Cbmi Nlm Fellows

CBMI NLM training fellows

Thursday, April 9, 2009

1.the law surrounds us, even in its absence.



free/libre open source


open culture


open access


the right to make and distribute “copies”

the right to make and distribute “derivatives”


the digital commons - another network layer.


computers

documents

knowledge

tcp/ip

html/http

commons


open rights.

multiplicity of incentives.

distributed workloads.


commons as infrastructureThursday, April 9, 2009

open science?


is the goal freedom or methodology? or both?

or something else?


2.science on the net: digitized, not digital.


no metcalfe’s law for science yet.


no metcalfe’s law for science yet.


stable systems have “immune” responses to change.






web assumptions and web scale FAIL




the model is at the center of value creation and capture



would you share your map?Thursday, April 9, 2009

1,596,270,108 internet users(http://www.internetworldstats.com/stats.htm)


http://www.internetworldstats.com/stats.htm

http://www.internetworldstats.com/stats.htm


.0001 of internet users = wikipedia


.0001 of geneticists = ?


there is no crowd.


3.make the few more powerful via

object-orientation...


computers

documents

knowledge

tcp/ip

html/http

semantics


making computers understand things


Web page Web pagelinks to

making computers understand links between documents


drinking coffee feel awakecauses

making computers understand relationships between ideas


coffee

“coffee”

“cafe”

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

URLs for concepts, not just pages


http://ontology.foo.org/receptor

http://ontology.foo.org/receptor

www


4.hard to do, but not impossible.


digital content

research tools

digital content

technology


research tools

digital contentThursday, April 9, 2009

coming soon.Thursday, April 9, 2009


digital content

digital contentThursday, April 9, 2009

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

>1000 journals under CC


what do these ideas mean in

a world of integrated data?


interoperate with the public domain.


announcing: personal genomes underCC∅, available via filesharing networks






digital content

technology


http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1

990+ databases




“find me signal transduction genes in pyramidal neurons”


“read 189,000 pages” is not the ideal

answer.



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

you need four data sources to answer the question.


http://purl.org/obo/owl/GO#


http://www.w3.org/2000/01/rdf-schema#


http://www.w3.org/2002/07/owl#


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


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


http://www.obofoundry.org/ro/ro.owl#


http://purl.org/commons/hcls/pubmesh









http://purl.org/commons/hcls/goa


http://purl.org/commons/hcls/20070416/classrelations


http://purl.org/obo/owl/obo#part_of


http://purl.org/commons/hcls/gene


http://purl.org/commons/hcls/20070416


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`

precise answers to complex questions


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 turn ugly query code into a link
















































we can turn ugly query code into a link


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}

}

users can view and edit source


























collaborative question answering


open = pleasant surprises.


google maps for brain images

http://sparql.neurocommons.org:8890/map/#Kcnip3@2850,Kcnd1@2800


http://sparql.neurocommons.org:8890/map/

http://sparql.neurocommons.org:8890/map/

“it’s the links, dummy”- James Boyle

aka “Boyle’s Law 2.0”


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

“papers”


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

“networked knowledge”










http://ucsdbiolit.codeplex.com/

http://blogs.msdn.com/exscientia/

http://tinyurl.com/deypwt

(video)

(developer blog)

(project site)


http://ucsdbiolit.codeplex.com

http://ucsdbiolit.codeplex.com




what can you do?


what can you do?

1. solve locally, share globally.

2. standards, standards, standards.

3. lead by example.


thank you

[email protected]

http://sciencecommons.org


mailto:[email protected]

mailto:[email protected]



Documents

Cbmi Nlm Fellows