JournalClub
From ImageWeb
Contents |
Schedule
- Tuesday 24th June, 1230-1330 -- Semantic Publishing (Katie)
- Wednesday 2 July, 1230-1330 -- Bio2RDF (David/Jun)
Topic Suggestions
Stick any ideas you have for journal club topics here, don't forget to add your name so we know who proposed what.
Semantic Publishing -- Katie
Reading:
- Semantic enrichment
- Richard Kidd, "Semantic enrichment boosts information retrieval", Research Information Issue 8 April 2007 http://www.researchinformation.info/features/feature.php?feature_id=127
- Linking to data sets
- OECD Statlinks: http://www.oecd.org/dataoecd/36/3/35690106.pdf
- Citation networks
- "Citation Map on the HighWire Portal: Find the Best Articles on a New Topic—Fast!" The Physiologist Vol. 46,No. 5, 2003 p260 http://www.the-aps.org/publications/tphys/images/tphys10x03.pdf
More: Semantic Publishing
Further thoughts from David 24 June
See http://portal.acm.org/citation.cfm?doid=503124.503150 for further neat ideas:
- Additional Information: cited by collaborative colleagues peer to peer
- Tools and Actions: Review this Article
- Index terms as a classification hierarchy
David adds: New ideas for Semantic Publishing – 20 June 2008
The chemists are really showing us the way. The following features are shown in the International Union of Crystallography paper http://journals.iucr.org/a/issues/2003/01/00/au0310/index.html. All these features are ones that we could implement for the PLoS paper:
- The optional navigation bar at the top provides links to sections.
- Paper has a ‘cited in’ button that takes you to a page listing papers in Crystallography Journals Online (only) citing this one!
- Paper has a button permitting download of the correct citation of this paper in a variety of formats: EndNote, RefMan, Refer, Medline, CIF, SGM, Plain Text
- In-text links:
Each reference citation in the text is followed by a blue arrow linking to the reference in the list. Each citation of Table or Figure followed by a light blue arrow linking to the table or figure. Each equation is followed by green arrow linking to the equation.
- Each reference in the reference list is followed by links:
The CrossRef link links to a DOI which resolves as the online paper cited. The ChemPort link links to a page with for a $2 fee will give you a list of citing documents! The 'details' link links to the paper also.
- Books (e.g. Authier, A. (2001). Dynamical Theory of X-ray Diffraction, 1st ed. Oxford University Press) do not have links. But would it not be a good idea to supply a publisher link http://www.oup.com/uk/catalogue/?ci=9780198528920, or an Amazon link http://www.amazon.co.uk/Dynamical-Theory-Diffraction-International-Crystallography/dp/0198528922/ref=sr_1_1?ie=UTF8&s=books&qid=1213990077&sr=8-1?
Bio2RDF -- David/Jun
Reading:
- The Bio2RDF paper at WWW2007:
François Belleau, Marc-Alexandre Nolin, Nicole Tourigny, Philippe Rigault, Jean Morissette (2007). Bio2RDF: Towards A Mashup To Build Bioinformatics Knowledge System. Proc. WWW 2007, 8-12 May 2007, Banff, Canada. http://www2007.org/workshops/paper_143.pdf.
- The Bio2RDF paper in Journal of Biomedical Informatics (21 March 2008):
François Belleau, Marc-Alexandre A Nolin, Nicole Tourigny, Philippe Rigault, Jean Morissette (2008) Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. doi:10.1016/j.jbi.2008.03.004. http://tinyurl.com/4xncfm.
- The Bio2RDF web site: http://bio2rdf.org/.
- The Bio2RDF blog: http://bio2rdf.blogspot.com/.
Diversity, Connectivity and Innovation -- Alistair
Reading:
- Kaufmann (1995) "At Home in the Universe", chapters 3 and 12
In chapter 3, Kaufmann describes a model of auto-catalytics sets of chemicals, suggesting that both the degree of connectivity within the network of possible reactions and the diversity of chemical species are the two main factors determining whether a chemical soup will go "super-critical" and catalyse both it's own creation and an explosion of novel chemical species.
In chapter 12, Kaufmann transfers this model to technological innovation, and suggests that diversity is a major factor underlying economic growth (although he doesn't talk about connectivity, unfortunately).
How might these models and metaphors affect our own understanding and motivations behind the semantic publishing proposals? For example, we could argue that technological innovation is a major economic driver, and that scientific innovation and discover are major drivers of technological innovation. Therefore, how should we best "catalyse" scientific innovation? If a network of scientific ideas and practices is to go "super-critical", does it depend on the diversity of ideas and the extent to which those ideas are connected or can be discovered in conjunction? Does this help understand why current models of scientific publishing might actually be hindering scientific innovation, because content cannot be repurposed and hence connected and rediscovered in a diversity of settings and contexts?
- Scientists are studying the networks for friends on Facebook: http://www.nytimes.com/2007/12/17/style/17facebook.html, and not surprisingly, the networks shows a lot of commonality as any other networks, such as evolution, citation networks (Jun).
Experimental algorithmics -- Graham
Reading:
- CACM, Volume 50, Issue 11 (November 2007), http://portal.acm.org/citation.cfm?doid=1297797.1297818
This article is part of a special issue about experimental computer science, and the role of empirical studies in developing better understanding of algorithm performance, which stands in contrast to the traditional approach of formal theoretical analysis of algorithms.
I think this paper hints at resonances with the complexity reading mentioned above by Alistair (see my email to bioimage: http://lists.ontonet.org/mailman/private/bioimage/2008q2/001482.html).
I also think it is relevant to discussion about semantic web reasoner performance. The DL community make much capital out of the theoretical decidability properties of DLs, but many expressible problems remain intractable for DL reasoners. Maybe here is an approach to understanding tractability of reasoning problems that is more practically useful?
The article doesn't contain much technical detail, but may act to sensitize one to alternative ways of looking at the issues concerned.
OAI-ORE Briefing -- Alistair
Reading:
Further reading:
- See links from http://www.openarchives.org/ore/
The OAI-ORE initiative is getting a lot of attention lately. So what's it all about?
Chado -- Graham
Chado is more than just the database shcema for FlyBase. It aimed at providing a generic structure for sequence-related data for any organism, to be applicable for local or global databases. The Bioinformatics paper discusses the purpose and goals of Chado, and introduces a few of its key technical features. A study of Chado might event prove to be an interesting way to introduce software engineers to the essentials of genetics and bioinformatics.
BioBike - Graham
BioBike is a combination knowledge base and web-accessible easy-to-use programming environment for biologists. I think it may embody some ideas that are relevant to OpenDataForge, but is less web-centric. I particularly like the use of a functional language (LISP) as the basis for programming access to and analysis of the knowledge base. While it seems quite well integrated as a human web application, I'm less sure (on very brief casual review) whether it's very easy to access data from the web in general.
Linked Data Workshop, WWW2008
I think a brief review of the papers from this workshop might be a useful topic for discussion. I found many to be uninspiring, but I may well be missing something here, and would welcome an opportunity to hear others' views.
