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john wilbankscreative commons / science commons
Open Innovation, Institutional Policy, and the Digital Commons
10 november 2008haas school of business
knowledge gapsprocess failures
transaction costslost opportunities
knowledge gapsprocess failures
transaction costslost opportunities
is the answer more products?
the discovery process:
the discovery process:
thanks to the products, we already know a lot...
we need process innovationsto match product innovations.
collaborative workflowsstandard data formatscollaboration software
secure legal frameworks
we need process innovationsto match product innovations.
most products advance incrementally
business model: sell more, faster, cheaper
business model: sell more, faster, cheaper
does the ability to ask more questions, faster, lead us to more
knowledge or just more data?
what’s different about communications and computers?
1. we know stuff.
1. we know stuff.2. open networks.
physical
code
content
1.
the “digital commons” represents a methodology to bring network externalities to the sciences
“the commons”
knowledge rights
“digital commons”
interoperabilitylow transaction costslaw and technology
user interface to copyright
140,000,000+ digital objects online under our licenses
licenses “ported” to 45+ countries
integrated with Google, Yahoo, Firefox, Microsoft Office...
physical
code
content
physical
code
content
innovation
2.
the digital commons is a innovation-friendly way to manage data,
materials, and content for science.
“think market”
project development
funding
pro bono
community
“do no harm”
“running code”
early focus on life sciencesexploring climate change, geospatial, elsewhere
what would move via the science network?
Open AccessResearch Tools
making the tacit knowledge encoded in materials and data available at high speed and low
transaction costs.
user interface to technology transfer
core contract grants the right to do research
“one-click” for DNA and
materials
ibridge
build offer through simple set of choices(post-authentication)
Scientist readable
Lawyer readable
Machine readable
service opportunity:
amazon, e-bay, paypal, shipping, materials prep
“one-click” for clinical data
service opportunity:
data cleaning, data integration, data analytics,
“virtual” clinical trials, storage, escrow, etc.
Open Access Content
making knowledge legally and technically available for re-use and composition into new knowledge.
we use digital tools to replicate paper technology
© creative expression
© ideas or facts
e=mc2
the container, not the facts.
the container, not the facts.
but © locks the container.
IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
indexing: disallowed.
image from the public library of sciencelicensed to the public under CC-BY 3.0
>1000 journals under CC
c
service opportunity:
enhanced publishing, document markup,
literature-data integration, indexing and search
3.
we have to build infrastructure for data into the web of documents that we have.
solves the legal problem
but not the container problem.
web 2.0, science 3.0, what about making Google work better?
over 200years at
one paper/day
what you want is a list of genes.
not a list of documents.
building a web for data:the “semantic web”
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
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
192.168.1.1
we need a Domain Name System for concepts:
http://sciencecommons.org
coffee http://ontology.foo.org/coffee
coffee
“coffee”
“cafe”
“kopi” http://ontology.foo.org/coffee
use the web to integrate information from different places and different names
bed
get out of bed
get out of beddrink 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
(too much work for coffee)
(distributed, networked approaches start to look pretty good)
Open SourceData Integration
formatting digital knowledge into modular building blocks for
composition into new knowledge.
e pluribus unum.
500,000,000+ RDF “triples”pre-formatted queries
pathway analytic software donated by MLNMuses $5,000 of off-the-shelf hardwarebundled with open source triple store
download, mirror, fork.http://neurocommons.org
uses:
“DNS for life sciences”enhanced document markupmodular data distributions
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
“While brain maps until now have been similar to a traditional encyclopedia, the Allen Brain Atlas is more like Google Earth.”
“mashups” in science
open systems do things you don’t expect, that are occasionally more valuable...
service opportunity:
distribution and services, database conversion, ontology creation,
namespace servers, registries
they’re coming.
changes from a guild culture of knowledge
physical
code
content
knowledge
http://sciencecommons.org
