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Semweb Scionline09

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Semantic Web slides for my workshop at Science Online 09.

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Semweb Scionline09

  1. 1. 1. simple + open = WIN
  2. 2. individual manufacture design institution source: Rossini & Wilbanks
  3. 3. individual manufacture design institution
  4. 4. individual manufacture design institutionally mediated institution
  5. 5. “Joy’s Law”: most of the smart people work somewhere else.
  6. 6. individual manufacture design institution
  7. 7. open innovation: purposive inflows and outflows of knowledge to accelerate internal innovation expand the capacity of the external market to generate internally useful knowledge the business model is at the center of value creation and capture
  8. 8. depends on the quantity, requires both new quality, legal availability, behavior by R&D and technical usability of entities and the the knowledge emergence of intermediaries
  9. 9. individual manufacture design institution
  10. 10. individual network mediated manufacture design institution
  11. 11. user innovation: “all innovation is local” knowledge is sticky users solve their own problems
  12. 12. traditional collaboration: negotiated, low-volume, high-density information sharing
  13. 13. distributed collaboration: automated, high- volume, low-density information sharing
  14. 14. the real “tragedy of the commons” = we can do this for shoes, not for science.
  15. 15. scientists don’t share what they know very well.
  16. 16. IPR. funding models. inertia. incentive structures.
  17. 17. IPR. funding models. inertia. incentive structures. no web for data.
  18. 18. 2. building the web for data.
  19. 19. the “semantic web”
  20. 20. making computers understand things
  21. 21. making computers understand links between documents links to Web page Web page
  22. 22. making computers understand relationships between concepts causes drinking coffee feel awake
  23. 23. causes drink coee feel awake
  24. 24. bed person get out of located at last subevent does not want wants get out of after causes drink coee feel awake first subevent subevent causes feel jittery open eyes after after make coee pour coee pick up cup drink is a is for located in coee cafe property of often near often near wet cup sugar
  25. 25. 3. blood and guts: what the semantic web is.
  26. 26. lots of specifications.
  27. 27. we need a Domain Name System for concepts: 192.168.1.1 http://sciencecommons.org coffee http://ontology.foo.org/coffee
  28. 28. http://ontology.foo.org/causes causes drinking coffee feel awake http://ontology.foo.org/drinking coffee http://ontology.foo.org/feel awake
  29. 29. use the web to integrate information from different places and different names “coffee” coffee “cafe” http://ontology.foo.org/coffee “kopi”
  30. 30. Resource Description Framework directed - every arc has a direction labelled - every arc has a label pseudo-graph - there can be more then one arc between the same two nodes http://www.betaversion.org/~stefano/linotype/news/57/
  31. 31. “literals” this blog ---(contains)--- this news this news ---(has title)--- quot;Semantic Web 101quot; this news ---(was written on)--- quot;20040404quot;[date] this news ---(has content)--- quot;htmlbody.../body/htmlquot; “reification” this news ---(has category)--- quot;semantic webquot; [this news ---(has category)--- quot;semantic webquot;] ---(added by)--- stefano
  32. 32. bootstrap via GRDDL http://www.w3.org/TR/grddl/
  33. 33. RDFa - RDF in HTML
  34. 34. http://www.w3.org/2006/07/SWD/RDFa/primer/
  35. 35. Web Ontology Language
  36. 36. Web Ontology Language this property is transitive. (owl:TransitiveProperty) [Example of transitive properties are quot;belongs to the same organizationquot;, while quot;is friend ofquot; is not] this property is symmetric. (owl:SymmetricProperty) [Example of a symmetric property is quot;works withquot;, while quot;being father ofquot; is not.] this property is the inverse of this other one (owl:inverseOf) [Example of two inverse properties are quot;being parent ofquot; and quot;being child ofquot;] this property is equivalent to that one (owl:equivalentProperty) this node is the same as that one (owl:sameAs) this relationship can appear only these many times (owl:cardinality) [Example, one can have only one biological father]
  37. 37. SPARQL
  38. 38. 4. a proof of concept: the Neurocommons project
  39. 39. open source data integration
  40. 40. formatting digital knowledge into re- usable building blocks for composition into new knowledge.
  41. 41. e pluribus unum.
  42. 42. uses: “DNS for life sciences” API to the public domain enhanced document markup activity center analysis
  43. 43. get precise answers out of existing databases and resources 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# Pubmed: Journal Articles select ?genename ?processname 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 {?process rdfs:subClassOf go:GO_0007166 }} GO: Signal Transduction ?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} }
  44. 44. 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 `
  45. 45. transforms complex queries into links 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%7Dformat=maxrows=50
  46. 46. transforms complex queries into links
  47. 47. view source, 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 Mesh: Cancer mesh:D009369 { ?paper ?p . ?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 go:GO_0006610} {{?process http://purl.org/obo/owl/obo#part_of union go:GO_0006610 }} GO: Ribosomal Protein {?process rdfs:subClassOf ?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} }
  48. 48. “mashups” in science “While brain maps until now have been similar to a traditional encyclopedia, the Allen Brain Atlas is more like Google Earth.”
  49. 49. that’s more like it.
  50. 50. 800,000,000+ RDF “triples” pre-formatted queries pathway analytic software donated by MLNM uses $5,000 of off-the-shelf hardware bundled with Virtuouso open source triple store download, mirror, fork. http://neurocommons.org

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