Presentation to Federation of Earth Science Information Partners
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ESIP semi-annual meetingwashington, dc6 january 2009
john wilbankscreative commons / science commons
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metcalfe’s law
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“information wants to be free”
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“if free, and technically enabled, information trends towards
connectivity and increased value”
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information knowledge?
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digitization changes knowledge
journals, databases, ontologies, wikis, annotations...
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why no disruptions like Metcalfe’s Law for knowledge?
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disruptive processes can’t be planned in advance.
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disruptive processes can’t be planned in advance.
planned innovation tends to be incremental, and slow.
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disruptive processes can’t be planned in advance.
planned innovation tends to be incremental, and slow.
...and not innovative.
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1.stable systems are resistant to change on
multiple levels.
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© creative expression
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the container, not the facts.
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the container, not the facts.
but © locks the container.
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IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
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IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
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http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
indexing: disallowed.
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creativework?
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40 minutes per year
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nih policy.
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Dorothea Salo, http://cavlec.yarinareth.net/2008/10/31/miniature-disasters-and-minor-catastrophes/
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the existing system is robust against disruption
the existing system is robust against disruption
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this is how evolved systems resist change: at multiple levels, with multiple fail-safes.
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2.the “digital commons” presents us with a
potential way out.
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“the commons”
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rivalrous v.
non-rivalrous
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small contributions.snap-together licensing.
technically enabled.
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“the commons”
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“intellectual property”
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knowledge rights
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copyright
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mostusesfree
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mostregulated usescommercial
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couldn’tlegally control
perfectly
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copyrightregulates“copies”
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in digital world
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every use=
“copy”
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thus, presumption: every userequires
permission
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All Rights Reserved
No Rights Reserved
Copyright
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All Rights Reserved
No Rights Reserved
Copyright
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Attribution
Non-Commercial No Derivative Works
Share Alike
licensingstep 1: choose conditions
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Ported to 50 Jurisdictions
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160M
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160M
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solves the legal problem
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but not the container problem.
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over 200years at
one paper/day
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what you want is a list of genes.
not a list of documents.
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building a web for data:the “semantic web”
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databases as unique entities, instead of nodes in a network
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“packages”
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scalable aggregation
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not-software
scalable
modular
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lots of peopleopen licenses
community norms
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3.reports from the front lines: building a
commons is really, really hard.
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whichever we choose, we need some way for computers to help us theorize, and to
leverage the work of others (either to build on or to use in creative anarchy)
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exponential content growth
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0
1.25
2.50
3.75
5.00
1990 1994 1998 2002
our brain capacity
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but if we can work together...
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open copyright, balanced incentives, and distributed workloads
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Open Access Content
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image from the public library of sciencelicensed to the public under CC-BY 3.0
>1000 journals under CC
c
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running policy code(w. SPARC)
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+
+
+ +
+
++ +
is it legal?
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conflicts with the protection instinct
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conflicts with the protection instinct
the protection instinct is sometimes an instinct to protect “freedom”
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http://visibleearth.nasa.gov/
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Open SourceData Integration
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a repository of ontologies, namespaces, and integrated
databases.
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e pluribus unum.
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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
we can transform complex queries into links
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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
we can transform complex queries into links
![Page 105: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/105.jpg)
we can transform complex queries into links
![Page 106: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/106.jpg)
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}}
we can help scholars “remix” queries
Mesh: Cancer
GO: Ribosomal Protein
![Page 107: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/107.jpg)
we can build a corpus of queries as links
![Page 108: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/108.jpg)
we can re-use cultural tools for scholarship
![Page 109: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/109.jpg)
![Page 110: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/110.jpg)
conclusion?
![Page 111: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/111.jpg)
don’t wait.
![Page 112: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/112.jpg)
use existing systems.
![Page 113: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/113.jpg)
hack around problems.
![Page 114: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/114.jpg)
create new ways to measure.
![Page 115: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/115.jpg)
build your own commons.
![Page 116: Presentation to Federation of Earth Science Information Partners](https://reader034.fdocuments.in/reader034/viewer/2022051612/54bc9c214a7959f6568b4619/html5/thumbnails/116.jpg)
thank you
http://sciencecommons.org