ISBER: The Bio-commons concept
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ISBER: The Bio-commons concept

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Meeting of the International Society for Biological and Environmental Repositories (ISBER) at the American Museum of Natural History, May, 2004, New York, New York

Meeting of the International Society for Biological and Environmental Repositories (ISBER) at the American Museum of Natural History, May, 2004, New York, New York

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ISBER: The Bio-commons concept ISBER: The Bio-commons concept Presentation Transcript

  • The Bio Commons ConceptMay, 2004Tom Moritz AMNH
  • Digital “Libraries”?
  • Stages of Digital Library Development Stage Date Sponsor Purpose NSF/ARPA/NASAI: Experiments on collections of digital materials 1994Experimental 1998/199II: Begin to consider custodianship, sustainability, user 9 NSF/ARPA/NASA, DLF/CLIRDeveloping communities ? Funded through normalIII: 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 haspublished 240,000+ pages of scientific literature.
  • “Modalities of Constraint” on Open Access to Data, Information, Knowledge Market Data Architecture Information (Technology) Law Knowledge NormsAdapted from: Lessig, L. Code and other laws of cyberspace. NY, Basic Books, 1999.August 30, 2002 BiodiversityCommons / WSSD BiodiversityCommons
  • The “Digital Divide”?
  • A graphic depiction of the digital dividehttp://antwrp.gsfc.nasa.gov/apod/image/0011/earthlights_dmsp_big.jpg
  • 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 10Environmental 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
  • What is to be done…?
  • “…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 contractuallyfor scirntific data in a highly protectionist intellectual property environment,” L a wa 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 commonsfor scirntific data in a highly protectionist intellectual property environment,” L a wa 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: AContractually Reconstructed Commons for Science and Innovation.http://www.law.duke.edu/pd/papers/ReichmanandUhlir.pdf
  • The CommonsTHE ROLE OF SCIENTIFIC AND TECHNICAL DATA AND INFORMATION IN THE PUBLIC DOMAIN PROCEEDINGS OF A SYMPOSIUMJulie M. Esanu and Paul F. Uhlir, Editors Steering Committee on the Role of Scientific and Technical Data and Information in the Public Domain Office ofInternational Scientific and Technical Information Programs Board on International Scientific Organizations Policy and Global Affairs Division, NationalResearch 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 PublicDomain Office of International Scientific and Technical Information Programs Board on International Scientific Organizations Policy andGlobal 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 aSymposium. Julie M. Esanu and Paul F. Uhlir, Eds. Steering Committee on the Role of Scientific and Technical Data andInformation in the Public Domain Office of International Scientific and Technical Information Programs Board on InternationalScientific 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 PublicDomain Office of International Scientific and Technical Information Programs Board on International Scientific Organizations Policy andGlobal 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 interoperabilityInteroperability, 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)
  • 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. ScientificName 13. Collector Person 2. Kingdom 14. Year 3. Phylum 15. Month Date 4. Class 16. Day 5. Order 17. CountryName 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(expeditionname)[print –alpha]Spatial Element (geographic place name) Date element (mm-dd-yyyy)[manuscript -- alpha] [manuscript -- alphanumeric] Specimen Label
  • Specimen Label + VersoAddress element (Specimen Field #) Nominal/ Descriptive element (Notes)[manuscript -- numeric] [manuscript -- alpha]
  • Address element (InstitutionalName) [print -- alpha] Negative # [print/stamp – alpha/numeric]Spatial Element (geographic placename) [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] Date element (mm-dd-yyyy) [manuscript -- alphanumeric]Nominal/ Descriptive element (ScientificName) [manuscript - alpha]Nominal/ Descriptive element(Common Name) [manuscript -alpha]Nominal/ Descriptive element (Sex)[manuscript -- icon] [ Responsibility (collector) [implied] ] [ Responsibility (expedition name) [implied] ] Nominal/ Descriptive element (Notes) [manuscript -- alpha]
  • Field Notebook TranscriptionField book name: Birds 7 Page #57 Taxonomic name ( Apaloderma narina brachyurum)Field #5736 Catalog #158883Locality ( Avakubi ) Date: June 03, 1914 Sex: MDescription: Larger Trogon (apaloderma narina brachyurum). Testes slightly enlarged. Stomach containedhairless 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] Nominal/ Descriptive element (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] Nominal/ Descriptive element (Sex) [print-- icon] Date element (mm-dd-[yy implicit]) [print-- alphanumeric] Nominal/ Descriptive element (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 nameNominal/ Descriptive Citation Taxonomic historyelement (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 LengthNominal/ 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 elementResponsibility(author)
  • Metadata?
  • MARC Record: an expensive 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 Canadas 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 Interchange of Museum InformationFrom 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
  • Mediated Dublin Core (xml): a somewhat less expensive CIMI: Consortium for the Computer Interchange of Museum Informationsolution 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 Berlands 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 (InstitutionalName) [print -- alpha] Negative # [print/stamp – alpha/numeric]Spatial Element (geographic placename) [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]“Native” or “Vernacular” Metadata” Negative Envelope
  • Transcription of “native” / “vernacular” Metadata from negative sleeves (Congo Project I)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.
  • <?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 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