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…
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…
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 …
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
…
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…
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…
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 …
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…
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…
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…