Search

Cbmi Nlm Fellows

Loading...

Flash Player 9 (or above) is needed to view presentations.
We have detected that you do not have it on your computer. To install it, go here.

0 comments

Post a comment

    Post a comment
    Embed Video
    Edit your comment Cancel

    Notes on slide 1

    Favorites, Groups & Events

    Cbmi Nlm Fellows - Presentation Transcript

    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

    + john wilbanksjohn wilbanks, 7 months ago

    custom

    478 views, 0 favs, 0 embeds more stats

    Presentation to the CBMI NLM Fellows (informaticist more

    More info about this document

    © All Rights Reserved

    Go to text version

    • Total Views 478
      • 478 on SlideShare
      • 0 from embeds
    • Comments 0
    • Favorites 0
    • Downloads 3
    Most viewed embeds

    more

    All embeds

    less

    Flagged as inappropriate Flag as inappropriate
    Flag as inappropriate

    Select your reason for flagging this presentation as inappropriate. If needed, use the feedback form to let us know more details.

    Cancel
    File a copyright complaint
    Having problems? Go to our helpdesk?

    Tags

    -->
    Search
    RSS Feed
    What's new?

    © 2009 SlideShare Inc. All Rights Reserved