university of michigan
  health informatics grand rounds
            ann arbor, mi
          13 january 2009

            ...
metcalfe’s law
“information wants to be free”
“if free, and technically enabled,
    information trends towards
connectivity and increased value”
information   knowledge?
digitization changes knowledge

journals, databases, ontologies, wikis, annotations...
why no disruptions like Metcalfe’s
      Law for knowledge?
disruptive processes can’t be
     planned in advance.
disruptive processes can’t be
      planned in advance.

planned innovation tends to be
    incremental, and slow.
disruptive processes can’t be
      planned in advance.

planned innovation tends to be
    incremental, and slow.

     ....
1.
stable systems are resistant to change on
              multiple levels.
©
creative expression
the container, not the facts.
the container, not the facts.

      © locks the container.
but
IGFBP-5 plays a role in the
regulation of cellular senescence
via a p53-dependent pathway
and in aging-associated
vascular...
IGFBP-5 plays a role in the
regulation of cellular senescence
via a p53-dependent pathway
and in aging-associated
vascular...
indexing: disallowed.




 http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
creative
 work?
40 minutes per year
nih policy.
Dorothea Salo, http://cavlec.yarinareth.net/2008/10/31/miniature-disasters-and-minor-catastrophes/
the existing system is robust against
              disruption



the existing system is robust against
              disr...
this is how evolved systems resist change:
 at multiple levels, with multiple fail-safes.
2.
the “digital commons” presents us with a
             potential way out.
“the commons”
rivalrous
      v.
non-rivalrous
small contributions.
snap-together licensing.
  technically enabled.
“the commons”
“intellectual property”
knowledge rights
Copyright
All Rights
Reserved



                         No Rights
                         Reserved
Copyright
All Rights
Reserved



                         No Rights
                         Reserved
licensing
step 1: choose conditions


  Attribution               Share Alike



  Non-Commercial            No Derivative...
Ported to 50
Jurisdictions
160M
160M
Photo: Dennis Stefani, (c) Mrs. Me, Inc., 2008, made available under a CC BY-NC-ND license
CC BY-NC-SA
3.
our knowledge containers are outdated.
solves the legal problem
but not the container
      problem.
over 200
   years at
one paper/day
what you want is
    a list of genes.

not a list of documents.
building a web for data:
  the “semantic web”
causes
drink coee            feel awake
we need a Domain Name System for concepts:

192.168.1.1             http://sciencecommons.org

  coffee                htt...
http://ontology.foo.org/causes



                                          causes
          drinking coffee              ...
bed
                                                                                    person

                          ...
databases as unique entities,
instead of nodes in a network
“packages”
scalable aggregation
4.
accelerating the scientific cycles via the
               commons.
whichever we choose, we need some way
  for computers to help us theorize, and to
leverage the work of others (either to b...
exponential content growth
our brain capacity


5.00



3.75



2.50



1.25



  0
   1990   1994                    1998   2002
but if we can work together...
Open Access Content
making knowledge legally and
technically available for re-use and
composition into new knowledge.
c
1000 journals under CC

  image from the public library of science
  licensed to the public under CC-BY 3.0
running policy code
    (w. SPARC)
+        +         +




    is it legal?
+                  +




+        +         +
conflicts with the protection instinct
conflicts with the protection instinct

the protection instinct is sometimes an instinct to
                protect “freedo...
“a biologist would rather share her toothbrush than her data.”
                        - carole goble
Open Source
Data Integration
a repository of ontologies,
namespaces, and integrated
         databases.
e pluribus unum.
uses:
   “DNS for life sciences”
  API to the public domain
enhanced document markup
    activity center analysis
we can transform complex queries into links


                                                                  Mesh: Pyra...
DRD1, 1812      adenylate cyclase activation
ADRB2, 154      adenylate cyclase activation
ADRB2, 154      arrestin mediate...
we can transform complex queries into links
http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3Chttp%3A%2F%2F...
we can transform complex queries into links
we can help scholars “remix” queries
  prefix go: http://purl.org/obo/owl/GO#
  prefix rdfs: http://www.w3.org/2000/01/rdf-s...
we can build a corpus of queries as links
“mashups” in science




“While brain maps until now have
been similar to a traditional
encyclopedia, the Allen Brain Atla...
...that’s better.
5.
 reports from the front lines: the same things
that prevent change can foster change...
open law, balanced incentives, and distributed
                 workloads
Open Access
Research Tools
making the tacit knowledge
encoded in materials and data
available at high speed and low
        transaction costs.
user interface to
  technology transfer

core contract grants the
  right to do research
“one-click”
for clinical data
“one-click”
for DNA and
   materials
ibridge
build offer through simple set of choices
          (post-authentication)
scientist readable




                     lawyer readable




                             machine readable
the public domain
conclusion?
don’t wait.
use existing systems.
hack around problems.
create new ways to measure.
build your own commons.
thank you

wilbanks@creativecommons.org

  http://sciencecommons.org
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University of Michigan, Health Informatics Grand Rounds presentation, 13 January 2009.

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Transcript of "Umich Grand Rounds"

  1. 1. university of michigan health informatics grand rounds ann arbor, mi 13 january 2009 john wilbanks creative commons / science commons
  2. 2. metcalfe’s law
  3. 3. “information wants to be free”
  4. 4. “if free, and technically enabled, information trends towards connectivity and increased value”
  5. 5. information knowledge?
  6. 6. digitization changes knowledge journals, databases, ontologies, wikis, annotations...
  7. 7. why no disruptions like Metcalfe’s Law for knowledge?
  8. 8. disruptive processes can’t be planned in advance.
  9. 9. disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow.
  10. 10. disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow. ...and not innovative.
  11. 11. 1. stable systems are resistant to change on multiple levels.
  12. 12. © creative expression
  13. 13. the container, not the facts.
  14. 14. the container, not the facts. © locks the container. but
  15. 15. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  16. 16. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  17. 17. indexing: disallowed. http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
  18. 18. creative work?
  19. 19. 40 minutes per year
  20. 20. nih policy.
  21. 21. Dorothea Salo, http://cavlec.yarinareth.net/2008/10/31/miniature-disasters-and-minor-catastrophes/
  22. 22. the existing system is robust against disruption the existing system is robust against disruption
  23. 23. this is how evolved systems resist change: at multiple levels, with multiple fail-safes.
  24. 24. 2. the “digital commons” presents us with a potential way out.
  25. 25. “the commons”
  26. 26. rivalrous v. non-rivalrous
  27. 27. small contributions. snap-together licensing. technically enabled.
  28. 28. “the commons”
  29. 29. “intellectual property”
  30. 30. knowledge rights
  31. 31. Copyright All Rights Reserved No Rights Reserved
  32. 32. Copyright All Rights Reserved No Rights Reserved
  33. 33. licensing step 1: choose conditions Attribution Share Alike Non-Commercial No Derivative Works
  34. 34. Ported to 50 Jurisdictions
  35. 35. 160M
  36. 36. 160M
  37. 37. Photo: Dennis Stefani, (c) Mrs. Me, Inc., 2008, made available under a CC BY-NC-ND license
  38. 38. CC BY-NC-SA
  39. 39. 3. our knowledge containers are outdated.
  40. 40. solves the legal problem
  41. 41. but not the container problem.
  42. 42. over 200 years at one paper/day
  43. 43. what you want is a list of genes. not a list of documents.
  44. 44. building a web for data: the “semantic web”
  45. 45. causes drink coee feel awake
  46. 46. we need a Domain Name System for concepts: 192.168.1.1 http://sciencecommons.org coffee http://ontology.foo.org/coffee
  47. 47. http://ontology.foo.org/causes causes drinking coffee feel awake http://ontology.foo.org/drinking coffee http://ontology.foo.org/feel awake h
  48. 48. 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
  49. 49. databases as unique entities, instead of nodes in a network
  50. 50. “packages”
  51. 51. scalable aggregation
  52. 52. 4. accelerating the scientific cycles via the commons.
  53. 53. 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)
  54. 54. exponential content growth
  55. 55. our brain capacity 5.00 3.75 2.50 1.25 0 1990 1994 1998 2002
  56. 56. but if we can work together...
  57. 57. Open Access Content
  58. 58. making knowledge legally and technically available for re-use and composition into new knowledge.
  59. 59. c 1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0
  60. 60. running policy code (w. SPARC)
  61. 61. + + + is it legal? + + + + +
  62. 62. conflicts with the protection instinct
  63. 63. conflicts with the protection instinct the protection instinct is sometimes an instinct to protect “freedom”
  64. 64. “a biologist would rather share her toothbrush than her data.” - carole goble
  65. 65. Open Source Data Integration
  66. 66. a repository of ontologies, namespaces, and integrated databases.
  67. 67. e pluribus unum.
  68. 68. uses: “DNS for life sciences” API to the public domain enhanced document markup activity center analysis
  69. 69. 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} }
  70. 70. 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 `
  71. 71. 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%7Dformat=maxrows=50
  72. 72. we can transform complex queries into links
  73. 73. 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} }
  74. 74. we can build a corpus of queries as links
  75. 75. “mashups” in science “While brain maps until now have been similar to a traditional encyclopedia, the Allen Brain Atlas is more like Google Earth.”
  76. 76. ...that’s better.
  77. 77. 5. reports from the front lines: the same things that prevent change can foster change...
  78. 78. open law, balanced incentives, and distributed workloads
  79. 79. Open Access Research Tools
  80. 80. making the tacit knowledge encoded in materials and data available at high speed and low transaction costs.
  81. 81. user interface to technology transfer core contract grants the right to do research
  82. 82. “one-click” for clinical data
  83. 83. “one-click” for DNA and materials
  84. 84. ibridge
  85. 85. build offer through simple set of choices (post-authentication)
  86. 86. scientist readable lawyer readable machine readable
  87. 87. the public domain
  88. 88. conclusion?
  89. 89. don’t wait.
  90. 90. use existing systems.
  91. 91. hack around problems.
  92. 92. create new ways to measure.
  93. 93. build your own commons.
  94. 94. thank you wilbanks@creativecommons.org http://sciencecommons.org
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