Science and the Commons
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1. scholarly publishing: change is
coming, like it or not.
Tuesday, September 15, 2009
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when you make people more relevant than content containers, content industries get disrupted.
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media company response:adjust the physical media
force the cd format
ignore that people...like to make mixes.
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http://www.flickr.com/photos/diemer/cc-by-sa
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now a *computer* company dominates the music industry.
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and it’s a control culture. an “app store approval” culture.
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science “knowledge”
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containers grow, and we ignorethe radical shift.
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“article of the future”
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the “container” is still the “paper”
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the “container” is still the “paper”
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the “article of the future”is not an article.
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<people><acquire><leptospira><people><reside in><floodzones>
(computers love this stuff. people, not so much.)
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@prefix skos: <http://www.w3.org/2004/02/skos/core#> .@prefix sc: <http://purl.org/science/owl/sciencecommons/> .@prefix m: <http://purl.org/commons/record/mesh/> .m:D000001Q00000! skos:broader m:D00000" .m:D000001Q00000! sc:is_qualified_by m:Q00000! .m:D000001Q00000! skos:prefLabel "Calcimycin - administration # dosage".m:D000001Q00000$ skos:broader m:D00000" .m:D000001Q00000$ sc:is_qualified_by m:Q00000$ .m:D000001Q00000$ skos:prefLabel "Calcimycin - adverse effects".m:D000001Q00003" skos:broader m:D00000" .m:D000001Q00003" sc:is_qualified_by m:Q00003" .m:D000001Q00003" skos:prefLabel "Calcimycin - analogs # derivatives".m:D000001Q00003% skos:broader m:D00000" .m:D000001Q00003% sc:is_qualified_by m:Q00003% .m:D000001Q00003% skos:prefLabel "Calcimycin - analysis".m:D000001Q00003& skos:broader m:D00000" .m:D000001Q00003& sc:is_qualified_by m:Q00003& .m:D000001Q00003& skos:prefLabel "Calcimycin - antagonists # inhibitors".m:D000001Q00009' skos:broader m:D00000" .m:D000001Q00009' sc:is_qualified_by m:Q00009' .
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registrationcertification
disseminationpreservation
publishing tradition:
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registrationcertification
disseminationpreservation
publishing tradition:
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registrationcertification
disseminationpreservation
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registrationcertification
disseminationpreservation
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registrationcertification
disseminationpreservation
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so what’s left for publishers?
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when a layer gets commoditized, value can be created in adjacent layers.
(clayton christensen)
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when a layer gets commoditized, value can be created in adjacent layers.
(clayton christensen)
(hint: networks make copies of content into commodities)
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integrationannotationfederation
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integrationannotationfederation
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integrationannotationfederation
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coffee
cafe
kopi
cafezinho
koffee
espresso
latte
mocha americano
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integrationannotationfederation
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content services are much more valuable when the content itself becomes a commodity.
but if your focus is on preventing copying, you’ll miss the shift.
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exponential content growth
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0
0.25
0.50
0.75
1.00
1990 1994 1998 2002
our brain capacity
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“...we don’t ask what the incentive is for the electrons to leave home. we say that the current results from an emergent property of the system, which we call induction.”
eben moglen
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“...we don’t ask what the incentive is for the electrons to leave home. we say that the current results from an emergent property of the system, which we call induction.”
The question we ask is ‘what’s the resistance of the wire?’
eben moglen
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ignoring the law does not scale.
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computers
documents
knowledge
tcp/ip
html/http
commons
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image from the public library of science
licensed to the public under cc-by-3.0
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2. there is real tension between interoperability and choice,
and in science, we need interoperability more.
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cc for oa? good.
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but...cc for oa? good.
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attribution
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©in relation to data...
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category errors
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is it creative?
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is it creative?
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is it creative?
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Non-Commercial
the problem of...
for data
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Non-Commercial
what’s a commercial useof the data web?
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Share Alike
the problem of...
for data
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Attribution
the problem of...
for data
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the problem of...
for data
any license
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if property is the accepted metaphor, allof these terms will eventually appear.
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uses triggered by “making a copy”
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unmet expectations
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attribution = licensecitation = norms
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attribution = licensecitation = norms
(which one applies whether or nota copy is made?)
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waive all rights necessary for data extraction and re-use
no obligations (share-alike, contract) to limit downstream use
request behavior (citation) through norms
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interoperability...
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3.value of legally interoperable
data depends on technical interoperability, too.
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coffee
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coffee
cafe
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coffee
cafe
kopi
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coffee
cafe
kopi
cafezinho
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coffee
cafe
kopi
cafezinho
koffee
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coffee
cafe
kopi
cafezinho
koffee
espresso
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coffee
cafe
kopi
cafezinho
koffee
espresso
latte
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coffee
cafe
kopi
cafezinho
koffee
espresso
latte
mocha
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coffee
cafe
kopi
cafezinho
koffee
espresso
latte
mocha americano
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coffee
“coffee”
“cafe”
“kopi” http://ontology.foo.org/1234567
converge on common names.
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103 databases - just molecular biology
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“read (89,00) papers” is not the ideal answer.
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select ?gene_name ?process_namewhere{ PropertyValue(?pubmed_record, ?p, mesh:D017966) PropertyValue(?article, sc:identified_by_pmid , ?pubmed_record) PropertyValue(?gene_record, sc:describes_gene_or_gene_product_mentioned_by, ?article) SubClassOf(?protein, some(ro:has_function, some(ro:realized_as, ?process))) SubClassOf(?process, or(go:GO_0007166, some(ro:part_of, go:GO_0007166)) SubClassOf(?protein, some(sc:is_protein_gene_product_of_dna_described_by,?gene_record)) Annotation(?gene_record,rdfs:label,{?gene_name}) Annotation(?process,rdfs:label,?process_name)}
Mesh: *yramidal +eurons
Pubmed: ,ournal -rticles
Entrez .ene: .enes
GO: /ignal 0ransduction
better answers through better formats:
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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`
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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
turn ugly query code into a link
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4. the commons, like the internet,
changes the physical world, not just the digital one.
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stem cells
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non-digital.
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“start by melting iron ore...”
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change.
whether we like it or not.
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interoperability...Tuesday, September 15, 2009
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two futures.
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c:\
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the digital commons...
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the right to create.
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law + technology + content + community
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at best, we’re partially right.
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at worst, we’re really wrong.
at best, we’re partially right.
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the right to fix our mistakes.
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“1 propose the seeming paradox that in science, private property is established by
having its substance freely given to others…”
Merton
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thank you
John 2. and 3atherine 0. 4acArthur 5oundationEwing 4arion 6auffman 5oundationCHD1 5oundationOmidyar +etworkNike, 7nc.
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