Thanks, Chuck for this detailed response. You are quite right that we need
to be clear what we mean by "specimen". Your clarification of MOBOT's use
of identifiers shows not only that there are many identifiers in use, but
also they may apply to any in a series of increasingly refined objects (or
sets of objects), and that there are good reasons for wanting to be able to
identify each item in that series. If we think of this in software modeling
terms, each of these could be a separate object which could be manipulated
and referenced independently of the others.
Different communities within biological collections, will clearly have
different series of identifiable objects. For example an entomological
collection could have the following series:
(Survey?) -> Contents of an (malaise/light/water/etc.) trap -> Individual
insect -> Insect part (genitalia preparation, leg removed for DNA analysis)
-> (DNA preparation?)
Handling of plankton samples, culture collections and seedbank accessions
will be different again. Within botanical collections, is there any attempt
to indicate that two separate collecting events relate to the same plant or
clonal population?
Depending on the needs and purpose of an individual collection, it may track
different items in these series. Individual insects may be part of a
numbered series or have their own numbers.
As Chuck suggests, this means that it is not clear that we have a single
common definition of "specimen" that would be accepted by all of us. My use
of the word "subsample" and the phrase "identifiable set" in my original
question was an attempt to recognise that one group's specimen may be seen
by another group as just a part of a specimen or as a set of specimens. The
ABCD Schema uses the general term Unit to reflect the variation between
different items recorded by different providers.
It seems to me that there are various ways that we can try to handle this:
1. We could try to develop wording that explains what we agree to be a
reasonable shared definition of a specimen that can be applied by each
collection to select an appropriate identifier or require them to generate a
new one. This seems unlikely ever to be successful given the wide range of
situations, collections and databases that need to be covered.
2. We could let each provider give an indication of the nature of the
item being referenced (sample with multiple organisms, individual organism,
tissue, etc.; living material, dead material) using terminology that is
appropriate to their community. This may help human readers of the data to
interpret the data but does not allow us to reason reliably about the data
we receive. This is close to the approach followed today by Darwin Core
(BasisOfRecord) and the ABCD Schema (Unit/RecordBasis).
3. We could work as a community to develop and enforce a controlled
terminology for the nature of items referenced. By limiting the range of
terms that can be used, it should in many cases be possible to reason more
clearly about what each record describes.
4. We could go further and manage the controlled terminology as an
ontology that includes hierarchically-arranged definitions (e.g. a
CultureCollection isA LiveUnit, a HerbariumSheet isA DeadUnit) and other
relationships (e.g. a Tissue derivesFrom a DeadUnit). There would be more
work in doing this, but the BioMOBY project provides one example of how to
build such an ontology as an open community activity.
As we consider the use of GUIDs, I would really also like us to think about
the fourth of these options. Any "Unit" (or whatever else we may use as a
generic term for a biological item being recorded) can be identified as
belonging to a particular class of objects identified within a shared
ontology. We can do this by having an element whose value must be the
identifier for an object class registered in the ontology. This allows an
institution to make an assertion that one record relates to an individual
dead organism and that another relates to a tissue sample, and for those
assertions to be ones that software applications can process. Better still,
the presence of GUIDs for each of these records would allow us to add an
extra element to the tissue sample record that securely identifies the
specimen from which it was taken.
The bottom line here is that we certainly need to do some work to make sure
that we know what we are talking about when we speak of a "specimen" (or any
other similar term), but that we can use a combination of GUIDs and a shared
ontology to transcend the difficulties this could present, and to construct
subtle and informative webs of information.
Donald
---------------------------------------------------------------
Donald Hobern ( <mailto:dhobern@gbif.org> dhobern(a)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
---------------------------------------------------------------
_____
From: Taxonomic Databases Working Group GUID Project
[mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU] On Behalf Of Chuck Miller
Sent: 22 October 2005 00:40
To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU
Subject: Re: Topic 2: GUIDs for Collections and Specimens
I am responding to Donald's questions as they apply at Missouri Botanical
Garden.
As several have described, there are multiple layers of identification that
occur with specimens, particularly botanical specimens.
Our physical herbarium specimens are structured in a hierarchy, starting
from the original plant that was collected down to individual pieces with
labels.
COLLECTION
Identification begins at collection. Multiple "samples" are usually taken
from one plant or an entire small plant may be taken, a collector's number
is assigned to the sample in the collector's field book along with notes and
samples also numbered. Samples of other plants of the same kind may also be
taken with different numbers assigned to each in the field book and on the
sample. Samples may be made up of multiple pieces - leaves and stems,
fruits, seeds, bark, etc. - some may be dried, others left wet. All of the
pieces/samples of the one plant described in one numbered field book entry
belong to the one organism noted by the collector.
PREPARATION
The pieces of dried or wet samples are shipped back to MBG with their
identifying numbers. Nowadays, the information from the field book is
recorded in Tropicos including the collector's number. A unique TropicosID
number is assigned in database to the specimen or "sample" and the data from
the field book is recorded including the collector's name and number.
Accession numbers are assigned to each of the pieces of the sample that will
be "mounted" in a different way. A mounting sheet has the accession number
pre-printed on the sheet and the number applies to whatever is mounted on
the sheet. But, a separate large fruit from the same plant would be put in
a bag for instance and assigned a different accession number. Nowadays,
these accession numbers are also recorded in Tropicos. A label is printed
for the sheet and duplicate labels are printed for each of the related
"accessions". They are all the same label with the TropicosID and
collector's number on them.
DUPLICATES
Labels are also printed for the "duplicate" samples but no accession numbers
are assigned to them and they are not mounted. The duplicates may be sent
unmounted to specialists for determination or to other herbaria. The
identification of these samples/specimens is what is printed on the included
label - which includes Tropicos ID, Collector's Name and Collector's Number.
The receiving institution may or may not assign additional numbers, mount
the sample on a sheet, database it, etc. Totally up to them.
MOUNTING
The flat pieces are mounted on the sheets, large samples may require
multiple sheets for one copy. Large things (fruits, bark, branches) may be
put into bags or other holding methods. A barcode number is attached to the
sheet and any additional pieces/accessions and recorded in Tropicos. A
different barcode is on each piece or accession. So, barcodes have a
one-to-one match to accession numbers. The duplicate printed labels are
also attached to the sheet and any related pieces/accessions. If an
attached barcode comes off and is lost, a new, replacement barcode is
attached and updated in Tropicos.
The use of Lead Collector's Last Name and field book (also called catalog)
number is very common in botany - eg. CROAT 10100. The collector-number
method is frequently used in reference literature plus the addition of the
Index Herbariorium code for the institution where the specimen was seen or
gotten from. Duplicates of CROAT 10100 could be at MO, K, P, F, etc. and
those sheets may have different accession numbers or no accession number at
all.
Donald's Questions:
1. What identifiers (how many per specimen) get assigned to specimens
in your organisation or domain (field numbers, catalogue numbers, etc.)?
On one mounted specimen sheet at MBG are the following numbers/identifiers:
- Accession number (100% unique)
- Barcode number (100% unique)
- Tropicos ID (applies to all accessions and barcodes for one
sample/specimen)
- Collector's name and number (applies to all accessions, barcodes,
TropicosIDs, and duplicate samples/labels sent to other institutions from
the original collected organism)
All of these numbers are recorded in the Tropicos database.
2. What is the scope of uniqueness for each of these identifiers
(notebook page, collector, database, institution, global, etc.)?
I attempted to describe this above.
Collector's numbers are commonly unique to a collector and don't repeat
across notebooks, but the numbers are not unique themselves and are only
unique when combined with Collector's name
Accession numbers and barcodes are unique to the sheet/bag they are attached
to and are one-to-one with each other and are unique within the institution
TropicosID is unique within the database and the institution and is supposed
to be one-to-one with collector/collector number.
Lead collector last name plus number is unique within the database and
within the institution but not unique globally.
3. Can you explain the life cycle of each of these identifiers (who
assigns them, how they are subsequently tracked)?
Described at the beginning.
4. Can you give examples of how these identifiers are used to retrieve
the specimen and/or information on the specimen?
The primary search for specimens in Tropicos is by collector name and
number.
5. Would there be any social or technical roadblocks to replacing these
identifiers with a single identifier that was guaranteed to be unique?
Technically, it would require addition of an "alias" identifier and
additional programming to enable searching on the alias.
Since there are 4 identifiers in hierarchical relationship, which of them
could be the "single" identifier? This goes to my continuing question of
"what are we trying to identify"? The original specimen (and its
duplicates), a specific sheet, a specific part of a sheet, or part of a
specimen in an alcohol bottle separate from the sheet?
6. In the case of subsamples from a specimen, can you identify issues
around associating the sample and associated information with the source
specimen and associated information?
By subsample, are we referring to the occurrence of "duplicates" of the
original organism or rather to the pieces of it, like bark, fruit, leaves?
What constitutes the "specimen" versus the sample? We really need to
sharpen the language in these discussions to eliminate the round-robin
responses that occur as everyone states their opinion of what they think the
terms mean but no one decides exactly the definition to be used by everyone.
The biggest issue to me is that there are no standards for identification of
anything below the level of the original collecting event and even the
collector name + number is just a common practice in botany, not a
"standard" and not universal by any means. The term "accession" means
different things to different institutions. Accession number at MBG refers
to an associated part of a specimen, not the whole specimen. Does catalog
number mean the same thing everywhere? To some it means the collector's
number.
I suppose another issue is that because of the common practice in botany of
collecting duplicate samples and sending them around to other institutions,
any worldwide count of databased specimens that does not account for these
duplicates will overstate the real number.
The subject of specimen identifiers is somewhat linked to that of collection
identifiers, since Darwin Core and the ABCD Schema have used institution and
collection codes together with catalogue numbers to identify specimens in
the absence of GUIDs. It would also be useful here to collect information
on the following:
7. How are your specimens organised into larger identifiable sets
(collections, named collections, databases, institutions, etc.)?
We don't separate our collections into sets, they are all part of one
herbarium collection.
Accessions combine into one specimen.
Duplicate specimens can be at other institutions.
We do record the institutions where we know duplicates of a specimen are
located but we do not record the other institution's catalog numbers
8. What identifiers get assigned to each of these sets in your
organization or domain (institution codes, collection codes, Index Herbarium
acronyms, etc.)?
9. Can you explain the life cycle of each of these identifiers (who
assigns them, how they are subsequently tracked)?
10. Can you give examples of how these identifiers are used to locate
the set and/or information on the set?
11. Would there be any social or technical roadblocks to replacing these
identifiers with a single identifier that was guaranteed to be unique?
Previously discussed.
