Knowledge sharing and the Commons

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A presentation on semantics and the need for Open Access, given at the 1st Conference on Open Access Scholarly Publishing in Lund, Sweden (13-16 Sept).

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Knowledge sharing and the Commons

  1. 1. knowledge sharing and the commons kaitlin thaney program manager, science commons lund, sweden - COASP - 15 sep 2009 This presentation is licensed under the CreativeCommons-Attribution-3.0 license. Wednesday, September 16, 2009
  2. 2. make sharing easy, legal and scalable integrated approach building part of the infrastructure for knowledge sharing Wednesday, September 16, 2009
  3. 3. com⋅mons (noun) - law, content, technology, community Wednesday, September 16, 2009
  4. 4. knowledge? journal articles data ontologies annotations plasmids and cell lines Wednesday, September 16, 2009
  5. 5. knowledge sharing is at the root of scholarship and science the system of scholarly publishing is a system of sharing knowledge it all starts with access to information Wednesday, September 16, 2009
  6. 6. scientific revolutions occur when a sufficient body of data accumulates to overthrow the dominant theories we use to frame reality a so-called paradigm shift - from thomas kuhn Wednesday, September 16, 2009
  7. 7. need to change the way we think of scholarly publishing, of knowledge sharing paradigm shift begin thinking of “papers” as containers of knowledge Wednesday, September 16, 2009
  8. 8. Wednesday, September 16, 2009
  9. 9. “the future is here ... just unevenly distributed” - william gibson (i.e., linked data, W3C, neurocommons...) Wednesday, September 16, 2009
  10. 10. 1. three layers of resistance: technical, semantic, legal save legal for last ... Wednesday, September 16, 2009
  11. 11. “read 189,000 papers” is not the ideal answer. Wednesday, September 16, 2009
  12. 12. DRD1, 1812 adenylate cyclase activation ADRB2, 154 adenylate cyclase activation ADRB2, 154 arrestin mediated desensitization of G-protein coupled receptor protein signaling pathway DRD1IP, 50632 dopamine receptor signaling pathway DRD1, 1812 dopamine receptor, adenylate cyclase activating pathway DRD2, 1813 dopamine receptor, adenylate cyclase inhibiting pathway GRM7, 2917 G-protein coupled receptor protein signaling pathway GNG3, 2785 G-protein coupled receptor protein signaling pathway GNG12, 55970 G-protein coupled receptor protein signaling pathway DRD2, 1813 G-protein coupled receptor protein signaling pathway ADRB2, 154 G-protein coupled receptor protein signaling pathway CALM3, 808 G-protein coupled receptor protein signaling pathway HTR2A, 3356 G-protein coupled receptor protein signaling pathway DRD1, 1812 G-protein signaling, coupled to cyclic nucleotide second messenger SSTR5, 6755 G-protein signaling, coupled to cyclic nucleotide second messenger MTNR1A, 4543 G-protein signaling, coupled to cyclic nucleotide second messenger CNR2, 1269 G-protein signaling, coupled to cyclic nucleotide second messenger HTR6, 3362 G-protein signaling, coupled to cyclic nucleotide second messenger GRIK2, 2898 glutamate signaling pathway GRIN1, 2902 glutamate signaling pathway GRIN2A, 2903 glutamate signaling pathway GRIN2B, 2904 glutamate signaling pathway ADAM10, 102 integrin-mediated signaling pathway GRM7, 2917 negative regulation of adenylate cyclase activity LRP1, 4035 negative regulation of Wnt receptor signaling pathway ADAM10, 102 Notch receptor processing ASCL1, 429 Notch signaling pathway HTR2A, 3356 serotonin receptor signaling pathway ADRB2, 154 transmembrane receptor protein tyrosine kinase activation (dimerization) PTPRG, 5793 transmembrane receptor protein tyrosine kinase signaling pathway EPHA4, 2043 transmembrane receptor protein tyrosine kinase signaling pathway NRTN, 4902 transmembrane receptor protein tyrosine kinase signaling pathway CTNND1, 1500 Wnt receptor signaling pathway ` Wednesday, September 16, 2009
  13. 13. better answers through better formats: Mesh: Pyramidal Neurons select ?gene_name ?process_name where Pubmed: Journal Articles { PropertyValue(?pubmed_record, ?p, mesh:D017966) PropertyValue(?article, sc:identified_by_pmid , ?pubmed_record) PropertyValue(?gene_record, sc:describes_gene_or_gene_product_mentioned_by, ?article) SubClassOf(?protein, some(ro:has_function, some(ro:realized_as, ?process))) SubClassOf(?process, or(go:GO_0007166, some(ro:part_of, go:GO_0007166)) Entrez Gene: Genes SubClassOf(?protein, some(sc:is_protein_gene_product_of_dna_described_by,?gene_record)) Annotation(?gene_record,rdfs:label,{?gene_name}) } Annotation(?process,rdfs:label,?process_name) GO: Signal Transduction Wednesday, September 16, 2009
  14. 14. technical Wednesday, September 16, 2009
  15. 15. traditional transfer of copyright agreement Wednesday, September 16, 2009
  16. 16. (1) KEGG - Kyoto Encyclopedia of Genes and Genomes “Non-academic users and Academic users intending to use KEGG for commercial purposes are requested to obtain a license agreement through KEGG's exclusive licensing agent, Pathway Solutions, for installation of KEGG at their sites, for distribution or reselling of KEGG data, for software development or any other commercial activities that make use of KEGG, or as end users of any third-party application that requires downloading of KEGG data or access to KEGG data via the KEGG API. (2) HapMap - human genetic variation data “The click-wrap license was designed as a temporary tool to continue the practice of providing rapid access to human genome data [...]. One consequence of the license requirement was that the [...] license prevented HapMap data from being integrated into major public databases, which require that data deposited carry no conditions on use ...” - Wellcome Trust, Sanger, Dec 2004 Wednesday, September 16, 2009
  17. 17. what companies think we’re doing with the web Wednesday, September 16, 2009
  18. 18. 2. people like stories ... (scientists are people ...) Wednesday, September 16, 2009
  19. 19. semantic agreement is hard. Wednesday, September 16, 2009
  20. 20. Wednesday, September 16, 2009
  21. 21. Wednesday, September 16, 2009
  22. 22. espresso coffee cafe kopi cafezinho latte koffee mocha americano Wednesday, September 16, 2009
  23. 23. “choice” or interoperability. (pick one) Wednesday, September 16, 2009
  24. 24. Wednesday, September 16, 2009
  25. 25. converge on common names “coffee” “cafe” coffee “kopi” http://ontology.foo.org/1234567 Wednesday, September 16, 2009
  26. 26. Wednesday, September 16, 2009
  27. 27. Wednesday, September 16, 2009
  28. 28. 3. the data “rights” conundrum... Wednesday, September 16, 2009
  29. 29. Open Access (OA) Photo Credit: Peter Jeffs Wednesday, September 16, 2009
  30. 30. © “creative expression” Wednesday, September 16, 2009
  31. 31. is it creative? Wednesday, September 16, 2009
  32. 32. is it creative? Wednesday, September 16, 2009
  33. 33. is it creative? Wednesday, September 16, 2009
  34. 34. category errors Wednesday, September 16, 2009
  35. 35. the problem of... Non-Commercial for data Wednesday, September 16, 2009
  36. 36. Non-Commercial what’s a commercial use of the data web? Wednesday, September 16, 2009
  37. 37. the problem of... Share Alike for data Wednesday, September 16, 2009
  38. 38. 1854 Wednesday, September 16, 2009
  39. 39. the problem of... Attribution for data Wednesday, September 16, 2009
  40. 40. Wednesday, September 16, 2009
  41. 41. Wednesday, September 16, 2009
  42. 42. the problem of... any license for data Wednesday, September 16, 2009
  43. 43. database protections based on jurisdiction sui generis, “sweat of the brow” Crown copyright the list goes on .... Wednesday, September 16, 2009
  44. 44. attribution = license citation = norms (which one applies whether or not a copy is made?) Wednesday, September 16, 2009
  45. 45. need for a legally accurate and simple solution reducing or eliminating the need to make the distinction of what’s protected requires modular, standards based approach to licensing Wednesday, September 16, 2009
  46. 46. Wednesday, September 16, 2009
  47. 47. Wednesday, September 16, 2009
  48. 48. CC Zero waiver + SC norms waive rights public domain attribution / citation through community norms, not a contract Wednesday, September 16, 2009
  49. 49. calls for data providers to waive all rights necessary for data extraction and re-use requires provider place no additional obligations (like share-alike) to limit downstream use request behavior (like attribution) through norms and terms of use Wednesday, September 16, 2009
  50. 50. infrastructure for a data web the digital commons law + content + technology + community Wednesday, September 16, 2009
  51. 51. data without structure and annotation is a lost opportunity. data should flow in an open, public, and extensible infrastructure support recombination and reconfiguration into computer models, queryable by search engine treated as public good Wednesday, September 16, 2009
  52. 52. resist the temptation to treat as property embrace the potential to treat instead as a network resource Wednesday, September 16, 2009
  53. 53. 4. at best, we’re partially right. at worst, we’re really wrong. Wednesday, September 16, 2009
  54. 54. the right to fix our mistakes. Wednesday, September 16, 2009
  55. 55. (remember Prodigy and AOL?) Wednesday, September 16, 2009
  56. 56. design for maximum reuse ensure the freedom to integrate leverage existing open infrastructure allows for snap together integration of the tools, data, research literature Wednesday, September 16, 2009
  57. 57. thank you kaitlin@creativecommons.org sciencecommons.org neurocommons.org Wednesday, September 16, 2009

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