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uncommon knowledge, open innovation




Wednesday, March 11, 2009
how do we make the web work for science?




Wednesday, March 11, 2009
we need more from what we know.




Wednesday, March 11, 2009
we need more from what we know.




Wednesday, March 11, 2009
“compatibly communicating”
                                     devices.




Wednesday, March 11, 2009
“compatibly communicating”
                                  knowledge?




Wednesday, March 11, 2009
1.
      science on the net: digitized, not digital.




Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
stable systems have “immune”
                                 responses to change.




Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
there is no crowd.
Wednesday, March 11, 2009
the knowledge is uncommon.




Wednesday, March 11, 2009
2.
                      the digital commons - another
                               network layer.




Wednesday, March ...
computers    tcp/ip

                 documents   html/http

                 knowledge   commons


Wednesday, March 11, 2...
Wednesday, March 11, 2009
socially constructed rights
Wednesday, March 11, 2009
“rivalrous goods”



Wednesday, March 11, 2009
socially constructed exceptions




Wednesday, March 11, 2009
the tragedy
                            “rivalrous goods”the
                                            is
              ...
open rights.

   multiplicity of incentives.

      distributed workloads.




Wednesday, March 11, 2009
Wednesday, March 11, 2009
commons as infrastructure
Wednesday, March 11, 2009
computers    tcp/ip

                 documents   html/http

                 knowledge   semantics


Wednesday, March 11,...
“papers”



                            IGFBP-5 plays a role in the regulation of cellular
                            sen...
“networked
         knowledge”



                            IGFBP-5 plays a role in the regulation of cellular
         ...
making computers understand things




Wednesday, March 11, 2009
making computers understand links between documents




                                       links to
                  ...
making computers understand relationships between ideas




                                              causes
         ...
URLs for concepts,
                                         not just pages
                            “coffee”




      ...
www


Wednesday, March 11, 2009
3.
                      hard to do, but not impossible.




Wednesday, March 11, 2009
digital content




                research tools           technology

Wednesday, March 11, 2009
research tools

Wednesday, March 11, 2009
coming soon.
Wednesday, March 11, 2009
Wednesday, March 11, 2009
digital content




Wednesday, March 11, 2009
>1000 journals under CC
                               image from the public library of science
                          ...
what do these
               ideas mean in
                 a world of
             integrated data?




Wednesday, March ...
interoperate with the public domain.




Wednesday, March 11, 2009
announcing: personal genomes under
                            CC∅, available via filesharing networks




Wednesday, March...
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
technology

Wednesday, March 11, 2009
exponential content growth
Wednesday, March 11, 2009
our brain capacity


                1.00



                0.75



                0.50



                0.25



     ...
990+ databases




                            http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1



Wednesday, ...
“find me signal transduction genes in pyramidal neurons”




Wednesday, March 11, 2009
“read 189,000 pages”
                               is not the ideal
                                   answer.



Wednesd...
Wednesday, March 11, 2009
Wednesday, March 11, 2009
you need four data sources to answer the question.


                                                                     ...
precise answers to complex questions
                            DRD1, 1812      adenylate cyclase activation
            ...
we can turn ugly query code into a link
              http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3Cht...
we can turn ugly query code into a link




Wednesday, March 11, 2009
users can view and edit source
                                          prefix go: <http://purl.org/obo/owl/GO#>
        ...
collaborative question answering




Wednesday, March 11, 2009
open = pleasant surprises.




Wednesday, March 11, 2009
google maps for brain images




                            http://sparql.neurocommons.org:8890/map/#Kcnip3@2850,Kcnd1@28...
“one last thing”



Wednesday, March 11, 2009
“it’s the links, dummy”
                                  - James Boyle

                            aka “Boyle’s Law 2.0”...
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
Wednesday, March 11, 2009
http://ucsdbiolit.codeplex.com/
                                      (project site)

                            http://b...
closing the loop to open innovation:
                         freedom to operate.




Wednesday, March 11, 2009
reconstructing the research exemption




Wednesday, March 11, 2009
Wednesday, March 11, 2009
thank you

                            wilbanks@creativecommons.org

                              http://sciencecommons.o...
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Etech Wilbanks

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Transcript of "Etech Wilbanks"

  1. 1. uncommon knowledge, open innovation Wednesday, March 11, 2009
  2. 2. how do we make the web work for science? Wednesday, March 11, 2009
  3. 3. we need more from what we know. Wednesday, March 11, 2009
  4. 4. we need more from what we know. Wednesday, March 11, 2009
  5. 5. “compatibly communicating” devices. Wednesday, March 11, 2009
  6. 6. “compatibly communicating” knowledge? Wednesday, March 11, 2009
  7. 7. 1. science on the net: digitized, not digital. Wednesday, March 11, 2009
  8. 8. Wednesday, March 11, 2009
  9. 9. Wednesday, March 11, 2009
  10. 10. Wednesday, March 11, 2009
  11. 11. Wednesday, March 11, 2009
  12. 12. Wednesday, March 11, 2009
  13. 13. stable systems have “immune” responses to change. Wednesday, March 11, 2009
  14. 14. Wednesday, March 11, 2009
  15. 15. Wednesday, March 11, 2009
  16. 16. Wednesday, March 11, 2009
  17. 17. there is no crowd. Wednesday, March 11, 2009
  18. 18. the knowledge is uncommon. Wednesday, March 11, 2009
  19. 19. 2. the digital commons - another network layer. Wednesday, March 11, 2009
  20. 20. computers tcp/ip documents html/http knowledge commons Wednesday, March 11, 2009
  21. 21. Wednesday, March 11, 2009
  22. 22. socially constructed rights Wednesday, March 11, 2009
  23. 23. “rivalrous goods” Wednesday, March 11, 2009
  24. 24. socially constructed exceptions Wednesday, March 11, 2009
  25. 25. the tragedy “rivalrous goods”the is anti-commons Wednesday, March 11, 2009
  26. 26. open rights. multiplicity of incentives. distributed workloads. Wednesday, March 11, 2009
  27. 27. Wednesday, March 11, 2009
  28. 28. commons as infrastructure Wednesday, March 11, 2009
  29. 29. computers tcp/ip documents html/http knowledge semantics Wednesday, March 11, 2009
  30. 30. “papers” IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases Wednesday, March 11, 2009
  31. 31. “networked knowledge” IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases Wednesday, March 11, 2009
  32. 32. making computers understand things Wednesday, March 11, 2009
  33. 33. making computers understand links between documents links to Web page Web page Wednesday, March 11, 2009
  34. 34. making computers understand relationships between ideas causes drinking coffee feel awake Wednesday, March 11, 2009
  35. 35. URLs for concepts, not just pages “coffee” coffee “cafe” http://ontology.foo.org/1234567 “kopi” Wednesday, March 11, 2009
  36. 36. www Wednesday, March 11, 2009
  37. 37. 3. hard to do, but not impossible. Wednesday, March 11, 2009
  38. 38. digital content research tools technology Wednesday, March 11, 2009
  39. 39. research tools Wednesday, March 11, 2009
  40. 40. coming soon. Wednesday, March 11, 2009
  41. 41. Wednesday, March 11, 2009
  42. 42. digital content Wednesday, March 11, 2009
  43. 43. >1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0 Wednesday, March 11, 2009
  44. 44. what do these ideas mean in a world of integrated data? Wednesday, March 11, 2009
  45. 45. interoperate with the public domain. Wednesday, March 11, 2009
  46. 46. announcing: personal genomes under CC∅, available via filesharing networks Wednesday, March 11, 2009
  47. 47. Wednesday, March 11, 2009
  48. 48. Wednesday, March 11, 2009
  49. 49. Wednesday, March 11, 2009
  50. 50. Wednesday, March 11, 2009
  51. 51. technology Wednesday, March 11, 2009
  52. 52. exponential content growth Wednesday, March 11, 2009
  53. 53. our brain capacity 1.00 0.75 0.50 0.25 0 1990 1994 1998 2002 Wednesday, March 11, 2009
  54. 54. 990+ databases http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1 Wednesday, March 11, 2009
  55. 55. “find me signal transduction genes in pyramidal neurons” Wednesday, March 11, 2009
  56. 56. “read 189,000 pages” is not the ideal answer. Wednesday, March 11, 2009
  57. 57. Wednesday, March 11, 2009
  58. 58. Wednesday, March 11, 2009
  59. 59. you need four data sources to answer the question. Mesh: Pyramidal Neurons prefix go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> prefix mesh: <http://purl.org/commons/record/mesh/> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix ro: <http://www.obofoundry.org/ro/ro.owl#> select ?genename ?processname Pubmed: Journal Articles where { graph <http://purl.org/commons/hcls/pubmesh> { ?paper ?p mesh:D017966 . ?article sc:identified_by_pmid ?paper. ?gene sc:describes_gene_or_gene_product_mentioned_by ?article. } graph <http://purl.org/commons/hcls/goa> Entrez Gene: Genes { ?protein rdfs:subClassOf ?res. ?res owl:onProperty ro:has_function. ?res owl:someValuesFrom ?res2. ?res2 owl:onProperty ro:realized_as. ?res2 owl:someValuesFrom ?process. graph <http://purl.org/commons/hcls/20070416/classrelations> {{?process <http://purl.org/obo/owl/obo#part_of> go:GO_0007166} union GO: Signal Transduction {?process rdfs:subClassOf go:GO_0007166 }} ?protein rdfs:subClassOf ?parent. ?parent owl:equivalentClass ?res3. ?res3 owl:hasValue ?gene. } graph <http://purl.org/commons/hcls/gene> { ?gene rdfs:label ?genename } graph <http://purl.org/commons/hcls/20070416> { ?process rdfs:label ?processname} } Wednesday, March 11, 2009
  60. 60. precise answers to complex questions 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, March 11, 2009
  61. 61. we can turn ugly query code into a link http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3Chttp%3A%2F%2Fpurl.org%2Fobo%2Fowl%2FGO%23%3E %0Aprefix%20rdfs%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0Aprefix%20owl%3A %20%3Chttp%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23%3E%0Aprefix%20mesh%3A%20%3Chttp%3A%2F%2Fpurl.org %2Fcommons%2Frecord%2Fmesh%2F%3E%0Aprefix%20sc%3A%20%3Chttp%3A%2F%2Fpurl.org%2Fscience%2Fowl %2Fsciencecommons%2F%3E%0Aprefix%20ro%3A%20%3Chttp%3A%2F%2Fwww.obofoundry.org%2Fro%2Fro.owl%23%3E%0A %0Aselect%20%3Fgenename%20%3Fprocessname%0Awhere%0A%7B%20%20graph%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons %2Fhcls%2Fpubmesh%3E%0A%20%20%20%20%20%7B%20%3Fpaper%20%3Fp%20mesh%3AD017966%20.%0A %20%20%20%20%20%20%20%3Farticle%20sc%3Aidentified_by_pmid%20%3Fpaper.%0A%20%20%20%20%20%20%20%3Fgene %20sc%3Adescribes_gene_or_gene_product_mentioned_by%20%3Farticle.%0A%20%20%20%20%20%7D%0A%20%20%20graph %20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2Fgoa%3E%0A%20%20%20%20%20%7B%20%3Fprotein%20rdfs %3AsubClassOf%20%3Fres.%0A%20%20%20%20%20%20%20%3Fres%20owl%3AonProperty%20ro%3Ahas_function.%0A %20%20%20%20%20%20%20%3Fres%20owl%3AsomeValuesFrom%20%3Fres2.%0A %20%20%20%20%20%20%20%3Fres2%20owl%3AonProperty%20ro%3Arealized_as.%0A %20%20%20%20%20%20%20%3Fres2%20owl%3AsomeValuesFrom%20%3Fprocess.%0A%20%20%20graph%20%3Chttp%3A%2F %2Fpurl.org%2Fcommons%2Fhcls%2F20070416%2Fclassrelations%3E%0A%20%20%20%20%20%7B%7B%3Fprocess%20%3Chttp %3A%2F%2Fpurl.org%2Fobo%2Fowl%2Fobo%23part_of%3E%20go%3AGO_0007166%7D%0A%20%20%20%20%20%20%20union %0A%20%20%20%20%20%20%7B%3Fprocess%20rdfs%3AsubClassOf%20go%3AGO_0007166%20%7D%7D%0A %20%20%20%20%20%20%20%3Fprotein%20rdfs%3AsubClassOf%20%3Fparent.%0A%20%20%20%20%20%20%20%3Fparent %20owl%3AequivalentClass%20%3Fres3.%0A%20%20%20%20%20%20%20%3Fres3%20owl%3AhasValue%20%3Fgene.%0A %20%20%20%20%20%20%7D%0A%20%20%20graph%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2Fgene%3E%0A %20%20%20%20%20%7B%20%3Fgene%20rdfs%3Alabel%20%3Fgenename%20%7D%0A%20%20%20graph%20%3Chttp%3A%2F %2Fpurl.org%2Fcommons%2Fhcls%2F20070416%3E%0A%20%20%20%20%20%7B%20%3Fprocess%20rdfs%3Alabel %20%3Fprocessname%7D%0A%7D&format=&maxrows=50 Wednesday, March 11, 2009
  62. 62. we can turn ugly query code into a link Wednesday, March 11, 2009
  63. 63. users can view and edit source prefix go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> prefix mesh: <http://purl.org/commons/record/mesh/> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix ro: <http://www.obofoundry.org/ro/ro.owl#> select ?genename ?processname where { graph <http://purl.org/commons/hcls/pubmesh> { ?paper ?p mesh:D009369 . ?article sc:identified_by_pmid ?paper. ?gene sc:describes_gene_or_gene_product_mentioned_by ?article. } graph <http://purl.org/commons/hcls/goa> { ?protein rdfs:subClassOf ?res. ?res owl:onProperty ro:has_function. ?res owl:someValuesFrom ?res2. ?res2 owl:onProperty ro:realized_as. ?res2 owl:someValuesFrom ?process. graph <http://purl.org/commons/hcls/20070416/classrelations> {{?process <http://purl.org/obo/owl/obo#part_of> go:GO_0006610} union {?process rdfs:subClassOf go:GO_0006610 }} ?protein rdfs:subClassOf ?parent. ?parent owl:equivalentClass ?res3. ?res3 owl:hasValue ?gene. } graph <http://purl.org/commons/hcls/gene> { ?gene rdfs:label ?genename } graph <http://purl.org/commons/hcls/20070416> { ?process rdfs:label ?processname} } Wednesday, March 11, 2009
  64. 64. collaborative question answering Wednesday, March 11, 2009
  65. 65. open = pleasant surprises. Wednesday, March 11, 2009
  66. 66. google maps for brain images http://sparql.neurocommons.org:8890/map/#Kcnip3@2850,Kcnd1@2800 Wednesday, March 11, 2009
  67. 67. “one last thing” Wednesday, March 11, 2009
  68. 68. “it’s the links, dummy” - James Boyle aka “Boyle’s Law 2.0” Wednesday, March 11, 2009
  69. 69. Wednesday, March 11, 2009
  70. 70. Wednesday, March 11, 2009
  71. 71. Wednesday, March 11, 2009
  72. 72. Wednesday, March 11, 2009
  73. 73. Wednesday, March 11, 2009
  74. 74. Wednesday, March 11, 2009
  75. 75. Wednesday, March 11, 2009
  76. 76. Wednesday, March 11, 2009
  77. 77. Wednesday, March 11, 2009
  78. 78. http://ucsdbiolit.codeplex.com/ (project site) http://blogs.msdn.com/exscientia/ (developer blog) http://tinyurl.com/deypwt (video) Wednesday, March 11, 2009
  79. 79. closing the loop to open innovation: freedom to operate. Wednesday, March 11, 2009
  80. 80. reconstructing the research exemption Wednesday, March 11, 2009
  81. 81. Wednesday, March 11, 2009
  82. 82. thank you wilbanks@creativecommons.org http://sciencecommons.org Wednesday, March 11, 2009
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