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Etech Wilbanks

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    Etech Wilbanks - Presentation Transcript

    1. uncommon knowledge, open innovation Wednesday, March 11, 2009
    2. how do we make the web work for science? Wednesday, March 11, 2009
    3. we need more from what we know. Wednesday, March 11, 2009
    4. we need more from what we know. Wednesday, March 11, 2009
    5. “compatibly communicating” devices. Wednesday, March 11, 2009
    6. “compatibly communicating” knowledge? Wednesday, March 11, 2009
    7. 1. science on the net: digitized, not digital. Wednesday, March 11, 2009
    8. Wednesday, March 11, 2009
    9. Wednesday, March 11, 2009
    10. Wednesday, March 11, 2009
    11. Wednesday, March 11, 2009
    12. Wednesday, March 11, 2009
    13. stable systems have “immune” responses to change. Wednesday, March 11, 2009
    14. Wednesday, March 11, 2009
    15. Wednesday, March 11, 2009
    16. Wednesday, March 11, 2009
    17. there is no crowd. Wednesday, March 11, 2009
    18. the knowledge is uncommon. Wednesday, March 11, 2009
    19. 2. the digital commons - another network layer. Wednesday, March 11, 2009
    20. computers tcp/ip documents html/http knowledge commons Wednesday, March 11, 2009
    21. Wednesday, March 11, 2009
    22. socially constructed rights Wednesday, March 11, 2009
    23. “rivalrous goods” Wednesday, March 11, 2009
    24. socially constructed exceptions Wednesday, March 11, 2009
    25. the tragedy “rivalrous goods”the is anti-commons Wednesday, March 11, 2009
    26. open rights. multiplicity of incentives. distributed workloads. Wednesday, March 11, 2009
    27. Wednesday, March 11, 2009
    28. commons as infrastructure Wednesday, March 11, 2009
    29. computers tcp/ip documents html/http knowledge semantics Wednesday, March 11, 2009
    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. “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. making computers understand things Wednesday, March 11, 2009
    33. making computers understand links between documents links to Web page Web page Wednesday, March 11, 2009
    34. making computers understand relationships between ideas causes drinking coffee feel awake Wednesday, March 11, 2009
    35. URLs for concepts, not just pages “coffee” coffee “cafe” http://ontology.foo.org/1234567 “kopi” Wednesday, March 11, 2009
    36. www Wednesday, March 11, 2009
    37. 3. hard to do, but not impossible. Wednesday, March 11, 2009
    38. digital content research tools technology Wednesday, March 11, 2009
    39. research tools Wednesday, March 11, 2009
    40. coming soon. Wednesday, March 11, 2009
    41. Wednesday, March 11, 2009
    42. digital content Wednesday, March 11, 2009
    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. what do these ideas mean in a world of integrated data? Wednesday, March 11, 2009
    45. interoperate with the public domain. Wednesday, March 11, 2009
    46. announcing: personal genomes under CC∅, available via filesharing networks Wednesday, March 11, 2009
    47. Wednesday, March 11, 2009
    48. Wednesday, March 11, 2009
    49. Wednesday, March 11, 2009
    50. Wednesday, March 11, 2009
    51. technology Wednesday, March 11, 2009
    52. exponential content growth Wednesday, March 11, 2009
    53. our brain capacity 1.00 0.75 0.50 0.25 0 1990 1994 1998 2002 Wednesday, March 11, 2009
    54. 990+ databases http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1 Wednesday, March 11, 2009
    55. “find me signal transduction genes in pyramidal neurons” Wednesday, March 11, 2009
    56. “read 189,000 pages” is not the ideal answer. Wednesday, March 11, 2009
    57. Wednesday, March 11, 2009
    58. Wednesday, March 11, 2009
    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. 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. 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. we can turn ugly query code into a link Wednesday, March 11, 2009
    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. collaborative question answering Wednesday, March 11, 2009
    65. open = pleasant surprises. Wednesday, March 11, 2009
    66. google maps for brain images http://sparql.neurocommons.org:8890/map/#Kcnip3@2850,Kcnd1@2800 Wednesday, March 11, 2009
    67. “one last thing” Wednesday, March 11, 2009
    68. “it’s the links, dummy” - James Boyle aka “Boyle’s Law 2.0” Wednesday, March 11, 2009
    69. Wednesday, March 11, 2009
    70. Wednesday, March 11, 2009
    71. Wednesday, March 11, 2009
    72. Wednesday, March 11, 2009
    73. Wednesday, March 11, 2009
    74. Wednesday, March 11, 2009
    75. Wednesday, March 11, 2009
    76. Wednesday, March 11, 2009
    77. Wednesday, March 11, 2009
    78. http://ucsdbiolit.codeplex.com/ (project site) http://blogs.msdn.com/exscientia/ (developer blog) http://tinyurl.com/deypwt (video) Wednesday, March 11, 2009
    79. closing the loop to open innovation: freedom to operate. Wednesday, March 11, 2009
    80. reconstructing the research exemption Wednesday, March 11, 2009
    81. Wednesday, March 11, 2009
    82. thank you wilbanks@creativecommons.org http://sciencecommons.org Wednesday, March 11, 2009
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