The Bio Commons Concept: Digital "Libraries

The Bio Commons Concept

May, 2004
Tom Moritz
AMNH

Stages of Digital Library Development

Stage Date Sponsor Purpose

NSF/ARPA/NASA
I: Experiments on collections of digital materials
1994
Experimental

1998/199
II: Begin to consider custodianship, sustainability, user
9 NSF/ARPA/NASA, DLF/CLIR
Developing communities

?
Funded through normal
III: Mature Real sustainable interoperable digital libraries
channels?

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

Zoological Record Citations by Publisher Type
(1978-2002)

Natural History Association
Institutions/ Other
Non-profit 0% University
9%
Government
Commercial
10%
Commercial Association Government
17% 58%
University NH Institutions/Non-
6% profit
Other

For example: the
American Museum of
Natural History has
published 240,000+ pages
of scientific literature.

“Modalities of Constraint” on Open Access
to Data, Information, Knowledge

Market

Data
Architecture Information
(Technology)
Law
Knowledge

Norms
Adapted from: Lessig, L. Code and other laws of cyberspace. NY, Basic Books, 1999.
August 30, 2002 BiodiversityCommons / WSSD
BiodiversityCommons

A graphic depiction of the digital divide

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

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

“The field of knowledge is the common
property of all mankind “
Thomas Jefferson 1807

Universal Declaration of Human
Rights
Article 19.
Everyone has the right to freedom of
opinion and expression; this right
includes freedom to hold opinions
without interference and to seek,
receive and impart information and
ideas through any media and
regardless of frontiers.
(emphasis added)
http://www.un.org/Overview/rights.html

RIO DECLARATION ON ENVIRONMENT AND
DEVELOPMENT (1992)
Principle 10
Environmental issues are best handled with
participation of all concerned citizens, at the relevant
level. At the national level, each individual shall have
appropriate access to information concerning the
environment that is held by public authorities,
including information on hazardous materials and
activities in their communities, and the opportunity
to participate in decision-making processes. States
shall facilitate and encourage public awareness and
participation by making information widely available.
Effective access to judicial and administrative
proceedings, including redress and remedy, shall be
provided

Convention on Biological Diversity: Article 17

Exchange of Information

3. The Contracting Parties shall facilitate the exchange of
information, from all publicly available sources, relevant to
the conservation and sustainable use of biological
diversity, taking into account the special needs of
developing countries.

2. Such exchange of information shall include exchange
of results of technical, scientific and socio-economic
research, as well as information on training and
surveying programmes, specialized knowledge,
indigenous and traditional knowledge as such and in
combination with the technologies referred to in
Article 16, paragraph 1. It shall also, where feasible,
include repatriation of information.

http://www.biodiv.org/convention/articles.asp?lg=0&a=cbd-17

“…we propose a dual strategy, one that
c o n t r a c t u a l l y r e in f o r c e s t h e p u b l ic
d o ma in for data that exists within the ambit of the federal
government and a n o t h e r t h a t
c ont r ac t ual l y r ec ons t r uc t s a
r e s e a r c h c o mmo n s f o r d a t a (a n d
o t h e r f o r ms o f in f o r ma t io n ) in
a c a d e mia a n d t h e p r iv a t e s e c t o r . We
argue that excessively rigid efforts to keep scientific data
free of private control will end by yielding less and less
data to the public domain, whereas a contractually
reconstructed commons for data, while less pure in theory,
will in practice make more data more accessible for
H. research purposes in the long run. reconstructed research commons
Reichman and Paul F. Uhlir, “A contractually
for scirntific data in a highly protectionist intellectual property environment,” L a w
a n d C o n t e mp o r a r y P r o b l e ms V o l . 6 6 : 3 15 - 4 6 2 W i n t e r -
S p r in g 2 0 0 3 .

“To make this strategy work, the funding agencies,
universities, and scientific organizations mu s t
a g r e e t o a b a s ic s e t o f g r o u n d
r u l e s , wit h t h e g o a l o f p r e s e r v in g
b
t h e d a t a c o mmo n s f o r r e s e a r c h
p u r p o s e s wit h o u t imp e d in g
in s t it u t io n a l a c t o r s o r s in g l e
r e s e a r c h e r s f r o m e n j o y in g t h e
b e n e f it s o f a p p r o p r ia t e
c o mme r c ia l iz a t io n in t h e p r iv a t e
s ec t or .“

J. H. Reichman and Paul F. Uhlir, “A contractually reconstructed research commons
for scirntific data in a highly protectionist intellectual property environment,” L a w
a n d C o n t e mp o r a r y P r o b l e ms V o l . 6 6 : 3 15 - 4 6 2 W i n t e r -
S p r in g 2 0 0 3 .

A definition of the “Public Domain”
“The public domain is a range of uses of information that
any person is privileged to make absent individualized
facts that make a particular use by a particular person
unprivileged.”
Conversely:
“The enclosed domain is the range of uses of information
as to which someone has an exclusive right, and that no
other person may make absent individualized facts that
indicate permission from the holder of the right, or
otherwise privilege the specific use under the stated
facts.”

Yochai Benkler, “Free as the air to common use: First Amendment constraints
on enclosure of the Pulic Domain,” NYU Law Review Vol. 74 (May,
1999):362.

November 11, 2002 BiodiversityCommons / World Heritage
BiodiversityCommons

What is a “Commons” ???
• A commons is a limited and conditional zone of fair
use (defined both legally and technically)
• A commons permits sustainable use of a resource
without jeopardizing original ownership rights
• Supports control of patrimonial / property rights
required by owners as required by owners (for
example: indigenous peoples, national governments);
protects against unauthorized commercial use
• BUT also does permit authorized commercial uses
(i.e. is compatible with market mechanisms )
• protects organizational/individual “moral rights” (i.e.
rights of authors)

Digital Commons?

Digital resources as “public goods” are:
• non-rivalrous (near-zero cost for additional
increments of use)
• non-excludable (i.e.of potentially universal benefit)
• universally accessible (potentially)
(But economic inequities and newly emergent
legal/technical barriers may deny these benefits)

Reichman, Jerome H. and Paul F. Uhlir, Promoting Public Good Uses of Scientific Data: A
Contractually Reconstructed Commons for Science and Innovation.
http://www.law.duke.edu/pd/papers/ReichmanandUhlir.pdf

The Commons

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

Digital “Objects”???

Formats?
Heritability?
(Metadata?)

Conservation data information and
knowledge
is widely dispersed but vaguely
synthesized and weakly “integrated”
 Time-based media (film,
 Specimen collections video, recorded sounds)
preserved & living (museums,  Bibliographic indices (e.g.
Zoological Record 1864-
herbaria, botanical gardens,
present) & Authority Files
zoos, aquaria and culture
 Observational data on
collections)
occurrences of species
 Derivatives and “virtual”  Maps (analog or digital)
specimens and samples
 Environmental Data
 Collateral collections (nests,  Archives and manuscripts
etc) (field and lab notes)
 Genetic sequence data  Expertise: the experience-
 Scientific publications & based knowledge of
“gray literature” individuals or cultures
 Images of all types (satellite
to electro-micrographs)

“Image Families”
Optimal use of digital objects
depends on “heritability”--
defined in terms of:
•technical integrity (of
image)
•semantic properties
•legal ownership
Each arrow implies the
necessary transfer of
a complete set of metadata

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

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 independently, and the resulting data
independently
sets from such studies generally are heterogeneous and unstandardized, with
unstandardized
few of the individual data holdings deposited in public data repositories or
openly shared.
The data exist in various twilight states of accessibility, depending on
accessibility
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 disaggregated components of
an incipient network that is only as effective as the individual transactions
that put it together. Openness and sharing are not ignored, but they are not
together
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

“the zone of
informal data exchanges,”

(credited to: Stephen Hilgartner and Sherry Brandt-Rauf )

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

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
independently, and the resulting data sets from such studies generally are
independently
heterogeneous and unstandardized, with few of the individual data holdings deposited
unstandardized
in public data repositories or openly shared.
The data exist in various twilight states of accessibility,
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 disaggregated components of an
incipient network that is only as effective as the individual transactions that put it
together. Openness and sharing are not ignored, but they are not necessarily dominant
together
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

Synthesis? Integration?
Interoperability?

“Synthesis”? / “Integration”?
“Synthesis” :
The analytical, logical effort to complete integral information
sets by well-defined, rigorous inference.

“Integration” :
The design and implementation of technology for the digital
capture, and coherent linking of data, information and/or
knowldege

“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, 1995
IITA Digital Libraries Workshop August 22, 1995 Clifford Lynch ( clifford.lynch@ucop.edu)

Toward a possible “ontology” of conservation 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. ScientificName 13. Collector Person
2. Kingdom 14. Year
3. Phylum 15. Month Date
4. Class 16. Day
5. Order 17. Country
Name 6. Family 18. State/Province
7. Genus 19. County
8.
9.
Species
Subspecies
20.
21.
Locality
Longitude
Place
10. InstitutionCode 22. Latitude

Address 11.
12.
CollectionCode
CatalogNumber
23.
24.
BoundingBox
Julian Day

Dave Vieglais Species Analyst 4/20/2000
http://habanero.nhm.ukans.edu/presentations/Gainesville_May2000_files/v3_document.htm

The Darwin Core model (Version 1.0) suggests a
rudimentary synthetic ontological framework for
natural history information that can support and inform
searching across our full corpus of literature.

This ontology has broader applicability to most types of
digital information objects in conservation and can be
supplemented by other core elements.

Address element (Institutional Name) [print -- alpha]
+ (Specimen #) [manuscript -- numeric] Nominal/ Descriptive element (Sex)
[manuscript -- icon]
Nominal/ Descriptive element (Scientific Name)
[manuscript -- alpha] Responsibility (collectors) [print – alpha]

Responsibility
(expedition
name)
[print –alpha]

Spatial Element (geographic place name) Date element (mm-dd-yyyy)
[manuscript -- alpha] [manuscript -- alphanumeric]

Specimen Label

Specimen Label + Verso

Address element (Specimen Field #) Nominal/ Descriptive element (Notes)
[manuscript -- numeric] [manuscript -- alpha]

Address element (Institutional
Name) [print -- alpha] Negative # [print/stamp – alpha/numeric]
Spatial Element (geographic place
name) [print/typescript -- alpha]
Responsibility (expedition name)
[print –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]

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

Negative Envelope

Field Notebook

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

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

(Common Name) [manuscript -
alpha]
[manuscript -- icon]

[ Responsibility (collector) [implied] ]

[ Responsibility (expedition name) [implied] ]

(Notes) [manuscript -- alpha]

Field Notebook Transcription

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

Address element (Institutional Name)
Nominal/ Descriptive [print -- alpha]
element (Scientific Name)
[manuscript -- alpha] element (mm-dd-yyyy)
Date
[manuscript -- alphanumeric] Responsibility (collector)
[manuscript –
alpha]

(Sex) [manuscript -- icon]

Address element: (Specimen #) Spatial Element (geographic place name)
[print -- numeric] [manuscript -- alpha]

Specimen Catalog

Nominal/ Descriptive element (Scientific Name)
“Taxon Treatment” [print-- alpha]

Responsibility (author) [print – alpha]

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

[print-- icon]

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

(Notes) [print – alpha
(continued on following pages)

Cryo Collections “Freezerworks” record structure (I)
Entity supertype Entity subtype
BARCODE ID
NUMBERADMINISTRATIVE AMNH reg. #
DATA Dept/Partner#
ISIS #
Studbook #
Field cat. #
Other ID #
Coll. By?
Responsibility Donor
Expedition #
Accession date
Voucher #
eVoucher#
Disposition
Data source
Availability
Restrictions
Permission
Notification
Administrative notes
TAXONOMY
Kingdom
Phylum
Class
Order
Family
Sub-Family
Genus
Species
Nominal/ Descriptive Sub-species
element (Scientific Name) Determined by?
Authority
Type
Questionable ID
Common name
Nominal/ Descriptive Citation
Taxonomic history
element (Common Name)

Cryo Collections “Freezerworks” record structure (II)
FIELD DATA Collected date 1
Collected date 2
Date Time of collection
Season of collection
Continent
Body of Water
City
Province
State
County
Spatial Element Specific locality
UTM
Latitude
Longitude
CPI
Purpose of storage
Ancillary collection
Prepared by?
Field Preparation method
Storage method
Field notes
Habitat description

Physical characteristic Sex
Age
Height
Weight
Length
Nominal/ Descriptive element Molt status
(Sex) Reproduction condition
Date of death
Cause of death
Birth type
Preservation type
Physical characteristic comments

Cryo Collections “Freezerworks” record structure III

ALIQUOT

Position

Vat
Section
Rack
Box
Results tab Position
Initial
Current

Protocol Aliquot type
Assay
Results
Medium
Protocol date
Protocol

Preservation History Storage Medium
Loan date
Loan

Preservation History

Nominal
(Sci &
Common
Name)

Date
element

Responsibility
(author)

MARC Record: an expensive solution
ID 10507973BASE DG STS n REC am ENC I DCF a ENT 960314
INT REP GOV CNF 0 FSC 0 INX 1 CTY onc ILS ab
MEI FIC 0 BIO MOD CSC d CON b LAN eng PD 1995
006 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 of
Nature. <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$b19960618
Hol: 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 $aocm34363082
Hol: 920 $aCUVA 922 $aUCD 924 $aCU-A 926 $aShields 930 $cQH106.M67 1995

CIMI: Consortium for the Computer Interchange
of Museum Information
From Guide to Best Practice: Dublin Core (DC 1.0 =
RFC 2413)
Final Version 12 August 1999

The 15 Dublin Core Elements
Resource Type
Format
Title
Description
Subject and Keywords
Author or Creator
Other Contributor
Publisher
Date
Resource Identifier
Source
Relation
Language
Coverage
Rights

Mediated Dublin Core (xml):
a somewhat less expensive
CIMI: Consortium for the Computer Interchange of Museum Information
solution 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>

Address element (Institutional
Name) [print -- alpha] Negative # [print/stamp – alpha/numeric]
Spatial Element (geographic place
name) [print/typescript -- alpha]
Responsibility (expedition name)
[print –alpha]

Responsibility (collectors) [print – alpha]

[print/typescript – alpha/numeric]

(Common Name) [print - alpha]
[typescript -- alpha]

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

“Native” or “Vernacular”
Metadata” Negative Envelope

Transcription of “native” / “vernacular” Metadata from
negative sleeves (Congo Project I)
221276 Medje, Congo Belge, Gamangui
Feb. 6, 1910
Leopard, male, shot by a Pygmy, with an arrow in the heart.
The two men are the Pygmies.

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

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

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

<?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/DC
Blue = 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 applications

1
“Semantic Web” Definitions

“ONTOLOGIES”: C o lle c t io n s of
s t a t e m e n t s w r it t e n in a la n g u a g e
s u c h a s R D F t h a t d e f in e t h e
r e la t io n s b e t w e e n c o n c e p t s a n d
s p e c if y lo g ic a l r u le s f o r r e a s o n in g
a b o u t t h e m . C o m p u t e r s w ill
“u n d e r s t a n d ” t h e m e a n in g o f s e m a n t ic
d a t a o n a We b p a g e b y f o llo w in g lin k s
t o s p e c if ie d o n t o lo g ie s .

TheSemanticWeb. T im B e r n e r s -L e e , J a m e s H e n d le r a n d O r a L a s s ila
S C IE N T IF IC AME R IC AN S P E C IAL O N L IN E IS S U E AP R IL 2 0 0 2

1
“Semantic Web” Definitions
“RDF”: R e s o u r c e D e s c r ip t io n F r a m e w o r k . A s c h e m e
f o r d e f in in g in f o r m a t io n o n t h e We b . R D F
p r o v id e s t h e t e c h n o lo g y f o r e x p r e s s in g t h e
m e a n in g o f t e r m s a n d c o n c e p t s in a f o r m
t h a t c o m p u t e r s c a n r e a d ily p r o c e s s . R D F c a n
u s e X ML f o r it s s y n t a x a n d U R Is t o s p e c if y
e n t it ie s , c o n c e p t s , p r o p e r t ie s a n d r e la t io n s .
“ONTOLOGIES”: C o lle c t io n s o f s t a t e m e n t s w r it t e n in
a la n g u a g e s u c h a s R D F t h a t d e f in e t h e
r e la t io n s b e t w e e n c o n c e p t s a n d s p e c if y
lo g ic a l r u le s f o r r e a s o n in g a b o u t t h e m .
C o m p u t e r s w ill “u n d e r s t a n d ” t h e m e a n in g o f
s e m a n t ic d a t a o n a We b p a g e b y f o llo w in g
lin k s t o s p e c if ie d o n t o lo g ie s .
“AGENT”: A p ie c e o f s o f t w a r e t h a t r u n s w it h o u t
d ir e c t h u m a n c o n t r o l o r c o n s t a n t
s TheSemanticWeb. ioim Bte o n a r sc-L em p J a m e sg H eanls le p rao v id r ad L b s s ila
u p e r v is T n r e c o e , lis h o d r nd Oe ay
a u s C IE N TAgIC n t sR IC ANp S P a C IAL cOo L IN E t ,S f E AP R IL a2n0d 2
S e r . IF e AME t y ic E lly N lle c IS U ilt e r 0

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.

http://www.fishbase.org/Summary/SpeciesSummary.cfm?ID=862&genusname=Carcharhinus&speciesname=amboinensis

http://www.fishbase.org/Summary/SpeciesSummary.cfm?id=862&lang=Chinese

http://www.fishbase.org/Summary/SpeciesSummary.cfm?id=862&lang=Greek

http://www.fishbase.org/Photos/ThumbnailsSummary.cfm?ID=862

http://www.redlist.org/search/details.php?species=39366

http://64.95.130.5/Map/OccurrenceTSAMapList.cfm?ID=862&GenusName=Carcharhinus&SpeciesName=amboinensis

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The Bio Commons Concept: Digital "Libraries

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