Harvard Shared Informatics Retreat Talk

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    Harvard Shared Informatics Retreat Talk - Presentation Transcript

    1. uncommon knowledge and open innovation 16 january 2009 john wilbanks creative commons / science commons
    2. metcalfe’s law
    3. “if free, and technically enabled, information trends towards connectivity and increased value”
    4. information knowledge?
    5. digitization changes knowledge journals, databases, ontologies, wikis, annotations...
    6. why no disruptions like Metcalfe’s Law for knowledge?
    7. disruptive processes can’t be planned in advance.
    8. disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow.
    9. disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow. ...and not innovative.
    10. 1. stable systems are resistant to change on multiple levels.
    11. © creative expression
    12. the container, not the facts.
    13. the container, not the facts. © locks the container. but
    14. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
    15. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
    16. indexing: disallowed. http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
    17. creative work?
    18. 40 minutes per year
    19. Dorothea Salo, http://cavlec.yarinareth.net/2008/10/31/miniature-disasters-and-minor-catastrophes/
    20. the existing system is robust against disruption the existing system is robust against disruption
    21. 2. the “digital commons” presents us with a potential way out.
    22. “the commons”
    23. small contributions. snap-together licensing. technically enabled.
    24. “the commons”
    25. knowledge rights
    26. Copyright All Rights Reserved No Rights Reserved
    27. Copyright All Rights Reserved No Rights Reserved
    28. Ported to 50 Jurisdictions
    29. 160M
    30. CC BY-NC-SA
    31. 3. our knowledge containers are outdated.
    32. solves the legal problem
    33. over 200 years at one paper/day
    34. building a web for data: the “semantic web”
    35. causes drink coee feel awake
    36. 192.168.1.1 http://sciencecommons.org coffee http://ontology.foo.org/coffee
    37. bed person get out of bed located at last subevent does not want wants get out of bed after causes drink coee feel awake first subevent subevent causes feel jittery open eyes after after make coee pour coee pick up cup drink is a is for located in coee cafe property of often near often near wet cup sugar
    38. “packages”
    39. scalable aggregation
    40. 4. accelerating the scientific cycles via the commons.
    41. whichever we choose, we need some way for computers to help us theorize, and to leverage the work of others (either to build on or to use in creative anarchy)
    42. exponential content growth
    43. our brain capacity 5.00 3.75 2.50 1.25 0 1990 1994 1998 2002
    44. but if we can work together...
    45. Open Access Content
    46. making knowledge legally and technically available for re-use and composition into new knowledge.
    47. c >1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0
    48. + + + is it legal? + + + + +
    49. conflicts with the protection instinct
    50. conflicts with the protection instinct the protection instinct is sometimes an instinct to protect “freedom”
    51. “a biologist would rather share her toothbrush than her data.” - carole goble
    52. Open Source Data Integration
    53. a repository of ontologies, namespaces, and integrated databases.
    54. e pluribus unum.
    55. uses: “DNS for life sciences” API to the public domain enhanced document markup activity center analysis
    56. we can transform complex queries into links 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> { ?protein rdfs:subClassOf ?res. Entrez Gene: Genes ?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} }
    57. 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 `
    58. we can transform complex queries into links 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
    59. we can transform complex queries into links
    60. we can help scholars “remix” queries 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> Mesh: Cancer mesh:D009369 { ?paper ?p . ?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> go:GO_0006610} {{?process <http://purl.org/obo/owl/obo#part_of> union GO: Ribosomal Protein go:GO_0006610 }} {?process rdfs:subClassOf ?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} }
    61. we can build a corpus of queries as links
    62. “mashups” in science “While brain maps until now have been similar to a traditional encyclopedia, the Allen Brain Atlas is more like Google Earth.”
    63. ...that’s better.
    64. 5. reports from the front lines: the same things that prevent change can foster change...
    65. open law, balanced incentives, and distributed workloads
    66. Open Access Research Tools
    67. making the tacit knowledge encoded in materials and data available at high speed and low transaction costs.
    68. user interface to technology transfer core contract grants the right to do research
    69. “one-click” for DNA and materials
    70. ibridge
    71. build offer through simple set of choices (post-authentication)
    72. scientist readable lawyer readable machine readable
    73. the public domain
    74. eco-patent commons linux patent commons company a company b “sharing networks”
    75. commercial use academic research control freedom corporate research “some rights reserved”
    76. conclusion?
    77. use existing systems.
    78. hack around problems.
    79. create new ways to measure.
    80. build your own commons.
    81. thank you wilbanks@creativecommons.org http://sciencecommons.org
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