Synthesis and Integration in the Natural History Commons

@ AAAS 2004

American Association for the Advancement of Science Seattle, WashingtonFebruary 16, 2004

Virtual Science Museum Development:Virtual Science Museum Development: Technology, Interoperability & CollaborationTechnology, Interoperability & Collaboration

Synthesis and Integrationin the Natural History Commons

Tom Moritz Harold Boeschenstein Director, Library Services

American Museum of Natural History

“The field of knowledge is the common property of all mankind “

Thomas Jefferson 1807

Julian Birkinshaw and Tony Sheehan, “Managing the Knowledge Life Cycle,” MIT Sloan Management Review, 44 (2) Fall, 2002: 77.

Is natural history knowledge a “commodity” ???

International Context: Digital Divide

http://antwrp.gsfc.nasa.gov/apod/image/0011/earthlights_dmsp_big.jpg

$0.00$5,000.00

$10,000.00$15,000.00$20,000.00$25,000.00$30,000.00$35,000.00$40,000.00

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Internet Hosts

Some prior thoughts…

Moritz, T. Toward community standards in systematics, Spectra v.16:2 Summer, 1989, p.18,20.

The “small science,” independent investigator approach traditionally has characterized a large area of experimental laboratory sciences, such as chemistry or biomedical research, and field work and studies, such as biodiversity, ecology, microbiology, soil science, and anthropology. The data or samples are collected and analyzed independentlycollected and analyzed independently, and the resulting data sets from such studies generally are heterogeneous and unstandardizedheterogeneous and unstandardized, with few of the individual data holdings deposited in public data repositories or openly shared. The data exist in various twilight exist in various twilight states of accessibilitystates of accessibility, depending on the extent to which they are published, discussed in papers but not revealed, or just known about because of reputation or ongoing work, but kept under absolute or relative secrecy. The data are thus data are thus disaggregated components of an incipient network that disaggregated components of an incipient network that is only as effective as the individual transactions that is only as effective as the individual transactions that put it togetherput it together. Openness and sharing are not ignored, but they are not necessarily dominant either. These values must compete with strategic considerations of self-interest, secrecy, and the logic of mutually beneficial exchange, particularly in areas of research in which commercial applications are more readily identifiable.

The Role of Scientific and Technical Data and Information in the Public Domain: Proceedings of a Symposium. Julie M. Esanu and Paul F. Uhlir, Eds. Steering Committee on the Role of Scientific and Technical Data and Information in the Public Domain Office of International Scientific and Technical Information Programs Board on International Scientific Organizations Policy and Global Affairs Division, National Research Council of the National Academies, p. 8

and much prior (and ongoing) analysis and development…

Figure: The “Association of Systematic Collections, Information Model for Biological Collections”.

[After ASC, 1993; simplified.]

http://research.calacademy.org/taf/proceedings/intro.html

Stan Blum “Introduction,”Taxonomic Authority Files Workshop, Washington, DC, June 22-23, 1998

For example:

Figure: Flow of Basic Taxonomic Data.

http://research.calacademy.org/taf/proceedings/intro.html Stan Blum “Introduction,”Taxonomic Authority Files Workshop, Washington, DC, June 22-23, 1998

Figure: An object-oriented representation of the data structure for a Collection-Object

http://research.calacademy.org/taf/proceedings/intro.html Stan Blum “Introduction,”Taxonomic Authority Files Workshop, Washington, DC, June 22-23, 1998

A proposed definition: “Natural History”???

“The comparative study of variation in organisms, natural systems and human

cultures over time and space.”-- TD Moritz

Thus, in natural history, the collected object

and, by logical extension the collecting eventthe collecting event

(rigorously defined) are of primary importance

““Legacy Data”Legacy Data”

• Very rough estimate of 3 Billion Specimens in 6,500 natural history museums (Nature, 1998)

• A single “digital object” may result in a complex of multiple “derivatives”

• At a single large institution scale could be in the 10’s of millions of digital objects

• At community scale – in a fully developed virtual environment, we must be prepared to cope with many hundreds of millions of digital objectsmany hundreds of millions of digital objects

Natural History data information and knowledge

widely distributed but vaguely synthesized and weakly “integrated”

Specimen collections preserved & living (museums, herbaria, botanical gardens, zoos, aquaria and culture collections)

Derivatives and “virtual” specimens and samples

Collateral collections (nests, etc)

Genetic sequence data Scientific publications &

“gray literature” Images of all types (satellite to

electro-micrographs)

Time-based media (film, video, recorded sounds)

Bibliographic indices (e.g. Zoological Record 1864-present) & Authority Files

Observational data on occurrences of species

Maps (analog or digital) Archives and

manuscripts (field and lab notes)

Expertise: the experience-based knowledge of individuals or cultures

Strategic decisions about investment, design and access

must be consciously and explicitly mission-drivenmission-driven

November 11, 2002 BiodiversityBiodiversityCommonsCommons // World Heritage

The act to incorporate the American Museum of Natural History, which passed the New York State Congress on April 6, 1869, states:

The American Museum of Natural History, to be located in the City of New York for the purpose of establishing and maintaining in said city a Museum and Library of Natural History; of encouraging and developing the study of Natural Science; of advancing the general knowledge of kindred subjects, and to that end of furnishing popular instruction.

The 1996 strategic plan, adopted by the Board of Trustees on December 10, includes the following statement of mission:

To discover, interpret, and disseminate -- through scientific research and education -- knowledge about human cultures, the natural world, and the universe.

Institutional Mission of a “Not-for-Profit”

The “New” Natural History ???

View from the north of the Ngoc Linh Mountain Range in Vietnam's Central Highlands. This image was created by draping a LandSat scene (1998) over a three-dimensional model.

Courtesy AMNH Center for Biodiversity and Conservation

AMNH entomologist Dr. Christine Johnson checking

pitfall trap lines at Ngoc LinhLooking northwest from the Ngoc Linh

escarpment in the Central (Western) Highlands of Vietnam. In 1999 survey teams visited the

range's northeastern slopes.

CBC Program Director Dr. Eleanor J. Sterling examining an orchid at Ngoc Linh; orchids (Orchidaceae) are the most species

rich plant family in Southeast Asia.

Homemade snare used to trap mammals and large ground-dwelling birds (foreground, Dr. Nguyen Tien

AMNH ornithologist Paul Sweet removing an owl from mist nets.

Ornithological specimens from Ngoc Linh (Quang Nam Province).

Elaphe mandarina, the Mandarin Rat Snake, from Rao An, Huong Son District, Ha Tinh Province, Vietnam (Northern Truong Son Mountains Herpetofaunal Survey 1998).

Ornithological specimens from Ngoc Linh (Quang Nam Province).

http://research.amnh.org/biodiversity/center/cbcnews/archive/sprng_sum01/song.html

http://birds.cornell.edu/publications/birdscope/Summer2002/ivory_bill_absent.html

Source: Voss & Emmons, AMNH Bull. No. 230, 1996(by permission: T. Erwin)

Recent site map from Peru

depicting elements of “collecting effort”

Rheinardia ocellata, the Crested Argus. Photographed at night by an automatic camera-trap in the Ngoc Linh foothills (Quang Nam Province).

Dryshippers:

The AM-CC provides researchers with dry-shippers allowing control-rate freezing type of samples collected in the field. Recently, the AM-CC has managed to outfit the small dryshipper (content: 80 vials on cryo-canes) in a external frame backpack, making its transport more manageable.

A manual on how to fill and how to use the dryshipper is provided with it.

http://research.amnh.org/amcc/labfacilities6.html

The Ambrose Monell Collection for Molecular and Microbial Research is the American Museum of Natural History's newest research collection. Launched in May

2001, the Monell Collection will house approximately one million frozen tissue samples representing the DNA of a wide range of species. Potentially the largest and most comprehensive initiative of its kind, the Museum's frozen tissue collection will support a broad range of research, and allow scientists, today and in the future, to

take full advantage of advances in genomic technology.

AMNH Ambrose Monell Collection for Molecular and Microbial Research

http://research.amnh.org/amcc/labfacilities6.html

http://research.amnh.org/amcc/

http://www.sandiegozoo.org/wildideas/kids/job_ryder.html

Source: Voss & Emmons, AMNH Bull. No. 230, 1996(by permission)

Collecting Methods

CollectingCollecting Methods

Pitfall trap lines with drift fences for capturing small mammals;

located in bamboo forest c. 2000m on Mt. Tay Con Linh II

(Ha Giang).

CBC-AMNH herpetologist Raoul Bain establishing pitfall trap lines c.

1400m at Mt. Tay Con Linh II.

Collecting fish with seine nets in a Ha Giang

stream.

Collecting Effort

The Ecology of the Digital Commons?

August 30, 2002 BiodiversityBiodiversityCommonsCommons // WSSD

Information

Adapted from: Lessig, L. Code and other laws of cyberspace. NY, Basic Books, 1999.

Law“Architecture” (technology)

Market

“Modalities of Constraint” on Open Access to Information

OECD Follow Up Group on Issues of Access to Publicly Funded Research Data. Promoting Access to Public Research Data for Scientific,Economic, and Social Development: Final Report March 2003.

Information

Market

A brief digression:

Who is involved?How do we “cooperate”?

Organizations

Networks of practice

Knowledge Flows:“Leaking”? or “Conscious Sharing”?

• Subcontracting• Joint ventures• Cross licensing• Portfolio Sharing• Collaborative Research Grants• Universities (as vectors)

• PUBLIC DOMAINPUBLIC DOMAIN • COMMONSCOMMONS• OPEN SOURCEOPEN SOURCE

Digital “Objects”???

Formats?Heritability?(Metadata?)

Traditional natural history information is maintained in a variety of formats:

formal publications (paper/print) archival records (paper-digital/ manuscript-

typescript- digital files – including LIST

discussions) field/lab notes (paper-digital / manuscript-

typescript-digital file) museum collections records (paper-digital/

manuscript-typescript-digital files)

specimen/artifact labels (paper/ manuscript- typescript) specimens/artifacts (object) “institutional memory” / personal expertise

Each of these formats has one or more digital format-equivalents.

The Raw Material

“Image Families”

From:Howard Besser. The Next Stage: Moving from Isolated Digital Collections to Interoperable Digital Libraries by First Monday, volume 7, number 6 (June 2002),URL: http://firstmonday.org/issues/issue7_6/besser/index.html

Optimal use of digital objects depends on “heritability”-- defined in terms of:

•technical integrity (of image)

•semantic properties

•legal ownership

“Synthesis” & “Integration”?

“Integration”?

““Synthesis”Synthesis” : The analytical, logical effort to complete integral information sets

by well-defined, rigorous inference.

““Integration”Integration” : The design and implementation of technology for the digital capture,

and coherent linking of data, information and/or knowldege

Who Who is being served?

Have their needs been rigorously and thoroughly assessed?

Design must be needs-based…

““Legacy Data”Legacy Data”

• Very general estimate of 3 Billion Specimens in 6,500 natural history museums (Nature, 1998)

• A single “digital object” may result in a complex of multiple “derivatives”

• At a single large institution scale could be in the 10’s of millions of digital objects

• At community scale – in a fully developed virtual environment, we must be prepared to cope with many hundreds of millions of digital objects

Digital Libraries? / Digital Libraries? / Digital Museums? Digital Museums?

Stages of Digital Library Development

Stage Date Sponsor Purpose

I: Experimental

1994NSF/ARPA/NASA Experiments on collections of digital materials

II: Developing

1998/1999 NSF/ARPA/NASA, DLF/CLIR Begin to consider custodianship, sustainability,

user communities

III: Mature? Funded through normal

channels? Real sustainable interoperable digital libraries Howard Besser. Adapted from The Next Stage: Moving from Isolated Digital Collections to Interoperable Digital Libraries by First Monday, volume 7, number 6 (June 2002),URL: http://firstmonday.org/issues/issue7_6/besser/index.html

Information

Market

OECD Follow Up Group on Issues of Access to Publicly Funded Research Data. Promoting Access to Public Research Data for Scientific,Economic, and Social Development: Final Report March 2003

References to “Intellectual Property” in U.S. federal cases

"IntellectualProperty"

"Intellectual Property" 1 0 4 9 15 11 56 341 1721

1900-1919

1920-1929

1930-1939

1940-1949

1950-1959

1960-1969

1970-1979

1980-1989

1990-1999

“Professor Hank Greely” Cited in Lessig, L. The future of ideas: the fate of the commons in a connrcted world. NY, Random House, 2001. P. 294.

http://www.arl.org/newsltr/218/costimpact.html

Year Number of Titles Average Price Percentage Increase Index

1984 94 78.35 — 100.0

1985 94 90.75 15.8 115.8

1986 94 102.83 13.3 131.2

1987 94 112.91 9.8 144.1

1988 94 127.33 12.8 162.5

1989 94 142.14 11.6 181.4

1990 94 153.78 8.2 196.3

1991 94 172.56 12.2 220.2

1992 94 197.89 14.7 252.6

1993 94 219.58 11.0 280.3

1994 94 243.38 10.8 310.6

1995 94 266.72 9.6 340.4

1996 94 299.84 12.4 382.7

1997 94 338.31 12.8 431.8

1998 94 385.40 13.9 491.9

1999 94 433.79 12.6 553.7

2000 94 470.43 8.4 600.4

2001 94 510.53 8.5 651.6

2002 94 543.96 6.5 694.3

U.S. Periodical Prices—2002

TABLE VII: Zoology(1 title dropped; 1 title added)

(52% of the titles increased in price)

http://www.ala.org/Content/NavigationMenu/Products_and_Publications/Periodicals/American_Libraries/Selected_articles/7zoology.htm

A “Third World” Problem”?

The American Museum of Natural History has published 240,000+ pages of scientific literature.

We expect this entire corpus of literature to be digitized and available by mid-2004.

Zoo Record Citations by Publisher Type(1978-2002)

Association58%

University6%

Commercial17%

Other0%

NH Institutions/No

n-prof it9%Government

Association

University

Commercial

Government

NH Institutions/Non-prof it

Analysis by BIOSIS and AMNH (currently unpublished)

Biodiversity Informatics Infrastructure:Biodiversity Informatics Infrastructure:

An Information Commons for the Biodiversity CommunityAn Information Commons for the Biodiversity CommunityGladys A. Cotter and Barbara T. Bauldock

U.S. Geological Survey U.S. Geological Survey

300 National Center 300 National Center

Reston, VA 20192 Reston, VA 20192

USA USA

gladys_cotter@usgs.gov barbara_bauldock@usgs.gov

Abstract

This paper provides an overview of efforts to create an informatics infrastructure for the

biodiversity community. A vast amount of biodiversity information exists, but no comprehensive

infrastructure is in place to provide easy assess and effective use of this information. The

advent of modern information technologies provides a foundation for a remedy. Biodiversity

informatics infrastructures are being called for at national, regional, and global levels, and plans

are in place to coordinate these efforts to ensure interoperability. The paper reviews some essential

requirements and some challenges related to building this infrastructure.

Proceedings of the 26th International Conference on Very

Large Databases, Cairo, Egypt, 2000

D-Lib MagazineJune 2002

Volume 8 Number 6ISSN 1082-9873

Building the Biodiversity Commons

(This Opinion piece presents the opinions of the author. It does not necessarily reflect the views of D-Lib Magazine, its publisher, the Corporation for National Research Initiatives, or its sponsor.)

Provision of free, universal access to biodiversity information is a practical imperative for the international conservation community — this goal should be accomplished by promotion of the Public Domain and by development of a sustainable Biodiversity Information Commons adapting emergent legal and technical mechanisms to provide a free, secure and persistent environment for access to and use of biodiversity information and data.

http://www.dlib.org/dlib/june02/moritz/06moritz.html

Thomas Moritz American Museum of Natural Historytmoritz@amnh.org

“the zone of informal data exchanges,”(credited to: Stephen Hilgartner and Sherry Brandt-

Rauf )

The “small science,” independent investigator approach traditionally has characterized a large area of experimental laboratory sciences, such as chemistry or biomedical research, and field work and studies, such as biodiversity, ecology, microbiology, soil science, and anthropology. The data or samples are collected and analyzed independentlycollected and analyzed independently, and the resulting data sets from such studies generally are heterogeneous and unstandardizedheterogeneous and unstandardized, with few of the individual data holdings deposited in public data repositories or openly shared. The data exist in various twilight exist in various twilight states of accessibilitystates of accessibility, depending on the extent to which they are published, discussed in papers but not revealed, or just known about because of reputation or ongoing work, but kept under absolute or relative secrecy. The data are thus data are thus disaggregated components of an incipient network that disaggregated components of an incipient network that is only as effective as the individual transactions that is only as effective as the individual transactions that put it togetherput it together. Openness and sharing are not ignored, but they are not necessarily dominant either. These values must compete with strategic considerations of self-interest, secrecy, and the logic of mutually beneficial exchange, particularly in areas of research in which commercial applications are more readily identifiable.

THE ROLE OF SCIENTIFIC AND TECHNICAL DATA AND INFORMATION IN THE PUBLIC DOMAIN PROCEEDINGS OF A SYMPOSIUM Julie M. Esanu and Paul F. Uhlir, Editors Steering Committee on the Role of Scientific and Technical Data and Information in the Public Domain Office of International Scientific and Technical Information Programs Board on International Scientific Organizations Policy and Global Affairs Division, National Research Council of the National Academies, p. 5

The Commons

Interoperability???

“a full spectrum of views on interoperability…”

• the use of common tools and interfaces that provide a superficial uniformity for navigation and access but rely almost entirely on human intelligence to provide any coherence of content

• primarily syntactic interoperability (the interchange of metadata and the use of digital object transmission protocols and formats based on this metadata rather than simply common navigation, query, and viewing interfaces) as a means of providing limited coherence of content, supplemented by human interpretation.

• deep semantic interoperability

Interoperability, Scaling, and the Digital Libraries Research Agenda: A Report on the May 18-19, 1995IITA Digital Libraries Workshop August 22, 1995 Clifford Lynch ( clifford.lynch@ucop.edu)Hector Garcia-Molina ( hector@db.stanford.edu

Ontological Synthesis?

Toward a possible “ontology” of natural history information?

“Ontology”? :

“A formal explicit specification of a shared conceptualization”

(T.A. Gruber. A translation approach to portable ontologies, Knowledge 7.)

“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. County20. Locality21. Longitude22. Latitude23. BoundingBox24. Julian Day

Dave Vieglais Species Analyst 4/20/2000

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

PersonDate

Address

The Darwin Core model (Version 1.0) suggests a rudimentary synthetic ontological frameworksynthetic ontological framework for biodiversity information that can support and inform searching across a complete range of knowledge resources.

This ontology has broader applicability to most types of digital information objects in natural history.

Nominal/ Descriptive element (Sex) [manuscript -- icon]

Date element (mm-dd-yyyy) [manuscript -- alphanumeric]

Responsibility (collectors) [print – alpha]Nominal/ Descriptive element (Scientific Name) [manuscript -- alpha]

Spatial Element (geographic place name) [manuscript -- alpha]

Address element (Institutional Name) [print -- alpha] + (Specimen #) [manuscript -- numeric]

Responsibility (expedition name) [print –alpha]

Specimen Label

Specimen Label + Verso

Address element (Specimen Field #) [manuscript -- numeric]

Nominal/ Descriptive element (Notes) [manuscript -- alpha]

Spatial Element (geographic place name) [print/typescript -- alpha]

Responsibility (collectors) [print – alpha]

Date element (mm-dd-yyyy) [print/typescript – alpha/numeric]

Nominal/ Descriptive element (Common Name) [print - alpha]

Nominal/ Descriptive element (Sex) [typescript -- alpha]

Address element (Institutional Name) [print -- alpha]

Negative Envelope

Negative # [print/stamp – alpha/numeric]

“Catalog No.” (Collection #) [print – alpha/numeric]

Nominal/ Descriptive element (Scientific Name) [manuscript - alpha]

Nominal/ Descriptive element (Common Name) [manuscript - alpha]

[ Responsibility (collector) [implied] ]

[ Responsibility (expedition name) [implied] ]

Nominal/ Descriptive element (Notes) [manuscript -- alpha]

Field Notebook

Field book name: Birds 7 Page #57

Taxonomic name ( Apaloderma narina brachyurum)

Field #5736 Catalog #158883

Locality ( Avakubi ) Date: June 03, 1914

Sex: M

Description: Larger Trogon (apaloderma narina brachyurum). Testes slightly enlarged. Stomach contained hairless caterpillars and insects (an orthopter and a beetle). (Water color of head). When freshly killed, these trogons have the iris always red brown, but if allowed to lie long, it may appear deep red.

http://diglib1.amnh.org/cgi-bin/database/index.cgi

Field Notebook Transcription

Responsibility (collector) [manuscript – alpha]

Nominal/ Descriptive element (Scientific Name) [manuscript -- alpha]

Address element: (Specimen #) [print -- numeric]

Specimen Catalog

Nominal/ Descriptive element (Scientific Name) [print-- alpha]

Spatial Element (geographic place name) [print -- alpha]

Nominal/ Descriptive element (Sex) [print-- icon]

“Taxon Treatment”

Responsibility (author) [print – alpha]

Date element (mm-dd-[yy implicit]) [print-- alphanumeric]

Nominal/ Descriptive element (Notes) [print – alpha (continued on following pages)

Entity supertypeBARCODE ID NUMBERADMINISTRATIVE DATA

Entity subtype

AMNH reg. #Dept/Partner#ISIS #Studbook #Field cat. #Other ID #Coll. By?DonorExpedition #Accession dateVoucher #eVoucher#DispositionData sourceAvailabilityRestrictionsPermissionNotificationAdministrative notes KingdomPhylumClassOrderFamilySub-FamilyGenusSpeciesSub-speciesDetermined by?AuthorityTypeQuestionable IDCommon nameCitationTaxonomic history

Cryo Collections “Freezerworks” record structure (I)

Nominal/ Descriptive element (Scientific Name)

TAXONOMY

Responsibility

Nominal/ Descriptive element (Common Name)

Cryo Collections “Freezerworks” record structure (II)

Spatial Element

Nominal/ Descriptive element (Sex)

FIELD DATA Physical characteristic

Collected date 1Collected date 2Time of collectionSeason of collectionContinentBody of WaterCityProvinceStateCountySpecific localityUTMLatitudeLongitudeCPIPurpose of storageAncillary collectionPrepared by?Field Preparation methodStorage methodField notesHabitat description SexAgeHeightWeightLengthMolt statusReproduction conditionDate of deathCause of deathBirth typePreservation typePhysical characteristic comments

ALIQUOT Position Results tab Protocol Medium Preservation History

VatSectionRackBoxPositionInitialCurrent Aliquot typeAssayResults Protocol dateProtocol Storage MediumLoan dateLoan Preservation History

Cryo Collections “Freezerworks” record structure III

Date element

Responsibility (author)

Nominal (Sci & Common Name)

Type of Information /DataSpecimen Label

Field Note Manuscript Catalog

Publication (“Taxon Treatment”)

Database Red List

Scientific Name

Common Name

Address (Inst. / Cat. #)

Responsibility

Date Element

Spatial Element

Descriptive (Sex, etc.)

lements

Logical Integration Matrix for Natural History Information

Toward “optimal” (most efficient, most parsimonious)

solutions…

“Utility”???

Imaginge-Text (capture)

Mark-up/ Metadata

Library Research/ Innovation

Library Investment?

Standards?

MARC Record: an expensiveexpensive solutionID 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>

Mediated Dublin Core (xml): a somewhat less expensiveless expensive

solution

Spatial Element (geographic place name) [print/typescript -- alpha]

Responsibility (collectors) [print – alpha]

Date element (mm-dd-yyyy) [print/typescript – alpha/numeric]

Nominal/ Descriptive element (Common Name) [print - alpha]

Nominal/ Descriptive element (Sex) [typescript -- alpha]

Negative Envelope

Negative # [print/stamp – alpha/numeric]

“Catalog No.” (Collection #) [print – alpha/numeric]

“Native” or “Vernacular”

Metadata”

221276 Medje, Congo Belge, GamanguiFeb. 6, 1910Leopard, male, shot by a Pygmy, with an arrow in the heart. The two men are the Pygmies.

221277 Faradje, Congo BelgeMar. 28, 1911Leopard, male. Entire side view.

221278 Near Faradje, Congo BelgeJan. 5, 1912Matari with Lion, male.

221279 Faradje, Congo BelgeJan. 5, 1912Lion, male. Entire specimen, side view.

Transcription of “native” / “vernacular” Metadata from negative sleeves (Congo Project I)

<?xml version="1.0"?><!DOCTYPE rdf:RDF PUBLIC "-//DUBLIN CORE//DCMES DTD 2002/07/31//EN""http://dublincore.org/documents/2002/07/31/dcmes-xml/dcmes-xml-dtd.dtd"><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/"><rdf:Description><dc:title>Leopard, male, shot by a Pygmy, with an arrow in the heart.The two men are the Pygmies.</dc:title><dc:creator>Lang, Herbert, 1879-1957.</dc:creator><dc:subject>Panthera pardus</dc:subject><dc:publisher>American Museum of Natural History</dc:publisher><dc:contributor>American Museum Congo Expedition,1909-1915</dc:contributor><dc:date>Feb. 6, 1910</dc:date><dc:type>Image.photographic</dc:type><dc:format>jpg</dc:format><dc:source>image number 221276</dc:source><dc:coverage>Medje, Congo Belge, Gamangui</dc:coverage><dc:rights>For conditions of use see:http://library.amnh.org/diglib/conditions.html</dc:rights></rdf:Description></rdf:RDF>

Transformation of native metadata record to RDF/DCBlue = native record natural language

Green = native record inferred/derived elements

Toward an “Ontological” Approach

• Application of rigorous, reductionist, “ontological” analysis of the problem domain

• Development of reference model for key facets• Application of state-of-the-art tools and methodologies

Hence:

Semantic Web applicationsSemantic Web applications

“Semantic Web” Definitions1

“ONTOLOGIES”: Collections of statements written in a language such as RDF that define the relations between concepts and specify logical rules for reasoning about them. Computers will “understand” the meaning of semantic data on a Web page by following links to specified ontologies.

The Semantic Web. Tim Berners-Lee, James Hendler and Ora LassilaSCIENTIFIC AMERICAN SPECIAL ONLINE ISSUE APRIL 2002

“Semantic Web” Definitions1

“RDF”: Resource Description Framework. A scheme for defining information on the Web. RDF provides the technology for expressing the meaning of terms and concepts in a form that computers can readily process. RDF can use XML for its syntax and URIs to specify entities, concepts, properties and relations.

“ONTOLOGIES”: Collections of statements written in a language such as RDF that define the relations between concepts and specify logical rules for reasoning about them. Computers will “understand” the meaning of semantic data on a Web page by following links to specified ontologies.

“AGENT”: A piece of software that runs without direct human control or constant supervision to accomplish goals provided by a user. Agents typically collect, filter and process information found on the Web, sometimes with the help of other agents.

The Semantic Web. Tim Berners-Lee, James Hendler and Ora LassilaSCIENTIFIC AMERICAN SPECIAL ONLINE ISSUE APRIL 2002

Key Web services will be:

a digital gazetteer • Alexandria Project http://www.alexandria.ucsb.edu/; • TGN: http://www.getty.edu/research/tools/vocabulary/tgn/; • GEOnet Names Server: http://164.214.2.59/gns/html/index.html; a biological names resolver • ITIS: http://www.itis.usda.gov/; • Species 2000: http://www.sp2000.org/; • UbIO: < http:/www.ubio.org/>;

• A time authority system (including geologic time) • An NLM UMLS-style macro-thesaurus of entomological and

zoological descriptors.

Formal Publications

Unstructured Information

Bibliographic Indices: [e.g. Zoological Record? BIOSIS?]

WEB QUERIES

BIODIVERSITY COMMONS: a rough sketch (Universe of Biodiversity Information & Knowledge)

Metadata Registry / Ontological Processor

Structured Metadata

Metadata Repository

Native Metadata

= Dublin Core x Darwin Core

"...organic processes have an historical contingency that prevents universal

explanation."

Richard Lewontin in The Triple Helix

Synthesis and Integration in the Natural History Commons

Science

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