CBMI NLM training fellows




Thursday, April 9, 2009
1.
         the law surrounds us, even in its absence.




Thursday, April 9, 2009
Thursday, April 9, 2009
free/libre open source

Thursday, April 9, 2009
open culture

Thursday, April 9, 2009
open access

Thursday, April 9, 2009
the right to make and distribute “copies”

                          the right to make and distribute “derivatives”




Th...
the digital commons - another
                                   network layer.




Thursday, April 9, 2009
computers    tcp/ip

                   documents    html/http

                    knowledge   commons


Thursday, April ...
open rights.

    multiplicity of incentives.

       distributed workloads.




Thursday, April 9, 2009
commons as infrastructure
Thursday, April 9, 2009
open science?




Thursday, April 9, 2009
is the goal freedom or methodology?
                        or both?
                  or something else?



Thursday, Apr...
2.
       science on the net: digitized, not digital.




Thursday, April 9, 2009
no metcalfe’s law for science yet.




Thursday, April 9, 2009
no metcalfe’s law for science yet.




Thursday, April 9, 2009
stable systems have “immune”
                               responses to change.




Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
web assumptions and web scale FAIL




Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
the model is at the center of
                  value creation and capture
Thursday, April 9, 2009
Thursday, April 9, 2009
would you share your map?
Thursday, April 9, 2009
1,596,270,108 internet users
                          (http://www.internetworldstats.com/stats.htm)
Thursday, April 9, 20...
Thursday, April 9, 2009
.0001 of internet users = wikipedia
Thursday, April 9, 2009
.0001 of geneticists = ?
Thursday, April 9, 2009
there is no crowd.
Thursday, April 9, 2009
3.
                    make the few more powerful via
                          object-orientation...




Thursday, April ...
computers    tcp/ip

                   documents    html/http

                    knowledge   semantics


Thursday, Apri...
making computers understand things




Thursday, April 9, 2009
making computers understand links between documents




                                          links to
               ...
making computers understand relationships between ideas




                                            causes
           ...
URLs for concepts,
                                       not just pages
                          “coffee”




          ...
www


Thursday, April 9, 2009
4.
                          hard to do, but not impossible.




Thursday, April 9, 2009
digital content




                  research tools         technology

Thursday, April 9, 2009
research tools

Thursday, April 9, 2009
coming soon.
Thursday, April 9, 2009
Thursday, April 9, 2009
digital content




Thursday, April 9, 2009
>1000 journals under CC
                             image from the public library of science
                            ...
what do these
                 ideas mean in
                   a world of
               integrated data?




Thursday, A...
interoperate with the public domain.




Thursday, April 9, 2009
announcing: personal genomes under
                          CC∅, available via filesharing networks




Thursday, April 9,...
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
technology

Thursday, April 9, 2009
990+ databases




                          http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1



Thursday, Apr...
“find me signal transduction genes in pyramidal neurons”




Thursday, April 9, 2009
“read 189,000 pages”
                             is not the ideal
                                 answer.



Thursday, A...
Thursday, April 9, 2009
you need four data sources to answer the question.


                                                                     ...
precise answers to complex questions
                          DRD1, 1812      adenylate cyclase activation
              ...
we can turn ugly query code into a link
                http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3C...
we can turn ugly query code into a link




Thursday, April 9, 2009
users can view and edit source
                                        prefix go: <http://purl.org/obo/owl/GO#>
          ...
collaborative question answering




Thursday, April 9, 2009
open = pleasant surprises.




Thursday, April 9, 2009
google maps for brain images




                          http://sparql.neurocommons.org:8890/map/#Kcnip3@2850,Kcnd1@2800...
“it’s the links, dummy”
                                - James Boyle

                          aka “Boyle’s Law 2.0”



...
“papers”



                          IGFBP-5 plays a role in the regulation of cellular
                          senesce...
“networked
           knowledge”



                          IGFBP-5 plays a role in the regulation of cellular
         ...
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
Thursday, April 9, 2009
http://ucsdbiolit.codeplex.com/
                                    (project site)

                          http://blogs...
Thursday, April 9, 2009
what can you do?




Thursday, April 9, 2009
what can you do?

                            1. solve locally, share globally.

                          2. standards, s...
thank you

                          wilbanks@creativecommons.org

                            http://sciencecommons.org

...
Upcoming SlideShare
Loading in...5
×

Cbmi Nlm Fellows

1,400

Published on

Presentation to the CBMI NLM Fellows (informaticists mainly) monthly course.

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
1,400
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
4
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Cbmi Nlm Fellows

  1. 1. CBMI NLM training fellows Thursday, April 9, 2009
  2. 2. 1. the law surrounds us, even in its absence. Thursday, April 9, 2009
  3. 3. Thursday, April 9, 2009
  4. 4. free/libre open source Thursday, April 9, 2009
  5. 5. open culture Thursday, April 9, 2009
  6. 6. open access Thursday, April 9, 2009
  7. 7. the right to make and distribute “copies” the right to make and distribute “derivatives” Thursday, April 9, 2009
  8. 8. the digital commons - another network layer. Thursday, April 9, 2009
  9. 9. computers tcp/ip documents html/http knowledge commons Thursday, April 9, 2009
  10. 10. open rights. multiplicity of incentives. distributed workloads. Thursday, April 9, 2009
  11. 11. commons as infrastructure Thursday, April 9, 2009
  12. 12. open science? Thursday, April 9, 2009
  13. 13. is the goal freedom or methodology? or both? or something else? Thursday, April 9, 2009
  14. 14. 2. science on the net: digitized, not digital. Thursday, April 9, 2009
  15. 15. no metcalfe’s law for science yet. Thursday, April 9, 2009
  16. 16. no metcalfe’s law for science yet. Thursday, April 9, 2009
  17. 17. stable systems have “immune” responses to change. Thursday, April 9, 2009
  18. 18. Thursday, April 9, 2009
  19. 19. Thursday, April 9, 2009
  20. 20. Thursday, April 9, 2009
  21. 21. Thursday, April 9, 2009
  22. 22. web assumptions and web scale FAIL Thursday, April 9, 2009
  23. 23. Thursday, April 9, 2009
  24. 24. Thursday, April 9, 2009
  25. 25. the model is at the center of value creation and capture Thursday, April 9, 2009
  26. 26. Thursday, April 9, 2009
  27. 27. would you share your map? Thursday, April 9, 2009
  28. 28. 1,596,270,108 internet users (http://www.internetworldstats.com/stats.htm) Thursday, April 9, 2009
  29. 29. Thursday, April 9, 2009
  30. 30. .0001 of internet users = wikipedia Thursday, April 9, 2009
  31. 31. .0001 of geneticists = ? Thursday, April 9, 2009
  32. 32. there is no crowd. Thursday, April 9, 2009
  33. 33. 3. make the few more powerful via object-orientation... Thursday, April 9, 2009
  34. 34. computers tcp/ip documents html/http knowledge semantics Thursday, April 9, 2009
  35. 35. making computers understand things Thursday, April 9, 2009
  36. 36. making computers understand links between documents links to Web page Web page Thursday, April 9, 2009
  37. 37. making computers understand relationships between ideas causes drinking coffee feel awake Thursday, April 9, 2009
  38. 38. URLs for concepts, not just pages “coffee” coffee “cafe” http://ontology.foo.org/1234567 “kopi” Thursday, April 9, 2009
  39. 39. www Thursday, April 9, 2009
  40. 40. 4. hard to do, but not impossible. Thursday, April 9, 2009
  41. 41. digital content research tools technology Thursday, April 9, 2009
  42. 42. research tools Thursday, April 9, 2009
  43. 43. coming soon. Thursday, April 9, 2009
  44. 44. Thursday, April 9, 2009
  45. 45. digital content Thursday, April 9, 2009
  46. 46. >1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0 Thursday, April 9, 2009
  47. 47. what do these ideas mean in a world of integrated data? Thursday, April 9, 2009
  48. 48. interoperate with the public domain. Thursday, April 9, 2009
  49. 49. announcing: personal genomes under CC∅, available via filesharing networks Thursday, April 9, 2009
  50. 50. Thursday, April 9, 2009
  51. 51. Thursday, April 9, 2009
  52. 52. Thursday, April 9, 2009
  53. 53. Thursday, April 9, 2009
  54. 54. technology Thursday, April 9, 2009
  55. 55. 990+ databases http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1 Thursday, April 9, 2009
  56. 56. “find me signal transduction genes in pyramidal neurons” Thursday, April 9, 2009
  57. 57. “read 189,000 pages” is not the ideal answer. Thursday, April 9, 2009
  58. 58. Thursday, April 9, 2009
  59. 59. you need four data sources to answer the question. 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> 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 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} } Thursday, April 9, 2009
  60. 60. precise answers to complex questions 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 ` Thursday, April 9, 2009
  61. 61. we can 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 Thursday, April 9, 2009
  62. 62. we can turn ugly query code into a link Thursday, April 9, 2009
  63. 63. users can view and edit source 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> { ?paper ?p mesh:D009369 . ?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> {{?process <http://purl.org/obo/owl/obo#part_of> go:GO_0006610} union {?process rdfs:subClassOf go:GO_0006610 }} ?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} } Thursday, April 9, 2009
  64. 64. collaborative question answering Thursday, April 9, 2009
  65. 65. open = pleasant surprises. Thursday, April 9, 2009
  66. 66. google maps for brain images http://sparql.neurocommons.org:8890/map/#Kcnip3@2850,Kcnd1@2800 Thursday, April 9, 2009
  67. 67. “it’s the links, dummy” - James Boyle aka “Boyle’s Law 2.0” Thursday, April 9, 2009
  68. 68. “papers” IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases Thursday, April 9, 2009
  69. 69. “networked knowledge” IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases Thursday, April 9, 2009
  70. 70. Thursday, April 9, 2009
  71. 71. Thursday, April 9, 2009
  72. 72. Thursday, April 9, 2009
  73. 73. Thursday, April 9, 2009
  74. 74. Thursday, April 9, 2009
  75. 75. Thursday, April 9, 2009
  76. 76. Thursday, April 9, 2009
  77. 77. Thursday, April 9, 2009
  78. 78. http://ucsdbiolit.codeplex.com/ (project site) http://blogs.msdn.com/exscientia/ (developer blog) http://tinyurl.com/deypwt (video) Thursday, April 9, 2009
  79. 79. Thursday, April 9, 2009
  80. 80. what can you do? Thursday, April 9, 2009
  81. 81. what can you do? 1. solve locally, share globally. 2. standards, standards, standards. 3. lead by example. Thursday, April 9, 2009
  82. 82. thank you wilbanks@creativecommons.org http://sciencecommons.org Thursday, April 9, 2009
  1. Gostou de algum slide específico?

    Recortar slides é uma maneira fácil de colecionar informações para acessar mais tarde.

×