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The Ontogenesis Kblog: Light-Weight Publishing about Semantics with Light-Weight Semantic Publishing
- 1. The Ontogenesis Kblog Light-Weight Publishing about Semantics with Light-Weight Semantic Publishing Robert Stevens BioHealth Informatics Group University of Manchester
- 2. 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”
- 3. ID_REF VALUE 1007_s_at 2.867330709 1053_at 10.50302152 117_at 2.702517066 121_at 3.052316166 1255_g_at 2.278998026 1294_at 5.360226024 1316_at 5.496447322 1320_at 4.475412175 1405_i_at 2.301359647 Example Data Source name vascular endothelial iris cells Organism Homo sapiens Characteristics 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/1617 0129). 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
- 4. Old Ways with New Technology
- 5. 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
- 6. 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
- 7. 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….)
- 8. Our Solution: Light Publishing, Standard Environments
- 9. ASCIIDOC
- 11. Target Content • Just about anything, but… • Grey literature; • The long tail; • Publishing the unpublishable…. • Things that can play the role of books
- 12. 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
- 13. 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….
- 14. Light Semantics in Kblog • The “Ontology entities” experience; • Citations; • Use of short codes…
- 15. 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.
- 16. Kcite (development) [cite]10.1371/journal.pone.0012258[/cite] <span property=“cite”>10.1371..</span> { {[Lord, P],[Stevens,R] }
- 17. 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.
- 18. 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.
- 19. 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.
- 20. 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)
Editor's Notes
- This slide shows some papers, some microarray probe Ids, miami, so statistical plots. But the data from the long tail and big science is different. While big science generally produces Sequence data, which is generally all of the same type. The long tail doesn’t. For example, We start with microarray expression data. Then we have MIAME compliant metadata, An RNA degredation plot and finally a paper, in this case a random one that I found on PLoS Yesterday. Of these, we have data standards for many parts – the second part, often called “metadata” even Though it isn’t, whichuses MIAME which is one of the older information content standards in Bioinformatics. To me, all of this is data. Without the later three, the “raw data” is just junk.
- A slide build with icons – latex, pdf, another pdf, word, XML, then to both PDF and HTML. It’s the PLoS One publication system. Consider for example this process from one of the major publishers that I have Published with. I wrote my article in latex. I converted it to PDF. The website converted it to another PDF (which I had to check). The publishers then (and this is true) converted it to a word doc. From there, they turn it into XML, which was finally converted to HTML and, yes, you guessed It, another PDF. Now, not only is this a waste of time, but it’s inaccurate. Errors happen. And trying to get Structured or data linked publications through this process. You might as well give up.
- A slide build – starts with an outdoor shop clock, then shows a set of coins (the one with overlapping images On the back, then the PDF icon). So, what is the problem. Well first the process of publishing is very time-consuming. Secondly, it’s very expensive. And finally, it’s a process where, to misquote Douglas Adams Which is so amazingly primitive that we still think PDFs are a pretty neat idea. But in general, this form of data capture only happens for the most cherry picked data. The positive data, the significant data, the data where the experiment worked. What about The negative data, the insignificant, what about the standard operating procedure, what about the tutorial Information and so on. This is not a small issue – the massive publication bias in biology hampers Our understanding of the way that organisms function. In medicine, people die because not through lack of knowledge, but because we cannot collate information that exists.
- My solution. Wordpress. Actually, more importantly, commodity software. And by commodity, I mean commodity, and not research. There are some excellent tools from academia – widely used. Open Journal Systems, for example, powers 6000 journals. Wordpress is behind 10% of ALL websites.
- Slide shows wordpress icon, surrounded by icons of software that can be used to get data in. Word, latex, libreoffice, email, asciidoc.
- Knowledgeblog (we need a logo!) surrounded by icons for EditFlow, Mathjax, co-author-plus screenshot, Datacite, ePub, UK Web Archive.
- Slide shows current kcite version -- short code is transformed to (unsemantic) HTML presentation. We are also addressing referencing. The current version of kcite is entirely non-semantic, as everything happens in wordpress. We take short codes which have standard identifiers and replace them with a presentation HTML
- Kcite in development. Shortcode transformed by Wordpress to RDFa marked up in text citation, and citation info in JSON. The development version, however, transforms the intext citation into a span tag markup (we are migrating to RDFa). The Bibliographic information is turned into JSON, currently inline, but this will be served asynchronously eventually.
- RDFa and JSON transformed into presentation using Citeproc-js. The intext citation will remain semantic with RDFa underneath. Citeproc allows us to change the HTML client side (so user can choose). We believe that the intext citation needs to be semantic, But the bibliography list itself is a presentation thing anyway, so we don’t care, particularly as it will require a lot of modification of citeproc. This also means that when the bibliographic info is not available or has not loaded yet, the user will still see something useful in text (a link to a DOI, URL, whatever).