Post on 20-Dec-2015
Collection Documentation
Francisco PandoGBIF - Spain
2nd SYNTHESYS Course in Management, Conservation and Care of Natural History Collections
Madrid, 2 October 2007
Contents
• Definitions & caveats• General aspects• Collection documentation• Specimen documentation• Wrap-up: Check-list for good
practices in documentation
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.)..
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
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, collection’s conceptual framework exists within the context of the institution's mission and resources.
General aspects
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
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
Collection (s.s.) documentation
• Adquisitions
• Collection Guide
• Annual Reports
• Visitors
• Communication
• Treatments & incidents
Acquisitions
• Exchange • Gift• Deposit• Purchase• Permanent loan• … • Who, when, special
conditions• Record and acknowledge
Examplehttp://www.rjb.csic.es/colecciones_herbario_cripto.php
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
References
• Arrangement• E.g.: Family arrangement follows Engler-
Prantl Die natürlichen Pflanzenfamilien
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
Visitors
Visitor´s book:Who, when, what
… Computer application:Who, when, what
Correspondence Record
We have gone from paper communication to email in ten years. Archiving procedures have not gone in pace with this. Have they?
What do we do with email?
http://www.popularmechanics.com/technology/industry/4201645.html?
Treatments & incidents
Treatments• Treatments• Fumigation• Climate control• Poisoning• Freezing
• When• Supplier• Product / equipment
incidents• Pests• Other disasters
Specimen documentation
• Labels• Cross-link specimens• Labile data (color, smell, etc.)• Destructive sampling and
documentation• Identifications• Georeference• Paper documentation• Digital documentation
Labels
• people (...)
• habitat / ecologic
• molecular studies
• historic / phenologic
• taxonomic
• locality / distribution
Cross-link specimens
Labile data (color, smell, etc.)
Destructive sampling and documentation
Destructive sampling and documentation
Identifications: explicit and implicit knowledge
name
who
when
…
Identifications: what we are talking about
• Identifications, names, concepts (taxa)
from Nozomi Ytow & al.
Example: male fernFl. 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
Dryopteris filix-mas
ssp. borreri
ssp. filix-mas
ssp. oreades
Dryopteris villarii
ssp. submontana
ssp. balearica
ssp. affinis
D. affinisD. filix-mas
spp. filix-mas
D. filix-mas
D. oreades
ssp. oreades
ssp. stilluppensis
ssp. borrerissp. borreri
Fl. iberica Fl. Paisos Catalans
Example: names and concepts
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.
We need to make explicit that information…
Who made the identificationwhen • Reliability • Precision (identification qualifiers)• Accuracy ( reference to a taxonomic
framework)
Identification reliability (1)
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.
From: Australian National Fish Collection (in use since 1993)
Identification reliability (2)
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.
From: Chapman (2005) Principles of Data Quality. GBIF
Identification qualifier
close to
compare
group
section
sensu lato
species multae
series
sensu stricto
pro parte
doubtPrecision
*based on ITF2, a TDWG standard (www.tdwg.org)”
Accuracy (ref. to a taxonomy)
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
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
Datums
Traditional Horizontal Datums
NAD 27(Clarke Ellipsoid )
ED 50(International Ellipsoid)
From US Navy (n.dat.)
Datum Shifts
Datum Shifts
Arthur D. Chapman et al. (2006)
http://www.gbif.org/prog/digit/Georeferencing
Paper documentation
• Documentation is in everything: original materials, arrangemenent of materials
• one database multiple indexing multiple uses
• one (card) index n-1 difficult tasks
Digital documentation
Digital documentation: more than just storing it
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
Virtuality, reality and databases
Documentation & Data outlets in the digital era
• Conditions and provisos for use • Feedback
• "how to cite"
Collection website, GBIF, OBIS, REMIB,…
Conditions and provisos for use
Feedback
http://data.gbif.org/occurrences/76377384/
Proporcionar al usuario la posibilidad de reportar errores o comentarios
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
Some common recommendations (1)
Store metadata on imagesWhat?
• Technical data• Color data• Curatorial metadata (including IPR)• Content metadata
Digital documentation: images
Some common recommendations (2)
Store metadata on imagesHow?... 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
Some common recommendations (3)
Store metadata on imagesWhere?
• a) Via database• b) Within image file (EXIF specifications,
JPEG2000)• Not in the file name; not in the folder
name
Digital documentation: images
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
Digital documentation: backups
Suggestion:Working with two on-line backup locations and save data to them everyday alternatively
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