Topic 3: GUIDs for Taxon Names and Taxon Concepts

Donald Hobern dhobern at GBIF.ORG
Sun Oct 30 09:31:54 CET 2005


[ Another topic for comments.  Please keep the Topic number in responses. ]



Topic 3: GUIDs for Taxon Names and Taxon Concepts



Another key area in which TDWG has recognised the need for globally unique
identifiers is in connection with taxon names and the various concepts
associated with them.  This issue actually also intersects with that of
identifiers for taxonomic publications.



Definitions



In the following discussion, a "taxon name" is a scientific name string
which simply identifies a name assigned in the taxonomic literature.  In
many cases such a name may have been applied in different ways by the
original author and subsequent taxonomists.  Each such application of a
taxon name by a taxonomist to a set of organisms is here referred to as a
"taxon concept".  An understanding of the taxon concept adopted by a
researcher is frequently essential if data are to be interpreted correctly.
In its most basic form a "taxon concept" can be considered to be the use of
a given "taxon name" in a given "taxonomic publication", in other words
something that could be represented as, "Agenus aspecies Author1 Year1 sec.
Author2 Year2".    One possible approach to assigning identifiers to taxon
concepts would therefore be to assign identifiers to taxon names and to
taxonomic publications and to use a combination these identifiers to
identify each taxon concept.



Note that a taxon concept may be defined at least in part by a set of
assertions about the relationship between the present concept and the
concepts adopted by earlier taxonomists.  In addition it is possible for
other researchers to make their own assertions about the relationships
between the concepts published by different taxonomists.  Much of the
interest and value to be gained from modeling taxonomy relates to the
interpretation of these asserted relationships.



Although the distinction between taxon names and taxon concepts may seem
(over-)subtle, it is important that we should know whether we are referring
simply to a nomenclaturally valid name, quite independently of any set of
organisms to which it may be applied, or to a taxon concept which somehow
applies such a name to such a set of organisms.  Without this distinction,
we will be restricted in our ability to develop biodiversity informatics,
although of course there will be many cases in which all we can say is that
a data set refers to some unspecified taxon concept associated with a given
taxon name.



Identifiers



Clearly there are many situations in which a taxon name can itself be
treated as a unique identifier without any apparent ambiguity about which
name is being referenced (e.g. Turdus merula; Poa annua), but the existence
of homonyms prevents this from being generally true.  Even when taxon names
include citations of the original publications (e.g. Turdus merula Linnaeus,
1758; Poa annua L.), they can be very difficult to compare since the form of
the citations may vary greatly.  Even where there is no ambiguity about
which name is being referenced, such a name does not by itself serve to
identify which associated concept is being referenced.



There are many different systems in place for associating other identifiers
with either taxon names or taxon concepts.  ITIS (http://www.itis.usda.gov/,
http://www.cbif.gc.ca/pls/itisca, http://siit.conabio.gob.mx/) assigns
Taxonomic Serial Numbers (TSNs) to each name in its system.  Other species
databases have their own identifiers for taxon concepts.  Recording schemes
often have their own identifiers for taxa (e.g. Bradley and Fletcher numbers
for Lepidoptera in the UK, various systems of four-letter codes for North
American bird species).  These are often used to provide some stability and
clarity in the taxonomy used by a given project.



Questions



I would like therefore to ask the following questions of any of you who use
scientific names in your databases (either taxonomic databases recording a
list of taxa, or databases recording information about taxa, specimens,
observations, etc.):



1.      Is your data organised using taxon names or to taxon concepts?
2.      Do you assign any reusable identifiers to taxon names or concepts
(i.e. identifiers used in more than one database)?
3.      If so, what is the process in assigning new identifiers for
additional taxa and for accommodating taxonomic change?
4.      Where are these identifiers used (other organizations, databases,
data exchange, recording forms, etc.)?
5.      Do you use identifiers from any external classification within your
database?
6.      Would there be any social or technical roadblocks to replacing these
identifiers with a single identifier that was guaranteed to be unique?



As before I am looking for information on existing practices and any
requirements that would need to be accommodated within any general system of
identifiers.



Thanks,



Donald

---------------------------------------------------------------
Donald Hobern (dhobern at gbif.org)
Programme Officer for Data Access and Database Interoperability
Global Biodiversity Information Facility Secretariat
Universitetsparken 15, DK-2100 Copenhagen, Denmark
Tel: +45-35321483   Mobile: +45-28751483   Fax: +45-35321480
---------------------------------------------------------------




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<div class=3DSection1>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial'>[ <font color=3Dnavy><span =
style=3D'color:navy'>Another </span></font>topic<font
color=3Dnavy><span style=3D'color:navy'> </span></font>for comments. =
&nbsp;Please
keep the Topic number in responses<font color=3Dnavy><span =
style=3D'color:navy'>.</span></font>
]<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><b><font size=3D2 face=3DArial><span lang=3DEN-GB
style=3D'font-size:10.0pt;font-family:Arial;font-weight:bold'>Topic =
<font
color=3Dnavy><span style=3D'color:navy'>3</span></font>: <font =
color=3Dnavy><span
style=3D'color:navy'>GUIDs for Taxon Names and Taxon =
Concepts</span></font><o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Another key area in which TDWG has
recognised the need for globally unique identifiers is in connection =
with taxon
names and the various concepts associated with them.&nbsp; This issue =
actually
also intersects with that of identifiers for taxonomic =
publications.&nbsp; <o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><b><font size=3D2 color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial;color:navy;font-weight:bold'>=
Definitions<o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>In the following discussion, a
&#8220;taxon name&#8221; is a scientific name string which simply =
identifies a
name assigned in the taxonomic literature.&nbsp; In many cases such a =
name may
have been applied in different ways by the original author and =
subsequent
taxonomists.&nbsp; Each such application of a taxon name by a taxonomist =
to a
set of organisms is here referred to as a &#8220;taxon =
concept&#8221;.&nbsp; An
understanding of the taxon concept adopted by a researcher is frequently
essential if data are to be interpreted correctly.&nbsp; In its most =
basic form
a &#8220;taxon concept&#8221; can be considered to be the use of a given
&#8220;taxon name&#8221; in a given &#8220;taxonomic publication&#8221;, =
in
other words something that could be represented as, &#8220;<i><span
style=3D'font-style:italic'>Agenus aspecies</span></i> Author1 Year1 =
sec. Author2
Year2&#8221;.&nbsp;&nbsp;&nbsp; One possible approach to assigning =
identifiers
to taxon concepts would therefore be to assign identifiers to taxon =
names and
to taxonomic publications and to use a combination these identifiers to
identify each taxon concept.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Note that a taxon concept may be =
defined
at least in part by a set of assertions about the relationship between =
the
present concept and the concepts adopted by earlier taxonomists.&nbsp; =
In
addition it is possible for other researchers to make their own =
assertions
about the relationships between the concepts published by different
taxonomists.&nbsp; Much of the interest and value to be gained from =
modeling
taxonomy relates to the interpretation of these asserted =
relationships.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Although the distinction between =
taxon
names and taxon concepts may seem (over-)subtle, it is important that we =
should
know whether we are referring simply to a nomenclaturally valid name, =
quite
independently of any set of organisms to which it may be applied, or to =
a taxon
concept which somehow applies such a name to such a set of =
organisms.&nbsp;
Without this distinction, we will be restricted in our ability to =
develop biodiversity
informatics, although of course there will be many cases in which all we =
can
say is that a data set refers to some unspecified taxon concept =
associated with
a given taxon name.&nbsp;&nbsp; <o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><b><font size=3D2 color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial;color:navy;font-weight:bold'>=
Identifiers<o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Clearly there are many situations =
in which
a taxon name can itself be treated as a unique identifier without any =
apparent
ambiguity about which name is being referenced (e.g. <i><span =
style=3D'font-style:
italic'>Turdus merula</span></i>; <i><span =
style=3D'font-style:italic'>Poa annua</span></i>),
but the existence of homonyms prevents this from being generally =
true.&nbsp;
Even when taxon names include citations of the original publications =
(e.g. <i><span
style=3D'font-style:italic'>Turdus merula</span></i> Linnaeus, 1758; =
<i><span
style=3D'font-style:italic'>Poa annua</span></i> L.), they can be very =
difficult
to compare since the form of the citations may vary greatly.&nbsp; Even =
where
there is no ambiguity about which name is being referenced, such a name =
does
not by itself serve to identify which associated concept is being =
referenced.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>There are many different systems in =
place
for associating other identifiers with either taxon names or taxon
concepts.&nbsp; ITIS (<a =
href=3D"http://www.itis.usda.gov/">http://www.itis.usda.gov/</a>,
<a =
href=3D"http://www.cbif.gc.ca/pls/itisca">http://www.cbif.gc.ca/pls/itisc=
a</a>,
<a href=3D"http://siit.conabio.gob.mx/">http://siit.conabio.gob.mx/</a>) =
assigns
Taxonomic Serial Numbers (TSNs) to each name in its system.&nbsp; Other =
species
databases have their own identifiers for taxon concepts.&nbsp; Recording
schemes often have their own identifiers for taxa (e.g. Bradley and =
Fletcher
numbers for Lepidoptera in the <st1:country-region =
w:st=3D"on"><st1:place w:st=3D"on">UK</st1:place></st1:country-region>,
various systems of four-letter codes for North American bird =
species).&nbsp;
These are often used to provide some stability and clarity in the =
taxonomy used
by a given project.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><b><font size=3D2 color=3Dnavy face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial;color:navy;font-weight:bold'>=
Questions<o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>I would like therefore to ask the
following questions of any of you who use scientific names in your =
databases (either
taxonomic databases recording a list of taxa, or databases recording
information about taxa, specimens, observations, =
etc.):<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<ol style=3D'margin-top:0cm' start=3D1 type=3D1>
 <li class=3DMsoNormal style=3D'color:navy;mso-list:l1 level1 =
lfo3'><font size=3D2
     color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>Is
     your data organised using taxon names or to taxon =
concepts?<o:p></o:p></span></font></li>
 <li class=3DMsoNormal style=3D'color:navy;mso-list:l1 level1 =
lfo3'><font size=3D2
     color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>Do
     you assign any reusable identifiers to taxon names or concepts =
(i.e.
     identifiers used in more than one =
database)?<o:p></o:p></span></font></li>
 <li class=3DMsoNormal style=3D'color:navy;mso-list:l1 level1 =
lfo3'><font size=3D2
     color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>If
     so, what is the process in assigning new identifiers for additional =
taxa
     and for accommodating taxonomic =
change?<o:p></o:p></span></font></li>
 <li class=3DMsoNormal style=3D'color:navy;mso-list:l1 level1 =
lfo3'><font size=3D2
     color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>Where
     are these identifiers used (other organizations, databases, data =
exchange,
     recording forms, etc.)?<o:p></o:p></span></font></li>
 <li class=3DMsoNormal style=3D'color:navy;mso-list:l1 level1 =
lfo3'><font size=3D2
     color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>Do
     you use identifiers from any external classification within your =
database?<o:p></o:p></span></font></li>
 <li class=3DMsoNormal style=3D'color:navy;mso-list:l1 level1 =
lfo3'><font size=3D2
     color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>Would
     there be any social or technical roadblocks to replacing these =
identifiers
     with a single identifier that was guaranteed to be =
unique?<o:p></o:p></span></font></li>
</ol>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>As before I am looking for =
information on
existing practices and any requirements that would need to be =
accommodated
within any general system of identifiers.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Thanks,</span></font><font size=3D2
face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p=
>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial'>Donald<br>
&nbsp;<br>
---------------------------------------------------------------<br>
Donald Hobern (<a =
href=3D"mailto:dhobern at gbif.org">dhobern at gbif.org</a>)<br>
Programme Officer for Data Access and Database Interoperability <br>
Global Biodiversity Information Facility Secretariat <br>
Universitetsparken 15, DK-2100 <st1:place w:st=3D"on"><st1:City =
w:st=3D"on">Copenhagen</st1:City>,
 <st1:country-region =
w:st=3D"on">Denmark</st1:country-region></st1:place><br>
Tel: +45-35321483&nbsp;&nbsp; <st1:place w:st=3D"on"><st1:City =
w:st=3D"on">Mobile</st1:City></st1:place>:
+45-28751483&nbsp;&nbsp; Fax: +45-35321480<br>
---------------------------------------------------------------<o:p></o:p=
></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
lang=3DEN-GB
style=3D'font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>

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