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MAJESTy seminar

           john wilbanks
science commons / creative commons
             2 october
            tokyo, jap...
most of the useful knowledge
       is inaccessible.
most of the useful knowledge
 is in the wrong technology.

we don’t h...
1. an answer lies in a
 cultural innovation
this presentation:
public domain in 2158
“By open access to the literature, we mean its free availability
on the public internet, permitting users to read, downloa...
“The only constraint on reproduction and distribution, and
the only role for copyright in this domain, should be to give
a...
c
Open Access Content




Open Source                        Open Access
Knowledge Management               Research Tools
(the web doesn’t work for research
   the way it works for culture)
Open Access Content
it all starts with the scholarly digital
   content: journals and databases
c
>1000 journals under CC

  image from the public library of science
  licensed to the public under CC-BY 3.0
promote
author’s
  rights
a protocol, not a license
solves the access
problem via contract.
Open Access
Research Tools
research materials represent an
 incredible investment in tacit
          knowledge
office supplies
   for science
there are no office
  superstores for
      science
no internet
marketplaces
 for science
everyone has to
 pre-authorize
    through
  institutions
needs
funding
the commons allows for
 “some rights reserved”
    options to share
Open Source
Knowledge Management
the commons approach works
 better than the regular Web
to manage science knowledge
88,400
results...
88,400
  results...
mainly papers.
over 200
   years at
one paper/day
what you want is
   a list of genes.

not a list of documents.
a mapped set of databases
integrated query
    endpoint
write code to answer questions:

            prefix go: <http://purl.org/obo/owl/GO#>
    prefix rdfs: <http://www.w3.org/...
88,400
  results...
mainly papers.
DRD1, 1812      adenylate cyclase activation
ADRB2, 154      adenylate cyclase activation
ADRB2, 154      arrestin mediate...
we can transform complex queries into links

            prefix go: <http://purl.org/obo/owl/GO#>
    prefix rdfs: <http:/...
we can transform complex queries into links

http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3Chttp%3A%2F%2...
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/...
the “view source” method of building
          a knowledge web
mashup-enabled
but it is now.
build your own.
  download ours.
   make it yours.
http://neurocommons.org
Open Access Content




Open Source                        Open Access
Knowledge Management               Research Tools
2. how do we enable
   construction of
knowledge models?
in the past, human-based model
  building could compete with
mathematics and data analysis...
models have to be composed
of sub-units - which in turn have
to be legally and technically
  available to model-builders
DNA
the two key discoveries:
one was revealed in a regular
     laboratory report.
the two key facts:
one was revealed without
      permission
humans can’t build
 models to scale
   anymore.
it’s not just life sciences.
3. the commons lets us
 transform knowledge
into model-compatible
        elements.
common knowledge
common knowledge

“things we all know”
common knowledge

 “things someone
knows, somewhere”
“the web”


no organizing topics
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...
all the data and all the
 ideas: building blocks
indexing: disallowed.




  http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
solves the legal problem
but not the
technical problem.
common knowledge

“things we can all build
        upon”
what do you have to do to some
  objects to get them to compose
 something - to bring into existence
some further thing ma...
common knowledge

 “things that are in a
knowledge network”
physical
01-23-45-67-89-ab
code

physical
C:
content

 code

physical
papers contain
     ideas,
  like boxes
         </html>
contain books
knowledge

 content

  code

 physical
causes
drink coffee            feel awake




 a network
of concepts
bed
                                                                                 person

  located at                 ...
(too much work
   for coffee)
extending the commons to science:

connecting the right collaborators.
    facilitating big discoveries.
  ensuring credit...
with a little help from our friends.

    (crowds and computers)
destroying a guild
culture of knowledge
knowledge

 content

  code

 physical
creating a network
culture of knowledge
thank you

wilbanks@creativecommons.org

  http://sciencecommons.org
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
Waseda John Wilbanks
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Waseda John Wilbanks

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Transcript of "Waseda John Wilbanks"

  1. 1. MAJESTy seminar john wilbanks science commons / creative commons 2 october tokyo, japan
  2. 2. most of the useful knowledge is inaccessible. most of the useful knowledge is in the wrong technology. we don’t have enough people working on it.
  3. 3. 1. an answer lies in a cultural innovation
  4. 4. this presentation: public domain in 2158
  5. 5. “By open access to the literature, we mean its free availability on the public internet, permitting users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal or technical barriers other than those inseparable from gaining access to the internet itself.” image from the public library of science image from the public library of science licensed to the public under CC-BY 3.0 licensed to the public under CC-BY 3.0
  6. 6. “The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited” - the Budapest Open Access Initiative image from the public library of science image from the public library of science licensed to the public under CC-BY 3.0 licensed to the public under CC-BY 3.0
  7. 7. c
  8. 8. Open Access Content Open Source Open Access Knowledge Management Research Tools
  9. 9. (the web doesn’t work for research the way it works for culture)
  10. 10. Open Access Content
  11. 11. it all starts with the scholarly digital content: journals and databases
  12. 12. c >1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0
  13. 13. promote author’s rights
  14. 14. a protocol, not a license
  15. 15. solves the access problem via contract.
  16. 16. Open Access Research Tools
  17. 17. research materials represent an incredible investment in tacit knowledge
  18. 18. office supplies for science
  19. 19. there are no office superstores for science
  20. 20. no internet marketplaces for science
  21. 21. everyone has to pre-authorize through institutions
  22. 22. needs funding
  23. 23. the commons allows for “some rights reserved” options to share
  24. 24. Open Source Knowledge Management
  25. 25. the commons approach works better than the regular Web to manage science knowledge
  26. 26. 88,400 results...
  27. 27. 88,400 results... mainly papers.
  28. 28. over 200 years at one paper/day
  29. 29. what you want is a list of genes. not a list of documents.
  30. 30. a mapped set of databases
  31. 31. integrated query endpoint
  32. 32. write code to answer questions: prefix go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> Mesh: Pyramidal Neurons 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> Pubmed: Journal Articles { ?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 {?process rdfs:subClassOf go:GO_0007166 }} ?protein rdfs:subClassOf ?parent. ?parent owl:equivalentClass ?res3. GO: Signal Transduction ?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} }
  33. 33. 88,400 results... mainly papers.
  34. 34. 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 `
  35. 35. we can transform complex queries into links prefix go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> Mesh: Pyramidal Neurons 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> Pubmed: Journal Articles { ?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 {?process rdfs:subClassOf go:GO_0007166 }} ?protein rdfs:subClassOf ?parent. ?parent owl:equivalentClass ?res3. GO: Signal Transduction ?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} }
  36. 36. 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
  37. 37. we can transform complex queries into links
  38. 38. 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:D009369 { ?paper ?p ?article sc:identified_by_pmid ?paper. . Mesh: Cancer ?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 go:GO_0006610 }} {?process rdfs:subClassOf ?protein rdfs:subClassOf ?parent. GO: Ribosomal Protein ?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} }
  39. 39. the “view source” method of building a knowledge web
  40. 40. mashup-enabled
  41. 41. but it is now.
  42. 42. build your own. download ours. make it yours. http://neurocommons.org
  43. 43. Open Access Content Open Source Open Access Knowledge Management Research Tools
  44. 44. 2. how do we enable construction of knowledge models?
  45. 45. in the past, human-based model building could compete with mathematics and data analysis...
  46. 46. models have to be composed of sub-units - which in turn have to be legally and technically available to model-builders
  47. 47. DNA
  48. 48. the two key discoveries: one was revealed in a regular laboratory report.
  49. 49. the two key facts: one was revealed without permission
  50. 50. humans can’t build models to scale anymore.
  51. 51. it’s not just life sciences.
  52. 52. 3. the commons lets us transform knowledge into model-compatible elements.
  53. 53. common knowledge
  54. 54. common knowledge “things we all know”
  55. 55. common knowledge “things someone knows, somewhere”
  56. 56. “the web” no organizing topics
  57. 57. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  58. 58. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  59. 59. all the data and all the ideas: building blocks
  60. 60. indexing: disallowed. http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
  61. 61. solves the legal problem
  62. 62. but not the technical problem.
  63. 63. common knowledge “things we can all build upon”
  64. 64. what do you have to do to some objects to get them to compose something - to bring into existence some further thing made up of those objects?
  65. 65. common knowledge “things that are in a knowledge network”
  66. 66. physical
  67. 67. 01-23-45-67-89-ab
  68. 68. code physical
  69. 69. C:
  70. 70. content code physical
  71. 71. papers contain ideas, like boxes </html> contain books
  72. 72. knowledge content code physical
  73. 73. causes drink coffee feel awake a network of concepts
  74. 74. bed person located at get out of bed last subevent does not want wants get out of bed after causes drink coffee feel awake first subevent subevent causes feel jittery open eyes after after make coffee pour coffee pick up cup drink is a is for located in coffee cafe property of often near often near wet cup sugar
  75. 75. (too much work for coffee)
  76. 76. extending the commons to science: connecting the right collaborators. facilitating big discoveries. ensuring credit for one’s work.
  77. 77. with a little help from our friends. (crowds and computers)
  78. 78. destroying a guild culture of knowledge
  79. 79. knowledge content code physical
  80. 80. creating a network culture of knowledge
  81. 81. thank you wilbanks@creativecommons.org http://sciencecommons.org
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