isber: the bio-commons concept

The Bio Commons ConceptThe Bio Commons Concept

May, 2004 Tom Moritz

AMNH

Digital “Libraries”?Digital “Libraries”?

Stages of Digital Library Development

Stage Date Sponsor Purpose

I: Experimental

1994

NSF/ARPA/NASAExperiments 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 

Zoological Record Citations by Publisher Type(1978-2002)

Association

58%

University

6%

Commercial

17%

Other

0%

Natural History

Institutions/ Non-prof it

9%Government

10%

Association

University

Commercial

Government

NH Institutions/Non-prof it

Other

For example: the American Museum of Natural History has

published 240,000+ pages of scientific literature.

August 30, 2002 BiodiversityBiodiversityCommonsCommons // WSSD

Market

Law

Norms

Architecture (Technology)

Data Information Knowledge

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

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

The “Digital Divide”?

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

A graphic depiction of the digital divide

BioDiverse Areas of the World

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

A schematic representation

“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

1. 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

What is to be done…?

“…we propose a dual strategy, one that contractually reinforces the public domain for data that exists within the ambit of the federal government and another that contractually reconstructs a research commons for data (and other forms of information) in academia and the private sector. 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 research purposes in the long run.

H. Reichman and Paul F. Uhlir, “A contractually reconstructed research commons for scirntific data in a highly protectionist intellectual property environment,” Law and Contemporary Problems Vol. 66:315-462 Winter-Spring 2003.

“To make this strategy work, the funding

agencies, universities, and scientific organizations must agree to a basic set of ground rules, with the goal of preserving the data commons for research purposes without impeding institutional actors or single researchers from enjoying the benefits of appropriate commercialization in the private sector. “

J. H. Reichman and Paul F. Uhlir, “A contractually reconstructed research commons for scirntific data in a highly protectionist intellectual property environment,” Law and Contemporary Problems Vol. 66:315-462 Winter-Spring 2003.

b

November 11, 2002 BiodiversityBiodiversityCommonsCommons // World Heritage

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.

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 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

Digital “Objects”???

Formats?

Heritability?

(Metadata?)

Conservation data information and knowledge

is widely dispersed 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) Environmental Data Archives and

manuscripts (field and lab notes)

Expertise: the experience-based knowledge of individuals or cultures

“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

Each arrow implies the necessary transfer of a complete set of metadata

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

“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 collected and analyzed independentlyindependently, 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 states of exist in various twilight states of accessibilityaccessibility, 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 data are thus disaggregated components of an incipient network that is only as effective as the individual incipient network that is only as effective as the individual transactions that put it togethertransactions that put 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

Synthesis? Integration? Interoperability?

“Synthesis”? / “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

“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)Hector Garcia-Molina ( hector@db.stanford.edu

Ontological Synthesis?

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. 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

Name

Person

Date

Place

Address

The Darwin Core model (Version 1.0) suggests a rudimentary synthetic ontological frameworksynthetic 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.

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 (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]

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]

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

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

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

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

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

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

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

Responsibility (collector) [manuscript – alpha]

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

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

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

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)

Date

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)

Metadata?

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 (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]

Address element (Institutional Name) [print -- 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/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 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 Lassila

SCIENTIFIC 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 Lassila

SCIENTIFIC 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.

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