open content and the commons
DESCRIPTION
My presentation from RECSUS on IP issues for scientific communication in a digital age - March 11 - Sherbrooke QCTRANSCRIPT
![Page 1: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/1.jpg)
open content and the commons
kaitlin thaneyprogram manager, science at creative commons
sherbrooke, quebec - 11 march 2010
This presentation is licensed under the CreativeCommons-Attribution-3.0 license.
Thursday, March 11, 2010
![Page 2: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/2.jpg)
make sharing easy, legal and scalable
integrated approach
building part of the infrastructure for knowledge sharing
Thursday, March 11, 2010
![Page 3: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/3.jpg)
knowledge?
journal articlesdata
ontologiesannotations
grey literatureplasmids and stem cells
Thursday, March 11, 2010
![Page 4: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/4.jpg)
(1) the “paradigm shift”
(2) access ... (content) (research tools) (data)
(3) technical / semantic
Thursday, March 11, 2010
![Page 5: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/5.jpg)
1. the “paradigm shift”
it’s no longer about the container.
Thursday, March 11, 2010
![Page 6: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/6.jpg)
scientific revolutions occur when a sufficient body of data accumulates to
overthrow the dominant theorieswe use to frame reality,
... a so-called paradigm shift
- thomas kuhn
Thursday, March 11, 2010
![Page 7: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/7.jpg)
Thursday, March 11, 2010
![Page 8: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/8.jpg)
media company response:adjust the physical media
force the cd format
ignore that people...like to make mixes.
Thursday, March 11, 2010
![Page 9: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/9.jpg)
facing the same shift
for education, science
Thursday, March 11, 2010
![Page 10: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/10.jpg)
scholarship entrenched in idea of transmitting knowledge via paper
mentality reflected even in the way we describe “papers”
static, one-dimensional documents
Thursday, March 11, 2010
![Page 11: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/11.jpg)
information sharing is at the root of scholarship and science
the system of print publishing is a system of communicating knowledge
then came the move to digital ...
Thursday, March 11, 2010
![Page 12: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/12.jpg)
in the digital world, “papers” can become living, breathing works
no longer static PDF documents
linking to data sets, other relevant papers, information, plasmids, genes
Thursday, March 11, 2010
![Page 13: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/13.jpg)
oldest scientific journal
published in english-
speaking world
1665
Thursday, March 11, 2010
![Page 14: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/14.jpg)
Thursday, March 11, 2010
![Page 15: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/15.jpg)
Thursday, March 11, 2010
![Page 16: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/16.jpg)
Thursday, March 11, 2010
![Page 17: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/17.jpg)
need to change the way we think of scholarly publishing,
of knowledge sharing
paradigm shift
begin thinking of “papers” as containers of knowledge
Thursday, March 11, 2010
![Page 18: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/18.jpg)
the container is still the paper
what’s changed is how we use itThursday, March 11, 2010
![Page 19: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/19.jpg)
Thursday, March 11, 2010
![Page 20: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/20.jpg)
2.access is step one
content needs to be legally and technically accessible
Thursday, March 11, 2010
![Page 21: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/21.jpg)
indexing, translation, redistribution: disallowed
Thursday, March 11, 2010
![Page 22: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/22.jpg)
“ By open access to the literature, we mean its free availability on the public internet,
permitting users to read, download, copy, distribute, print, search, or link to the full texts of the articles, crawl them for indexing, pass them as data to software, or use them for any other lawful
purpose, without financial, legal or technical barriers other than those inseparable from gaining
access to the internet itself.”
Image from the Public Library of Science, licensed to the public, under CC-BY-3.0
Thursday, March 11, 2010
![Page 23: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/23.jpg)
“The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the
integrity of their work and the right to be properly acknowledged and cited.”
Thursday, March 11, 2010
![Page 24: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/24.jpg)
Thursday, March 11, 2010
![Page 25: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/25.jpg)
Thursday, March 11, 2010
![Page 26: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/26.jpg)
Thursday, March 11, 2010
![Page 27: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/27.jpg)
Thursday, March 11, 2010
![Page 28: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/28.jpg)
legal implementation
Thursday, March 11, 2010
![Page 29: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/29.jpg)
image from the public library of sciencelicensed to the public under CC-BY 3.0
>1000 journals under CC
Open Access journals
Thursday, March 11, 2010
![Page 30: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/30.jpg)
... what about the physical materials?
Thursday, March 11, 2010
![Page 31: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/31.jpg)
non-digital.
Thursday, March 11, 2010
![Page 32: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/32.jpg)
non-digital.
Thursday, March 11, 2010
![Page 33: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/33.jpg)
non-digital.
Thursday, March 11, 2010
![Page 34: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/34.jpg)
ideally ...
contact author, obtain material, recreate experiment
build on the existing work, publish
and repeat ...
Thursday, March 11, 2010
![Page 35: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/35.jpg)
the reality ... materials difficult to find, fulfill, lack
resources
reagents and assays often re-invented or reverse engineered
locked in contracts, bureaucracy, deliberate withholding, “club mentality”
Thursday, March 11, 2010
![Page 36: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/36.jpg)
Thursday, March 11, 2010
![Page 37: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/37.jpg)
Thursday, March 11, 2010
![Page 38: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/38.jpg)
solves the access problem via contract
SLA
SCMTA
UBMTA (standardized material transfer agreements, or
MTAs)
standard icons, CC methodology, metadata
Thursday, March 11, 2010
![Page 39: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/39.jpg)
Thursday, March 11, 2010
![Page 40: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/40.jpg)
build offer through simple set of choicessimilar way to license chooser
Thursday, March 11, 2010
![Page 41: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/41.jpg)
scientist
lawyer
machine
Thursday, March 11, 2010
![Page 42: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/42.jpg)
Thursday, March 11, 2010
![Page 43: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/43.jpg)
and scaling ...
Thursday, March 11, 2010
![Page 44: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/44.jpg)
access to data
the data “rights” conundrum...
Thursday, March 11, 2010
![Page 45: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/45.jpg)
legal implications
in short, it’s complicated.
Thursday, March 11, 2010
![Page 46: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/46.jpg)
©“creative expression”
Thursday, March 11, 2010
![Page 47: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/47.jpg)
is it creative?
Thursday, March 11, 2010
![Page 48: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/48.jpg)
is it creative?
Thursday, March 11, 2010
![Page 49: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/49.jpg)
is it creative?
Thursday, March 11, 2010
![Page 50: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/50.jpg)
category errors
Thursday, March 11, 2010
![Page 51: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/51.jpg)
Non-Commercial
the problem of...
for data
Thursday, March 11, 2010
![Page 52: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/52.jpg)
Non-Commercial
what’s a commercial useof the data web?
Thursday, March 11, 2010
![Page 53: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/53.jpg)
Share Alike
the problem of...
for data
Thursday, March 11, 2010
![Page 54: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/54.jpg)
1854 Thursday, March 11, 2010
![Page 55: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/55.jpg)
issue of license proliferation
whatever you do to the least of the databases, you do to the integrated system
(the most restrictive wins)
risk for unintended consequences
Thursday, March 11, 2010
![Page 56: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/56.jpg)
Attribution
the problem of...
for data
Thursday, March 11, 2010
![Page 57: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/57.jpg)
Thursday, March 11, 2010
![Page 58: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/58.jpg)
Thursday, March 11, 2010
![Page 59: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/59.jpg)
the problem of...
for data
any license
Thursday, March 11, 2010
![Page 60: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/60.jpg)
national law / jurisdiction-based hurdles
sui generis, “sweat of the brow”
Crown copyright “level of skill”
how internat’l data sharing efforts are affected?
Thursday, March 11, 2010
![Page 61: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/61.jpg)
attribution vs. citation
which one applies? which is best fit?what’s the difference?
“credit where credit is due”
Thursday, March 11, 2010
![Page 62: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/62.jpg)
attribution:(legal entity)
“triggered by making of a copy”does it apply to facts?
how to attribute? (papers, ontologies, data)
“in a manner specified by ...”attribution stacking
Thursday, March 11, 2010
![Page 63: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/63.jpg)
citation:(gentle(wo)man’s club)
legal requirement? interoperability?
credit where credit is dueentrenched scientific norm
Thursday, March 11, 2010
![Page 64: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/64.jpg)
we shouldn’t use the law to make it hard to do the wrong thing ...
Thursday, March 11, 2010
![Page 65: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/65.jpg)
need for a legally accurate and simple solution
reducing or eliminating the need to make the distinction of what’s protected
requires modular, standards based approach to licensing
Thursday, March 11, 2010
![Page 66: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/66.jpg)
Thursday, March 11, 2010
![Page 67: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/67.jpg)
Thursday, March 11, 2010
![Page 68: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/68.jpg)
Thursday, March 11, 2010
![Page 69: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/69.jpg)
Thursday, March 11, 2010
![Page 70: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/70.jpg)
... must promote legal predictability and certainty.
... must be easy to use and understand.
... must impose the lowest possible transaction costs on users.
full text: http://sciencecommons.org/projects/publishing/open-access-data-protocol/
Thursday, March 11, 2010
![Page 71: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/71.jpg)
norms approach
set of principles (not license)
open, accessible, interoperable
create legal zones of certainty
Thursday, March 11, 2010
![Page 72: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/72.jpg)
calls for data providers to waive all rights necessary for data extraction and re-use
requires provider place no additional obligations (like share-alike) to limit
downstream use
request behavior (like attribution) through norms and terms of use
Thursday, March 11, 2010
![Page 73: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/73.jpg)
Thursday, March 11, 2010
![Page 74: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/74.jpg)
Thursday, March 11, 2010
![Page 75: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/75.jpg)
Thursday, March 11, 2010
![Page 76: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/76.jpg)
Thursday, March 11, 2010
![Page 77: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/77.jpg)
Thursday, March 11, 2010
![Page 78: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/78.jpg)
3.technical considerations
(semantics, annotation, standards)
Thursday, March 11, 2010
![Page 79: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/79.jpg)
“read 189,000 papers” is not
the ideal answer.
Thursday, March 11, 2010
![Page 80: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/80.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`
Thursday, March 11, 2010
![Page 81: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/81.jpg)
technical
Thursday, March 11, 2010
![Page 82: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/82.jpg)
semantic agreement
is hard.
Thursday, March 11, 2010
![Page 83: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/83.jpg)
Thursday, March 11, 2010
![Page 84: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/84.jpg)
Thursday, March 11, 2010
![Page 85: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/85.jpg)
cafekopi
cafezinho
koffee
espresso
latte
mocha americano
coffee
Thursday, March 11, 2010
![Page 86: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/86.jpg)
(pick one)
“choice” or interoperability.
Thursday, March 11, 2010
![Page 87: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/87.jpg)
coffee
“coffee”
“cafe”
“kopi” http://ontology.foo.org/1234567
converge on common names
Thursday, March 11, 2010
![Page 88: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/88.jpg)
Thursday, March 11, 2010
![Page 89: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/89.jpg)
Thursday, March 11, 2010
![Page 90: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/90.jpg)
Thursday, March 11, 2010
![Page 91: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/91.jpg)
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: Pyramidal Neurons
Pubmed: Journal Articles
Entrez Gene: Genes
GO: Signal Transduction
better answers through better formats:
Thursday, March 11, 2010
![Page 92: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/92.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`
Thursday, March 11, 2010
![Page 93: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/93.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
turn ugly query code into a link
Thursday, March 11, 2010
![Page 94: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/94.jpg)
Thursday, March 11, 2010
![Page 95: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/95.jpg)
Thursday, March 11, 2010
![Page 96: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/96.jpg)
one man’s observation is another man’s closed book or flight of
fancy.
- willard van orman quine
Thursday, March 11, 2010
![Page 97: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/97.jpg)
data without structure and annotation is a lost opportunity.
work towards maximum reuse of information, interoperability
support recombination and reconfiguration into computer models, queryable by search
engine
treat knowledge as public good
Thursday, March 11, 2010
![Page 98: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/98.jpg)
resist the temptation to treatas property
embrace the potential to treat instead as a network resource
Thursday, March 11, 2010
![Page 99: Open Content and the Commons](https://reader033.vdocuments.site/reader033/viewer/2022051616/5553564db4c905cf188b4672/html5/thumbnails/99.jpg)
thank you.
slideshare.net/kaythaney
Thursday, March 11, 2010