dcc conference
        edinburgh, scotland

radical sharing: transforming science?

            john wilbanks
creative com...
1. the “alternative” to radical sharing is sharing
                  inefficiently.
science is not unlike wikipedia...
science is not unlike wikipedia...
it is based on publishing (make public)
it advances via individual action
it advances discrete edit by discrete edit
science is not unlike wikipedia...
science is not unlike wikipedia...




...except authenticated, and expensive.
given trust ratings by peer review
science is not unlike wikipedia...




...except authenticated, and expensive.
             (and slow!)
and what of the curator?
“necessarily involves tangible objects of
               some sort”
from a technical perspective
from a technical perspective
inefficient and expensive ecosystem of
  processes to peer-produce and
     review scholarly content
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.

     ....
2.
stable systems are resistant to change on
              multiple levels.
©
creative expression
the container, not the facts.
the container, not the facts.

but   © locks the container.
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
what do these
 ideas mean in
   a world of
integrated data?
creative
 work?
40 minutes per year
nih policy.
i can has
repository staff?
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...
3.
  reports from the front lines: building a
commons is really, really hard - and can’t
      be done without sharing.
Open Access Content
“running code”
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?   +




+        +         +
a protocol, not a license
conflicts with the protection instinct
conflicts with the protection instinct

the protection instinct is sometimes an instinct to
                protect “freedo...
solves the legal problem
but not the container
      problem.
building a web for data:
  the “semantic web”
making computers understand links between documents



                     links to
       Web page                    We...
making computers understand relationships between concepts




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



                                          causes
          drinking coffee              ...
use the web to
           integrate information
            from different places
             and different names
“coffee...
(too much work for
      coffee)
(radical sharing starts to
   look pretty good)
web 2.0, science 3.0, what about making
          Google work better?
over 200
   years at
one paper/day
what you want is
    a list of genes.

not a list of documents.
Open Source
Data Integration
a repository of ontologies,
namespaces, and integrated
         databases.
DRD1, 1812      adenylate cyclase activation
ADRB2, 154      adenylate cyclase activation
ADRB2, 154      arrestin mediate...
e pluribus unum.
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%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/rd...
we can build a corpus of queries as links
we can re-use cultural tools for scholarship
4.
radical sharing is a smart choice.
simple + open = WIN
content

 code

physical
knowledge

 content

  code

 physical
open copyright, balanced incentives, and
        distributed workloads
the infrastructure for this is very, very shaky.
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix rdfs: <http://www.w3...
what are the odds that the organizations making the
 namespaces will be here in 50 years? 100 years?
and what about ontologies?
•and junk) (quality control: spam
 extension


•integrity and attribution) loss of
 remix (brand confusion,


•common(fail...
“it’s complicated”
“In any case, it is clear that a library containing all possible
 books, arranged at random, is equivalent (as a source of...
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...
conclusion?
don’t wait.
use existing systems.
enlist everyone to curate.
create new ways to measure.
invest in curation.
free as in speech
free as in speech
 free as in beer
free as in speech
 free as in beer
free as in a puppy
free as in speech
                                         free as in beer

Average Cost Of 100 Pound Dog
                ...
thank you

wilbanks@creativecommons.org

  http://sciencecommons.org
DCC Radical Sharing Meeting
DCC Radical Sharing Meeting
DCC Radical Sharing Meeting
DCC Radical Sharing Meeting
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DCC Radical Sharing Meeting
DCC Radical Sharing Meeting
DCC Radical Sharing Meeting
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DCC Radical Sharing Meeting
DCC Radical Sharing Meeting
DCC Radical Sharing Meeting
DCC Radical Sharing Meeting
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DCC Radical Sharing Meeting
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DCC Radical Sharing Meeting

  1. 1. dcc conference edinburgh, scotland radical sharing: transforming science? john wilbanks creative commons / science commons
  2. 2. 1. the “alternative” to radical sharing is sharing inefficiently.
  3. 3. science is not unlike wikipedia...
  4. 4. science is not unlike wikipedia...
  5. 5. it is based on publishing (make public)
  6. 6. it advances via individual action
  7. 7. it advances discrete edit by discrete edit
  8. 8. science is not unlike wikipedia...
  9. 9. science is not unlike wikipedia... ...except authenticated, and expensive.
  10. 10. given trust ratings by peer review
  11. 11. science is not unlike wikipedia... ...except authenticated, and expensive. (and slow!)
  12. 12. and what of the curator?
  13. 13. “necessarily involves tangible objects of some sort”
  14. 14. from a technical perspective
  15. 15. from a technical perspective
  16. 16. inefficient and expensive ecosystem of processes to peer-produce and review scholarly content
  17. 17. disruptive processes can’t be planned in advance.
  18. 18. disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow.
  19. 19. disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow. ...and not innovative.
  20. 20. 2. stable systems are resistant to change on multiple levels.
  21. 21. © creative expression
  22. 22. the container, not the facts.
  23. 23. the container, not the facts. but © locks the container.
  24. 24. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  25. 25. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  26. 26. indexing: disallowed. http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
  27. 27. what do these ideas mean in a world of integrated data?
  28. 28. creative work?
  29. 29. 40 minutes per year
  30. 30. nih policy.
  31. 31. i can has repository staff?
  32. 32. Dorothea Salo, http://cavlec.yarinareth.net/2008/10/31/miniature-disasters-and-minor-catastrophes/
  33. 33. the existing system is robust against disruption the existing system is robust against disruption
  34. 34. 3. reports from the front lines: building a commons is really, really hard - and can’t be done without sharing.
  35. 35. Open Access Content
  36. 36. “running code”
  37. 37. c >1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0
  38. 38. running policy code (w. SPARC)
  39. 39. +
  40. 40. + + + + is it legal? + + + +
  41. 41. a protocol, not a license
  42. 42. conflicts with the protection instinct
  43. 43. conflicts with the protection instinct the protection instinct is sometimes an instinct to protect “freedom”
  44. 44. solves the legal problem
  45. 45. but not the container problem.
  46. 46. building a web for data: the “semantic web”
  47. 47. making computers understand links between documents links to Web page Web page
  48. 48. making computers understand relationships between concepts causes drinking coffee feel awake
  49. 49. http://ontology.foo.org/causes causes drinking coffee feel awake http://ontology.foo.org/drinking coffee http://ontology.foo.org/feel awake h
  50. 50. use the web to integrate information from different places and different names “coffee” “cafe” coffee http://ontology.foo.org/coffee “kopi”
  51. 51. (too much work for coffee)
  52. 52. (radical sharing starts to look pretty good)
  53. 53. web 2.0, science 3.0, what about making Google work better?
  54. 54. over 200 years at one paper/day
  55. 55. what you want is a list of genes. not a list of documents.
  56. 56. Open Source Data Integration
  57. 57. a repository of ontologies, namespaces, and integrated databases.
  58. 58. 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 `
  59. 59. e pluribus unum.
  60. 60. 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> { ?protein rdfs:subClassOf ?res. ?res owl:onProperty ro:has_function. ?res owl:someValuesFrom ?res2. Entrez Gene: Genes ?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} }
  61. 61. 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
  62. 62. we can transform complex queries into links
  63. 63. 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} }
  64. 64. we can build a corpus of queries as links
  65. 65. we can re-use cultural tools for scholarship
  66. 66. 4. radical sharing is a smart choice.
  67. 67. simple + open = WIN
  68. 68. content code physical
  69. 69. knowledge content code physical
  70. 70. open copyright, balanced incentives, and distributed workloads
  71. 71. the infrastructure for this is very, very shaky.
  72. 72. prefix dc: <http://purl.org/dc/elements/1.1/> prefix skos: <http://www.w3.org/2004/02/skos/core#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix foaf: <http://xmlns.com/foaf/0.1/>
  73. 73. what are the odds that the organizations making the namespaces will be here in 50 years? 100 years?
  74. 74. and what about ontologies?
  75. 75. •and junk) (quality control: spam extension •integrity and attribution) loss of remix (brand confusion, •common(failure to adhere to formats protocols or technology) •of all Web things...) persistence (the transient nature
  76. 76. “it’s complicated”
  77. 77. “In any case, it is clear that a library containing all possible books, arranged at random, is equivalent (as a source of information) to a library containing zero books.” http://en.wikipedia.org/wiki/The_Library_of_Babel
  78. 78. exponential content growth
  79. 79. our brain capacity 5.00 3.75 2.50 1.25 0 1990 1994 1998 2002
  80. 80. but if we can work together...
  81. 81. conclusion?
  82. 82. don’t wait.
  83. 83. use existing systems.
  84. 84. enlist everyone to curate.
  85. 85. create new ways to measure.
  86. 86. invest in curation.
  87. 87. free as in speech
  88. 88. free as in speech free as in beer
  89. 89. free as in speech free as in beer free as in a puppy
  90. 90. free as in speech free as in beer Average Cost Of 100 Pound Dog free as in a puppy Over A Year Good Quality Dog Food $70 x 12 = $840 Dog Accessories (collar, leash, etc.) $30 Dog Toys $30 - $50 Vaccines $35 Flea, Tick, & Heartworm Prevention $320 Dog Treats $200 Boarding $100 - $200 (at $15 - $20 a day) Emergency Costs $0 - $2500 or more Total $1375 or much more
  91. 91. thank you wilbanks@creativecommons.org http://sciencecommons.org
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