Donat Agosti - Copyright, Biopiracy and the Taxonomic Impediment

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  • An image from a recent (Dec. 1 I think) issue of Nature showing some ongoing digitization efforts.
  • If the publications are marked up in XML they can be searched and indexex, but parts of it can be displayed by dedicated servers, such as ispecies, antweb, etc.. For example, if publishers would agree to insert taxonomically relevant XML-mark-up, then the distribution and online discovery of new species descriptions could be almost instantaneous.
  • This is an example using a species with a long nomenclatorial history, a large body of biological literature, and one of the worst invasive species in the world, and thus an extensive body of information should be online accessible.
  • Searching for „Argentine Ant“ in google scholar results in 1,320 hits. The return is also interesting in sofar as it shows the problem of missspellings. Whereas record 2 has been found because of „Argentiine ant“ it would not have been found because of the missspelling of Linepithema as I. inepithema.
  • The search using the scientific name is less successful.
  • This is the latest taxonomic treatment of the Argentine ant. It lists 6 scientific variants of the name, which are either synonyms, subspecies or missspellings.
  • This is uBIO‘s approach, using 9 different variants of Linepithema humile is more successful than either of google‘s approach. The reason being, that uBIO is using for its searches different variants of its name which it derives from ist NameBank. However, its searcg does not yet include the vernacular name „Argentine ant“.
  • In fact, the search could be even more powerful, if ALL the 19 variants of this species‘ name would be included, this does not inlcude yet misspellings and short forms, such as L. humile. Antbase/Hymenoptera Name Server so far focused on recovering all those names, which are of nomenclatorial importance. But there is a body of ca 90,000 pages of legacy publications out to extract all different variants of names, not to speak of over 30,000 scientific publications on ant behavio, pest control, and then all the public literature…. Not having access to all this information is recognized as on the worts impediments for effective conservation, ie the taxonomic impediment. To open up this treasure trove would not only allow a look back, but allow a lot of new ways we look and act in our world.
  • Donat Agosti - Copyright, Biopiracy and the Taxonomic Impediment

    1. 1. Copyright, Biopiracy andthe Taxonomic ImpedimentDonat AgostiNaturhistorisches Museum der Burgergemeinde Bern,SwitzerlandandAmerican Museum of Natural History, New York, USA
    2. 2. Access to ant taxonomic publications through antbase.org /Smithsonian Institution, including currently theentire body of non-copyrighted publications since 1758 (>4,000 publications or 85,000 pages covering11840 species. Source: (Agosti 2005)Copyright
    3. 3. This seems little better than biopiracy:taking biodiversity material from thedeveloping world for profit, without sharingbenefit or providing the people who live therewith access to this crucial information.Biopiracy(Agosti, 2006 Nature 439: 392)
    4. 4. Taxonomic ImpedimentCan systematics publications be copyrighted?• factual knowledge• cultural heritage (Universal Declaration on Cult.Div.)• access and benefit sharing (CBD)Why ought they to be open access – ethic issues?• Conservation Commons• Biodiversity Crisis: unability to to identify and thusprotect biodiversity• descriptions equals gen sequences• impediment for future research: the genomics case.• fusion of retro- and prospective data dissemination
    5. 5. What is a systematics publication – or what do systematists do?They are part of a more or less closed systemTaxonomic Impediment
    6. 6. ScanningPdf-conversion(WWW)Electronic revolution? Not yet.
    7. 7. One Step closer…
    8. 8. From text document to XML-documentTaxon-xschema
    9. 9. ms submission(„Taxon-x-version“)new ms alertPosting for reviewEdited msRevised msPublication: pdfPublication: hard copyPublication database(„taxon-x-version“)ontologybibliographyanalysis &ms preparationZoobankCharacter DBSpecimen DBDescription DBDistribution DBChar. Matrix DBPhyl. Tree DBChar-state Im.Specimen Im.Habitat ImageLeg. Publicat.TaxonDBNew DatafeedbackAccepted msNew taxon alertWhere the past meets the future: deconstruction and machine generation of publications
    10. 10. The New Taxonomy: a point of view1: Taxon Data Standard2: Taxon Transfer Protocol3: ApplicationsTaxonDB (1)InputQueryResponse(2)variaDBs(3)Change Notification system(3)
    11. 11. Usage of published data: data mash-ups
    12. 12. Taxonomic ImpedimentCan systematics publications be copyrighted?• factual knowledge• cultural heritage• access and benefit sharing (CBD)Why ought they to be open access – ethic issues?• Conservation Commons• Biodiversity Crisis: unability to to identify and thusprotect biodiversity• descriptions equals gen sequences• impediment for future research: the genomics case.• fusion of retro- and prospective data dissemination
    13. 13. SolutionsAll systematics publications are open access (eg creativecommons licence; subscription to ConservationCommons principles)The content of all systematics publications is open access:eg mark-up and exposure of publications; selfrespositoriesAll descriptions are open access (description = gensequence): eg mark-up and exposure of descriptions;submission of descriptions to dedicated databases, suchas ZooBank or taxon specific DBAbandoning traditional publications and integratingpublications into populations process of DB. (publication= version control of knowledge)
    14. 14. The Argentine Ant(Linepithema humile)A well known ant
    15. 15. Search using the vernacular name
    16. 16. Search using the currently valid scientific name „Linepithema humile“
    17. 17. HNS20351 Wild, A. L. 2004. Taxonomy and distribution of the Argentine ant, Linepithema humile (Hymenoptera:Formicidae). Ann. Entomol. Soc. Amer. 97(6): 1204-1215. (http://antbase.org/ants/publications/20351/20351.pdf)6 variants of the nameLinepithema humile
    18. 18. +
    19. 19. Linepithema humileHypoclinea (Iridomyrmex) humilis MayrHypoclinea humilis MayrIridomyrmex humilis (Mayr)Linepithema humile (Mayr)Linepithema riograndense (Borgmeier)Linepithema humile angulatumIridomyrmex humilis subsp. angulatusLinepithema humile arrogansIridomyrmex humilis var. arrogansIridomyrmex humilis st. breviscapa SantschiLinepithema humile breviscapum (Santschi)Dorymyrmex gallardoi BrèthesLinepithema humile gallardoi (Brèthes)Linepithema humile humile (Mayr)Iridomyrmex humilis r. platensis ForelLinepithema humile platense (Forel)Iridomyrmex humilis st. scotti SantschiLinepithema humile scotti (Santschi)19 Variants
    20. 20. Taxonomic ImpedimentSolution:Either make all systematics publications online accessibleAllow the actual descriptions be open access, not the entire publication
    21. 21. Biopiracy
    22. 22. The potential of the OA movement, heargues, doesn’t begin with policyconditions aimed at altering the operatingconditions for a small subset of journalpublishers. Rather, it needs a muchbroader-based effort to make institutionalself-archiving a routine and unquestionedpart of the work of scholarship – as basicas including bibliographies and referencelists at the end of any paper.
    23. 23. How do academics feel about self-archiving? “Authors haven’t picked it up,”says Dr. Willinsky at UBC. “It has a lot todo with the fact that the focus of[academics’] work is getting published, notgetting circulated.”John Lorinc The bottom line on open accessby University Affairs, March 2006
    24. 24. Stevan Harnard and Tim Brody, 2004. Comparing the Impact of Open Access (OA) vs. Non-OA Articles in the Same Journals. D-LibMagazine, June 2004, Volume 10 Number 6Figure 1 shows the total number of journal articles in physics indexed by the Institute of Scientific Information from 1992-2001 (gray), thepercentage of these that have been made open-access (OA) by author self-archiving (green), and the ratio of the citation counts for the OAarticles to the citation counts for the non-OA articles (red). (Analyses are by Brody et al. (2004) and are based on the ®ISI CD-ROM* citationdatabase metadata and references from 14,000,000 articles in 7,000 leading journals from 1991 to 2001 licensed to the Observatoire dessciences et des technologies <http://www.ost.qc.ca> and from the 260,000 articles self-archived in <http://www.arxiv.org>.)
    25. 25. • FURTHER RECOGNIZING that underArticle 17 of the Convention on BiologicalDiversity, Parties shall facilitate theexchange of information, from all publiclyavailable sources, relevant to theconservation and sustainable use ofbiological diversity, taking into account thespecial needs of developing countries;
    26. 26. “…we propose a dual strategy, one that contractuallyreinforces the public domain for data that existswithin the ambit of the federal government and anotherthat contractually reconstructs a researchcommons for data (and other forms ofinformation) in academia and the privatesector. We argue that excessively rigid efforts to keepscientific data free of private control will end by yieldingless and less data to the public domain, whereas acontractually reconstructed commons for data, while lesspure in theory, will in practice make more data moreaccessible for research purposes in the long run.H. Reichman and Paul F. Uhlir, “A contractually reconstructed research commonsfor scirntific data in a highly protectionist intellectual property environment,” Lawand Contemporary Problems Vol. 66:315-462 Winter-Spring 2003.
    27. 27. Approved by 148 against 2 votes (4abstentions) by the GeneralConference of UNESCO in Paris,October 20
    28. 28. Universal Declaration on Cultural DiversityARTICLE 6 Towards access for all to cultural diversityWhile ensuring the free flow of ideas by word and image, careshould be exercised that all cultures can express themselves andmake themselves known.Freedom of expression, media pluralism, multilingualism, equalaccess to art and to scientific and technological knowledge,including in digital form, and the possibility for all cultures to haveaccess to the means of expression and dissemination are theguarantees of cultural diversity.

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