Re: [tdwg-tag] canonicalScientificName
Sorry, forgot to include TAG mailing list.
On Tue, Mar 13, 2012 at 15:27, Peter Desmet peter.desmet@umontreal.ca wrote:
Hi everyone,
In a recent tweet [1] Roderic Page reminded me that in Darwin Core, we don't have a ready-to-use scientificName field. The definition for scientificName [2] asks for the full verbose name, including authors. I think this is a good definition (see below), but it also means that in a lot of use cases, names need to be parsed before they can be used or matched. I am currently helping collections publish their data for Candensys [3] and as a data producer I am happy we can provide all the information we have in scientificName, but as a data user, I get frustrated every time I see those long verbose botanical names with multiple authors. I am convinced that our data would be more usable if we had an additional canonicalScientificName term.
Which is why I am now officially requesting it on the Darwin Core code site: http://code.google.com/p/darwincore/issues/detail?id=150 (see below). This has been discussed in detail before [4], but no consensus was reached. I hope we can get our act together this time!
Regards,
Peter Desmet
--
[1] https://twitter.com/#!/rustyrussell22/status/179500954901692417 [2] http://rs.tdwg.org/dwc/terms/index.htm#scientificName [3] http://www.canadensys.net [4] http://lists.tdwg.org/pipermail/tdwg-content/2010-November/thread.html#1976
==New Term Recommendation== Submitter: Peter Desmet
Justification: The scientific name is probably the most used element of an occurrence/taxon, but currently Darwin Core does not provide a single ready-to-use-field for this. A canonicalScientificName with the scientific name as a uninomial, binomial or trinomial could solve this problem. The current terms are not sufficient:
- scientificName: verbose, used to record all components of a
scientific name (if available), including authorship(s) and rankmarker(s). It is critical to keep this definition, as this term is sometimes the only place to share certain information, e.g.: quadrinomials, intermediate botanical authors, hybrid formulas, etc. The disadvantage of only having this verbose notation is that the user needs to parse the name before he/she can use or match it.
- genus, specificEpithet, infraspecificEpithet: concatenated, this
terms are identical to the canonicalScientificName for genera, species and infraspecific taxa. For higher taxa or infrageneric taxa, these terms are not sufficient. In addition, there is some ambiguity regarding the genus definition: for synonyms, is it the accepted genus or the genus that is part of the synonym name? See: http://lists.tdwg.org/pipermail/tdwg-content/2010-November/002052.html. In the former case, the genus cannot be used to concatenate a canonicalScientificName.
The need for this term has been discussed thoroughly already (see: http://lists.tdwg.org/pipermail/tdwg-content/2010-November/thread.html#1976), but no consensus was reached. I'd like to reopen the discussion and I hope that a consensus can be reached quickly, so our data can be used more easily.
Definition: The scientific name as a uninomial, binomial or trinomial. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain authorship(s), rankmarker(s) or identification qualifications. If the scientific name cannot be expressed as a uni-, bi- or trinomial (e.g. hybrid formulas), do not use this term (use scientificName instead).
Comment: Examples: "Carex" (genus), "Vulpes vulpes" (species), "Anaphalis margaritacea occidentalis" (plant variety)
Refines:
Has Domain:
Has Range:
Replaces:
ABCD 2.06:
-- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net
Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada
Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet@umontreal.ca / peter.desmet.cubc@gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet
There has in the past been discussions about a term for this purpose (in fact I believe the proposed term was canonicalScientificName). It's been a few years, and it would take me some time to dig up the details, but my recollection of the conclusion of those discussions was along the lines of the following:
- When providers had only a "text blob" to represent the scientific name, with or without authorship, with or without rank abbreviations and formatting, etc., and these providers lacked the time, inclination, skills, and/or local data structure to parse these text blobs, then the scientificName term fulfilled their needs.
- When providers had a text blob for the name, separate from the text blob for the authorship, they could concatenate the two for presentation in scientificName, and also provide the authorship bit in scientificNameAuthorship, and the consumers could easily strip the authorship from scientificName to produce the functional equivalent of a canonical name.
- When providers did have the time, inclination, skills, and local data structure to parse these text blobs, the elements of a canonical name could be provided via the genus | subgenus | specificEpithet | infraspecificEpithet | taxonRank | verbatimTaxonRank terms, and the consumer could easily assemble these into a single string with canonical form.
This led to the conclusion that the addition of yet another term in the dwc:Taxon class would have provided very little benefit, at the cost of confusion about what information to provide in which term, and inconsistent use.
Aloha, Rich
Richard L. Pyle, PhD Database Coordinator for Natural Sciences Associate Zoologist in Ichthyology Dive Safety Officer Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef@bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html
Note: This disclaimer formally apologizes for the disclaimer below, over which I have no control.
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of Peter Desmet Sent: Tuesday, March 13, 2012 12:59 PM To: TDWG content mailing list; Roderic D. M. Page; TDWG TAG mailing list Subject: Re: [tdwg-content] canonicalScientificName
Sorry, forgot to include TAG mailing list.
On Tue, Mar 13, 2012 at 15:27, Peter Desmet peter.desmet@umontreal.ca wrote:
Hi everyone,
In a recent tweet [1] Roderic Page reminded me that in Darwin Core, we don't have a ready-to-use scientificName field. The definition for scientificName [2] asks for the full verbose name, including authors. I think this is a good definition (see below), but it also means that in a lot of use cases, names need to be parsed before they can be used or matched. I am currently helping collections publish their data for Candensys [3] and as a data producer I am happy we can provide all the information we have in scientificName, but as a data user, I get frustrated every time I see those long verbose botanical names with multiple authors. I am convinced that our data would be more usable if we had an additional canonicalScientificName term.
Which is why I am now officially requesting it on the Darwin Core code site: http://code.google.com/p/darwincore/issues/detail?id=150 (see below). This has been discussed in detail before [4], but no consensus was reached. I hope we can get our act together this time!
Regards,
Peter Desmet
--
[1] https://twitter.com/#!/rustyrussell22/status/179500954901692417 [2] http://rs.tdwg.org/dwc/terms/index.htm#scientificName [3] http://www.canadensys.net [4] http://lists.tdwg.org/pipermail/tdwg-content/2010-
November/thread.html
#1976
==New Term Recommendation== Submitter: Peter Desmet
Justification: The scientific name is probably the most used element of an occurrence/taxon, but currently Darwin Core does not provide a single ready-to-use-field for this. A canonicalScientificName with the scientific name as a uninomial, binomial or trinomial could solve this problem. The current terms are not sufficient:
- scientificName: verbose, used to record all components of a
scientific name (if available), including authorship(s) and rankmarker(s). It is critical to keep this definition, as this term is sometimes the only place to share certain information, e.g.: quadrinomials, intermediate botanical authors, hybrid formulas, etc. The disadvantage of only having this verbose notation is that the user needs to parse the name before he/she can use or match it.
- genus, specificEpithet, infraspecificEpithet: concatenated, this
terms are identical to the canonicalScientificName for genera, species and infraspecific taxa. For higher taxa or infrageneric taxa, these terms are not sufficient. In addition, there is some ambiguity regarding the genus definition: for synonyms, is it the accepted genus or the genus that is part of the synonym name? See: http://lists.tdwg.org/pipermail/tdwg-content/2010-
November/002052.html.
In the former case, the genus cannot be used to concatenate a canonicalScientificName.
The need for this term has been discussed thoroughly already (see: http://lists.tdwg.org/pipermail/tdwg-content/2010-
November/thread.html
#1976), but no consensus was reached. I'd like to reopen the discussion and I hope that a consensus can be reached quickly, so our data can be used more easily.
Definition: The scientific name as a uninomial, binomial or trinomial. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain authorship(s), rankmarker(s) or identification qualifications. If the scientific name cannot be expressed as a uni-, bi- or trinomial (e.g. hybrid formulas), do not use this term (use scientificName instead).
Comment: Examples: "Carex" (genus), "Vulpes vulpes" (species), "Anaphalis margaritacea occidentalis" (plant variety)
Refines:
Has Domain:
Has Range:
Replaces:
ABCD 2.06:
-- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net
Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada
Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet@umontreal.ca / peter.desmet.cubc@gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
This message is only intended for the addressee named above. Its contents may be privileged or otherwise protected. Any unauthorized use, disclosure or copying of this message or its contents is prohibited. If you have received this message by mistake, please notify us immediately by reply mail or by collect telephone call. Any personal opinions expressed in this message do not necessarily represent the views of the Bishop Museum.
In the original TCS it was
TaxonName/CanonicalName/Simple This field should contain only the words that form the name. It should not contain rank, authorship or any other qualifiers. For scientific names it will contain one, two or three words. For cultivated plant names it may contain more but any special characters, including the quotes round the cultivar epithet, should be omitted.
Jessie -----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Richard Pyle Sent: 14 March 2012 17:11 To: 'Peter Desmet'; 'TDWG content mailing list'; 'Roderic D. M. Page'; 'TDWG TAG mailing list' Subject: Re: [tdwg-content] canonicalScientificName
There has in the past been discussions about a term for this purpose (in fact I believe the proposed term was canonicalScientificName). It's been a few years, and it would take me some time to dig up the details, but my recollection of the conclusion of those discussions was along the lines of the following:
- When providers had only a "text blob" to represent the scientific name, with or without authorship, with or without rank abbreviations and formatting, etc., and these providers lacked the time, inclination, skills, and/or local data structure to parse these text blobs, then the scientificName term fulfilled their needs.
- When providers had a text blob for the name, separate from the text blob for the authorship, they could concatenate the two for presentation in scientificName, and also provide the authorship bit in scientificNameAuthorship, and the consumers could easily strip the authorship from scientificName to produce the functional equivalent of a canonical name.
- When providers did have the time, inclination, skills, and local data structure to parse these text blobs, the elements of a canonical name could be provided via the genus | subgenus | specificEpithet | infraspecificEpithet | taxonRank | verbatimTaxonRank terms, and the consumer could easily assemble these into a single string with canonical form.
This led to the conclusion that the addition of yet another term in the dwc:Taxon class would have provided very little benefit, at the cost of confusion about what information to provide in which term, and inconsistent use.
Aloha, Rich
Richard L. Pyle, PhD Database Coordinator for Natural Sciences Associate Zoologist in Ichthyology Dive Safety Officer Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef@bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html
Note: This disclaimer formally apologizes for the disclaimer below, over which I have no control.
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of Peter Desmet Sent: Tuesday, March 13, 2012 12:59 PM To: TDWG content mailing list; Roderic D. M. Page; TDWG TAG mailing list Subject: Re: [tdwg-content] canonicalScientificName
Sorry, forgot to include TAG mailing list.
On Tue, Mar 13, 2012 at 15:27, Peter Desmet peter.desmet@umontreal.ca wrote:
Hi everyone,
In a recent tweet [1] Roderic Page reminded me that in Darwin Core, we don't have a ready-to-use scientificName field. The definition for scientificName [2] asks for the full verbose name, including authors. I think this is a good definition (see below), but it also means that in a lot of use cases, names need to be parsed before they can be used or matched. I am currently helping collections publish their data for Candensys [3] and as a data producer I am happy we can provide all the information we have in scientificName, but as a data user, I get frustrated every time I see those long verbose botanical names with multiple authors. I am convinced that our data would be more usable if we had an additional canonicalScientificName term.
Which is why I am now officially requesting it on the Darwin Core code site: http://code.google.com/p/darwincore/issues/detail?id=150 (see below). This has been discussed in detail before [4], but no consensus was reached. I hope we can get our act together this time!
Regards,
Peter Desmet
--
[1] https://twitter.com/#!/rustyrussell22/status/179500954901692417 [2] http://rs.tdwg.org/dwc/terms/index.htm#scientificName [3] http://www.canadensys.net [4] http://lists.tdwg.org/pipermail/tdwg-content/2010-
November/thread.html
#1976
==New Term Recommendation== Submitter: Peter Desmet
Justification: The scientific name is probably the most used element of an occurrence/taxon, but currently Darwin Core does not provide a single ready-to-use-field for this. A canonicalScientificName with the scientific name as a uninomial, binomial or trinomial could solve this problem. The current terms are not sufficient:
- scientificName: verbose, used to record all components of a
scientific name (if available), including authorship(s) and rankmarker(s). It is critical to keep this definition, as this term is sometimes the only place to share certain information, e.g.: quadrinomials, intermediate botanical authors, hybrid formulas, etc. The disadvantage of only having this verbose notation is that the user needs to parse the name before he/she can use or match it.
- genus, specificEpithet, infraspecificEpithet: concatenated, this
terms are identical to the canonicalScientificName for genera, species and infraspecific taxa. For higher taxa or infrageneric taxa, these terms are not sufficient. In addition, there is some ambiguity regarding the genus definition: for synonyms, is it the accepted genus or the genus that is part of the synonym name? See: http://lists.tdwg.org/pipermail/tdwg-content/2010-
November/002052.html.
In the former case, the genus cannot be used to concatenate a canonicalScientificName.
The need for this term has been discussed thoroughly already (see: http://lists.tdwg.org/pipermail/tdwg-content/2010-
November/thread.html
#1976), but no consensus was reached. I'd like to reopen the discussion and I hope that a consensus can be reached quickly, so our data can be used more easily.
Definition: The scientific name as a uninomial, binomial or trinomial. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain authorship(s), rankmarker(s) or identification qualifications. If the scientific name cannot be expressed as a uni-, bi- or trinomial (e.g. hybrid formulas), do not use this term (use scientificName instead).
Comment: Examples: "Carex" (genus), "Vulpes vulpes" (species), "Anaphalis margaritacea occidentalis" (plant variety)
Refines:
Has Domain:
Has Range:
Replaces:
ABCD 2.06:
-- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net
Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada
Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet@umontreal.ca / peter.desmet.cubc@gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet
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*Sigh*
So what I'm hearing is people can't figure out how to use Darwin Core without getting confused about pretty much the most basic thing, the taxonomic name. And we're OK with that?!
In many ways I don't actually care about Darwin Core, all I want is for people to serve canonical names whenever they can (and if they actually want people to use their data without those people pulling their hair out).
Regards
Rod
On 14 Mar 2012, at 17:11, Richard Pyle wrote:
There has in the past been discussions about a term for this purpose (in fact I believe the proposed term was canonicalScientificName). It's been a few years, and it would take me some time to dig up the details, but my recollection of the conclusion of those discussions was along the lines of the following:
When providers had only a "text blob" to represent the scientific name, with or without authorship, with or without rank abbreviations and formatting, etc., and these providers lacked the time, inclination, skills, and/or local data structure to parse these text blobs, then the scientificName term fulfilled their needs.
When providers had a text blob for the name, separate from the text blob for the authorship, they could concatenate the two for presentation in scientificName, and also provide the authorship bit in scientificNameAuthorship, and the consumers could easily strip the authorship from scientificName to produce the functional equivalent of a canonical name.
When providers did have the time, inclination, skills, and local data structure to parse these text blobs, the elements of a canonical name could be provided via the genus | subgenus | specificEpithet | infraspecificEpithet | taxonRank | verbatimTaxonRank terms, and the consumer could easily assemble these into a single string with canonical form.
This led to the conclusion that the addition of yet another term in the dwc:Taxon class would have provided very little benefit, at the cost of confusion about what information to provide in which term, and inconsistent use.
Aloha, Rich
Richard L. Pyle, PhD Database Coordinator for Natural Sciences Associate Zoologist in Ichthyology Dive Safety Officer Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef@bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html
Note: This disclaimer formally apologizes for the disclaimer below, over which I have no control.
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of Peter Desmet Sent: Tuesday, March 13, 2012 12:59 PM To: TDWG content mailing list; Roderic D. M. Page; TDWG TAG mailing list Subject: Re: [tdwg-content] canonicalScientificName
Sorry, forgot to include TAG mailing list.
On Tue, Mar 13, 2012 at 15:27, Peter Desmet peter.desmet@umontreal.ca wrote:
Hi everyone,
In a recent tweet [1] Roderic Page reminded me that in Darwin Core, we don't have a ready-to-use scientificName field. The definition for scientificName [2] asks for the full verbose name, including authors. I think this is a good definition (see below), but it also means that in a lot of use cases, names need to be parsed before they can be used or matched. I am currently helping collections publish their data for Candensys [3] and as a data producer I am happy we can provide all the information we have in scientificName, but as a data user, I get frustrated every time I see those long verbose botanical names with multiple authors. I am convinced that our data would be more usable if we had an additional canonicalScientificName term.
Which is why I am now officially requesting it on the Darwin Core code site: http://code.google.com/p/darwincore/issues/detail?id=150 (see below). This has been discussed in detail before [4], but no consensus was reached. I hope we can get our act together this time!
Regards,
Peter Desmet
--
[1] https://twitter.com/#!/rustyrussell22/status/179500954901692417 [2] http://rs.tdwg.org/dwc/terms/index.htm#scientificName [3] http://www.canadensys.net [4] http://lists.tdwg.org/pipermail/tdwg-content/2010-
November/thread.html
#1976
==New Term Recommendation== Submitter: Peter Desmet
Justification: The scientific name is probably the most used element of an occurrence/taxon, but currently Darwin Core does not provide a single ready-to-use-field for this. A canonicalScientificName with the scientific name as a uninomial, binomial or trinomial could solve this problem. The current terms are not sufficient:
- scientificName: verbose, used to record all components of a
scientific name (if available), including authorship(s) and rankmarker(s). It is critical to keep this definition, as this term is sometimes the only place to share certain information, e.g.: quadrinomials, intermediate botanical authors, hybrid formulas, etc. The disadvantage of only having this verbose notation is that the user needs to parse the name before he/she can use or match it.
- genus, specificEpithet, infraspecificEpithet: concatenated, this
terms are identical to the canonicalScientificName for genera, species and infraspecific taxa. For higher taxa or infrageneric taxa, these terms are not sufficient. In addition, there is some ambiguity regarding the genus definition: for synonyms, is it the accepted genus or the genus that is part of the synonym name? See: http://lists.tdwg.org/pipermail/tdwg-content/2010-
November/002052.html.
In the former case, the genus cannot be used to concatenate a canonicalScientificName.
The need for this term has been discussed thoroughly already (see: http://lists.tdwg.org/pipermail/tdwg-content/2010-
November/thread.html
#1976), but no consensus was reached. I'd like to reopen the discussion and I hope that a consensus can be reached quickly, so our data can be used more easily.
Definition: The scientific name as a uninomial, binomial or trinomial. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain authorship(s), rankmarker(s) or identification qualifications. If the scientific name cannot be expressed as a uni-, bi- or trinomial (e.g. hybrid formulas), do not use this term (use scientificName instead).
Comment: Examples: "Carex" (genus), "Vulpes vulpes" (species), "Anaphalis margaritacea occidentalis" (plant variety)
Refines:
Has Domain:
Has Range:
Replaces:
ABCD 2.06:
-- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net
Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada
Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet@umontreal.ca / peter.desmet.cubc@gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
This message is only intended for the addressee named above. Its contents may be privileged or otherwise protected. Any unauthorized use, disclosure or copying of this message or its contents is prohibited. If you have received this message by mistake, please notify us immediately by reply mail or by collect telephone call. Any personal opinions expressed in this message do not necessarily represent the views of the Bishop Museum.
--------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK
Email: r.page@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 Skype: rdmpage AIM: rodpage1962@aim.com Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
So what I'm hearing is people can't figure out how to use Darwin Core without getting confused about pretty much the most basic thing, the taxonomic name. And we're OK with that?!
Hmmm. not sure what you mean. Do you mean that people who have parsed names aren't providing them using the appropriate fields? Or are people using terms incorrectly? Or....?
Rich
This message is only intended for the addressee named above. Its contents may be privileged or otherwise protected. Any unauthorized use, disclosure or copying of this message or its contents is prohibited. If you have received this message by mistake, please notify us immediately by reply mail or by collect telephone call. Any personal opinions expressed in this message do not necessarily represent the views of the Bishop Museum.
- When providers had a text blob for the name, separate from the text blob
for the authorship, they could concatenate the two for presentation in scientificName, and also provide the authorship bit in scientificNameAuthorship, and the consumers could easily strip the authorship from scientificName to produce the functional equivalent of a canonical name.
this does not work for autonyms in botany, i.e. the infraspecific taxa where the infraspecific epithet and the specific epithet are the same. Here the author is before the infraspecific epithet. Inconvenient, but prevents the simplest solution.
participants (5)
-
Gregor Hagedorn -
Kennedy, Jessie -
Peter Desmet -
Richard Pyle -
Roderic Page