etech wilbanks
TRANSCRIPT
uncommon knowledge, open innovation
Wednesday, March 11, 2009
how do we make the web work for science?
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we need more from what we know.
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we need more from what we know.
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“compatibly communicating”
devices.
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“compatibly communicating”
knowledge?
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1.science on the net: digitized, not digital.
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stable systems have “immune” responses to change.
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there is no crowd.Wednesday, March 11, 2009
the knowledge is uncommon.
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2.the digital commons - another
network layer.
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computers
documents
knowledge
tcp/ip
html/http
commons
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socially constructed rights
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“rivalrous goods”
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socially constructed exceptions
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“rivalrous goods”the tragedy
is theanti-commons
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open rights.
multiplicity of incentives.
distributed workloads.
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commons as infrastructureWednesday, March 11, 2009
computers
documents
knowledge
tcp/ip
html/http
semantics
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IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
“papers”
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IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
“networked knowledge”
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making computers understand things
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Web page Web pagelinks to
making computers understand links between documents
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drinking coffee feel awakecauses
making computers understand relationships between ideas
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coffee
“coffee”
“cafe”
“kopi” http://ontology.foo.org/1234567
URLs for concepts, not just pages
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www
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3.hard to do, but not impossible.
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digital content
research tools
digital content
technology
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research tools
digital contentWednesday, March 11, 2009
coming soon.Wednesday, March 11, 2009
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digital content
digital contentWednesday, March 11, 2009
image from the public library of sciencelicensed to the public under CC-BY 3.0
>1000 journals under CC
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what do these ideas mean in
a world of integrated data?
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interoperate with the public domain.
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announcing: personal genomes underCC∅, available via filesharing networks
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digital content
technology
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exponential content growthWednesday, March 11, 2009
0
0.25
0.50
0.75
1.00
1990 1994 1998 2002
our brain capacity
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http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1
990+ databases
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“find me signal transduction genes in pyramidal neurons”
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“read 189,000 pages” is not the ideal
answer.
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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 ?processnamewhere
{ 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>
{ ?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. ?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}}
Mesh: Pyramidal Neurons
Pubmed: Journal Articles
Entrez Gene: Genes
GO: Signal Transduction
you need four data sources to answer the question.
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DRD1, 1812 adenylate cyclase activationADRB2, 154 adenylate cyclase activationADRB2, 154 arrestin mediated desensitization of G-protein coupled receptor protein signaling pathwayDRD1IP, 50632 dopamine receptor signaling pathwayDRD1, 1812 dopamine receptor, adenylate cyclase activating pathwayDRD2, 1813 dopamine receptor, adenylate cyclase inhibiting pathwayGRM7, 2917 G-protein coupled receptor protein signaling pathwayGNG3, 2785 G-protein coupled receptor protein signaling pathwayGNG12, 55970 G-protein coupled receptor protein signaling pathwayDRD2, 1813 G-protein coupled receptor protein signaling pathwayADRB2, 154 G-protein coupled receptor protein signaling pathwayCALM3, 808 G-protein coupled receptor protein signaling pathwayHTR2A, 3356 G-protein coupled receptor protein signaling pathwayDRD1, 1812 G-protein signaling, coupled to cyclic nucleotide second messengerSSTR5, 6755 G-protein signaling, coupled to cyclic nucleotide second messengerMTNR1A, 4543 G-protein signaling, coupled to cyclic nucleotide second messengerCNR2, 1269 G-protein signaling, coupled to cyclic nucleotide second messengerHTR6, 3362 G-protein signaling, coupled to cyclic nucleotide second messengerGRIK2, 2898 glutamate signaling pathwayGRIN1, 2902 glutamate signaling pathwayGRIN2A, 2903 glutamate signaling pathwayGRIN2B, 2904 glutamate signaling pathwayADAM10, 102 integrin-mediated signaling pathwayGRM7, 2917 negative regulation of adenylate cyclase activityLRP1, 4035 negative regulation of Wnt receptor signaling pathwayADAM10, 102 Notch receptor processingASCL1, 429 Notch signaling pathwayHTR2A, 3356 serotonin receptor signaling pathwayADRB2, 154 transmembrane receptor protein tyrosine kinase activation (dimerization)PTPRG, 5793 transmembrane receptor protein tyrosine kinase signaling pathwayEPHA4, 2043 transmembrane receptor protein tyrosine kinase signaling pathwayNRTN, 4902 transmembrane receptor protein tyrosine kinase signaling pathwayCTNND1, 1500 Wnt receptor signaling pathway`
precise answers to complex questions
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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
we can turn ugly query code into a link
Wednesday, March 11, 2009
we can turn ugly query code into a link
Wednesday, March 11, 2009
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 ?processnamewhere
{ 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}
}
users can view and edit source
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collaborative question answering
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open = pleasant surprises.
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google maps for brain images
http://sparql.neurocommons.org:8890/map/#Kcnip3@2850,Kcnd1@2800
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“one last thing”
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“it’s the links, dummy”- James Boyle
aka “Boyle’s Law 2.0”
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http://ucsdbiolit.codeplex.com/
http://blogs.msdn.com/exscientia/
http://tinyurl.com/deypwt
(video)
(developer blog)
(project site)
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closing the loop to open innovation: freedom to operate.
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reconstructing the research exemption
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thank you
http://sciencecommons.org
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