/
ScientificName.txt
210 lines (129 loc) · 14.9 KB
/
ScientificName.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
%META:TOPICINFO{author="JohnWieczorek" date="1205673993" format="1.1" version="1.9"}%
%META:TOPICPARENT{name="DarwinCoreDraftStandard"}%
---++Element Description: Scientific Name
The full name of the lowest level taxon to which the organism has been identified in the most recent accepted determination, specified as precisely as possible, including name-author, year or authorship, sensu or sec. (according to or following) author, and indication of uncertainty. Conceptually equivalent to a full taxonomic identification as given by the identifier (verbatim). Does not include the identifier name or date of identification. Examples: "Coleoptera" (an Order), "Vespertilionidae" (a Family), "Manis" (a Genus), "Ctenomys sociabilis" (Genus + !SpecificEpithet), "Ambystoma tigrinum diaboli" (Genus + !SpecificEpithet + !SubspecificEpithet), "Quercus agrifolia var. oxyadenia (Torr.) J.T. Howell" (Genus + !SpecificEpithet + !InfraspecificRank + !InfraspecificEpithet + !AuthorYearOfScientificName).
---++++ Open Questions:
• Recommend that the !ScientificName element be populated without Author and Year information. (Munro, see comment immediately above). -- Main.JohnWieczorek (per D. Munro)- 10 Aug 2005
---++++ Change Log:
• 04 Aug 2005 - made minor wording changes in the description of !ScientificName (Wieczorek, con Ginzbarg).
---+++ Comments
Use the space below to make comments about this page. -- Main.StephenLong - 24 Aug 2006
------
%ICON{bubble}% *ScientificName*
Posted by: Steven Ginzbarg [mailto:sginzbar@biology.as.ua.edu] Date: Tue, 05 Oct 2004, 22:35:30
Since the separate name fields can be used for searching, the !ScientificName field, which might better be called !TaxonomicIdentificationVerbatim, should, in my opinion, be free to show the identification more precisely. Examples could show, in addition to names which can be concatenated from the separate name fields, hybrid formulas, named hybrids whose hybrid indicators should be omitted from the separate names, and names where cf. is used to refer to different ranks. At least the description should make it clear that it can contain more than concatenated name parts. The ABCD equivalent says “as fully as possible”.
------
%ICON{bubble}% *Recommendation* Posted by -- Main.JohnWieczorek (per D. Munro)- 10 Aug 2005
The older versions of Darwin core required the full name of the lowest level of the taxon only and did not include the author and year etc as suggested in the current draft. I strongly recommend retaining the older definition (without author year etc.). On our CBIF !DiGIR portal we hyperlink the !ScientificName field to our ITIS nomenclator and search will fail (we only search on the taxon name). As far as I have seen most online nomenclators work this way. Adding the authorship will required alot of rewriting of nomenclators. The authorship can be presented in a separate element and it is very easy to concatonate the two together in applications.
------
%ICON{bubble}% *Re: !ScientificName* Posted by -- sginzbar - 20 Nov 2005
If the parts of the name are provided, can the portal concatenate them into a new searchable field !ScientificNameWithoutAuthors? If not, then perhaps two elements are needed: the current !ScientificName renamed !TaxonomicIdentificationVerbatim which would correspond to ABCD 2.06 !FullScientificNameString and a !ScientificNameWithoutAuthors element.
------
------
%ICON{bubble}% *ScientificName*
Posted by: Steven Ginzbarg [mailto:sginzbar@biology.as.ua.edu] Date: Thu, 08 Jun 2006
The change to include authors in !DwC 2 was on my suggestion. It was for compatibility with ABCD where the corresponding field, !TaxonIdentified/ScientificName/FullScientificNameString has documentation:
Concatenated scientific name, preferrably formed in accordance with a Code of Nomenclature, _i. e._ a monomial, bionomial, or trinomial plus author(s) or author team(s) and - where relevant - year, or the name of a cultivar or cultivar group, or a hybrid formula, as fully as possible.
The rational was that the atomized elements are available for searching which leaves the !ScientificName field free to provide the verbatim taxonomic identification as completely as possible.
There has been the following subsequent discussion in the comments below the !DwC2 Documentation HTML table, http://darwincore.calacademy.org/Documentation/DarwinCore2Draft_v1-4_HTML: [Note: migrated to http://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreDraftStandard ]
------
<DL>
<DD> %ICON{bubble}% Re: !ScientificName
From: charlie Lapham [mailto:lapham@scrtc.com]; Sent: Thursday, June 08, 2006 12:24 PM
Subject: FW: !ScientificName
I’m forwarding a copy of a dialog I have going with Larry Spears and Arthur Chapman of GBIF. It has to do with what I consider excessive flexibility in the !DwC !ScientificName field.
Charles J. Lapham; 16 Winn School Rd; Glasgow, KY 42141; (270)-646-4060; lapham@scrtc.com
</DL>
------
<DL>
<DD> %ICON{bubble}% Re: !ScientificName
From: Larry Speers [mailto:lspeers@gbif.org]; Sent: Thursday, June 08, 2006 2:59 AM
Subject: RE: !ScientificName
Charlie-
Thanks for the explanation. Both Arthur and I agree you have raised some very interesting points and I will forward your query to the !DwC team and to the data interoperability group here at the secretariat for comment. ...
Larry Speers; Senior Programme Officer; Digitization of Natural History Collections; Global Biodiversity Information Facility; Universitetsparken 15; 2100 Copenhagen Ø
Denmark; Tel: +45 35 32 14 75; Fax: +45 35 32 14 80; Email: lspeers@gbif.org
</DL>
------
<DL>
<DD> %ICON{bubble}% Re: !ScientificName
From: charlie Lapham [mailto:lapham@scrtc.com]; Sent: 07 June 2006 17:59
Subject: RE: !ScientificName
The only required taxonomic filed in !DwC is the !ScientificName. Atomized data may, or may not, be provided. I agree with Arthur it should be and SERNEC will be doing this, but lots of folks aren’t.
My question is: Should this !ScientificName string include the author, or not, or does it even matter?.
I am building a global IUCN !T&E taxa table so folks can know what to dummy up for the net. Arthur Chapman’s how to dummy data up for the net project needs to have a companion what to dummy up list to go with it. ...
As things sit now we will need taxon without author (ICUN format), taxon with single author (ITIS format) and taxon with multiple authors (Plants format) to match what your providers are providing as you illustrated in your example. We will be linking taxon and country (ISO 3166 list) to set a rare taxa flag. ...
Providers want to be able to use what they have which varies with the institution. TDWG is currently on their side and their definition is wide open. If we don’t restrict some of these options, the current complications regarding taxon searches will become permanent. ...
I thought !ScientificName was being slightly restricted when the GBIF data cleaner (proposed, as I recall), was flagging taxon with author as an error in one of the examples Arthur Chapman used.
Charles J. Lapham
</DL>
------
<DL>
<DD> %ICON{bubble}% Re: !ScientificName
From: Larry Speers [mailto:lspeers@gbif.org]; Sent: Wednesday, June 07, 2006 7:16 AM
Subject: !ScientificName
Charles-
Dr. Edwards asked me to respond to your query concerning ‘best practices’ as to representing scientific names in the !DwC. I apologize for the delayed reply but I wanted to check with Arthur and the !DwC team to make sure we are on the same page.
I’m not too sure just what you are referring to as how the workshop at the SPNHC disagrees with the current !DwC documentation. As Arthur responded to my query:
“From my point of view and what I advocate in the Data Cleaning (and as given in Albuquerque at SPNHC) one should always atomize the taxonomic information into separate Genus/Species/Rank/Infraspecies/Author fields etc. wherever possible. As I see !DWC2 - the Scientific Name Field as given in the original enquiry is a concatenation of the other fields - _e.g._ Family, Genus, !SpecificEpithet, !InfraspecificRank, !InfraspecificEpithet, !AuthorYearOfScientificName, etc.
Because there is this atomization - I don't see !DWC2 at anyway in conflict with what I am advocating - just the opposite - it supports it. I would always advocate both storing information and exchanging it in atomized form wherever possible. Any exchange in concatenated form would be additional information.”
There was a change from !DwC 1 and !DcW 2 and the inclusion of the authority information but I have not spoken to the developers as to the reasons for this change.
When I posed your question to Dave Remsen from UBIO he was wondering if you were referring to author information associated with different levels of the hierarchy.
As he pointed out: “Many non-animal subspecific combinations cite authorship for both species and subspecific epithets and in this case separation of name and authority results in a loss of the species-level authority. Do plant people have a problem with this loss of information when it's passed?
ITIS refers to "_Quercus agrifolia_ var. _oxyadenia_ (Torr.) J.T. Howell"
USDA plants refers to "_Quercus agrifolia_ Née var. _oxyadenia_ (Torr.) J.T. Howell."
ITIS refers to "_Acacia angustissima_ var. _cuspidata_ (Schlecht.) L. Benson"
USDA plants refers to "_Acacia angustissima_ (P. Mill.) Kuntze var. _cuspidata_ (Schlecht.) L. Benson"
This variation is accepted in !DwC2. ...
Sincerely
Larry Speers
</DL>
------
<DL>
<DD> <UL> <L1>%ICON{bubble}% Re: !ScientificName From: Paul Kirk [mailto:p.kirk@cabi.org]; Sent: Thursday, June 08, 2006 22:42:53
in botanical (and mycological) nomenclature the USDA plants form (at the end of this mailing) is wrong and the ITIS form is correct. If homonyms are involved, unless they are at the same time taxonomic synonyms (in which case the discussion is irrelevant), an infraspecific epithet 'assigned' to the illegitimate name would be taxonomically incorrect and a correct name should be published if one is not already available.
Paul
------
<L2>%ICON{bubble}% Re: !ScientificName From: Steven Ginzbarg; Sent: Friday, June 09, 2006 05:19:45
I agree. Some may think it doesn't hurt to include the other authors but, if we are striving for one correct spelling of a taxon name, we should provide sufficient information and only the necessary information to make the name unambiguous. "Only one set of authors should be provided" should be included in the description of the !ScientificName element in a botanical Darwin Core module.
------
<L3>%ICON{bubble}% Re: !ScientificName From: Steven Ginzbarg; Sent: Friday, June 09, 2006 20:49:12
I could find nothing in the ICBN about including species authors in infraspecific names but none of the examples in the code include them. Omitting them is standard practice in zoology as well as in botany. I think they should be omitted when providing scientific names to GBIF. The description of the !ScientificName element in !DwC should say "Only the final set of authors should be included."
Paul wrote "an infraspecific epithet 'assigned' to the illegitimate name would be taxonomically incorrect". Taxonomically incorrect names are still given in synonymies. However the chances of an author creating a double homonym (same genus, same epithet, different species authors, same infraspecific epithet, same taxon author) are too remote to be concerned about.
We should be concerned about information retrieval. A search with the LIKE operator for "_Spigelia gentianoides_ var. _alabamensis_" will find "_Spigelia gentianoides_ var. _alabamensis_ K. Gould" and "_Spigelia gentianoides_ var. _alabamensis_ Gould" but not "_Spigelia gentianoides_ Chapman ex A. DC. var. _alabamensis_ K. Gould".
</UL> </DL>
------
<DL>
<DD> %ICON{bubble}% Re: !ScientificName From: charlie Lapham [mailto:lapham@scrtc.com]; Sent: Monday, June 05, 2006 4:38 PM
Subject: !ScientificName
Is the best practice to include the author in the scientific name or is it best not to include the author in the name?
The !DwC documentation at calacademy.org disagrees with Arthur Chapman’s error checking presentation at SPHNC.
Charles J. Lapham
</DL>
------
------
%ICON{bubble}% *Re: !ScientificName* Posted by -- Lynn Kutner [mailto: Lynn_Kutner@natureserve.org] Friday, 09 June 2006, 13:58:09
Just wondering how the proposed DWC2 and ABCD relate to the Taxonomic Concept Transfer Schema that was approved by TDWG in fall 2005?
http://tdwg.napier.ac.uk/index.php?pagename=HomePage
It may have already been done, but my thinking is that it would be helpful for other standards to begin to incorporate (or be compatible with) the Taxonomic Concept Transfer Schema.
Thanks -
Lynn Kutner; NatureServe; www.natureserve.org; (303) 541-0360; lynn_kutner@natureserve.org
------
%ICON{bubble}% *ScientificName* Posted by -- Charlie Lapham - 11 Jun 2006
!ScientificName can be in several formats now because the field is an unrestricted text field. It may or may not include authors in practice.
Authors are generarally abbreviated and the abbreviations are quite inconsistent. The !ScienficName, if it includes the author(s), is not very practical for search purposes.
There are vast differences between the IPNI author strings used by the IUCN and ITIS author strings. This does not mean the authors are incorrect, only that the strings don't match.
A better choice for the required taxonomy would be the atomized taxonomy fields. This would take care of the possibility of identical names in different kingdoms and this can be done without increasing the data entry time!
If you reformat the ITIS hierarchical database into into a flat file, it will write atomized taxonomy for you when you click on a taxon. I have code that does this. Plants is already in a flat file.
The same can probably be done for any atomized taxonomic reference.
The flat files, or taxonomic dictionaries, can be used for verification of manually entered taxonomy as well. If you record which one was used, you can use several dictionaries or make your own.
I have downloaded the IUCN Red List of rare taxa (global in scope and including 5 kingdoms). We need to link it to our taxonomy so we can flag rare taxa and not put precise location data on the net.
This will require greater consistency in the required taxonomy data in !DwC than we presently have.
We need to restrict country to the ISO 3166 Countries list at the same tme. It is currently only a suggestion.
Authors are probably a minor consideration in this context. If the only problem is an author mismatch, it probably better to err on the side of not listing precise data on the web until the discrepancy is resolved anyway.
Charlie Lapham
------
%ICON{bubble}% *Re: !ScientificName* Posted by -- Steven Ginzbarg - Monday, 26 Jun 2006, 02:38:08
The Taxonomic Concept Transfer Schema, http://tdwg.napier.ac.uk, voted a TDWG standard in 2005, includes "author given only for the lowest nomenclatural rank" in the description of the Simple element, !ScientificName complex type (TCSv1.01).
------
%ICON{bubble}%