Building Linked Web Communities

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Building Linked Web Communities

  1. 1. building linked web communities in biomedicine 29 april 2009 boston, ma john wilbanks Thursday, June 4, 2009
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  3. 3. “compatibly communicating” Thursday, June 4, 2009
  4. 4. “compatibly communicating” devices. Thursday, June 4, 2009
  5. 5. what about knowledge? Thursday, June 4, 2009
  6. 6. what about knowledge? journal articles data ontologies annotations wikis Thursday, June 4, 2009
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  12. 12. “compatibly communicating” Thursday, June 4, 2009
  13. 13. “compatibly communicating” Thursday, June 4, 2009
  14. 14. 1. making it “web” - the access principle Thursday, June 4, 2009
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  18. 18. the right to make and distribute “copies” the right to make and distribute “derivatives” Thursday, June 4, 2009
  19. 19. the law surrounds us, even in its absence. Thursday, June 4, 2009
  20. 20. the law surrounds us, even in its absence. Thursday, June 4, 2009
  21. 21. ignoring the law does not scale. Thursday, June 4, 2009
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  25. 25. the digital commons - another network layer. Thursday, June 4, 2009
  26. 26. computers tcp/ip documents html/http knowledge commons Thursday, June 4, 2009
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  28. 28. Licensing Step 1: Choose Conditions Attribution Share Alike Non-Commercial No Derivative Works Thursday, June 4, 2009
  29. 29. Licensing Step 2: Receive a License Thursday, June 4, 2009
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  32. 32. International Jurisdictions Thursday, June 4, 2009
  33. 33. Licensed Objects via G/Y! Thursday, June 4, 2009
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  36. 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. 37. what do these ideas mean in a world of integrated data? Thursday, June 4, 2009
  38. 38. license propagation: whatsoever you do to the least of the databases, you do to the integrated knowledgebase Thursday, June 4, 2009
  39. 39. “community spirit - with teeth” norms + public domain Thursday, June 4, 2009
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  55. 55. open rights. multiplicity of incentives. distributed workloads. Thursday, June 4, 2009
  56. 56. 2. making it “linked” - the names and containers problem Thursday, June 4, 2009
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  60. 60. 990+ databases http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1 Thursday, June 4, 2009
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  62. 62. making computers understand things Thursday, June 4, 2009
  63. 63. making computers understand links between documents links to Web page Web page Thursday, June 4, 2009
  64. 64. making computers understand relationships between ideas causes drinking coffee feel awake Thursday, June 4, 2009
  65. 65. using the web to integrate data and databases “coffee” “cafe” coffee http://ontology.foo.org/1234567 “kopi” Thursday, June 4, 2009
  66. 66. www Thursday, June 4, 2009
  67. 67. “domain name system” Thursday, June 4, 2009
  68. 68. “domain name system” or, “when it’s worth being strict about ontologies” Thursday, June 4, 2009
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  70. 70. google maps for brain images? http://sparql.neurocommons.org:8890/map/#Kcnip3@2850,Kcnd1@2800 Thursday, June 4, 2009
  71. 71. “find me signal transduction genes in pyramidal neurons” “what are the potential ‘locks’ for alzheimers?” Thursday, June 4, 2009
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  73. 73. “read 189,000 papers” is not the ideal answer. Thursday, June 4, 2009
  74. 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. 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. 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. 77. we can turn ugly query code into a link Thursday, June 4, 2009
  78. 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. 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. 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. 81. users remix query code Thursday, June 4, 2009
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  92. 92. http://ucsdbiolit.codeplex.com/ (project site) http://blogs.msdn.com/exscientia/ (developer blog) http://tinyurl.com/deypwt (video) Thursday, June 4, 2009
  93. 93. 3. making it “community” - the induction problem Thursday, June 4, 2009
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  95. 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. 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
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  104. 104. what can you do? Thursday, June 4, 2009
  105. 105. what can you do? 1. solve locally, share globally. 2. standards, standards, standards. 3. lead by example. Thursday, June 4, 2009
  106. 106. thank you John D. and Catherine T. MacArthur Foundation Ewing Marion Kauffman Foundation CHDI Foundation Omidyar Network Nike Thursday, June 4, 2009

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