Download - Data linking with kblog
![Page 1: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/1.jpg)
Data linking with kblog
Phillip LordNewcastle University
![Page 2: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/2.jpg)
The Long Tail
http://en.wikipedia.org/wiki/File:La_Palmyre_041-crop.jpg
![Page 3: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/3.jpg)
Example DataID_REF VALUE1007_s_at 2.8673307091053_at 10.50302152117_at 2.702517066121_at 3.0523161661255_g_at 2.2789980261294_at 5.3602260241316_at 5.4964473221320_at 4.4754121751405_i_at 2.301359647
![Page 4: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/4.jpg)
Example DataID_REF VALUE1007_s_at 2.8673307091053_at 10.50302152117_at 2.702517066121_at 3.0523161661255_g_at 2.2789980261294_at 5.3602260241316_at 5.4964473221320_at 4.4754121751405_i_at 2.301359647
Source name vascular endothelial iris cells
Organism Homo sapiensCharacteristics tissue: iris
cell type: vascular endothelial cells
Treatment protocol Matched human ocular MVEC were isolated from anonymised paired human globes, enucleated within 24 hours of death and free of any known ocular disease. Isolation and culture of human macular inner choroidal endothelial cells utilising anti-CD31-coated Dynabeads (Dynal Ltd, Wirral, UK) was used with the substitution of macular choroidal tissue with isolated iris, retinal and choroidal tissues (PMID 16170129; http://www.ncbi.nlm.nih.gov/pubmed/16170129).
Growth protocol Cells were seeded onto fibronectin-coated 35mm culture dishes (Beckton Dickinson, Oxford, UK), and incubated at 37°C in a humidified atmosphere of 5% CO2.
![Page 5: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/5.jpg)
Example DataID_REF VALUE1007_s_at 2.8673307091053_at 10.50302152117_at 2.702517066121_at 3.0523161661255_g_at 2.2789980261294_at 5.3602260241316_at 5.4964473221320_at 4.4754121751405_i_at 2.301359647
Source name vascular endothelial iris cells
Organism Homo sapiensCharacteristics tissue: iris
cell type: vascular endothelial cells
Treatment protocol Matched human ocular MVEC were isolated from anonymised paired human globes, enucleated within 24 hours of death and free of any known ocular disease. Isolation and culture of human macular inner choroidal endothelial cells utilising anti-CD31-coated Dynabeads (Dynal Ltd, Wirral, UK) was used with the substitution of macular choroidal tissue with isolated iris, retinal and choroidal tissues (PMID 16170129; http://www.ncbi.nlm.nih.gov/pubmed/16170129).
Growth protocol Cells were seeded onto fibronectin-coated 35mm culture dishes (Beckton Dickinson, Oxford, UK), and incubated at 37°C in a humidified atmosphere of 5% CO2.
![Page 6: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/6.jpg)
Example DataID_REF VALUE1007_s_at 2.8673307091053_at 10.50302152117_at 2.702517066121_at 3.0523161661255_g_at 2.2789980261294_at 5.3602260241316_at 5.4964473221320_at 4.4754121751405_i_at 2.301359647
Source name vascular endothelial iris cells
Organism Homo sapiensCharacteristics tissue: iris
cell type: vascular endothelial cells
Treatment protocol Matched human ocular MVEC were isolated from anonymised paired human globes, enucleated within 24 hours of death and free of any known ocular disease. Isolation and culture of human macular inner choroidal endothelial cells utilising anti-CD31-coated Dynabeads (Dynal Ltd, Wirral, UK) was used with the substitution of macular choroidal tissue with isolated iris, retinal and choroidal tissues (PMID 16170129; http://www.ncbi.nlm.nih.gov/pubmed/16170129).
Growth protocol Cells were seeded onto fibronectin-coated 35mm culture dishes (Beckton Dickinson, Oxford, UK), and incubated at 37°C in a humidified atmosphere of 5% CO2.
![Page 7: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/7.jpg)
The paper
![Page 8: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/8.jpg)
The problem?
http://en.wikipedia.org/wiki/File:Clock_in_Kings_Cross.jpg
![Page 9: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/9.jpg)
The problem?
http://en.wikipedia.org/wiki/File:Clock_in_Kings_Cross.jpg
http://en.wikipedia.org/wiki/File:New_British_Coinage_2008.jpg
![Page 10: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/10.jpg)
The problem?
http://en.wikipedia.org/wiki/File:Clock_in_Kings_Cross.jpg
http://en.wikipedia.org/wiki/File:New_British_Coinage_2008.jpg
![Page 11: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/11.jpg)
Coach Building
250,000 articles per year240 million DownloadsCost: 1.5 Billion EuroElsevier
17 million articles > 20 languages365 million readersTotal Cost: 10 million dollarsWikipedia
http://commons.wikimedia.org/wiki/File:Hackney-coach,_about_1680.png
![Page 12: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/12.jpg)
The process
![Page 13: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/13.jpg)
The process
![Page 14: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/14.jpg)
The process
![Page 15: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/15.jpg)
The process
![Page 16: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/16.jpg)
The process
![Page 17: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/17.jpg)
The process
![Page 18: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/18.jpg)
The process
![Page 19: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/19.jpg)
Our Solution
![Page 20: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/20.jpg)
Wordpress
• Has one critical feature– It has an edit dialog– Word– Latex– Open Office– Asciidoc– Textile– Markdown– By email
![Page 21: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/21.jpg)
Features
• Reviewing• Metadata – coins, metatags *• Crawlability *• Multiple authors• Archiving (UKWA)• Searchability
![Page 22: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/22.jpg)
Features
• Bi-directional links• Permalinks (purls to follow)• DOIs (datacite!)• Versioning
• Extensibility– Nice maths * (and mathjax)– Syntax Highlighting– Bibliographic Support (with DOIs, and incompletely CiTO) *– ePUB and PDF (!?) export
![Page 23: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/23.jpg)
Data Linking
• Bi-directional links require support at both ends– Adding this generically– Adding this for specific data sets (microarray)
• Data linking into papers
![Page 24: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/24.jpg)
Old technology
• Most of this technology pre-exists• So why don’t people use it!• There is a good reason...• TECHNOLOGY IS BORING
![Page 25: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/25.jpg)
Content
• http://ontogenesis.knowledgeblog.org – Now has 15k page views (not hits!)– 25 articles, multiple authors– Seeking pubmed inclusion– Advertising: two blog articles about ontogenesis
happened with 1 day of first article. • http://taverna.knowledgeblog.org– 10 articles– About scientific workflows– Supplement to myExperiment
![Page 26: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/26.jpg)
Well...
• These stats are not going to scare either Elsevier or Wikipedia
• But, they are not bad either• And it allows primary scientific content of
many different forms• We believe it can form part of the scientific
landscape
![Page 27: Data linking with kblog](https://reader036.vdocument.in/reader036/viewer/2022062405/554ea2dab4c9055f7b8b4853/html5/thumbnails/27.jpg)
Acknowledgements
Phillip Lord (me!)Dan SwanSimon CockellRobert Stevens (Manchester)Georgina Moulton (Manchester)
Thanks also to JISC, David Shotton, BL, Datacite, and WordPress.