funder incentives and open science

           john wilbanks
vp for science @ creative commons

         18 january 2008
 ...
Science Commons
              http://sciencecommons.org


non profit organization, part of a global non-profit with
        ...
investors and support:
                                                  content partners:
       MacArthur Foundation
   ...
our hypothesis:

 the way we disseminate research results has a
direct impact on the translation of basic research
       ...
closed dissemination “default rule”




$800,000,000-$1,ooo,000,000 per success

               15-17 years
legal, technical, and policy elements are required to
  wrench life sciences into network collaboration

  experience show...
Open Access Content




  innovation
http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
Howard Hughes Medical Institute
moving beyond publications: data sharing
data sharing policy should carry a method for citations
innovation

             Open Access
             Research Tools
Uni A




                                               Uni C


                Uni B




Uni D                   distinc...
Alzheimer’s
         Disease



                                                  Multiple
                               ...
Alzheimer’s
  Disease               Multiple
                        Sclerosis

              Autism



Huntington’s
  Dis...
Alzheimer’s
         Disease



                                             Multiple
                                    ...
“Minimizing Administrative Impediments to Research”
1. Free dissemination for use in research that is far removed from any...
scientist readable




                     lawyer readable




                           machine readable
Provider Lab
                                  MTA



tracking         deposit                  Recipient Lab


          ...
innovation

Open Source
Knowledge Management
knowledge management
what you get
DRD1, 1812      adenylate cyclase activation
ADRB2, 154      adenylate cyclase activation
ADRB2, 154      arrestin mediate...
PDSPki

        Gene                 Reactome
       Ontology




                                                       B...
PDSPki

     Gene              Reactome                   NeuronDB
    Ontology
                                          ...
precise answers to complex questions

            prefix go: <http://purl.org/obo/owl/GO#>
    prefix rdfs: <http://www.w3...
DRD1, 1812              adenylate cyclase activation
ADRB2, 154              adenylate cyclase activation
ADRB2, 154      ...
http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3Chttp%3A%2F%2Fpurl.org%2Fobo%2Fowl%2FGO%23%3E%
0Aprefix%20r...
“view source” effect:
beneficial output of releasing control
                 prefix go: <http://purl.org/obo/owl/GO#>
     ...
collaborative, web-based, open, extensible
     open content is the infrastructure
Open Access Content




              innovation

Open Source                      Open Access
Knowledge Management       ...
funders can drive the issue through grant award
               terms and conditions:

1. open access to digital content cr...
right now:

  1. implement a public access policy for articles by
              cloning the NIH policy

 2. implement a pu...
thank you

     wilbanks@creativecommons.org
       http://sciencecommons.org

funded by: Kauffman Foundation, MacArthur
  ...
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
Briefing Tlh Sciencecommons Public
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Briefing Tlh Sciencecommons Public

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comments to the Florida Biological Research Advisory Council

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Briefing Tlh Sciencecommons Public

  1. 1. funder incentives and open science john wilbanks vp for science @ creative commons 18 january 2008 tallahassee, fl
  2. 2. Science Commons http://sciencecommons.org non profit organization, part of a global non-profit with operations in 50 countries exploring the role of funding agencies, government, universities, and other institutions in open innovation
  3. 3. investors and support: content partners: MacArthur Foundation SPARC/Ass’n of Research Libraries Kauffman Foundation Carnegie-Mellon University MIT CSAIL MIT HighQ Foundation Public Library of Science Omidyar Network BioMed Central Teranode Corporation Nature Precedings anonymous charitable foundations Springer Author Choice in-kind supporters research tool partners: knowledge management partners: iBridge Network W3C HCLS Addgene Millennium Pharmaceuticals StrainInfo.net National Center for Biomedical Ontology Cure Huntington’s Disease Initiative Virtuoso So/ware Emory University Hewlett-Packard City of Hope Hospital
  4. 4. our hypothesis: the way we disseminate research results has a direct impact on the translation of basic research into meaningful benefits
  5. 5. closed dissemination “default rule” $800,000,000-$1,ooo,000,000 per success 15-17 years
  6. 6. legal, technical, and policy elements are required to wrench life sciences into network collaboration experience shows: it takes funder incentives to change scientific cultures towards dissemination
  7. 7. Open Access Content innovation
  8. 8. http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
  9. 9. Howard Hughes Medical Institute
  10. 10. moving beyond publications: data sharing
  11. 11. data sharing policy should carry a method for citations
  12. 12. innovation Open Access Research Tools
  13. 13. Uni A Uni C Uni B Uni D distinct “silos” of research
  14. 14. Alzheimer’s Disease Multiple Sclerosis Autism Huntington’s distinct “silos” of funders Disease
  15. 15. Alzheimer’s Disease Multiple Sclerosis Autism Huntington’s Disease bilateral contracts and pooling
  16. 16. Alzheimer’s Disease Multiple Sclerosis Autism Huntington’s Disease “one to many” offers / networks
  17. 17. “Minimizing Administrative Impediments to Research” 1. Free dissemination for use in research that is far removed from any commercial product. 2. Use of standard agreements. 3. Dra/ agreements that are clear and comprehensible to scientists and business people. 4. Reasonable terms in the first dra/. http://www.nih.gov/news/researchtools/appenda.htm
  18. 18. scientist readable lawyer readable machine readable
  19. 19. Provider Lab MTA tracking deposit Recipient Lab fulfillment biobank searching / ordering takes a full e-commerce infrastructure
  20. 20. innovation Open Source Knowledge Management
  21. 21. knowledge management
  22. 22. what you get
  23. 23. 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 ADAM10, 102 GRM7, 2917 glutamate signaling pathway integrin-mediated signaling pathway negative regulation of adenylate cyclase activity what you want 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 `
  24. 24. PDSPki Gene Reactome Ontology BAMS NeuronDB Entrez Gene Antibodies Allen Brain Atlas BrainPharm Literature SWAN Homologene AlzGene PubChem Mammalian Phenotype MESH
  25. 25. PDSPki Gene Reactome NeuronDB Ontology BAMS Allen Brain BrainPharm Antibodies Atlas Entrez Gene MESH Literature PubChem Mammalian Phenotype SWAN AlzGene Homologene requires technical and legal integration
  26. 26. precise answers to complex questions prefix go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> Mesh: Pyramidal Neurons 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> Pubmed: Journal Articles { ?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. Entrez Gene: Genes ?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. GO: Signal Transduction ?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} }
  27. 27. 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 this functionality is not infrastructure for anyone outside of pharma, and it’s re-created again and again inside pharma
  28. 28. 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
  29. 29. “view source” effect: beneficial output of releasing control 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> { ?paper ?pmesh: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} }
  30. 30. collaborative, web-based, open, extensible open content is the infrastructure
  31. 31. Open Access Content innovation Open Source Open Access Knowledge Management Research Tools
  32. 32. funders can drive the issue through grant award terms and conditions: 1. open access to digital content created under funds 2. open access to research tools created under funds 3. technical standardization for databases created under funds
  33. 33. right now: 1. implement a public access policy for articles by cloning the NIH policy 2. implement a public access incentive for research tools by citing the NIH recommendations and adding fields to grant applications and reviews 3. implement an public access policy for databases by adding fields to grant applications and reviews *make it easy to opt out for good cause*
  34. 34. thank you wilbanks@creativecommons.org http://sciencecommons.org funded by: Kauffman Foundation, MacArthur Foundation, Omidyar Network, HighQ

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