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

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

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