically homogeneous.
I dont think we want to do the same for sex, but the most elegant way of sharing this mixed information would be to share separate occurrence records, each being homogenous in their sex and lifestage. This might not be feasable for some publishers, but if its possible I think thats the right way to go. If you want to break down counts to many dimensions you need to represent occurrences according to those dimensiions.
Markus
On 06 Feb 2015, at 03:57, Richard Pyle deepreef@bishopmuseum.org wrote:
Does the term “sex” need to be constrained to the case of one individual only, and not include individuals?
One thing to keep in mind: sex is actually best not thought of as a property of an individual, but rather a property of an individual at a particular time (i.e., an Occurrence) (Note to Chuck: I know this isn't what you were suggesting, but your suggestion reminded me of it). This is because many organisms change sex throughout their lifetimes. So if pinning "sex" (and "lifestage") down to a particular individual (for which we have the new DwC class "Organism"), it should not be represented as a property of an individual/organism, but rather as a property of an individual/organism at a particular point in time (which we represent as Occurrences).
This seems like a nit-pick, but if this conversation leads to changes in DwC, I think it's important that we not allow it to lead to a step backwards.
Aloha, Rich
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"If you want to break down counts to many dimensions you need to represent occurrences according to those dimensiions." I agree, and this is the approach we are taking (multiple lots with their own biocuration properties, see below).
To follow up with Rich's observations on sex (and things like "stage" etc). In our software we have introduced the concept of a Biocuration class. Individuals in this class are biologicaly derived concepts *that are used to organize collections*. As Rich noted you have to make a bit of a leap from asserting that an individual classified under the biocuration class "female" is in fact female. In our software, by default, we do not make this leap, but we are considering extending the system to allow users to add domain/range constraints that would assert additional classifications, e.g. if a specimen is classified under the biocuration class "female(s)", then that specimen can be classified as a http://www.ebi.ac.uk/efo/EFO_0001265.
We feel that the biocuration concept more closely approximates the day-to-day intent/usage of classifiers like sex, stage, "furs", "bones" etc. as organizational concepts used to manage collections, rather than a specific biological assertion about the specimen(s).
Cheers, Matt
On Fri, Feb 6, 2015 at 4:05 AM, Markus Döring m.doering@mac.com wrote:
Right, Rich. And this is exactly the reason why they are grouped under Occurrence now.
To me the problem of having mixed values for sex and lifestage in a “lot” is pretty much the same as having different taxa in it. And to avoid that mess we defined Organism, on which an occurrence is based, to be taxonomically homogeneous.
I dont think we want to do the same for sex, but the most elegant way of sharing this mixed information would be to share separate occurrence records, each being homogenous in their sex and lifestage. This might not be feasable for some publishers, but if its possible I think thats the right way to go. If you want to break down counts to many dimensions you need to represent occurrences according to those dimensiions.
Markus
On 06 Feb 2015, at 03:57, Richard Pyle deepreef@bishopmuseum.org wrote:
Does the term “sex” need to be constrained to the case of one
individual only, and not include individuals?
One thing to keep in mind: sex is actually best not thought of as a
property of an individual, but rather a property of an individual at a particular time (i.e., an Occurrence) (Note to Chuck: I know this isn't what you were suggesting, but your suggestion reminded me of it). This is because many organisms change sex throughout their lifetimes. So if pinning "sex" (and "lifestage") down to a particular individual (for which we have the new DwC class "Organism"), it should not be represented as a property of an individual/organism, but rather as a property of an individual/organism at a particular point in time (which we represent as Occurrences).
This seems like a nit-pick, but if this conversation leads to changes in
DwC, I think it's important that we not allow it to lead to a step backwards.
Aloha, Rich
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Dear all,
In the interest of seeking resolution on this subject, I would like to propose that the standard reflect that which is not in contention among the illustrative examples, and leave the rest for secondary documentation. There are linked discussion pages where these kinds of recommendations can go, and controlled vocabularies (outside the scope of Darwin Core term definitions) can accommodate discipline-specific norms with complete definitions of the recommended values within those vocabularies.
Does anyone have any objections to this. If none arise before 26 April, I will make a formal proposal to the Executive Committee recommending the terms as proposed in the first message in this thread.
Cheers,
John
On Tue, Feb 24, 2015 at 8:36 AM, Matt Yoder diapriid@gmail.com wrote:
"If you want to break down counts to many dimensions you need to represent occurrences according to those dimensiions." I agree, and this is the approach we are taking (multiple lots with their own biocuration properties, see below).
To follow up with Rich's observations on sex (and things like "stage" etc). In our software we have introduced the concept of a Biocuration class. Individuals in this class are biologicaly derived concepts *that are used to organize collections*. As Rich noted you have to make a bit of a leap from asserting that an individual classified under the biocuration class "female" is in fact female. In our software, by default, we do not make this leap, but we are considering extending the system to allow users to add domain/range constraints that would assert additional classifications, e.g. if a specimen is classified under the biocuration class "female(s)", then that specimen can be classified as a http://www.ebi.ac.uk/efo/EFO_0001265.
We feel that the biocuration concept more closely approximates the day-to-day intent/usage of classifiers like sex, stage, "furs", "bones" etc. as organizational concepts used to manage collections, rather than a specific biological assertion about the specimen(s).
Cheers, Matt
On Fri, Feb 6, 2015 at 4:05 AM, Markus Döring m.doering@mac.com wrote:
Right, Rich. And this is exactly the reason why they are grouped under Occurrence now.
To me the problem of having mixed values for sex and lifestage in a “lot” is pretty much the same as having different taxa in it. And to avoid that mess we defined Organism, on which an occurrence is based, to be taxonomically homogeneous.
I dont think we want to do the same for sex, but the most elegant way of sharing this mixed information would be to share separate occurrence records, each being homogenous in their sex and lifestage. This might not be feasable for some publishers, but if its possible I think thats the right way to go. If you want to break down counts to many dimensions you need to represent occurrences according to those dimensiions.
Markus
On 06 Feb 2015, at 03:57, Richard Pyle deepreef@bishopmuseum.org wrote:
Does the term “sex” need to be constrained to the case of one
individual only, and not include individuals?
One thing to keep in mind: sex is actually best not thought of as a
property of an individual, but rather a property of an individual at a particular time (i.e., an Occurrence) (Note to Chuck: I know this isn't what you were suggesting, but your suggestion reminded me of it). This is because many organisms change sex throughout their lifetimes. So if pinning "sex" (and "lifestage") down to a particular individual (for which we have the new DwC class "Organism"), it should not be represented as a property of an individual/organism, but rather as a property of an individual/organism at a particular point in time (which we represent as Occurrences).
This seems like a nit-pick, but if this conversation leads to changes
in DwC, I think it's important that we not allow it to lead to a step backwards.
Aloha, Rich
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participants (7)
-
Bryan -
Chuck Miller -
John Wieczorek -
Markus Döring -
Matt Yoder -
Richard Pyle -
Robert Guralnick