knowledge sharing and the commons

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


com⋅mons (noun) - law, content, technology,

community


knowledge?

journal articlesdata

ontologiesannotations

plasmids and cell lines


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


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


need to change the way we think of scholarly publishing,

of knowledge sharing

paradigm shift

begin thinking of “papers” as containers of knowledge


“the future is here ... just unevenly distributed”

- william gibson

(i.e., linked data, W3C, neurocommons...)


1.three layers of resistance: technical, semantic, legal

save legal for last ...


“read 189,000 papers” is not

the ideal answer.


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`


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:


technical


traditional transfer of copyright agreement


(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


what companies think we’re doing with the web


2.people like stories ...

(scientists are people ...)


semantic agreement

is hard.


cafekopi

cafezinho

koffee

espresso

latte

mocha americano

coffee


(pick one)

“choice” or interoperability.


coffee

“coffee”

“cafe”

“kopi” http://ontology.foo.org/1234567

converge on common names


http://ontology.foo.org/receptor

http://ontology.foo.org/receptor

3.the data “rights” conundrum...


Open Access (OA)

Photo Credit: Peter Jeffs


©“creative expression”


is it creative?


category errors


Non-Commercial

the problem of...

for data


Non-Commercial

what’s a commercial useof the data web?


Share Alike

the problem of...

for data


1854 Wednesday, September 16, 2009

Attribution

the problem of...

for data


the problem of...

for data

any license


database protections based on jurisdiction

sui generis, “sweat of the brow”

Crown copyright

the list goes on ....


attribution = licensecitation = norms

(which one applies whether or nota copy is made?)


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


CC Zero waiver + SC norms

waive rights public domain

attribution / citation through community norms, not a contract


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


infrastructure for a data web

the digital commons

law + content + technology + community


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


resist the temptation to treatas property

embrace the potential to treat instead as a network resource


at worst, we’re really wrong.

4.at best, we’re partially right.


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


thank [email protected]

sciencecommons.orgneurocommons.org


mailto:[email protected]

mailto:[email protected]

knowledge sharing and the commons

Education

dopamine receptor

serotonin receptor

notch receptor processingascl1

entrez gene

cyclic nucleotide

knowledge sharing paradigm

record propertyvalue

installationof kegg