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<div class="moz-cite-prefix">.... in my opinion, it would be worth
enhancing / adapting the Global Registry of Biological
repositories to have as distinct Museum IDs as possible. Also,
with a open system that allows various spellings / connotations,
it is possible to integrate e.g. various projects, previous museum
abbreviations (which should be kept for any reason), etc. <br>
<br>
In our fish collection we link voucher IDs & tissue IDs, e.g.
ZSM-PIS-043113 / P-AA-0338<br>
ZSM identifies the collection (based on the museum abbreviations
as in the Eschmeyer Catalog), PIS identifies the section "Pisces"
+ running number; tissues are identified by an unambiguous prefix
(P= section identifier, AA = project identifier + running number /
scan ID, etc.)<br>
<br>
In combination with a GUID or similar identifier, we would be able
to establish a unique identifier that would serve internal and
external (ABS) demands. All further IDs (Scan IDs of DNA-tubes,
GenBank numbers, etc.) should be associated to this master ID,
which - ideally - identifies corresponding vouchers (irrespective
if in lot based containers, sitting on individual pins, or still
stuck in unsorted batch samples).<br>
<br>
DNA-samples - as soon as they are extracted - need individual
sample IDs anyway, to allow identification of specimens
(regardless of the system applied, e.g. different barcode-scan
IDs, numbering, etc.). This also applies for bulk extractions of
multiple specimens or extractions out of storage fluids of
containers with multiple specimens, as (in most cases) you need to
log & link the resulting sequence to a single specimen (even
though you might want to save money & time while lumping and
processing samples together).<br>
<br>
Important in my view is, that the DNA-barcode IDs or any other IDs
created <u>by researchers</u> (= samples are accessioned at a
later point. i.e. after extraction) are 1) unambiguous, 2)
correspond to generated accession files and 3) are used as issued
for publication and e.g. GenBank uploads. This has not always been
the case (especially point 2), and earlier GenBank entries are a
good example for this (don't want to point to others here, just by
judging from own experiences from our DNA-repository).<br>
<br>
It might be worth to discuss this in more detail at one of the
next SPNHC meetings (Gainsville and/or Berlin), and perhaps to
launch a small workgroup that could present first ideas open for
discussion ?!?<br>
<br>
All the best<br>
Dirk <br>
<br>
<br>
Am 18.08.2014 23:53, schrieb Derek Sikes:<br>
</div>
<blockquote
cite="mid:CAFV61VGaEwopOniA4NFryYrB8x446hc88Dc_-gBqSzQCFOVW0w@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>Colin et al.<br>
<br>
</div>
I also think simple (dumb) numbers are best
for the reasons stated. We use 2D barcodes on
specimens and vials (e.g. UAM100057034).<br>
<br>
</div>
For lots we create a record in Arctos for each
identification. Thus a vial with three species,
12 specimens, becomes 3 Arctos records - each
with a part lot count, for example 1, 1, and 10.
All share the container 'vial' which has a
barcode. Each record gets a GUID like:<br>
<br>
UAM:Ento:247065<br>
<br>
</div>
Thus the GUIDs denote records (identifications),
the barcodes are for the containers the parts are
in (or in the case of pins, on).<br>
<br>
</div>
<div>Therefore, 10,000 of our vials might represent
30,000 records if there is an average of 3 taxa
identified per vial. (This is common for projects
with lots of specimens, we only mount on pins or
otherwise isolate a representative series of each
taxon).<br>
</div>
<div><br>
</div>
Preparations / parts (eg a leg in a cryovial) are
listed under the single GUID with each container
getting its own barcode. In many cases we have just
one part 'whole organism'. A single specimen (one
GUID) could have 3 parts (3 barcodes): body,
cryovial leg, and genitalia slide.<br>
<br>
</div>
<div>So a single container (barcode) can have multiple
taxa (GUIDs) and a single specimen can have multiple
barcoded containers.<br>
</div>
<div><br>
</div>
I like this way of managing bulk samples. For example,
a trap sample can be entered simply as one record
'Arthropoda' or, if inspected, a separate record for
each identification in the sample (Coleoptera,
Hemiptera, Hymenoptera, etc) can be made. This allows
this sample to be found if someone is searching for
any of these taxa.<br>
<br>
If all the Coleoptera are then removed from the sample
and pinned, the Coleoptera record from the bulk trap
sample can be turned into a pinned specimen record and
cloned to make all the remaining pinned specimen
records.<br>
</div>
</div>
<br>
</div>
<div>We are just now loaning out a long series of pinned
flies that have phoretic or parasitic mites on them. Each
pinned fly has two records in Arctos - one for the fly and
one for the mites. Both share the container 'pin' with a
shared barcode. If the mites get moved to a vial or slide,
their barcodes will change. Relationships between the fly
and mite will link these records together, for example a
beetle related to a vial of mites <a
moz-do-not-send="true"
href="http://arctos.database.museum/guid/UAM:Ento:104251">http://arctos.database.museum/guid/UAM:Ento:104251</a><br>
<br>
It can become difficult to isolate a single specimen of a
single taxon that has multiple specimens in a container
(eg 10 of the same spider species).<br>
</div>
<br>
</div>
For spiders in vials (eg 10 specimens of 1 species) that we
DNA barcode, rather than make a new vial (which would require
a new database record, new label, etc). We put the spider from
which a leg was removed inside a genitalia vial inside the
larger vial and a new small label that indicates the spider in
the genitalia vial is a DNA barcode voucher. If the spider is
too large for this we do transfer it to a new vial. We have
plans to move all our specimens that were successfully DNA
barcoded to cryovials into our -70 freezers to better preserve
their remaining genomic material.<br>
<br>
</div>
-Derek<br>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div><br>
+++++++++++++++++++++++++++++++++++<br>
Derek S. Sikes, Curator of Insects<br>
Associate Professor of Entomology<br>
University of Alaska Museum<br>
907 Yukon Drive<br>
Fairbanks, AK 99775-6960<br>
<br>
<a moz-do-not-send="true"
href="mailto:dssikes@alaska.edu">dssikes@alaska.edu</a><br>
<br>
phone: 907-474-6278<br>
FAX: 907-474-5469<br>
<br>
University of Alaska Museum -<br>
<a moz-do-not-send="true"
href="http://www.uaf.edu/museum/collections/ento/">http://www.uaf.edu/museum/collections/ento/</a><br>
+++++++++++++++++++++++++++++++++++<br>
<br>
Interested in Alaskan Entomology? Join the
Alaska Entomological<br>
Society and / or sign up for the email
listserv "Alaska Entomological Network" at<br>
<a moz-do-not-send="true"
href="http://www.akentsoc.org/contact.php">http://www.akentsoc.org/contact.php</a><br>
<div><br>
<br>
<div>
<div><br>
<br>
<div>
<div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On
Mon, Aug 18, 2014 at 6:28
AM, Chuck Miller <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Chuck.Miller@mobot.org"
target="_blank">Chuck.Miller@mobot.org</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px
solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="white"
link="blue"
vlink="purple"
lang="EN-US">
<div>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">Dirk,</span></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">There’s
a start on a
unique museum
identifier
repository at the
</span><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"
lang="EN">Global
Registry of
Biological
Repositories
(GRBio) at <a
moz-do-not-send="true"
href="http://www.grbio.org/" target="_blank">www.grbio.org</a></span><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">.
But it is
currently focused
on
biological/biodiversity
collections.</span></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">Chuck</span></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><i><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">Chuck
Miller | VP-IT
& CIO |
Missouri
Botanical Garden</span></i></p>
<p class="MsoNormal"><i><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">4344
Shaw Boulevard |
Saint Louis, MO
63110 | Phone <a
moz-do-not-send="true" href="tel:314-577-9419" value="+13145779419"
target="_blank">314-577-9419</a></span></i><i><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"></span></i></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"> </span></p>
<div>
<div
style="border-width:1pt
medium
medium;border-style:solid
none
none;border-color:rgb(181,196,223)
-moz-use-text-color
-moz-use-text-color;padding:3pt
0in 0in">
<p
class="MsoNormal"><b><span
style="font-size:10pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span
style="font-size:10pt;font-family:"Tahoma","sans-serif";color:windowtext">
<a
moz-do-not-send="true"
href="mailto:nhcoll-l-bounces@mailman.yale.edu" target="_blank">nhcoll-l-bounces@mailman.yale.edu</a>
[mailto:<a
moz-do-not-send="true"
href="mailto:nhcoll-l-bounces@mailman.yale.edu" target="_blank">nhcoll-l-bounces@mailman.yale.edu</a>]
<b>On Behalf
Of </b>Dirk
Neumann<br>
<b>Sent:</b>
Monday, August
18, 2014 4:03
AM<br>
<b>To:</b> <a
moz-do-not-send="true" href="mailto:nhcoll-l@mailman.yale.edu"
target="_blank">nhcoll-l@mailman.yale.edu</a></span></p>
<div class=""><br>
<b>Subject:</b>
Re: [Nhcoll-l]
Unique IDs for
museum objects
versus specimens</div>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal">Hi
all,</p>
<div>
<div class="h5"><br>
<br>
don't want to
add lengthy
comments, so
just briefly:<br>
<br>
The entering
into force of
the Nagoya
Protocol
stipulates
specific
reporting
requirements,
for those <b>collections
based in
countries that
ratified the
NP</b>. Among
other, <b><i>unique
identifiers</i></b><i>
</i>allowing
tracing and
origin of
genetic
resources <b>should
be applied
soon.</b>
Application of
unique
identifiers will
be part of and
further detailed
in the reporting
obligations of
respective
countries.<br>
<br>
To confirm
previous
comments: yes,
we do need a
flexible system
that allows
application of <i>unique
identifiers</i>
to identify
batch samples,
unsorted
materials, etc.
and <i>unique</i>
should not be
confused with
identifiers for
individual
specimens (as
some political
decision makers
did during
discussions
towards the
European
ABS-legislation).<br>
<br>
Unique
identifiers
should be unique
- many molecular
barcoding /
digitalisation
projects apply
various kinds of
barcodes,
without testing
if these are
really unique (a
high probability
rate that
barcodes would
surely be not
duplicated is
not sufficient
in this
context).<br>
<br>
Any barcode or
decimal
numbering is <b><i>not
unique</i></b>,
because
"123456.077"
might appear as
number in
various
collections or
museums, may
perfectly
translates into
other types of
numberings (e.g.
telephone /
insurance /
account
numbers), and
even adding an
abbreviation for
the institute ,
e.g.
INST-123456.077
might <br>
a) not result in
a be unique ID
inside this
museum, e.g. if
various
collections /
sections inside
this museum use
a similar
numbering
system, e.g.
compinations of
accession dates
& specimen
numbers, as John
suggested
(2014.11.3)<br>
b) not be unique
globally for
natural history
specimens,
unless we do
have a
obligatory list
of Museum
abbreviations
that excludes
any duplications<br>
<br>
Similar applies
e.g. for GenBank
numbers; GenBank
numbering might
be unique inside
GenBank, but the
encoding does
not allow to
decipher in
which collection
the
corresponding
specimen is
deposited. <br>
<br>
This adds an
second field
that should be
considered in
this discussion,
how can we link
<i>unique
identifiers </i>with
<i>unique museum
references.</i>
We need a kind
of master ID,
especially for
the tissue and
DNA collections
and publication
of samples
stored in these
collections.<br>
<br>
Sadly, this
receives limited
attention at the
moment, even
though many
barcoding &
digitisation
projects outbid
each other to
gather &
publish specimen
data. I would
appreciate if we
could enter a
active
discussion how
to deal with
this.<br>
<br>
All the best<br>
Dirk <br>
<br>
<br>
<br>
<br>
Am 14.08.2014
22:55, schrieb
Colin Favret:</div>
</div>
</div>
<div>
<div class="h5">
<blockquote
style="margin-top:5pt;margin-bottom:5pt">
<div>
<div>
<p
class="MsoNormal">
<span
style="font-family:"Verdana","sans-serif"">Thank
you to
everyone
participating
in this
interesting
discussion.
I'm at least
relieved to
know that
there is no
community
standard, yet,
and so I'm not
off kilter
having
developed my
own solution.
As I
understand it,
palaeontologists
assign
separate
unique
identifiers to
the different
fossil
specimens
in/on a single
object (?).
And Specify
seeks a
solution to
disambiguate
"Containers"
from
specimens.</span></p>
</div>
<div>
<p
class="MsoNormal"><span
style="font-family:"Verdana","sans-serif""> </span></p>
</div>
<div>
<p
class="MsoNormal"><span
style="font-family:"Verdana","sans-serif"">But
unique
identifiers
referring to
museum objects
or specimens
are not "dumb"
in the same
way that they
are for
localities,
collection
events, taxa,
etc. They
refer to
physical
objects
located in a
collection
that bear a
label with
that unique
identifier.
That unique
identifier is
thus part of
the object
retrieval
process for
collection
users, in
addition to
being for data
retrieval.</span></p>
</div>
<div>
<p
class="MsoNormal"><span
style="font-family:"Verdana","sans-serif""> </span></p>
</div>
<div>
<p
class="MsoNormal"><span
style="font-family:"Verdana","sans-serif"">So can we
envision a
system where
the unique
identifier for
the 77th
specimen on a
microscope
slide can also
be used as
part of the
object
retrieval
process? Or
have we
decided that,
given a unique
identifier for
the 77th
specimen, I'm
better off
having to go
to the
database to
reference the
museum
object's ID
before heading
into the
compactors?
Does anyone
have a
significant
objection to
the decimal
INST-123456.077
to uniquely
refer to the
77th specimen
in/on museum
object
INST-123456?</span></p>
</div>
<div>
<p
class="MsoNormal"><span
style="font-family:"Verdana","sans-serif""> </span></p>
</div>
<div>
<p
class="MsoNormal"><span
style="font-family:"Verdana","sans-serif"">Thanks
for the
continued
discussion!</span></p>
</div>
<div>
<p
class="MsoNormal"><span
style="font-family:"Verdana","sans-serif""> </span></p>
</div>
<div>
<p
class="MsoNormal"><span
style="font-family:"Verdana","sans-serif"">Colin</span></p>
</div>
</div>
<p
class="MsoNormal"><br>
<br>
<br>
</p>
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<pre>society. See <a moz-do-not-send="true" href="http://www.spnhc.org" target="_blank">http://www.spnhc.org</a> for membership information.</pre>
</blockquote>
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<br>
<br>
</p>
<pre>-- </pre>
<pre>Dirk Neumann</pre>
<pre> </pre>
<pre>Tel: 089 / 8107-111</pre>
<pre>Fax: 089 / 8107-300</pre>
<pre>email: Dirk.Neumann(a)<a moz-do-not-send="true" href="http://zsm.mwn.de" target="_blank">zsm.mwn.de</a></pre>
<pre> </pre>
<pre>Postanschrift:</pre>
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<pre>Staatliche Naturwissenschaftliche Sammlungen Bayerns</pre>
<pre>Zoologische Staatssammlung München</pre>
<pre>Dirk Neumann, Sektion Ichthyologie / DNA-Labor</pre>
<pre>Münchhausenstr. 21</pre>
<pre>81247 München</pre>
<pre> </pre>
<pre>Besuchen Sie unsere Sammlung:</pre>
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<pre> </pre>
<pre>---------</pre>
<pre> </pre>
<pre>Dirk Neumann</pre>
<pre> </pre>
<pre>Tel: <a moz-do-not-send="true" href="tel:%2B49-89-8107-111" value="+49898107111" target="_blank">+49-89-8107-111</a></pre>
<pre>Fax: <a moz-do-not-send="true" href="tel:%2B49-89-8107-300" value="+49898107300" target="_blank">+49-89-8107-300</a></pre>
<pre>email: Dirk.Neumann(a)<a moz-do-not-send="true" href="http://zsm.mwn.de" target="_blank">zsm.mwn.de</a></pre>
<pre> </pre>
<pre>postal address:</pre>
<pre> </pre>
<pre>Bavarian Natural History Collections</pre>
<pre>The Bavarian State Collection of Zoology</pre>
<pre>Dirk Neumann, Section Ichthyology / DNA-Lab</pre>
<pre>Muenchhausenstr. 21</pre>
<pre>81247 Munich (Germany)</pre>
<pre> </pre>
<pre>Visit our section at:</pre>
<pre><a moz-do-not-send="true" href="http://www.zsm.mwn.de/ich/" target="_blank">http://www.zsm.mwn.de/ich/</a></pre>
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<br>
<br>
<pre class="moz-signature" cols="72">--
Dirk Neumann
Tel: 089 / 8107-111
Fax: 089 / 8107-300
email: Dirk.Neumann(a)zsm.mwn.de
Postanschrift:
Staatliche Naturwissenschaftliche Sammlungen Bayerns
Zoologische Staatssammlung München
Dirk Neumann, Sektion Ichthyologie / DNA-Labor
Münchhausenstr. 21
81247 München
Besuchen Sie unsere Sammlung:
<a class="moz-txt-link-freetext" href="http://www.zsm.mwn.de/ich/">http://www.zsm.mwn.de/ich/</a>
---------
Dirk Neumann
Tel: +49-89-8107-111
Fax: +49-89-8107-300
email: Dirk.Neumann(a)zsm.mwn.de
postal address:
Bavarian Natural History Collections
The Bavarian State Collection of Zoology
Dirk Neumann, Section Ichthyology / DNA-Lab
Muenchhausenstr. 21
81247 Munich (Germany)
Visit our section at:
<a class="moz-txt-link-freetext" href="http://www.zsm.mwn.de/ich/">http://www.zsm.mwn.de/ich/</a>
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