knowledge sharing and the commons kaitlin thaney program manager, science commons lund, sweden - COASP - 15 sep 2009 This presentation is licensed under the CreativeCommons-Attribution-3.0 license. Wednesday, September 16, 2009
May 13, 2015
knowledge sharing and the commons
kaitlin thaneyprogram manager, science commonslund, sweden - COASP - 15 sep 2009
This presentation is licensed under the CreativeCommons-Attribution-3.0 license.
Wednesday, September 16, 2009
make sharing easy, legal and scalable
integrated approach
building part of the infrastructure for knowledge sharing
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com⋅mons (noun) - law, content, technology,
community
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knowledge?
journal articlesdata
ontologiesannotations
plasmids and cell lines
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knowledge sharing is at the root of scholarship and science
the system of scholarly publishing is a system of sharing knowledge
it all starts with access to information
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scientific revolutions occur when a sufficient body of data accumulates to
overthrow the dominant theorieswe use to frame reality
a so-called paradigm shift
- from thomas kuhn
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need to change the way we think of scholarly publishing,
of knowledge sharing
paradigm shift
begin thinking of “papers” as containers of knowledge
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“the future is here ... just unevenly distributed”
- william gibson
(i.e., linked data, W3C, neurocommons...)
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1.three layers of resistance: technical, semantic, legal
save legal for last ...
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“read 189,000 papers” is not
the ideal answer.
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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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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: Pyramidal Neurons
Pubmed: Journal Articles
Entrez Gene: Genes
GO: Signal Transduction
better answers through better formats:
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technical
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traditional transfer of copyright agreement
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(1) KEGG - Kyoto Encyclopedia of Genes and Genomes
“Non-academic users and Academic users intending to use KEGG for commercial purposes are requested to obtain a license agreement through KEGG's exclusive licensing agent, Pathway Solutions, for installation of KEGG at their sites, for distribution or reselling of KEGG data, for software development or any other commercial activities that make use of KEGG, or as end users of any third-party application that requires downloading of KEGG data or access to KEGG data via the KEGG API.
(2) HapMap - human genetic variation data
“The click-wrap license was designed as a temporary tool to continue the practice of providing rapid access to human genome data [...]. One consequence of the license requirement was that the [...] license prevented HapMap data from being integrated into major public databases, which require that data deposited carry no conditions on use ...” - Wellcome Trust, Sanger, Dec 2004
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what companies think we’re doing with the web
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2.people like stories ...
(scientists are people ...)
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semantic agreement
is hard.
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cafekopi
cafezinho
koffee
espresso
latte
mocha americano
coffee
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(pick one)
“choice” or interoperability.
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coffee
“coffee”
“cafe”
“kopi” http://ontology.foo.org/1234567
converge on common names
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3.the data “rights” conundrum...
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Open Access (OA)
Photo Credit: Peter Jeffs
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©“creative expression”
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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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category errors
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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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1854 Wednesday, September 16, 2009
Attribution
the problem of...
for data
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the problem of...
for data
any license
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database protections based on jurisdiction
sui generis, “sweat of the brow”
Crown copyright
the list goes on ....
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attribution = licensecitation = norms
(which one applies whether or nota copy is made?)
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need for a legally accurate and simple solution
reducing or eliminating the need to make the distinction of what’s protected
requires modular, standards based approach to licensing
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CC Zero waiver + SC norms
waive rights public domain
attribution / citation through community norms, not a contract
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calls for data providers to waive all rights necessary for data extraction and re-use
requires provider place no additional obligations (like share-alike) to limit
downstream use
request behavior (like attribution) through norms and terms of use
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infrastructure for a data web
the digital commons
law + content + technology + community
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data without structure and annotation is a lost opportunity.
data should flow in an open, public, and extensible infrastructure
support recombination and reconfiguration into computer models, queryable by search
engine
treated as public good
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resist the temptation to treatas property
embrace the potential to treat instead as a network resource
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at worst, we’re really wrong.
4.at best, we’re partially right.
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the right to fix our mistakes.Wednesday, September 16, 2009
(remember Prodigy and AOL?)Wednesday, September 16, 2009
design for maximum reuse
ensure the freedom to integrate
leverage existing open infrastructure
allows for snap together integration of the tools, data, research literature
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