ZBIG MEETING UNIVERSITY OF KANSAS(?) 1998 (?)

The AMNH Congo Expedition The AMNH Congo Expedition (1909-1915) (1909-1915)

“The Lang-Chapin Expedition”“The Lang-Chapin Expedition”

Colobus guereza or “Black & White Colobus”

DIGITAL @ AMNHThe Library American Museum of Natural History

AMNH Digital Library Project 2

Assessing...“Legacy Data”Assessing...“Legacy Data”

• 3 Billion Specimens in 6,500 natural history museums (Nature, 1998)

• Provides essential baseline for biodiversity • Major support available for national & regional

biodiversity studies (World Bank/GEF)• Museum data has not been comprehensively

applied/used (with a few exceptions…)


Assessing the Museum EnvironmentAssessing the Museum Environment

• Museum departments and their collections are defined by discipline (Anthropology,, Botany, Entomology, Paleontology, etc.)

• Museums are often decentralized & seldom organized in multi-disciplinary ways

• Data capture and processing typically occurs at individual-researcher or departmental level


Some possible definitions…Some possible definitions…

• “Data”: Observations, descriptions or measurements recorded and reported in some standard way…

• “Information”: Reasonable associations of data

• “Experience”: Personal or collective recollection and interpretation of events

• “Knowledge”: Rational assumptions derived from information and experience, presumed to be “true”and “reliable”

• “Expertise”: Individual or collective knowledge that is considered reliable by virtue of accomplishment


Collections trends at AMNH

Fishes

0

100000

200000

300000

400000

500000

600000

700000

1810

-181

9

1820

-182

9

1830

-183

9

1840

-184

9

1850

-185

9

1860

-186

9

1870

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9

1880

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9

1890

-189

9

1900

-190

9

1910

-191

9

1920

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9

1930

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9

1940

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9

1950

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9

1960

-196

9

1970

-197

9

1980

-198

9

1990

-199

920

00-

Decades 1810-2000

Spec

imen

s A

cqui

red


Collections trends at AMNH

Herps

0

10000

20000

30000

40000

50000

60000

1810

-181

9

1820

-182

9

1830

-183

9

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1860

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-191

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9

1950

-195

9

1960

-196

9

1970

-197

9

1980

-198

9

1990

-199

920

00-

Decades 1810-2000

Spec

imen

s A

cqui

red


Scientific SenateAd Hoc Committee of Data Access

Proposed Institutional Policy and Guidelineson Access to Collection-based Information

Preamble

Through their collections natural history institutions house a permanent record of theworld's biodiversity, earth history, and cultural change, as well as, in their libraries andarchives, a written record pertaining to these subjects.

These collections serve as essential resources for a broad user community, fromscientists and other scholars who seek to understand and interpret the naturalworld, to those concerned with preserving biological and cultural diversity, tocountries and peoples attempting to promote their well-being through sustainableuse and conservation of their natural resources, to societies in general througheducational outreach.

Because of the critical services that collections-based information provides to society, thecuratorial staff of the American Museum of Natural History endorses a policy thatmakes data freely available in a timely way to the user community, with restrictionsto be noted below.

Collection-based information

For the purposes of this document, collection information is defined to be those data(whether in electronic form or not) directly linked to the Museum's scientificcollections, including but not necessarily limited to specimen or object identification,provenance, and disposition, such as is provided by catalogs, label information,images and field notes deposited with collections, and other associated descriptors.

Excluded by this definition are unverified and preliminary data or notes as well asinterpretive data and conclusions that are derived from specimens/objects in the normalcourse of scientific and scholarly research. It is assumed that free, open, and timelyaccess to these kinds of data will result from standard avenues of scholarly publicationand dissemination.


1892-1996 Records

Source: Department of Herpetology, California Academy of Sciences (1999) (by permission)


1892-1996 + 1997-1998

Records

Source: Department of Herpetology, California Academy of Sciences (1999) (by permission)


AMNH Digital Library ProjectAMNH Digital Library Project

March 1999: Andrew W. Mellon Foundation Awards AMNH “Digital Library” Grant– Grant involves an 18 month “pilot phase” focused on

the AMNH “Lang-Chapin” Congo Expedition (1909-1915)

– second phase -- extends an additional 42 months and involves multiple “themes”


J.P. Morgan

William Rockefeller

Augustus Juilliard

Morris K. Jesup


James Chapin Herbert Lang


ArcView® GIS plot of collecting sites for the Lang-Chapin Expedition


Forminière [1909-1913]

in Archives, Tervuren Museum Brussels, Belgium

Geological site map sketched in Congo during Lang-Chapin era.


Source: Voss & Emmons, AMNH Bull. No. 230, 1996

(by permission: T. Erwin)

Recent site map from Peru

depicting elements of “collecting effort”


Biodiversity AssessmentBiodiversity Assessment

• Specimen Records

• Collecting/Observational Events

• “Collecting [sampling] Effort” in itself ( i.e. null results are significant)– pattern of sampling– comprehensive effort (collecting methodology)


Lang-Chapin Lang-Chapin Biological Collections at AMNHBiological Collections at AMNH

• Mammalogy 5800

• Ornithology 6200

• Herpetology 4800

• Ichthyology 6000

• Invertebrates 100,000+

• Botany (???)



(by permission)

Collecting Methods


Fishing Owl

The CongoAMNH Library Special Collections

Ceratogymna atrata / BLACK-CASQUED HORNBILL(Male in breeding season)

http://userwww.sfsu.edu/~parker/Parkerweb/media/pictures/bchmale.hot.jpg

Recording courtesy of Dr. Hans Slabbekoorn

Ctr for Trop. Res., San Francisco State University



(by permission)

CollectingCollecting Methods


Collecting Effort


SPATIAL

NOMINAL

CHRONOLOGIC

CONTEXT FOR NATURAL HISTORY INFORMATION


“Darwin Core” – Access Points

1. ScientificName2. Kingdom3. Phylum4. Class5. Order6. Family7. Genus8. Species9. Subspecies10. InstitutionCode11. CollectionCode12. CatalogNumber

13. Collector14.Year15.Month16.Day17.Country18.State/Province19.County 20. Locality 21. Longitude 22. Latitude 23. BoundingBox 24. Julian Day

Dave Vieglais Species Analyst 4/20/2000

http://habanero.nhm.ukans.edu/presentations/Gainesville_May2000_files/v3_document.htm


For resource discovery in specimen databases: For resource discovery in specimen databases: a a common denominator common denominator zoologicalzoological Specimen RecordSpecimen Record

Core descriptive elements:Collector [Person]Date [Chronologic]Place [Spatial]Name [Taxonomic]Institution/Collection [Instit. Address]Field Collection Code [discrete alphanum. string]

Accession (Catalog) Code[discrete alphanum. string]

Bibliographic [DOI/SICI?]


Barambo Chief

Hand-colored “Lantern Slide” taken from a Lang Negative

AMNH Library Special Collections


Mangebetu Hairpins

Anthropology Collection

Anthropological Artifacts


Watercolor by James ChapinOrnithology Archives


James Chapin in the fieldAMNH Library Special Collections


Field Notes from the Lang-Chapin Expedition

<?xml version="1.0"?> <document xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance" xsi:noNamespaceSchemaLocation="G:\DigitalLibrary\IT Working Group\XML\Sample_treatment.xsd"> <treatment taxon_level="species">

<nomenclature><taxon_name>Dimorphomyrmex andrei</taxon_name><authority>Emery, 1894: 73.</authority><history>(Later combinations: Aphomomyrmex andrei Emery, 1899: 494;

Cladomyrma andrei, Emery, 1925: 45). Syntype queen, BORNEO: Indonesia, South Kalimantan, Poulo Laut, Doherty; MCSN [examined].Cladomyrma cryptata Agosti, 1991: 304.Holotype queen, BORNEO: East-Malaysia, Sabah, Poring Hot Springs, 815, Ulrich Maschwitz, ex Callerya (=Millettia) nieuwenhuisii; BMNH. New syn.</history></nomenclature>


<treatment_body>

<diagnosis>Diagnosis: <morph>Major worker. AL 0.84-1.64, HL 0.86-1.42, HW 0.76-1.32, EL 0.16-0.30, SL 0.38-0.68, CI 89-98, EI 21-42, SI 44-53 (n = 8). Generally larger body size; pilosity and dorsum of alitrunk and gaster variable, generally short and not very dense; generally reddish dark brown to dark brown; clypeus angulate; gastral pubescence thin, hair at least as long as distance between their insertions.</morph>

<morph>Minor worker. AL 0.64-1.00, HL 0.59-1.04, HW 0.52-0.78, EL 0.13-0.22, SL 0.29-0.46, CI 83-95, EI 23-27, SI 55-66 (n = 8). Generally larger body size; pubescence on gaster dense, short, and appressed; metapleural gland orifice large.</morph><morph>Queen. AL 2.08-2.56, HL 1.30-1.46, HW 1.02-1.24, EL 0.47-0.54, SL 0.61-0.78, CI 76-86, EI 40-47, SI 58-66 (n = 17). Large body size (AL < 2.0 mm); body color usually dark brown to black (rarely uniform yellowish); head distinctly bicolored with genae and clypeus lighter than reminder of the head capsule; metapleural gland orifice large but covered with a bunch of hairs inserted ventral to the opening; petiole low and dorsally truncate; gaster with many long, erect hairs scattered all over the tergites and generally appressed, widely set pubescence. paratype: Queen AL 2.28, HL 1.36, HW 1.14, SL 0.68, EL 0.53, CI 84, EI 46, SI 60. </morph></diagnosis>


<comment>Comments: The species belongs to the larger Bornean species of Cladomyrma. At the same time, it is the most variable in size, in head shape from a very short to a medium long head, an almost black body color to brown (rarely uniform yellowish [one collection]), and long to short gastral hairs. The synonymy with cryptata indicates that the status of this species is similar to that of petalae (see below). Though there might be several species included, it is at the very moment impossible to separate them.The typical cryptata and andrei differ somewhat in the fine chagrinate sculpture on the head and the matte surface, which is very distinct in cryptata as opposed to the brilliant shining and completely smooth surface in andrei. The type series of cryptata includes one queen with a short head and one with an elongate head, which is similar to the type of andrei.Another variation includes workers from Poring Hot Springs (J. Moog, 95-018 and 95-017) which have a slightly elongated head, and very conspicuous long, heterogeneous hairs (some longer than others) on the dorsum of the alitrunk. In contrast, the workers of the typical andrei have subhomogeneous shorter setae. This variation is also the only population of andrei living in Drypetes longifolia (Euphorbiaceae). One collection (J. Moog, 93-061) shows a uniform yellowish-colored queen that closely resembles andrei (cryptata form) in most characters except body color. We observed a very slight difference in the density of the pubescence on the anterior and lateral parts of the mesonotum but since this character exhibits some variation in andrei, it was not used to erect a new species. Considerable variation in body color of queens may be a rather common phenomenon in Cladomyrma (see under petalae). </comment>


<biology_ecology>Biology and Distribution: The species has been found colonizing the endemic woody climbers Callerya (formerly Millettia) nieuwenhuisii (Maschwitz et al., 1989), Spatholobus oblongifolius (both Papilionaceae) and the tree genus Neonauclea (Rubiaceae). In general, liana saplings usually possess a primary stem diameter too thin to allow ant inhabitation. However, saplings of these host lianas (Callerya,Spatholobus) provide some stem internodes with distinctly enlarged diameter (ant domatia) to permit colonization by foundress queens (Moog et al., in press).</biology_ecology><distribution> In Poring Hot Springs, Sabah, samples of this species have been obtained on a canopy walkway from a huge Callerya, about 40m above ground. Its supposed that andrei is distributed over all of Borneo since the type specimen was collected in South Kalimantan (Poulo Laut). Most records are, however, from Sabah and Sarawak, but Kalimantan is poorly sampled.</distribution>


<materials_examined>Material Examined: type: INDONESIA, South Kalimantan, Poulo Laut, Doherty, MCSN, queen. other specimens: E-MALAYSIA, Sabah, Ranau, Poring Hot Springs, 11/14/1992, Brigitte Fiala, 0052, ex: Callerya (=Millettia) nieuwenhuisii; Sabah, Ranau, Poring Hot Springs, 1/22/1989, Ulrich Maschwitz, 0815, ex: Callerya (=Millettia) nieuwenhuisii; Sabah, Ranau, Poring Hot Springs, 1/28/1993, Joachim Moog, 93-061, ex: Callerya (=Millettia) nieuwenhuisii, alt.: ca. 600 m, colony size: 11 workers; Sabah, Ranau, Poring Hot Springs, 1/26/1995, Joachim Moog, 95-017, ex: Drypetes longifolia, young colony: ca. 200 workers in total, alt.: ca. 800 m; Sabah, Ranau, Poring Hot Springs, 1/26/1995, 95-018, Joachim Moog, ex: Drypetes longifolia, mature colony, alt.: ca. 800 m; Sabah, Ranau Poring Hot Springs, 5/2/1987, Burckhardt and Lobl; Sarawak, Lambir NP, Miri, 2/25/1992, Ulrich Maschwitz, 92-222, ex: Spatholobus oblongifolius; Sarawak, Lambir NP, Miri, 2/25/1992, Ulrich Maschwitz, 92-224, 92-224a and 92-224c, ex: Callerya (=Millettia) nieuwenhuisii; Sarawak, Lambir NP, Miri, 2/25/1992, U. Maschwitz, 92-227, ex: Callerya (=Millettia) nieuwenhuisii; Sarawak, Lambir NP, Miri, 2/17/1995, Joachim Moog, 95-060, ex: Spatholobus oblongifolius, mature colony. INDONESIA, Kalimantan, 11/14/1992, Brigitte Fiala, 0126, ex: Callerya (=Millettia) nieuwenhuisii; Kalimantan, Balikpapan, 11/16/1992, Brigitte Fiala, 0182, ex: Spatholobus oblongifolius.</materials_examined></treatment_body></treatment>


Bakango Fish TrapAMNH Library Special Collections


Congo River

Fishing PlatformAMNH Library Special Collections


CORC: Cooperative Online Resource Catalog

Access to museum

information through

standards and

international

cooperation.


ITIS*ca - Canadian version of

ITIS Integrated Taxonomic Information System

Taxon-based biological information system


AMNH Digital Library Infrastructure

• Hardware – SUN 250

• OS – Solaris Sun OS 2.6

• Database Environment– ORACLE 8i

• Interface– Web/XML– CD/DVD?

• Production/Scanning– MIX: In/Out-sourced

• Indexing/Cataloging

– Metadata Standards

• Bibliographic Utility

– OCLC/(CORC)

• Bibliographic Indices

– Zoological Record

• Integrated Online Library System(IOLS)

– Innovative Interfaces• (MOU on R&D)


A . W . M e llo n F o u n d a tio nA M N H D ig ita l L ib r a r y P r o je c t

A M N H W eb P ro g ra m(C o m m . & M a rk etin g )

E x tern a l D ig ita l L ib ra ryA d v iso rs /P a rtn ers /C o lla b o ra to rs

A M N H D ig ita lL ib ra ry W o rk in g G ro u p s

M ich elle K o oG IS S p ecia lis t (C o n tra cto r)

A M N H L ib ra ry A ssessm en t & E v a lu a tio nS a ra h Y ea tes /M a ry D eJ o n g

G o rd y S la ckC o n ten t D ev elo p er (C o n tra cto r)

A M N H L ib ra ry W eb D es ig n(M . D ejo n g )

A n th ro p o lo g y D ig itiza tio n P ro ject(O th er A M N H D ig ita l P ro jects )

A M N H M eta d a ta /C a ta lo g in g(R .B ru n o /D . S h ih )

A to n ia L o p ez d e V icto riaT ra n scrip tio n /D a ta E n try A sst.

A M N H N etw o rk S y stem s

D a n K a n ia ra sserilW eb /S erv er M a n a g er

J o h n A u b ryD a ta B a se M a n a g er

Isa b el M en d elso h nF ra n P o llitt

T ech n ica l A ss is ta m ts

M ik e M cC a ffreyW eb D es ig n er/J u n io r P ro g ra m m er

A n th o n y T ro n ca leD ig ita l C o llectio n s L ib ra ria n

S u sa n R a p p a p o rtA sst. D irecto r T ech n ica l S erv ices

T o m M o ritzB o esch en stein D irecto r L ib ra ry S erv ices

P rin cip a l In v estig a to r

Digital Library Process

Theme(s)

Content

Ownership(IPR)

Acquisition

Format Definitions

Conversion

Transcription

Arrangement

Storage

Mark-up

Metadata

Semantic Standards

(“authorities”)

Tagging

User Needs Assessment

Surveys

Focus Groups

Analysis

Data Modelling

Databasing

“Business Plan”

WorldWideWeb,

CD-ROM,

DVD

[Pre-processed &

On-demand]

FTP

printed reports and

Publications

Information Technology Infrastructure

AMNH Digital Library Project

AMNH

Digital Library Fundamental Tasks

Mark-up

Content-Formats

Metadata-Tags

Integrating Mechanisms

Access-Interfaces

Conversion to Digital

Clearances-IPR

WWW


AMNH DL: Publishing EnvironmentsAMNH DL: Publishing Environments

Digital Publishers (Digital Publishing Environments)

• BioOne (AIBS/SPARC/ ARL/

Allen Press/Univ. Kansas) • Highwire Press (Stanford)

• Columbia University Press ?

Digital Archives• JSTOR


Metadata is:Metadata is:

“Information which qualifies other information”

OR

“Data about other data”


AMNH DL: Cataloging EnvironmentAMNH DL: Cataloging Environment

Metadata Standards: • MARC • DC (CIMI) • GILS• FGDC• [ZR?/ “Dialog”?]

MARC Record

ID 10507973BASE DG STS n REC am ENC I DCF a ENT 960314INT REP GOV CNF 0 FSC 0 INX 1 CTY onc ILS abMEI FIC 0 BIO MOD CSC d CON b LAN eng PD 1995006 p <CAS>015 C95-980201-0 <DG>020 0660130734 : $c $45.00 Can. <DG,CAS>040 VXG $c VXG $d CUV <DG> 040 VXG $c VXG $d CSFA <CAS>041 0 engfre <DG,CAS> 043 n-cn--- <DG,CAS> 082 0 574.5/0971 $2 20 <DG>100 1 Mosquin, Theodore, $d 1932- <DG,CAS>245 10 Canada's biodiversity : $b the variety of life, its status, economic benefits,conservation costs, and unmet needs / $c by Ted Mosquin, Peter G. Whiting, and Don E.McAllister ; prepared for the Canadian Centre for Biodiversity, Canadian Museum ofNature. <DG,CAS>246 1 $i Title on diskette: $a Biodiversit_e du Canada : $b _etat actuel, avantages_economiques, co_uts de conservation et besoins non satisfaits <CAS>260 Ottawa, ON, Canada : $b Canadian Museum of Nature, $c c1995. <DG,CAS>300 xxiv, 293 p. : $b ill., maps ; $c 21 x 26 cm. <DG>300 xxiv, 293 p. : $b ill., maps ; $c 21 x 26 cm. + $e 1 computer disk (3 1/2 in.) <CAS>440 0 Henderson book series ; $v no. 23 <DG,CAS>500 "French text provided on diskette"--P. [4] of cover. <CAS>504 Includes bibliographical references (p. 259-286) and index. <DG,CAS>538 System requirements for diskette: WordPerfect 5.1, version MS-DOS. <CAS>650 0 Biological diversity $z Canada <DG,CAS>650 0 Biological diversity conservation $z Canada <DG,CAS>700 1 Whiting, Peter G. <DG,CAS>700 1 McAllister, D. E. <DG,CAS>710 2 Canadian Centre for Biodiversity <DG,CAS>CAS: 901 $aO$b34363082$cCAW 902 $a19960618224327.0 903 $aCAS 904$a19960618$b19960618$b19960618Hol: 920 $aCAWR 922 $aZCAS 924 $aCSFA 926 $aBiodiv 930 $aQH106$b.M67 1995 932$aRef. 935 1$lLI.96.100 DG: 901 $aV$b1374AKO$cDAVD 902 $a19980713093351.0 903$aDG 904 $a19980713$b19980713 910 $aocm34363082Hol: 920 $aCUVA 922 $aUCD 924 $aCU-A 926 $aShields 930 $cQH106.M67 1995


CIMI: Consortium for the Computer Interchangeof Museum Information

From Guide to Best Practice: Dublin Core (DC 1.0 =RFC 2413)

Final Version 12 August 1999

The 15 Dublin Core ElementsResource TypeFormatTitleDescriptionSubject and KeywordsAuthor or CreatorOther ContributorPublisherDateResource IdentifierSourceRelationLanguageCoverageRights


CIMI: Consortium for the Computer Interchange of Museum Information

Guide to Best Practice: Dublin Core (DC 1.0 = RFC 2413)Final Version (12 August 1999)

Example D-4 Record Describing a Natural History Specimen<?xml version=”1.0” ?><dc-record><type>physical object</type><type>original</type><type>natural</type><title>Prosorhynchoides pusilla</title><description>Specimen fixed in Berland's fluid and preserved in 80%

alcohol.</description><description>Prepared by: Taskinen, J.</description><description>Determiner: Gibson, D.I. </description><description>Determination date: 1993-08-21</description><subject>parasite</subject><subject>fluke</subject><subject>animal</subject><creator>Gibson D.I.</creator><contributor>Taskinen, J.</contributor><publisher>The Natural History Museum, London</publisher><date>1993-08-21</date><identifier>NHM 1994.1.19.1.</identifier><relation>IsPartOf Bucephalidae</relation><relation>Requires Esox lucius</relation><coverage>Battle River</coverage><coverage>Fabyan</coverage><coverage>Alberta</coverage><coverage>Canada</coverage><rights>http://www.nhm.ac.uk/generic/copy.html</rights></dc-record>


TAXONOMIC

ITIS ca ??

GEO-REFERENCINGAlexandria?Getty TGN?

SUBJECTTHESAURI(Controlled

Vocabularies)

CONTENT???

CIMI: Consortium for the Computer Interchange of Museum Information

Guide to Best Practice: Dublin Core (DC 1.0 = RFC 2413)Final Version (12 August 1999)

Example D-4 Record Describing a Natural History Specimen<?xml version=”1.0” ?><dc-record><type>physical object</type><type>original</type><type>natural</type><title>Prosorhynchoides pusilla</title><description>Specimen fixed in Berland's fluid and preserved in 80%

alcohol.</description><description>Prepared by: Taskinen, J.</description><description>Determiner: Gibson, D.I. </description><description>Determination date: 1993-08-21</description><subject>parasite</subject><subject>fluke</subject><subject>animal</subject><creator>Gibson D.I.</creator><contributor>Taskinen, J.</contributor><publisher>The Natural History Museum, London</publisher><date>1993-08-21</date><identifier>NHM 1994.1.19.1.</identifier><relation>IsPartOf Bucephalidae</relation><relation>Requires Esox lucius</relation><coverage>Battle River</coverage><coverage>Fabyan</coverage><coverage>Alberta</coverage><coverage>Canada</coverage><rights>http://www.nhm.ac.uk/generic/copy.html</rights></dc-record>


AMNH DL: Indexing EnvironmentAMNH DL: Indexing Environment

Subject Thesauri• Aq. Sci. & Fish. Abs.

(ASFIS)

• Art & Arch. Thesaurus (Getty)

• Conservation Thesaurus (IUCN)

• CABI

• GEOREF

• Zoological Record

Taxonomy• ITIS(US/Canada)

Geo-Referencing (Gazetteer)

• Alexandria Project (UCSB NCGIA

[NSF/DLI 1&2] )

• TGN (Getty)

ZBIG MEETING UNIVERSITY OF KANSAS(?) 1998 (?)

Education

Transcript of ZBIG MEETING UNIVERSITY OF KANSAS(?) 1998 (?)