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…