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the information commons
                          and new norms for science

                                          kai...
1.
                          the “data web”



Tuesday, August 4, 2009
resist the temptation to treat
                         data as property.

    embrace the potential to treat data
       ...
© a
                          law as source of, and solution
                          for, the resistance in the wire.


...
data? not necessarily.

                            (it’s complicated)



Tuesday, August 4, 2009
2.
                          three layers of resistance:
                           legal, technical, semantic


Tuesday, ...
at each layer, tension between
                 “choice” and interoperability



Tuesday, August 4, 2009
legal
Tuesday, August 4, 2009
technical



Tuesday, August 4, 2009
semantic



Tuesday, August 4, 2009
copyright and databases

                            what’s protected? is it legal?

                                  fac...
database protections based on jurisdiction

                              sui generis,
                          “sweat of...
Tuesday, August 4, 2009
3.
            the data “rights” conundrum...



Tuesday, August 4, 2009
©
                          “creative expression”
Tuesday, August 4, 2009
is it creative?




Tuesday, August 4, 2009
is it creative?




Tuesday, August 4, 2009
is it creative?




Tuesday, August 4, 2009
category errors




Tuesday, August 4, 2009
the problem of...
                             Non-Commercial


                             for data


Tuesday, August 4,...
Non-Commercial


                          what’s a commercial use
                             of the data web?

Tuesday,...
the problem of...
                            Share Alike


                             for data


Tuesday, August 4, 2009
Tuesday, August 4, 2009
the problem of...
                             Attribution


                             for data


Tuesday, August 4, 20...
Tuesday, August 4, 2009
Tuesday, August 4, 2009
the problem of...
                            any license

                             for data


Tuesday, August 4, 2009
if property is the accepted metaphor, all
   of these terms will eventually appear.




Tuesday, August 4, 2009
uses triggered by “making a copy”




Tuesday, August 4, 2009
what if use is orthogonal
       to “making a copy” ?




Tuesday, August 4, 2009
attribution = license
                            citation = norms




Tuesday, August 4, 2009
attribution = license
                            citation = norms

       (which one applies whether or not
             ...
need for a legally accurate and
                                   simple solution

           reducing or eliminating the...
Tuesday, August 4, 2009
Tuesday, August 4, 2009
CC Zero waiver + SC norms



                 waive rights   public domain

         attribution / citation through
      ...
calls for data providers to waive all rights
           necessary for data extraction and re-use

                    requ...
Tuesday, August 4, 2009
Tuesday, August 4, 2009
Tuesday, August 4, 2009
Tuesday, August 4, 2009
the problem: how to achieve data
                interoperability?



Tuesday, August 4, 2009
“panton principles”




Tuesday, August 4, 2009
4.
                  Explicit dedication of data from public
                  science into the public domain via
        ...
technical considerations:

                           persistent URLs
                       open, stable namespaces
     ...
Tuesday, August 4, 2009
Tuesday, August 4, 2009
coffee




Tuesday, August 4, 2009
coffee
                              cafe




Tuesday, August 4, 2009
coffee
                              cafe
                                     kopi




Tuesday, August 4, 2009
coffee
                              cafe
                                     kopi
                                      ...
coffee
                              cafe
                                     kopi
                                      ...
espresso
                     coffee
                              cafe
                                     kopi
        ...
espresso
                     coffee
                              cafe
                                     kopi
        ...
espresso
                     coffee
                                cafe
                                       kopi
    ...
espresso
                     coffee
                                cafe
                                       kopi
    ...
“choice” or interoperability.

                                   (pick one)



Tuesday, August 4, 2009
Tuesday, August 4, 2009
converge on common names.

                              “coffee”


                              “cafe”               cof...
Tuesday, August 4, 2009
Tuesday, August 4, 2009
Tuesday, August 4, 2009
“read 189,000
                          papers” is not the
                            ideal answer.



Tuesday, August 4,...
better answers through better formats:


                                                                                 ...
select ?gene_name ?process_name
                   where
                   { PropertyValue(?pubmed_record, ?p, mesh:D0179...
DRD1, 1812      adenylate cyclase activation
                          ADRB2, 154      adenylate cyclase activation
      ...
turn ugly query code into a link
                http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3Chttp%3A...
Tuesday, August 4, 2009
remember edit
                          select ?gene_name ?process_name
                          where                   ...
query construction via edit source




Tuesday, August 4, 2009
infrastructure for a data web

                           the digital commons

                          law + technology ...
resist the temptation to treat
                                 data as property.

       embrace the potential to treat d...
design for maximum reuse

                          ensure the freedom to integrate

                 leverage existing op...
thank you
                          kaitlin@creativecommons.org
                                sciencecommons.org
       ...
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Information Commons and New Norms for Science

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A presentation on the information commons, data sharing and new norms of science. Presented at GeoNorth in Fairbanks, Alaska - August 4, 2009

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Transcript of "Information Commons and New Norms for Science"

  1. 1. the information commons and new norms for science kaitlin thaney program manager, science commons fairbanks, alaska - 4 august 2009 This presentation is licensed under the CreativeCommons-Attribution-3.0 license. Tuesday, August 4, 2009
  2. 2. 1. the “data web” Tuesday, August 4, 2009
  3. 3. resist the temptation to treat data as property. embrace the potential to treat data as a network resource. Tuesday, August 4, 2009
  4. 4. © a law as source of, and solution for, the resistance in the wire. Tuesday, August 4, 2009
  5. 5. data? not necessarily. (it’s complicated) Tuesday, August 4, 2009
  6. 6. 2. three layers of resistance: legal, technical, semantic Tuesday, August 4, 2009
  7. 7. at each layer, tension between “choice” and interoperability Tuesday, August 4, 2009
  8. 8. legal Tuesday, August 4, 2009
  9. 9. technical Tuesday, August 4, 2009
  10. 10. semantic Tuesday, August 4, 2009
  11. 11. copyright and databases what’s protected? is it legal? facts are free to what extent is there creative expression? Tuesday, August 4, 2009
  12. 12. database protections based on jurisdiction sui generis, “sweat of the brow” Crown copyright the list goes on .... Tuesday, August 4, 2009
  13. 13. Tuesday, August 4, 2009
  14. 14. 3. the data “rights” conundrum... Tuesday, August 4, 2009
  15. 15. © “creative expression” Tuesday, August 4, 2009
  16. 16. is it creative? Tuesday, August 4, 2009
  17. 17. is it creative? Tuesday, August 4, 2009
  18. 18. is it creative? Tuesday, August 4, 2009
  19. 19. category errors Tuesday, August 4, 2009
  20. 20. the problem of... Non-Commercial for data Tuesday, August 4, 2009
  21. 21. Non-Commercial what’s a commercial use of the data web? Tuesday, August 4, 2009
  22. 22. the problem of... Share Alike for data Tuesday, August 4, 2009
  23. 23. Tuesday, August 4, 2009
  24. 24. the problem of... Attribution for data Tuesday, August 4, 2009
  25. 25. Tuesday, August 4, 2009
  26. 26. Tuesday, August 4, 2009
  27. 27. the problem of... any license for data Tuesday, August 4, 2009
  28. 28. if property is the accepted metaphor, all of these terms will eventually appear. Tuesday, August 4, 2009
  29. 29. uses triggered by “making a copy” Tuesday, August 4, 2009
  30. 30. what if use is orthogonal to “making a copy” ? Tuesday, August 4, 2009
  31. 31. attribution = license citation = norms Tuesday, August 4, 2009
  32. 32. attribution = license citation = norms (which one applies whether or not a copy is made?) Tuesday, August 4, 2009
  33. 33. need for a legally accurate and simple solution reducing or eliminating the need to make the distinction of what’s protected requires modular, standards based approach to licensing Tuesday, August 4, 2009
  34. 34. Tuesday, August 4, 2009
  35. 35. Tuesday, August 4, 2009
  36. 36. CC Zero waiver + SC norms waive rights public domain attribution / citation through community norms, not a contract Tuesday, August 4, 2009
  37. 37. calls for data providers to waive all rights necessary for data extraction and re-use requires provider place no additional obligations (like share-alike) to limit downstream use request behavior (like attribution) through norms and terms of use Tuesday, August 4, 2009
  38. 38. Tuesday, August 4, 2009
  39. 39. Tuesday, August 4, 2009
  40. 40. Tuesday, August 4, 2009
  41. 41. Tuesday, August 4, 2009
  42. 42. the problem: how to achieve data interoperability? Tuesday, August 4, 2009
  43. 43. “panton principles” Tuesday, August 4, 2009
  44. 44. 4. Explicit dedication of data from public science into the public domain via PDDL or CCZero is strongly recommended and ensures compliance with both the Science Commons Protocol for Implementing Open Access Data and the Open Knowledge Definition as applied to data. Tuesday, August 4, 2009
  45. 45. technical considerations: persistent URLs open, stable namespaces standards, standards, standards facilitate integration, interoperability and more ... Tuesday, August 4, 2009
  46. 46. Tuesday, August 4, 2009
  47. 47. Tuesday, August 4, 2009
  48. 48. coffee Tuesday, August 4, 2009
  49. 49. coffee cafe Tuesday, August 4, 2009
  50. 50. coffee cafe kopi Tuesday, August 4, 2009
  51. 51. coffee cafe kopi cafezinho Tuesday, August 4, 2009
  52. 52. coffee cafe kopi cafezinho koffee Tuesday, August 4, 2009
  53. 53. espresso coffee cafe kopi cafezinho koffee Tuesday, August 4, 2009
  54. 54. espresso coffee cafe kopi cafezinho latte koffee Tuesday, August 4, 2009
  55. 55. espresso coffee cafe kopi cafezinho latte koffee mocha Tuesday, August 4, 2009
  56. 56. espresso coffee cafe kopi cafezinho latte koffee mocha americano Tuesday, August 4, 2009
  57. 57. “choice” or interoperability. (pick one) Tuesday, August 4, 2009
  58. 58. Tuesday, August 4, 2009
  59. 59. converge on common names. “coffee” “cafe” coffee “kopi” http://ontology.foo.org/1234567 Tuesday, August 4, 2009
  60. 60. Tuesday, August 4, 2009
  61. 61. Tuesday, August 4, 2009
  62. 62. Tuesday, August 4, 2009
  63. 63. “read 189,000 papers” is not the ideal answer. Tuesday, August 4, 2009
  64. 64. better answers through better formats: Mesh: Pyramidal Neurons select ?gene_name ?process_name where Pubmed: Journal Articles { PropertyValue(?pubmed_record, ?p, mesh:D017966) PropertyValue(?article, sc:identified_by_pmid , ?pubmed_record) PropertyValue(?gene_record, sc:describes_gene_or_gene_product_mentioned_by, ?article) SubClassOf(?protein, some(ro:has_function, some(ro:realized_as, ?process))) SubClassOf(?process, or(go:GO_0007166, some(ro:part_of, go:GO_0007166)) Entrez Gene: Genes SubClassOf(?protein, some(sc:is_protein_gene_product_of_dna_described_by,?gene_record)) Annotation(?gene_record,rdfs:label,{?gene_name}) } Annotation(?process,rdfs:label,?process_name) GO: Signal Transduction Tuesday, August 4, 2009
  65. 65. select ?gene_name ?process_name where { PropertyValue(?pubmed_record, ?p, mesh:D017966) PropertyValue(?article, sc:identified_by_pmid , ?pubmed_record) PropertyValue(?gene_record, sc:describes_gene_or_gene_product_mentioned_by, ?article) SubClassOf(?protein, some(ro:has_function, some(ro:realized_as, ?process))) SubClassOf(?process, or(go:GO_0007166, some(ro:part_of, go:GO_0007166)) SubClassOf(?protein, some(sc:is_protein_gene_product_of_dna_described_by,?gene_record)) Annotation(?gene_record,rdfs:label,{?gene_name}) Annotation(?process,rdfs:label,?process_name) } why you need inference and rigor... Tuesday, August 4, 2009
  66. 66. 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 ` Tuesday, August 4, 2009
  67. 67. 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 Tuesday, August 4, 2009
  68. 68. Tuesday, August 4, 2009
  69. 69. remember edit select ?gene_name ?process_name where source? { PropertyValue(?pubmed_record, ?p, mesh:D009369) PropertyValue(?article, sc:identified_by_pmid , ?pubmed_record) PropertyValue(?gene_record, sc:describes_gene_or_gene_product_mentioned_by, ?article) SubClassOf(?protein, some(ro:has_function, some(ro:realized_as, ?process))) SubClassOf(?process, or(go:GO_0006610, some(ro:part_of, go:GO_0006610)) SubClassOf(?protein, some(sc:is_protein_gene_product_of_dna_described_by,?gene_record)) Annotation(?gene_record,rdfs:label,{?gene_name}) Annotation(?process,rdfs:label,?process_name) } Tuesday, August 4, 2009
  70. 70. query construction via edit source Tuesday, August 4, 2009
  71. 71. infrastructure for a data web the digital commons law + technology + content + community Tuesday, August 4, 2009
  72. 72. resist the temptation to treat data as property. embrace the potential to treat data as a network resource. Tuesday, August 4, 2009
  73. 73. design for maximum reuse ensure the freedom to integrate leverage existing open infrastructure allows for snap together integration of the tools, data, research literature Tuesday, August 4, 2009
  74. 74. thank you kaitlin@creativecommons.org sciencecommons.org neurocommons.org Tuesday, August 4, 2009
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