science and the commons

1. scholarly publishing: change is

coming, like it or not.

Tuesday, September 15, 2009

when you make people more relevant than content containers, content industries get disrupted.


media company response:adjust the physical media

force the cd format

ignore that people...like to make mixes.


http://www.flickr.com/photos/diemer/cc-by-sa


http://www.flickr.com/photos/diemer/

http://www.flickr.com/photos/diemer/

now a *computer* company dominates the music industry.


and it’s a control culture. an “app store approval” culture.


science “knowledge”


containers grow, and we ignorethe radical shift.


“article of the future”


the “container” is still the “paper”


the “article of the future”is not an article.


<people><acquire><leptospira><people><reside in><floodzones>

(computers love this stuff. people, not so much.)


@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' .


http://www.w3.org/2004/02/skos/core#

http://www.w3.org/2004/02/skos/core#

http://purl.org/science/owl/sciencecommons/

http://purl.org/science/owl/sciencecommons/

http://purl.org/commons/record/mesh/

http://purl.org/commons/record/mesh/

registrationcertification

disseminationpreservation

publishing tradition:


so what’s left for publishers?


when a layer gets commoditized, value can be created in adjacent layers.

(clayton christensen)


when a layer gets commoditized, value can be created in adjacent layers.

(clayton christensen)

(hint: networks make copies of content into commodities)


integrationannotationfederation


coffee

cafe

kopi

cafezinho

koffee

espresso

latte

mocha americano


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.


exponential content growth


0

0.25

0.50

0.75

1.00

1990 1994 1998 2002

our brain capacity


“...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


“...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


ignoring the law does not scale.


computers

documents

knowledge

tcp/ip

html/http

commons


image from the public library of science

licensed to the public under cc-by-3.0


2. there is real tension between interoperability and choice,

and in science, we need interoperability more.


cc for oa? good.


but...cc for oa? good.


attribution


©in relation to data...


category errors


is it creative?


Non-Commercial

the problem of...

for data


Non-Commercial

what’s a commercial useof the data web?


Share Alike

the problem of...

for data


Attribution

the problem of...

for data


the problem of...

for data

any license


if property is the accepted metaphor, allof these terms will eventually appear.


uses triggered by “making a copy”


unmet expectations


attribution = licensecitation = norms


attribution = licensecitation = norms

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


waive all rights necessary for data extraction and re-use

no obligations (share-alike, contract) to limit downstream use

request behavior (citation) through norms


interoperability...


3.value of legally interoperable

data depends on technical interoperability, too.


coffee


coffee

cafe


coffee

cafe

kopi


coffee

cafe

kopi

cafezinho


coffee

cafe

kopi

cafezinho

koffee


coffee

cafe

kopi

cafezinho

koffee

espresso


coffee

cafe

kopi

cafezinho

koffee

espresso

latte


coffee

cafe

kopi

cafezinho

koffee

espresso

latte

mocha


coffee

cafe

kopi

cafezinho

koffee

espresso

latte

mocha americano


coffee

“coffee”

“cafe”

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

converge on common names.


http://ontology.foo.org/receptor

http://ontology.foo.org/receptor

103 databases - just molecular biology


“read (89,00) papers” is not the ideal answer.


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:


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`


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
















































4. the commons, like the internet,

changes the physical world, not just the digital one.


stem cells


non-digital.


“start by melting iron ore...”


change.

whether we like it or not.


interoperability...Tuesday, September 15, 2009

two futures.


c:\


the digital commons...


the right to create.


law + technology + content + community


at best, we’re partially right.


at worst, we’re really wrong.

at best, we’re partially right.


the right to fix our mistakes.


“1 propose the seeming paradox that in science, private property is established by

having its substance freely given to others…”

Merton


thank you

John 2. and 3atherine 0. 4acArthur 5oundationEwing 4arion 6auffman 5oundationCHD1 5oundationOmidyar +etworkNike, 7nc.


science and the commons

Technology