Data linking with kblog

Phillip LordNewcastle University

The Long Tail

http://en.wikipedia.org/wiki/File:La_Palmyre_041-crop.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

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.

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.

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.

The paper

The problem?

http://en.wikipedia.org/wiki/File:Clock_in_Kings_Cross.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

The problem?

http://en.wikipedia.org/wiki/File:Clock_in_Kings_Cross.jpg

http://en.wikipedia.org/wiki/File:New_British_Coinage_2008.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

The process

The process

The process

The process

The process

The process

The process

Our Solution

Wordpress

• Has one critical feature– It has an edit dialog– Word– Latex– Open Office– Asciidoc– Textile– Markdown– By email

Features

• Reviewing• Metadata – coins, metatags *• Crawlability *• Multiple authors• Archiving (UKWA)• Searchability

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

Data Linking

• Bi-directional links require support at both ends– Adding this generically– Adding this for specific data sets (microarray)

• Data linking into papers

Old technology

• Most of this technology pre-exists• So why don’t people use it!• There is a good reason...• TECHNOLOGY IS BORING

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

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

Acknowledgements

Phillip Lord (me!)Dan SwanSimon CockellRobert Stevens (Manchester)Georgina Moulton (Manchester)

Thanks also to JISC, David Shotton, BL, Datacite, and WordPress.