crossref user meeting
            boston, ma
        18 november 2008

            john wilbanks
creative commons / scienc...
threadless
knowledge gaps
  process failures
 transaction costs
lost opportunities
knowledge gaps
                  process failures
                 transaction costs
                lost opportunities


...
knowledge gaps
  process failures
 transaction costs
lost opportunities
knowledge gaps
                  process failures
                 transaction costs
                lost opportunities


...
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.

     ....
process change comes more slowly than
      information product change
process change comes more slowly than
          information product change




the knowledge network requires multiple pro...
1.
stable systems are resistant to process
      change on multiple levels.
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
the pre-existing system has blocks in
place to prevent process disruption.
40 minutes per year
nih policy.
more staff,
 please.
Dorothea Salo, http://cavlec.yarinareth.net/2008/10/31/miniature-disasters-and-minor-catastrophes/
tension between meeting the demands
of adding content and providing
services
copyright + incentives + labor = FAIL
2.
   reports from the front lines: building a
process innovation is really, really hard.
“the commons”
knowledge rights
“digital commons”

   interoperability
low transaction costs
 law and technology
user interface to copyright
140,000,000+ digital objects online
        under our licenses

licenses “ported” to 45+ countries

  integrated with Goog...
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
creative
 work?
what do these
 ideas mean in
   a world of
integrated data?
+
+        +         +




+   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”
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   ...
•and junk) (quality control: spam
 extension


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

•co...
(too much work for
      coffee)
(distributed, networked
approaches start 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.
Project A        Project B        Project C




      A’s name         B’s name         C’s name
        for X            ...
Project A        Project B              Project C

                        common name
                           for X
  ...
naming: database records
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
3.
collaboration is the essential factor
        for the knowledge web.
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...
that’s what this “collaboration” stuff is all about
that’s what this “collaboration” stuff is all about




 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?
conclusion?
1. to crossref?
names for use in semantic web
doi:10.1007/
doi:10.1007/s10067-006-0283-5

               or

info:doi:10.1007/s10067-006-0283-5
doi:10.1007/s10067-006-0283-5

                    or

    info:doi:10.1007/s10067-006-0283-5


http://dx.doi.org/10.1007/...
2. to .org?
estate planning.
put a copy in a dark archive

give the keys to trusted 3rd parties
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
                ...
3. to .com?
services.
“In any case, it is clear that a library containing all possible
 books, arranged at random, is equivalent (as a source of...
thank you

wilbanks@creativecommons.org

  http://sciencecommons.org
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Crossref Wilbanks
Upcoming SlideShare
Loading in...5
×

Crossref Wilbanks

1,931

Published on

Published in: Education, Technology
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total Views
1,931
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
14
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide

Crossref Wilbanks

  1. 1. crossref user meeting boston, ma 18 november 2008 john wilbanks creative commons / science commons
  2. 2. threadless
  3. 3. knowledge gaps process failures transaction costs lost opportunities
  4. 4. knowledge gaps process failures transaction costs lost opportunities is the answer more information?
  5. 5. knowledge gaps process failures transaction costs lost opportunities
  6. 6. knowledge gaps process failures transaction costs lost opportunities is the answer more information? or process innovation?
  7. 7. disruptive processes can’t be planned in advance.
  8. 8. disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow.
  9. 9. disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow. ...and not innovative.
  10. 10. process change comes more slowly than information product change
  11. 11. process change comes more slowly than information product change the knowledge network requires multiple process changes to come into being.
  12. 12. 1. stable systems are resistant to process change on multiple levels.
  13. 13. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  14. 14. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  15. 15. indexing: disallowed. http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
  16. 16. the pre-existing system has blocks in place to prevent process disruption.
  17. 17. 40 minutes per year
  18. 18. nih policy.
  19. 19. more staff, please.
  20. 20. Dorothea Salo, http://cavlec.yarinareth.net/2008/10/31/miniature-disasters-and-minor-catastrophes/
  21. 21. tension between meeting the demands of adding content and providing services
  22. 22. copyright + incentives + labor = FAIL
  23. 23. 2. reports from the front lines: building a process innovation is really, really hard.
  24. 24. “the commons”
  25. 25. knowledge rights
  26. 26. “digital commons” interoperability low transaction costs law and technology
  27. 27. user interface to copyright
  28. 28. 140,000,000+ digital objects online under our licenses licenses “ported” to 45+ countries integrated with Google, Yahoo, Firefox, Microsoft Office...
  29. 29. Open Access Content
  30. 30. “running code”
  31. 31. c >1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0
  32. 32. creative work?
  33. 33. what do these ideas mean in a world of integrated data?
  34. 34. +
  35. 35. + + + + is it legal? + + + +
  36. 36. a protocol, not a license
  37. 37. conflicts with the protection instinct
  38. 38. conflicts with the protection instinct the protection instinct is sometimes an instinct to protect “freedom”
  39. 39. solves the legal problem
  40. 40. but not the container problem.
  41. 41. building a web for data: the “semantic web”
  42. 42. building a web for data: the “semantic web”
  43. 43. making computers understand links between documents links to Web page Web page
  44. 44. making computers understand relationships between concepts causes drinking coffee feel awake
  45. 45. •and junk) (quality control: spam extension •integrity(brand confusion, loss of remix and attribution) •common protocols or to formats (failure to adhere technology) •nature of all Web things...) persistence (the transient
  46. 46. (too much work for coffee)
  47. 47. (distributed, networked approaches start to look pretty good)
  48. 48. web 2.0, science 3.0, what about making Google work better?
  49. 49. over 200 years at one paper/day
  50. 50. what you want is a list of genes. not a list of documents.
  51. 51. Open Source Data Integration
  52. 52. a repository of ontologies, namespaces, and integrated databases.
  53. 53. Project A Project B Project C A’s name B’s name C’s name for X for X for X A’s version B’s version C’s version of, or info of, or info of, or info about, X about, X about, X
  54. 54. Project A Project B Project C common name for X common name common name for X for X shared ‘about’ RDF A’s version of, B’s version C’s version or info about, of, or info of, or info X about, X about, X
  55. 55. naming: database records
  56. 56. 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 `
  57. 57. e pluribus unum.
  58. 58. 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} }
  59. 59. 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
  60. 60. we can transform complex queries into links
  61. 61. 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} }
  62. 62. we can build a corpus of queries as links
  63. 63. we can re-use cultural tools for scholarship
  64. 64. 3. collaboration is the essential factor for the knowledge web.
  65. 65. exponential content growth
  66. 66. our brain capacity 5.00 3.75 2.50 1.25 0 1990 1994 1998 2002
  67. 67. but if we can work together...
  68. 68. that’s what this “collaboration” stuff is all about
  69. 69. that’s what this “collaboration” stuff is all about the infrastructure for this is very, very shaky.
  70. 70. 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/>
  71. 71. what are the odds that the organizations making the namespaces will be here in 50 years? 100 years?
  72. 72. conclusion?
  73. 73. 1. to crossref? names for use in semantic web
  74. 74. doi:10.1007/
  75. 75. doi:10.1007/s10067-006-0283-5 or info:doi:10.1007/s10067-006-0283-5
  76. 76. doi:10.1007/s10067-006-0283-5 or info:doi:10.1007/s10067-006-0283-5 http://dx.doi.org/10.1007/s10067-006-0283-5
  77. 77. 2. to .org? estate planning.
  78. 78. put a copy in a dark archive give the keys to trusted 3rd parties
  79. 79. free as in speech
  80. 80. free as in speech free as in beer
  81. 81. free as in speech free as in beer free as in a puppy
  82. 82. 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
  83. 83. 3. to .com? services.
  84. 84. “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
  85. 85. thank you wilbanks@creativecommons.org http://sciencecommons.org
  1. A particular slide catching your eye?

    Clipping is a handy way to collect important slides you want to go back to later.

×