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

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

"how to cite"

http://data.gbif.org/datasets/resource/240

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