CNI Project Briefing Tuesday, December 13, 2011, 10:30-11:30 a.m. Joyce L. Ogburn
Cni Fall 08 Briefing Science Commons
-
Upload
john-wilbanks -
Category
Education
-
view
1.903 -
download
1
description
Transcript of Cni Fall 08 Briefing Science Commons
![Page 1: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/1.jpg)
CNI fall 2008
e-research, data integration
john wilbankscreative commons / science commons
![Page 2: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/2.jpg)
1. e-research requires new approaches to data
integration.
![Page 3: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/3.jpg)
databases as unique entities, instead of nodes in a network
![Page 4: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/4.jpg)
http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1
![Page 5: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/5.jpg)
“packages”
![Page 6: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/6.jpg)
![Page 7: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/7.jpg)
not monolithicnot centralized
![Page 8: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/8.jpg)
![Page 9: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/9.jpg)
![Page 10: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/10.jpg)
scalable
![Page 11: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/11.jpg)
aggregation
![Page 12: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/12.jpg)
not-software
scalable
modular
![Page 13: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/13.jpg)
what about science?
![Page 14: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/14.jpg)
...except authenticated, and expensive.
science is not unlike wikipedia...
![Page 15: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/15.jpg)
inefficient and expensive ecosystem of processes to peer-produce and
review scholarly content
![Page 16: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/16.jpg)
from a technical perspective
![Page 17: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/17.jpg)
![Page 18: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/18.jpg)
2. multivariate connected barriers to new methods
of data integration
![Page 19: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/19.jpg)
cognitive barriers.
![Page 20: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/20.jpg)
![Page 21: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/21.jpg)
![Page 22: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/22.jpg)
![Page 23: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/23.jpg)
![Page 24: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/24.jpg)
the knowledge was human-scale
![Page 25: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/25.jpg)
![Page 26: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/26.jpg)
![Page 27: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/27.jpg)
web 2.0, science 3.0, what about making Google work better?
![Page 28: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/28.jpg)
over 200years at
one paper/day
![Page 29: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/29.jpg)
what you want is a list of genes.
not a list of documents.
![Page 30: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/30.jpg)
technical barriers.
![Page 31: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/31.jpg)
IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
![Page 32: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/32.jpg)
IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
![Page 33: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/33.jpg)
tradition barriers.
![Page 34: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/34.jpg)
![Page 35: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/35.jpg)
![Page 36: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/36.jpg)
legal barriers.
![Page 37: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/37.jpg)
http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
indexing: disallowed.
![Page 38: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/38.jpg)
http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1
legal integration: impossible.
![Page 39: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/39.jpg)
3. moving from a document web to a data web.
![Page 40: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/40.jpg)
a network of devices
![Page 41: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/41.jpg)
01-23-45-67-89-ab
![Page 42: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/42.jpg)
papers contain ideas,
like boxes contain books
a networkof
documents
![Page 44: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/44.jpg)
drink coffee feel awakecauses
a networkof ideas
![Page 45: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/45.jpg)
drink coffee feel awakecauses
http://foo.bar/ideas/causes
![Page 46: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/46.jpg)
“graph” networks
![Page 47: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/47.jpg)
Web page Web pagelinks to
making computers understand links between documents
![Page 48: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/48.jpg)
![Page 49: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/49.jpg)
drinking coffee feel awakecauses
making computers understand relationships between concepts
![Page 50: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/50.jpg)
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
![Page 51: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/51.jpg)
coffee
“coffee”
“cafe”
“kopi” http://ontology.foo.org/coffee
use the web to integrate information from different places and different names
![Page 52: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/52.jpg)
drink coffee feel awakecauses
![Page 53: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/53.jpg)
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
![Page 54: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/54.jpg)
4. basic requirements for modular, package-based
approaches to “knowledge”
![Page 55: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/55.jpg)
it starts with the public domain.
![Page 56: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/56.jpg)
![Page 57: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/57.jpg)
it takes ontologies.
![Page 58: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/58.jpg)
“Kant saw the mind could not function as an empty container that simply receives data from the outside. Something had to be giving order to the incoming data...”
- http://en.wikipedia.org/wiki/Immanuel_Kant
![Page 59: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/59.jpg)
![Page 60: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/60.jpg)
requires a modular, standards-based
approach to licensing.
![Page 61: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/61.jpg)
![Page 62: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/62.jpg)
+
+
+ +
+
++ +
is it legal?
![Page 63: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/63.jpg)
license propagation: whatsoever you do to the least of the databases, you do to the integrated knowledgebase
(the most restrictive license wins)
![Page 64: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/64.jpg)
a protocol, not a license
![Page 65: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/65.jpg)
it takes some namespace work.
![Page 66: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/66.jpg)
documentation that tells what a URI names
database record that is about a thing
![Page 67: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/67.jpg)
![Page 68: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/68.jpg)
1. The referent of the URI must be made clear through documentation.
2.Provision of such documentation via a widely deployed network protocol must be an ongoing concern.
3.The documentation provider must be responsive to community needs, such as the need to have mistakes fixed and the need for stability of reference.
4.Documentation must be open.
URI requirements
![Page 69: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/69.jpg)
![Page 70: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/70.jpg)
1. The referent of the URI must be made clear through documentation.
2. Provision of such documentation via a widely deployed network protocol must be an ongoing concern.
3. The documentation provider must be responsive to community needs, such as the need to have mistakes fixed and the need for stability of reference.
4. Documentation must be open.
URI requirements
![Page 71: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/71.jpg)
![Page 72: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/72.jpg)
1. The referent of the URI must be made clear through documentation.
2. Provision of such documentation via a widely deployed network protocol must be an ongoing concern.
3. The documentation provider must be responsive to community needs, such as the need to have mistakes fixed and the need for stability of reference.
4. Documentation must be open.
URI requirements
![Page 73: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/73.jpg)
Stability of reference (meaning, denotation)
Stability of documentation
Stability of the referent
![Page 74: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/74.jpg)
1. The referent of the URI must be made clear through documentation.
2. Provision of such documentation via a widely deployed network protocol must be an ongoing concern.
3. The documentation provider must be responsive to community needs, such as the need to have mistakes fixed and the need for stability of reference.
4. Documentation must be open.
URI requirements
![Page 75: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/75.jpg)
and what about ontologies?
![Page 76: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/76.jpg)
copyrightable?
“it’s complicated.”
![Page 77: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/77.jpg)
•extension (quality control: spam and junk)
•remix (brand confusion, loss of integrity and attribution)
•formats (failure to adhere to common protocols or technology)
•persistence (the transient nature of all Web things...)
![Page 78: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/78.jpg)
5. proof of concept - open source data integration for
neuroscience.
![Page 79: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/79.jpg)
a repository of ontologies, namespaces, and integrated
databases.
http://neurocommons.org
![Page 80: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/80.jpg)
e pluribus unum.
![Page 81: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/81.jpg)
![Page 82: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/82.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: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
![Page 83: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/83.jpg)
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`
![Page 84: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/84.jpg)
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 85: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/85.jpg)
we can transform complex queries into links
![Page 86: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/86.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 87: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/87.jpg)
we can build a corpus of queries as links
![Page 88: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/88.jpg)
we can re-use cultural tools for scholarship
![Page 90: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/90.jpg)
![Page 91: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/91.jpg)
“a running Neurocommons mirror consumes a fair amount of system resources”
![Page 92: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/92.jpg)
http://kingsley.idehen.name:8890
http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VirtEC2AMINeuroCommonsInstall
![Page 93: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/93.jpg)
![Page 94: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/94.jpg)
conclusion?
![Page 95: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/95.jpg)
a. it’s very hard work to use the semantic web right now
b. it’s worth it if you have the cognitive overload problem.
c. none of it works without an open knowledge approach
![Page 96: Cni Fall 08 Briefing Science Commons](https://reader033.fdocuments.net/reader033/viewer/2022051612/54bc9c1b4a79597e6e8b456d/html5/thumbnails/96.jpg)
thank you
http://sciencecommons.org