Building Linked Web Communities

building linked web communities in biomedicine

29 april 2009boston, ma

john wilbanks

Thursday, June 4, 2009


“compatibly communicating”



devices.


what about knowledge?


what about knowledge?

journal articlesdata

ontologiesannotations

wikis











1.making it “web” - the access principle





the right to make and distribute “copies”

the right to make and distribute “derivatives”


the law surrounds us, even in its absence.Thursday, June 4, 2009

the law surrounds us, even in its absence.Thursday, June 4, 2009

ignoring the law does not scale.Thursday, June 4, 2009




the digital commons - another network layer.


computers

documents

knowledge

tcp/ip

html/http

commons



Attribution

Non-Commercial No Derivative Works

Share Alike

LicensingStep 1: Choose Conditions


LicensingStep 2: Receive a License




International Jurisdictions


Licensed Objects via G/Y!




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?


license propagation: whatsoever you do to the least of the databases, you do to the integrated knowledgebase


“community spirit - with teeth”

norms + public domain

















open rights.

multiplicity of incentives.

distributed workloads.


2.making it “linked” - the names and containers problem





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

990+ databases





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

using the web to integrate data and databases


http://ontology.foo.org/receptor

http://ontology.foo.org/receptor

www


“domain name system”


“domain name system”

or, “when it’s worth being strict about ontologies”



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/

“find me signal transduction genes in pyramidal neurons”

“what are the potential ‘locks’ for alzheimers?”



“read 189,000 papers” 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

better answers through better formats:


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

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

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

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

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

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

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

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

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

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

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

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

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









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

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

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

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

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

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

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

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

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

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`


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


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)}



why you need inference and rigor...



remember edit source?


users remix query code












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



3.making it “community” - the induction problem



“...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.”


“...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?’”









what can you do?


what can you do?

1. solve locally, share globally.

2. standards, standards, standards.

3. lead by example.


thank you

John D. and Catherine T. MacArthur FoundationEwing Marion Kauffman Foundation

CHDI FoundationOmidyar Network

Nike


Education

Building Linked Web Communities