the ontogenesis kblog: light-weight publishing about semantics with light-weight semantic publishing

The Ontogenesis Kblog Light-Weight Publishing about Semantics with

Light-Weight Semantic Publishing

Robert StevensBioHealth Informatics Group

University of Manchester

Getting in the Acknowledgements First

• Phil Lord does vision, technology and content;• Simon cockell does technology;• Daniel Swan does technology;• Robert Stevens does content and shouts “hurrah”

ID_REF VALUE

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Example Data

Source name vascular endothelial iris cells

Organism Homo sapiens

Characteristics tissue: iriscell 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.

“…ape-descended life forms are so amazingly primitive that they still think PDFs are a pretty neat idea.” – after Douglas Adams

Old Ways with New Technology

It costs time and money

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

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

Publication is Currently “Coach Building”

• Coach building suggests hand-crafted, bespoke solutions (often of great beauty)

• Coach building is a barrier to semantics;• Addition of semantics to publications is coach building• It needs to be light• It can’t be a post-hoc process• It has to be done by authors without doing down the

authors

Requirements

• Straight from authors to publication• Must support aspects of academic credibility• Must support academic narcissism• DOIs, author lists, tables of contents, …• As easy as possible for authors; let them use their own

environments; don’t rely on post-analysis of text (especially for semantics….)

Our Solution: Light Publishing, Standard Environments

ASCIIDOC

The Knowledgeblog Environment

ePUB

Target Content

• Just about anything, but…• Grey literature;• The long tail;• Publishing the unpublishable….• Things that can play the role of books

The Ontogenesis Kblog

• Chased for years to do a bio-ontology book;• Wanted to write it, but not as a book (the usual

drawbacks);• Writing a book piecemeal on the topic of biomedical

semantics – ontologies• On a platform in which we can build in some light

semantics

The Kblog Publication Process

• Write a short piece in some authoring tool;• Post it as “under review”• Get some reviews and fix the article;• Post the final version;• All open, versions retained, linked as necessary• Now has 25+ articles, good “reading” numbers;

reviewing a bit broken….

Light Semantics in Kblog

• The “Ontology entities” experience;• Citations;• Use of short codes…

Kcite (current)

• [cite]10.1371/journal.pone.0012258[/cite]

(Lord and Stevens 2010)

P. Lord and R. Stevens. Adding a little reality to building ontologies for biology. PLoS One, 2010.

Kcite (development)

[cite]10.1371/journal.pone.0012258[/cite]

<span property=“cite”>10.1371..</span>

{{[Lord, P],[Stevens,R]

}

Kcite (development)

<span property=“cite”>10.1371..</span> {

{[Lord, P],[Stevens,R]}

(Lord and Stevens 2010)

P. Lord and R. Stevens. Adding a little reality to building ontologies for biology. PLoS One, 2010.

CiTO Support

• [cite cito=“refutes”]...[/cite]• Cito would be nice and can be added easily. • But will the users add the data?• Particularly when we hide the shortcodes.

Keeping it Light

• Semantics have to be of use for the consumer• This is easy to see for semantic mark up of experimental

data – the GO experience• Kcite short codes do something for me the author and

the reader• Who does the work?• Semantics for publishing have to be easy to administer

and have to be enough to draw people in• Wordpress gives us an environment into which we can

build in some semantic support without writing a new tool from the bottom up.

Extant Kblogs

• http://ontogenesis.knowledgeblog.org• http://taverna.knowledgeblog.org• http://bio-ontologies.knowledgeblog.org (pending)• http://health.knowledgeblog.org• http://bioinformatics.knowledgeblog.org (pending)