open pharma innovation and the commons

15 april 2008PRISM Forum workshop on open innovation

North Mymms, U.K.

property theory

the “digital commons”:

standard legal tools, accessible to non-lawyers, rendered in machine-readable

form, tilted towards sharing

the intersection of law and technology

c100,000,000 objects on the web

500+ peer-reviewed journalsuniprot.org

nature precedingsPLoS

"merck accounts for about 1% of biomedical research in the world...to tap into the remaining 99%, we must actively reach out...the cascade of knowledge flowing from biotechnology and the unraveling of the human genome...is far too complex for any one company to handle alone"

- merck annual report, 2000

why is it hard to capture value from all of this knowledge?

most of the useful knowledge is inaccessible

most of the useful knowledge is poorly formatted

traditional business models don’t support it

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

pharma deals with that complexity by limiting false positives

Nature Reviews Drug Discovery 7, 197-198 (March 2008)

pharma is already practicing open innovation.

the question is why it doesn’t more efficiently.

it’s a combination of formats and access

the problem:

knowledge access allows us to exploit technologies and accelerate the processes of scientific innovation

knowledge flow drives the processes by which we explore new areas of science

knowledge formats dictate our ability to exploit new technologies and

processes

1. access control restricts knowledge flow and blocks open innovation

IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases

“papers”

IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases

“networked knowledge”

http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf

using software to index articles: not allowed.

PubMedCentral ~ 1,000,000 articlespermissions granted: 50,000

(6% of PMC legal for transformative use)(.003 of all PubMed records)

databases as unique entities, instead of nodes in a network

license propagation: whatsoever you do to the least of the databases, you do to the integrated knowledgebase

(the most restrictive license wins)

http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1

impossible.

what about tacit knowledge?

Science Commons materials project

academic > commercial research MTAone-click contract software (open source)harvest biobank catalogs for integration

standard funder policy for grants

Alzheimer’sDisease

Huntington’sDisease

MultipleSclerosis

Autism

distinct “silos” of funded research

Alzheimer’sDisease

Huntington’sDisease

MultipleSclerosis

Autism

bilateral contracts and deals

Alzheimer’sDisease

Huntington’sDisease

MultipleSclerosis

Autism

“one to many” offers / networks

Provider Lab

BRC

Recipient Lab

MTA

deposittracking

fulfillment

searching / ordering

key change: commercial is

defined by status of USE, not status

of USER

1. access control restricts knowledge flow and blocks open innovation

look for places to “flip the default switch” - and make sure the public folks do, too...

2. technical design choices restrict data integration and block open innovation

“read 189,000 papers” is not the

ideal answer.

NeuronDBBAMS

Literature

Homologene

SWAN

Entrez Gene

Gene Ontology

Mammalian Phenotype

PDSPki

BrainPharm

AlzGene

Antibodies

PubChem

MESH

Reactome

Allen Brain Atlas

credit: W3C HCLS

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

better answers through better formats:

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`

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`

this query is probably prohibited in the presence of copyleft / non commercial licensing on the underlying databases

when “freedom” isn’t free:

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

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” effect: shared problem solving on information aggregation

permutation and recombination

information itself is part of the ICT infrastructurethus end-to-end principles need to apply as well...

collaborative innovation, based on good design, can defeat complexity

open innovation, based on strong technology design + increased access, can exploit complexity

2. technical design choices restrict data integration and block open innovation

invest in a well-formatted public domain

commonsacademics

pharma

free as in speech

free as in beer

free as in a puppy

3. business model designs affect the ability of business to exploit information flows and block

open innovation

if knowledge is going to flow, someone will claim rights on discoveries made with that knowledge.

business models must capture and share the value with minimal transaction costs - pre-negotiate.

Health Commons

“some rights reserved”

“rights to ramble” for research purposessafe harbors for NTD, orphan disease

pre-negotiated IP arrangementsescrow institutions

3. business model designs affect the ability of business to exploit information flows and block

open innovation

figure out how to share profitably.

1. how to see your internal information against the external information as well as possible?

2. how to figure out what information flows to create?

3. how to give/get credit for discoveries from information outflows?

4. how to get the biggest, most diverse crowd to work on those problems?

5. how to capture the value created?

challenges

call to action.

identify internal resources for outflowtest-drive collaborations and intermediaries

create networks between existing collaborationsinvest in public infrastructure

push policy makers to update the metaphors

thank you

wilbanks@creativecommons.org

http://sciencecommons.org