Collection Documentation

1
Collection Documentation
Francisco Pando GBIF - Spain
2nd SYNTHESYS Course in Management, Conservation
and Care of Natural History Collections

• Madrid, 2 October 2007

2
Contents

• Definitions caveats
• General aspects
• Collection documentation
• Specimen documentation
• Wrap-up Check-list for good practices in
  documentation

3
Definitions

• Collection - a group of specimens or artifacts
  with like characteristics or a common base of
  association (e.g., geographic, donor, cultural)
• Specimen A natural object, part of a collection
  that is the basic unit of study and handling
• Documentation - supporting evidence, recorded in
  a permanent manner using a variety of media
  (paper, photographic, etc.), of the
  identification, condition, history, or scientific
  value of a specimen, artifact, or collection.
• This encompasses information that is inherent to
  the individual specimen and its associations in
  its natural environment as well as that which
  reflects processes and transactions affecting the
  specimen (e.g., accessioning, cataloging,
  loaning, sampling, analysis, treatment, etc.)..

4
Caveats

• Documentation is an integral aspect of the use,
  management, and preservation of a specimen, or
  collection
• Inherent value of documentation and archival
  records Evidence of the identification,
  condition, history, or scientific value of a
  specimen, artifact, or collection when recorded
  in a permanent manner enhances the value of the
  specimen.
• These records may actually have to substitute for
  the specimen or artifact should the specimens
  themselves deteriorate or be destroyed.
• Documentation is the responsibility of all
  individuals who use, prepare, manage, or care for
  specimens or artifacts. All techniques and
  materials used in collection management, care,
  and conservation must be fully documented.
• Methods and approaches presented here are
  strongly based on those used at the Real Jardín
  Botánico- CSIC, Madrid

5
The idea of the collection vision and mission
(purpose)

• Documentation as anything else in the
  collection must be guided by what we want the
  collection to be (vision) and what we have to do
  to make the the vision a reality (mission)
• Of course, collections conceptual framework
  exists within the context of the institution's
  mission and resources.

General aspects
6
Principles

• Documentation is documented metadata
  (authorship, time)
• Documentation is never destroyed amends are made
  by adding documentation no by replacing it
• Document everything (identification, condition,
  history, transactions, samplings,)
• Documentation is in everything (original labels,
  mounting materials, arrangement of specimens,)
• Precautionary principle

General aspects
7
Explicit and implicit knowledge

• Knowledge context, if you prefer-- is very
  elusive but vital for the best use of specimens
  and collections
• Documentation provides context
• IT tecnologies are bringing collection back to
  the front of science and societal matters, but in
  this process data gets decontextualized
• That makes documentation more important now than
  ever
• Go against the everybody knows that syndrome

General aspects
8
Collection (s.s.) documentation

• Adquisitions
• Collection Guide
• Annual Reports
• Visitors
• Communication
• Treatments incidents

9
Acquisitions

• Exchange
• Gift
• Deposit
• Purchase
• Permanent loan
• Who, when, special conditions
• Record and acknowledge

10
Example
http//www.rjb.csic.es/colecciones_herbario_cripto
.php
11
(No Transcript)
12
The Collection Guide"

• Arrangement
• Map
• Codes
• Catalogs, files, databases, publications
• Facilities
• Policy for handling specimens
• Procedures (opening hours, safety, sampling, etc.)

of course this is now a web site
13
References

• Arrangement
• E.g. Family arrangement follows Engler-Prantl
  Die natürlichen Pflanzenfamilien

14
Annual reports

• Compilation of major collection events
• Holdings
• Transactions (visitors, loans,..)
• Treatments (e.g. fumigation)
• New or changed procedures
• New or improved facilities
• Staff
• Report problems

think of it as a tool for you --or your
succesors-- rather that an annoying obligation
15
Visitors

• Visitors book
• Who, when, what

Computer application Who, when, what
16
Correspondence Record

• We have gone from paper communication to email
  in ten years. Archiving procedures have not gone
  in pace with this. Have they?

http//www.popularmechanics.com/technology/industr
y/4201645.html?
What do we do with email?
17
Treatments incidents

• Treatments
• Treatments
• Fumigation
• Climate control
• Poisoning
• Freezing

• When
• Supplier
• Product / equipment

• incidents
• Pests
• Other disasters

18
Specimen documentation

• Labels
• Cross-link specimens
• Labile data (color, smell, etc.)
• Destructive sampling and documentation
• Identifications
• Georeference
• Paper documentation
• Digital documentation

19
Labels

• taxonomic

• people (...)

• habitat / ecologic

• locality / distribution

• historic / phenologic

• molecular studies

20
Cross-link specimens
21
Labile data (color, smell, etc.)
22
Destructive sampling and documentation
23
Destructive sampling and documentation
24
Identifications explicit and implicit knowledge
name
who
when

25
Identifications what we are talking about

• Identifications, names, concepts (taxa)

from Nozomi Ytow al.
26
Example male fern
Fl. iberica Dryopteris filix-mas Dryopteris
affinis ssp. affinis ssp. borreri ssp.
stilluppensis Dryopteris oreades Dryopteris
submontana Dryopteris pallida ssp. pallida spp.
balearica Dryopteris carthusana Dryopteris
expansa Dryopteris dilatata
Fl. Països Catalans   Dryopteris austriaca ssp.
assimilis ssp. dilatata ssp. spinulosa   Dryopte
ris filix-mas ssp. borreri ssp. filix-mas ssp.
oreades   Dryopteris villarii ssp.
submontana ssp. balearica
27
Example names and concepts
Fl. iberica
Fl. Paisos Catalans
D. filix-mas
D. affinis
ssp. borreri
ssp. borreri
ssp. stilluppensis
spp. filix-mas
ssp. oreades
D. oreades
28
Where are we?

• To establish the meaning of an identification is
  at its best- an exercise of guesswork based
  upon implicit knowledge and assumptions
• This is a huge obstacle for the potential use of
  the collection, and thus an issue not to be
  dismiss.

29
We need to make explicit that information

• Who made the identification
• when
• Reliability
• Precision (identification qualifiers)
• Accuracy (? reference to a taxonomic framework)

30
Identification reliability (1)
From Australian National Fish Collection (in use
since 1993)

• Level 1 Highly reliable identification
• Specimen identified by (a) an internationally
  recognised authority of the group, or (b) a
  specialist that is presently studying or has
  reviewed the group in the Australian region.
• Level 2 Identification made with high degree of
  confidence at all levels
• Specimen identified by a trained identifier who
  had prior knowledge of the group in the
  Australian region or used available literature to
  identify the specimen.
• Level 3 Identification made with high confidence
  to genus but less so to species
• Specimen identified by (a) a trained identifier
  who was confident of its generic placement but
  did not substantiate their species identification
  using the literature, or (b) a trained identifier
  who used the literature but still could not make
  a positive identification to species, or (c) an
  untrained identifier who used most of the
  available literature to make the identification.
• Level 4 Identification made with limited
  confidence
• Specimen identified by (a) a trained identifier
  who was confident of its family placement but
  unsure of generic or species identifications (no
  literature used apart from illustrations), or (b)
  an untrained identifier who had/used limited
  literature to make the identification.
• Level 5 Identification superficial
• Specimen identified by (a) a trained identifier
  who is uncertain of the family placement of the
  species (cataloguing identification only), (b) an
  untrained identifier using, at best, figures in a
  guide, or (c) where the status expertise of the
  identifier is unknown.

31
Identification reliability (2)
From Chapman (2005) Principles of Data Quality.
GBIF

• Suggestion
• identified by World expert in the taxa with high
  certainty
• identified by World expert in the taxa with
  reasonable certainty
• identified by World expert in the taxa with some
  doubts
• identified by regional expert in the taxa with
  high certainty
• identified by regional expert in the taxa with
  reasonable certainty
• identified by regional expert in the taxa with
  some doubts
• identified by non-expert in the taxa with high
  certainty
• identified by non-expert in the taxa with
  reasonable certainty
• identified by non-expert in the taxa with some
  doubt
• identified by the collector with high certainty
• identified by the collector with reasonable
  certainty
• identified by the collector with some doubt.

32
Identification qualifier
close to
compare
group
section
sensu lato
species multae
series
sensu stricto
pro parte
doubt
Precision
based on ITF2, a TDWG standard (www.tdwg.org)
33
Accuracy (ref. to a taxonomy)
34
Georeference data

• Example
• Locality 2 nm NNE of North Head Light House off
  Sydney Heads
• Lat/Long -33.79916, 151.32054
• Datum WGS84
• GPS Accuracy 6 m
• Extent 50 m
• Remarks Garmin Etrex Summit GPS for coordinates
  and accuracy
  

35
Coordinates formats

Type Example
Degreesºminutes'seconds"NS Degreesºminutes'seconds"EW 30º50'15"N 2º30'10"W
-Degrees. Decimals - Degrees. Decimals 20.20 -2.80
UseZoneX100LetterY100LetterEastingNorthing 30TUV4050
UseZone Easting Northing 30T 440 4650

36
Datums

• Traditional Horizontal Datums

NAD 27
ED 50
(Clarke Ellipsoid )
(International Ellipsoid)
From US Navy (n.dat.)
37
Datum Shifts
38
Datum Shifts
39
Arthur D. Chapman et al. (2006)

• http//www.gbif.org/prog/digit/Georeferencing

40
Paper documentation

• Documentation is in everything original
  materials, arrangemenent of materials

41
Digital documentation

• one (card) index
• ? n-1 difficult tasks

• one database ? multiple indexing ? multiple uses

42
Digital documentation more than just storing it
43
Virtuality, reality and databases
Open issue To what extend shall the specimen
bear physically all the information generated on
it? e.g. Ref. to Genbank or specimen name vs.
Collection name
44
Virtuality, reality and databases
45
Documentation Data outlets in the digital era

• Collection website, GBIF, OBIS, REMIB,

• Conditions and provisos for use
• Feedback
• "how to cite"

46
Conditions and provisos for use
47
Feedback
Proporcionar al usuario la posibilidad de
reportar errores o comentarios

• http//data.gbif.org/occurrences/76377384/

48
"how to cite"
http//data.gbif.org/datasets/resource/240
49
Digital documentation images
http//www.gbif.es/imagenes_in.php
http//sciweb.nybg.org/science2/herbarium_imaging/

http//mcz-28168.oeb.harvard.edu/etypes/index.htm
50
Some common recommendations (1)

• Store metadata on images
• What?
• Technical data
• Color data
• Curatorial metadata (including IPR)
• Content metadata

Digital documentation images
51
Some common recommendations (2)

• Store metadata on images
• How?... standards
• EXIF (used by digital camera manufacturers
• DIG35 (xml industrial std.)International Imaging
  Industry Association
• Z39.87 (NISO std.) U.S.A.

Digital documentation images
52
Some common recommendations (3)

• Store metadata on images
• Where?
• a) Via database
• b) Within image file (EXIF specifications,
  JPEG2000)
• Not in the file name not in the folder name

Digital documentation images
53
Digital documentation backups

• Save all of your work in one place
• Create a DVD every (week, month)
• Setup off-site, on-line backup
• Test your backups

54
Digital documentation backups
Suggestion Working with two on-line backup
locations and save data to them everyday
alternatively
55
Check-list for good practices in documentation

• Know your Center /Institute Strategic Plan-
  Vision - Mission
• Vision and mission for the collection
• Collection guide
• Annual reports
• Specimen documentation
• -- Never throw away a label --
• What it is
• What it goes through
• Image repository with a documentation plan
• Backup system