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Building Linked Web Communities

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  • 1. building linked web communities in biomedicine 29 april 2009 boston, ma john wilbanks Thursday, June 4, 2009
  • 2. Thursday, June 4, 2009
  • 3. “compatibly communicating” Thursday, June 4, 2009
  • 4. “compatibly communicating” devices. Thursday, June 4, 2009
  • 5. what about knowledge? Thursday, June 4, 2009
  • 6. what about knowledge? journal articles data ontologies annotations wikis Thursday, June 4, 2009
  • 7. Thursday, June 4, 2009
  • 8. Thursday, June 4, 2009
  • 9. Thursday, June 4, 2009
  • 10. Thursday, June 4, 2009
  • 11. Thursday, June 4, 2009
  • 12. “compatibly communicating” Thursday, June 4, 2009
  • 13. “compatibly communicating” Thursday, June 4, 2009
  • 14. 1. making it “web” - the access principle Thursday, June 4, 2009
  • 15. Thursday, June 4, 2009
  • 16. Thursday, June 4, 2009
  • 17. Thursday, June 4, 2009
  • 18. the right to make and distribute “copies” the right to make and distribute “derivatives” Thursday, June 4, 2009
  • 19. the law surrounds us, even in its absence. Thursday, June 4, 2009
  • 20. the law surrounds us, even in its absence. Thursday, June 4, 2009
  • 21. ignoring the law does not scale. Thursday, June 4, 2009
  • 22. Thursday, June 4, 2009
  • 23. Thursday, June 4, 2009
  • 24. Thursday, June 4, 2009
  • 25. the digital commons - another network layer. Thursday, June 4, 2009
  • 26. computers tcp/ip documents html/http knowledge commons Thursday, June 4, 2009
  • 27. Thursday, June 4, 2009
  • 28. Licensing Step 1: Choose Conditions Attribution Share Alike Non-Commercial No Derivative Works Thursday, June 4, 2009
  • 29. Licensing Step 2: Receive a License Thursday, June 4, 2009
  • 30. Thursday, June 4, 2009
  • 31. Thursday, June 4, 2009
  • 32. International Jurisdictions Thursday, June 4, 2009
  • 33. Licensed Objects via G/Y! Thursday, June 4, 2009
  • 34. Thursday, June 4, 2009
  • 35. Thursday, June 4, 2009
  • 36. >1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0 Thursday, June 4, 2009
  • 37. what do these ideas mean in a world of integrated data? Thursday, June 4, 2009
  • 38. license propagation: whatsoever you do to the least of the databases, you do to the integrated knowledgebase Thursday, June 4, 2009
  • 39. “community spirit - with teeth” norms + public domain Thursday, June 4, 2009
  • 40. Thursday, June 4, 2009
  • 41. Thursday, June 4, 2009
  • 42. Thursday, June 4, 2009
  • 43. Thursday, June 4, 2009
  • 44. Thursday, June 4, 2009
  • 45. Thursday, June 4, 2009
  • 46. Thursday, June 4, 2009
  • 47. Thursday, June 4, 2009
  • 48. Thursday, June 4, 2009
  • 49. Thursday, June 4, 2009
  • 50. Thursday, June 4, 2009
  • 51. Thursday, June 4, 2009
  • 52. Thursday, June 4, 2009
  • 53. Thursday, June 4, 2009
  • 54. Thursday, June 4, 2009
  • 55. open rights. multiplicity of incentives. distributed workloads. Thursday, June 4, 2009
  • 56. 2. making it “linked” - the names and containers problem Thursday, June 4, 2009
  • 57. Thursday, June 4, 2009
  • 58. Thursday, June 4, 2009
  • 59. Thursday, June 4, 2009
  • 60. 990+ databases http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1 Thursday, June 4, 2009
  • 61. Thursday, June 4, 2009
  • 62. making computers understand things Thursday, June 4, 2009
  • 63. making computers understand links between documents links to Web page Web page Thursday, June 4, 2009
  • 64. making computers understand relationships between ideas causes drinking coffee feel awake Thursday, June 4, 2009
  • 65. using the web to integrate data and databases “coffee” “cafe” coffee http://ontology.foo.org/1234567 “kopi” Thursday, June 4, 2009
  • 66. www Thursday, June 4, 2009
  • 67. “domain name system” Thursday, June 4, 2009
  • 68. “domain name system” or, “when it’s worth being strict about ontologies” Thursday, June 4, 2009
  • 69. Thursday, June 4, 2009
  • 70. google maps for brain images? http://sparql.neurocommons.org:8890/map/#Kcnip3@2850,Kcnd1@2800 Thursday, June 4, 2009
  • 71. “find me signal transduction genes in pyramidal neurons” “what are the potential ‘locks’ for alzheimers?” Thursday, June 4, 2009
  • 72. Thursday, June 4, 2009
  • 73. “read 189,000 papers” is not the ideal answer. Thursday, June 4, 2009
  • 74. better answers through better formats: 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> 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 {?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} } Thursday, June 4, 2009
  • 75. 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, June 4, 2009
  • 76. 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, June 4, 2009
  • 77. we can turn ugly query code into a link Thursday, June 4, 2009
  • 78. 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) } Thursday, June 4, 2009
  • 79. 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... Thursday, June 4, 2009
  • 80. 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) } Thursday, June 4, 2009
  • 81. users remix query code Thursday, June 4, 2009
  • 82. Thursday, June 4, 2009
  • 83. Thursday, June 4, 2009
  • 84. Thursday, June 4, 2009
  • 85. Thursday, June 4, 2009
  • 86. Thursday, June 4, 2009
  • 87. Thursday, June 4, 2009
  • 88. Thursday, June 4, 2009
  • 89. Thursday, June 4, 2009
  • 90. Thursday, June 4, 2009
  • 91. Thursday, June 4, 2009
  • 92. http://ucsdbiolit.codeplex.com/ (project site) http://blogs.msdn.com/exscientia/ (developer blog) http://tinyurl.com/deypwt (video) Thursday, June 4, 2009
  • 93. 3. making it “community” - the induction problem Thursday, June 4, 2009
  • 94. Thursday, June 4, 2009
  • 95. “...we don’t ask what the incentive is for the electrons to leave home. We say that the current results from an emergent property of the system, which we call induction.” Thursday, June 4, 2009
  • 96. “...we don’t ask what the incentive is for the electrons to leave home. We say that the current results from an emergent property of the system, which we call induction.” “The question we ask is ‘what’s the resistance of the wire?’” Thursday, June 4, 2009
  • 97. Thursday, June 4, 2009
  • 98. Thursday, June 4, 2009
  • 99. Thursday, June 4, 2009
  • 100. Thursday, June 4, 2009
  • 101. Thursday, June 4, 2009
  • 102. Thursday, June 4, 2009
  • 103. Thursday, June 4, 2009
  • 104. what can you do? Thursday, June 4, 2009
  • 105. what can you do? 1. solve locally, share globally. 2. standards, standards, standards. 3. lead by example. Thursday, June 4, 2009
  • 106. thank you John D. and Catherine T. MacArthur Foundation Ewing Marion Kauffman Foundation CHDI Foundation Omidyar Network Nike Thursday, June 4, 2009