Just finished watching, Dr Alice Robert and the incredible human journey. I've not seen her before, although apparently she's been around a bit; she's not a bad presenter; she's enthusiastic without being gushing, explains clearly without being cringe-worthy simplification. Her semi-plummy tones are slightly irritating, but I guess I can live with that. The programme was also slightly irritating; the production is rather portentous. From the spoken intro "they say this is where it all began" to "come with me in the footsteps of our ancestors", sets the tone. I disliked the implication that she was going to sort it all out ("one woman on a global mission, to answer one question") --- it's not her journey, after all, she's reviewing the work mostly done by other…

Ah, it does on and on. After my last attempt at literate OWL programming, called omnsplit, I decided that there was a problem; this version splits the OWL file into individual statements, and puts them into files with the same name as the OWL class (property, or whatever). The problem is that, for an ontology like OBI, you get 1400 individual files; this is just inconvienient as many applications don't like this many files in a directory. Also, there is a naming constraint; you can only use characters legal in the file system; this doesn't include ":" if you want to be Windows (NTFS) compliant. So, for my new system, I decided to generate an index file, which just points at locations in the ontology file. Initially, I was just going to index the main ontology file; in the end, I …

Just finished two new books in a row. It's an unusual feature of my life that I am relaxed enough to do this; normally, when my head is too full of stuff, or my diary is too full of deadlines, I tend to be too tired in the evening to give my full attention to reading. At the moment, most of my colleagues seem to be chasing exam marking deadlines, so I feel slightly guilty at this, perhaps, but then I've been using the time to think about some new ideas for research, so not too guilty. And, as I mentioned, reading some books; so, onto these. Both were birthday presents, neither my choice, which made them all the more interesting. The first was by Barack Obama --- never been a great one for political memoirs; why spend money on buying a book full of lies; or, at least, honest attempts at dec…

After a bit of struggle, I now have another literate OWL tool working, along the lines discussed in a previous blog post. Rather than generating the OWL documentation, I now split a Manchester syntax file up, so that I can refer to bits of it. I have this working with OBI, using Protege to produce a single merged ontology file, in Manchester syntax. The current implementation is rather simple; it produces one file-per-entity in the OWL file which I don't think is entirely good. When run on OBI, it creates over 1400 files which is a lot. The other problem is that I've had to do some dubious hacking to get the file names work out. Firstly, I have to remove spaces and "\"'s, as wel as ":" which is illegal on NTFS. There's also a problem with some of the OWL. Unfortunately,…

Just upgraded to Wordpress 2.8. The automatic update didn't work; this seems to be a continual problem which stems from wordpress not being in the default location. For some reason, it wants to push from the new version rather than pull under these circumstances. Not good. So, I did the manual upgrade; unfortunately the admin page crashed out with an error: PHP Fatal error: Call to a member function read() on a non-object in wp-includes/theme.php on line 387 This has been reported here and here It's this bit of code causing the problems. $template_dir = @ dir("$theme_root/$template"); if ( $template_dir ) { while ( ($file = $template_dir->read()) !== false ) { // etc It appeared to be only be my modified version of the theme (Evanesence) causing the proble…

The weekend just gone was the Northern Rock cyclone weekend. With three events: the Leazes Criterium, Cyclone and Beaumont Trophy it's a bit a of feast for a cycling nutter like myself. The criterium is a short race just down from my work, the latter is a long, elite rider race. The cyclone is a fun run; on a bike. It's a bit of an embarrasement of riches, to be honest. Both this year and last, I've not seen all of the Criterium and totally missed the Beaumont because I wanted to sleep early or been knackered from the cyclone. I went for the 62 mile ride this year, as last. I quite fancied trying the 100, but in the end decided that it was a bit beyond me; I think it would have taken 7 or 8 hours. In the end, I was quite glad about this; I managed 80 miles a couple of weekends a go, but th…

Well, after a reasonable degree of struggle, I managed to get the first version of my literate OWL system working. As well as learning python, I've had a go with git; my repo is hosted on github at git://github.com/phillord/literate_omn.git. There are three components. omnextract.py : this pulls out all the referenced omn files from the TeX document and produces the complete omn file. omn.sty : this is a driver for the listings package which does syntax highlighting in TeX. omndoc.sty : this provides commands for including files into the TeX. It's a thin wrapper around the listings package. I decided to make omn.sty seperate from omndoc.sty as it works standalone, if you just want to use the listings package on its own. At the moment, you can only include files; environments don't wo…

Learning a new language is always a bit stressful. I thought that I would learn python; I need a new, rapid development, build some scripts, but don't look as awful as perl type language. I've recently learnt lua which was fun, but then it's meant as a very small, quick langauge. It's nice, but not really the perl-u-like that I wanted. I have actually been through the process of learning python in the past; I used to generate my website with ht2html which was quite cute and did the job; it was written in python, and I needed some skills to fiddle with it's output. In the end, I decided that table within table presentation was not ideal and that CSS was the way to go, so I moved to muse which I still use nowadays. As always, learning a new language is frustrating as you realise that you don…

Class: BiologicalFunction Annotations: rdfs:comment "Definition: A biological function is a realizable entity that inheres in continuant which is realized in an activity, and where the homologous structure(s) of individuals of closely related species (or identical species) fulfil this same biological function.", SubClassOf: Function

My next blog post was going to be about function, as I have just had a paper about it accepted. But, I got slightly side-tracked along the way, thinking about Literature Programming as it applies to OWL. While an ontology is (or, to my mind, should be) a computational artifact, it's a bit different from a program; the main thing is that it doesn't run; it doesn't have that functional test that a program does. This is not to say that an ontology is not an application-dependent entity. It can be, but even then it needs to have a program built on it. One of the upshots of this is that a narrative justification for an Ontology is fairly important; currently, we spend far too long on mailing lists, arguing about ontology terms and, to my mind, not enough of this is reflected in the final outcom…