Some Updates to omn-mode

I have described my experiences of using Emacs for writing ontologies previously [@url:www.russet.org.uk/blog/2161] I was not entirely happy with omn-mode, even after recent changes [@url:www.russet.org.uk/blog/2185] so I have taken the opportunity to update it a little more. This article most describes some implementation changes. Originally, omn-mode was based on generic.el; this is a package which enables development of simple major modes. However, the emphasis was on simple, and my code was getting a little bit complex; generic.el was starting to get in the way. Moving to the define-derived-mode was not pain-free; it involved redoing already functioning code which is always a bit down heartening but probably worthwhile. One thing that I did have problems with was getting comments to wo…

Contradictions in Karyotypes

Recently, I and my PhD student, Jennifer Warrender have become interested in the representation of karyotypes. There are descriptions of chromosome complement of an individual. In essence, they are a birds-eye view of the genome. Normally, they are described using a karyotype string, so my karyotype would be 46,XY (probably!) which is normal male. When describing abnormalities, these can get very complex; take, for example, 46,XX,der(9),t(9;11)(p22;q23)t(11;12)(p13;q22)c,der(11)t(9;11)t(11;12)c,der(12)t(11;12)c[20] which describes a patient with multiple translocations. There are a couple of reasons why we thought that it would be interesting to turn this into an ontological representation. The karyotype strings are not very parsable, and lack a computable specification which makes it very…

Extending the Process

After a reasonably long hiatus, I have started to work on the Process Knowledgeblog again. Particularly with the creation of kblog-metadata [@url:knowledgeblog.org/kblog-metadata] the need for more documentation was pressing, and the process kblog seems the obvious place to put it; putting full documentation in the plugin "readme" file is a little painful and hard to debug. As with all articles on a kblog, these will not be changed or updated, except for non-semantic error correction. Rather, I will add new articles outdating existing ones, maintaining a full record of what has happened before. I've also started to take advantage of a feature of kblogs that we have explored with Ontogenesis [@url:ontogenesis.knowledgeblog.org/] we do not have to wait for all the documentation to …

Colour is not enough

Recently, I was surprised to be told that we could not have colour figures in our paper [@url:www.russet.org.uk/blog/2170] even though it was online only. Our assumption is that this is an enormous legacy issue; the publisher in question, OUP, still produces a tree-based version of the journal, Bioinformatics. The distinction between colour and monochrome is important here. Of course, it is easy to criticise others for being trapped in a legacy situation. The reality is, though, it can to happen anyone; it is not possible to always take a step back, to reassess standard procedure, to think whether it still makes sense. The paper based publication process still affects all of our ways of thinking and this includes myself. The paper in question contains graphs showing a time course, in this …

Omn-mode now released

I recently published about my experiences of using Emacs for Ontology building [@url:www.russet.org.uk/blog/2161] A fairly niche subject area, but I was did get a couple of responses asking for my code; curiously, it appears that although I started to write this 6 or 7 years ago, even before this working draft was produced, I forgot to ever release it publically. The code is now available on my website. I have also taken the opportunity to move my versioning to Mercurial for all of my Emacs packages --- originally I used Subversion. This is fine, but the servers tend to get deleted over time for projects that are rarely updated. With a DVS, I keep the entire project history on my local machine which is a considerable advantage. This is also available from Google code. omn-mode is a work in…

Simple HTML

A while back, I submitted a grant to JISC on digital preservation. The basic idea was to move a set of files that I had as Word docs, post them all on the knowledgeblog platform. The practical upshot of this is that the files, instead of rusting, become accessible to the world at large and, also, they also get digitially preserved by the various web preservation engines around. We called this digital preservation by stealth; putting something on the web is useful anyway, the preservation occurs as a happy by-product. And along the way, we get stats on whether the content was actually used by anyone. Nice idea, I thought. Still, the grant bounced. There were several reasons for this: the preservation was so stealthy that one of the reviewers could not see it all at; another thought that the…

Bringing Things to Life

Tim Berners-Lee sitting at a computer desk, typing on his machine. Around him, 10,000 camera flashes flare, fireworks fire reds and blues into the sky, and the shades of a thousand costumes, filling his eyes. Then, on cue, he sees 50 metre high letters, brillant orange, spelling out "This is for everyone" in homage to his creation, to the Web. He smiles, feeling overwhelmed by the brilliance, and the sheer scale of the event, and the strangeness that his abstract creation has bought him here, to the start of the Olympics, a celebration of muscle and bone. But, somewhere, admist the multiple hues of London 2012, a doubt gnaws at him. He knows that there is a flaw, a problem, something wrong with his creation. Surely, he realises for the first time, it would have been better, more …

Ontology Building with Emacs

I have just started to build an ontology and I have to admit that it has been a while since I have done this; I think that the last time was when writing a paper about function [@url:dx.doi.org/10.1186/2041-1480-1-S1-S4] so I was interested to see how it would work. I've have been engaged in discussions recently about syntactic aspects of OWL [@url:www.russet.org.uk/blog/2040] the main reason for this is my long-held believe of the need for editing tools that work at the syntactic level; this allows us to plug in to the enormous body of programming tools supporting building, collaborative development, versioning and so on. So, I decided to build the entire thing using Emacs; the nature of the ontology also meant that I wanted to reboot my long-neglected attempts to bring literate developme…

Open Access and the Semantic Web

As I alluded to in my recent post [@url:www.russet.org.uk/blog/2151] the paper that we submitted to Sepublica [@url:www.russet.org.uk/blog/2054] was accepted for a special issue associated with the main conference Extended Semantic Web Conference, as one of the best papers from the Workshops. The problem that this is published by Springer, and I want my publication to remain open access. We did enquire of the conference and Springer whether there was an open access option; their website mentions open choice, at the rather eye watering price of 2000EUR. Initially, we were told that they would do this, at 480EUR (40EUR a page), but it turns out that they have stopped doing this for single papers in a conference proceedings. So, we turned down the publication offer. Perhaps not a sensible thi…

Trying arXiv

We were pleased that our paper [@url:www.russet.org.uk/blog/2054] was accepted in a special issue associated with the Extended Semantic Web Conference, as one of the best papers from the Workshops. Of course, it is lovely to be acknowledged in this way, and we're very grateful to the organisers of Sepublica for this. However, it did place us in the difficult position. In the end, I decided to turn this offer down on the grounds that I did not want to publish with Springer if it meant that the article would become Toll Access. Spurred on by this, therefore, I have finally got around to submitting a paper to arXiv. Pretty poor show on my behalf, I fear, as I should have done this years ago with most of my papers. I was put off by the possibility of extra work. As a result of which I have onl…