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1.
simple + open = WIN
institution
individual
design
manufacture
source: Rossini & Wilbanks
institution
individual
design
manufacture
institution
individual
design
manufacture
institutionally mediated
“Joy’s Law”:
most of the smart people work somewhere else.
institution
individual
design
manufacture
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
requires both new behavior by R&D entities and the emergence of intermediaries
depends on the quantity, quality, legal availability,
and technical usability of the knowledge
institution
individual
design
manufacture
institution
individual
design
manufacture
network mediated
user innovation:
“all innovation is local”knowledge is sticky
users solve their own problems
traditional collaboration: negotiated, low-volume, high-density information sharing
distributed collaboration: automated, high-volume, low-density information sharing
the real “tragedy of the commons” =
we can do this for shoes, not for science.
scientists don’t share what they know very well.
IPR.funding models.
inertia.incentive structures.
IPR.funding models.
inertia.incentive structures.
no web for data.
2.building the web for data.
the “semantic web”
making computers understand things
Web page Web pagelinks to
making computers understand links between documents
drinking coffee feel awakecauses
making computers understand relationships between concepts
drink coffee feel awakecauses
bed
get out of
get out of
drink coffee
open eyes
located atlast subevent
first subevent
after
drink
coffee
wet
cup
is a
property ofoften near
make coffee
is for
subevent
feel awake
person
feel jittery
does not wantwants
causes
causes
pour coffee pick up cupafter after
cafe
sugar
often near
located in
3.blood and guts: what the
semantic web is.
lots of specifications.
192.168.1.1
we need a Domain Name System for concepts:
http://sciencecommons.org
coffee http://ontology.foo.org/coffee
drinking coffee feel awakecauses
http://ontology.foo.org/drinking coffee http://ontology.foo.org/feel awake http://ontology.foo.org/receptor
http://ontology.foo.org/causes
coffee
“coffee”
“cafe”
“kopi” http://ontology.foo.org/coffee
use the web to integrate information from
different places and different names
Resource Description Framework
directed -> every arc has a directionlabelled -> 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/
this blog ---(contains)---> this newsthis news ---(has title)---> "Semantic Web 101"this news ---(was written on)---> "20040404"[date]this news ---(has content)---> "<html><body>...</body></html>"
this news ---(has category)---> "semantic web"[this news ---(has category)---> "semantic web"] ---(added by)---> stefano
“literals”
“reification”
http://www.betaversion.org/~stefano/linotype/news/57/
http://www.w3.org/TR/grddl/
bootstrap via GRDDL
RDFa - RDF in HTML
http://www.w3.org/2006/07/SWD/RDFa/primer/
Web Ontology Language
Web Ontology Language
“married to” is a symmetric property
“father of ” is not
“human” is a subclass of “animal”
“person” is equivalent to “human”
there can only be one biological mother
“son of ” is the inverse of “father of ”
SPARQL
RDF Statements retain their meaning in isolation, unlike XML elements that are meaningful only in their XPath context.
makes RDF data naturally mixable.
(more debt to Stefano)
+
+
+ +
+
++ +
is it legal?
conflicts with the protection instinct
conflicts with the protection instinct
the protection instinct is sometimes an instinct to protect “freedom”
“a biologist would rather share her toothbrush than her data.”- carole goble
4.a proof of concept: the Neurocommons project
open sourcedata integration
formatting digital knowledge into re-usable building blocks for
composition into new knowledge.
e pluribus unum.
uses:“DNS for life sciences”
API to the public domainenhanced document markup
activity center analysis
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
get precise answers out of existing databases and resources
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`
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
transforms complex queries into links
transforms complex queries into links
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}}
view source, edit source.
Mesh: Cancer
GO: Ribosomal Protein
“While brain maps until now have been similar to a traditional encyclopedia, the Allen Brain Atlas is more like Google Earth.”
“mashups” in science
that’s more like it.
800,000,000+ RDF “triples”pre-formatted queries
pathway analytic software donated by MLNMuses $5,000 of off-the-shelf hardware
bundled with Virtuouso open source triple store
download, mirror, fork.http://neurocommons.org
resources
Search tools:
SwoogleSindiceSchemaweb, Umbel, Zitgist, OLS, Bioportal
Collections of ontologies:
dbpediaLinked Open Databio2rdfOpen Biomedical Ontologies
http://www.w3.org/DesignIssues/Semantic.htmlhttp://www.youtube.com/watch?v=mVFY52CH6Bc
http://www.w3.org/2001/sw/http://neurocommons.org/page/IAP_2009
