Ucla GSEIS

13 november 2008

ucla graduate school of education and information sciences

the knowledge web

knowledge gapsprocess failures

transaction costslost opportunities

knowledge gapsprocess failures

transaction costslost opportunities

is the answer more information?

many information products advance

incrementally

the discovery process:

the discovery process:

thanks to the products, we already know a lot...

we need information innovationsand process innovations

to match product innovations.

1.

the “digital commons” represents a methodology that lowers the cost and

increases the volume of transactions at the “knowledge layer” of the net

does the ability to ask more questions, faster, lead us to more

knowledge or just more data?

what’s different about communications and computers?

1. we know stuff.

1. we know stuff.2. open networks.

physical

code

content

physical

code

content

physical

code

content

knowledge

knowledge rights

knowledge rights

“the commons”

“digital commons”

interoperabilitylow transaction costslaw and technology

user interface to copyright

140,000,000+ digital objects online under our licenses

licenses “ported” to 50+ countries

integrated with Google, Yahoo, Firefox, Microsoft Office...

2.

the digital commons is a stable methodology to manage data,

materials, and content for science.

“think market”

project development

funding

pro bono

community

“do no harm”

“running code”

early focus on life sciencesexploring climate change, geospatial, elsewhere

what would move via the science network?

Open Access Content

making knowledge legally and technically available for re-use and composition into new knowledge.

we use digital tools to replicate paper technology

© creative expression

© ideas or facts

e=mc2

the container, not the facts.

the container, not the facts.

but © locks the container.

IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases

IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases

http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf

indexing: disallowed.

image from the public library of sciencelicensed to the public under CC-BY 3.0

>1000 journals under CC

c

PubMedCentral ~ 1,000,000 articlespermissions granted: 50,000

(6% of PMC legal for transformative use)(.003 of all PubMed records)

what do these ideas mean in

a world of integrated data?

creativework?

“So, out of all of this discussion my

question is whether ChemSpider is

Content or Data.” - Antony Williams

“The motivation behind this memorandum is interoperability of scientific data.”

is it legal?

+

+

+

+ +

+

++ +

is it legal?

1 Converge on the public domain by waiving all rights based on intellectual property

2 Converge on the public domain by waiving other statutory or intellectual property rights.

3 Converge on the public domain by imposing no contractual controls.

4 Provide for interoperation with databases not available under the Protocol through open metadata

a protocol, not a license.

conflicts with the protection instinct

conflicts with the protection instinct

the protection instinct is frequently an instinct to protect “freedom”

3.

we have to build infrastructure for data into the web of documents that we have.

solves the legal problem

but not the container problem.

web 2.0, science 3.0, what about making Google work better?

over 200years at

one paper/day

what you want is a list of genes.

not a list of documents.

building a web for data:the “semantic web”

Web page Web pagelinks to

making computers understand links between documents

drinking coffee feel awakecauses

making computers understand relationships between concepts

drink coffee feel awakecauses

drinking coffee feel awakecauses

http://ontology.foo.org/drinking coffee http://ontology.foo.org/feel awake http://ontology.foo.org/receptor

http://ontology.foo.org/causes

192.168.1.1

we need a Domain Name System for concepts:

http://sciencecommons.org

coffee http://ontology.foo.org/coffee

coffee

“coffee”

“cafe”

“kopi” http://ontology.foo.org/coffee

use the web to integrate information from different places and different names

bed

get out of bed

get out of beddrink coffee

open eyes

located atlast subevent

first subevent

after

drink

coffee

wet

cup

is a

property ofoften near

make coffee

is for

subevent

feel awake

person

feel jittery

does not wantwants

causes

causes

pour coffee pick up cupafter after

cafe

sugar

often near

located in

(too much work for coffee)

(distributed, networked approaches start to look pretty good)

Open SourceData Integration

formatting digital knowledge into modular building blocks for

composition into new knowledge.

e pluribus unum.

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

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

we can transform complex queries into links

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

we can build a corpus of queries as links

we can re-use cultural tools for scholarship

we can make science user-driven.

4.

institutions have to provide a stable foundation for the knowledge web.

Parkinson’s

Huntington’s

ALS

Multiple Sclerosis

Autism

process revolutions: the network

Parkinson’s

Huntington’s

ALS

Multiple Sclerosis

Autism

institutional revolutions: the network

the library to me:location, structure, discovery, preservation

the infrastructure for this is very, very shaky.

prefix dc: <http://purl.org/dc/elements/1.1/> prefix skos: <http://www.w3.org/2004/02/skos/core#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix foaf: <http://xmlns.com/foaf/0.1/>

what are the odds that the organizations making the namespaces will be here in 50 years? 100 years?

Huntington’s

Parkinson’s

Huntington’s

ALS

Multiple Sclerosis

Autism

Parkinson’s

Huntington’s

ALS

Multiple Sclerosis

Autism

library

“In any case, it is clear that a library containing all possible books, arranged at random, is equivalent (as a source of

information) to a library containing zero books.”

http://en.wikipedia.org/wiki/The_Library_of_Babel

exponential content growth

0

1.25

2.50

3.75

5.00

1990 1994 1998 2002

our brain capacity

1. Books are for use. 2. Every reader his [or her] book. 3. Every book its reader. 4. Save the time of the User. 5. The library is a growing organism.

1. Books are for use. 2. Every reader his [or her] book. 3. Every book its reader. 4. Save the time of the User. 5. The library is a growing organism.

what’s the digital version of the five laws?

call to action:

1. join up with the semantic people - support discipline-drivennamespaces and ontologies

2. queries are the interface - average user doesn’t knowhow to ask complicated questions on the research web.

3. make the library the hub of the research web.

thank you

[email protected]

http://sciencecommons.org