An Exercise in Irrelevance

Thankful, the talk is over. It went okay, didn’t stumble too much and most importantly, got a few laughs.

The main questions where about the things that I thought they would be. First, was the question about the apparent circularity of the definition; I thought to take this out, because I knew it might cause trouble, but it produces a much more unwieldy definition. A second, was the question about orphan functions — genes with new functions or functions of duck-billed platypus. My answer is that all things have homologues even if they don’t exist any more.

Not sure people were entirely convinced; if you look at the axiomatisation, then my feeling is that it doesn’t make much difference anyway. You build your process hierarachy; functions and roles then just drop out because they are defined. So you don’t need to answer questions about homology when building the ontology at all; just when thinking about the instances.

Should have made that point. Damn.

Blogs are generally seen as a slightly dubious part of the scientific publishing landscape. This is not, of course, unreasonable. I put stuff up here, for example, such as my idea for IDs that I’ve thought about for a few days, but that I am unlikely to follow any further, or stuff opinion pieces on bees about which I have as little expertise as the average journalist.

Fundamentally, though, despite it’s current use, a blog is just a media channel; you can use them to transfer anything you like. A scientific paper, for instance. This might be useful. While, for instance, I love open access publication, it’s quite expensive particularly as the cash tends to come out of my own budget, at least until I can get the library to pay.

So, I’ve been thinking about a cheap and cheerful blog-based system. It would work like this. The author would simply publish their paper onto their own blog. Next, they would send a request (using one of these pingback or trackback thingies that I haven’t worked out yet) to a “journal” which would also be a blog, in this case a private one. The editor would then invite comments from willing reviewers using same technique. Reviewers could then read the blog post, comment on it using their own blog. After the normal revision cycle, the editor would make a decision. If it was accepted, the authors blog post would be linked from the journals main feed (probably grabbing an archival copy at the same time). If it was not accepted, the author could try another journal, this time with initial reviews in-hand; the process would not beed to be reiterated.

This would have several advantages over the current system. Formatting and presentational problems would disappear because they would be controlled by the authors. Prepublication would become unnecessary, because submission and publication would become the same thing. The role of the journal would be limited to what they are best at; getting reviewers in and rubber stamping a seal of approval on worthy papers. Finally, the tireless work of reviewers would be publically acknowledged; their own blogs would have a record of every review that they have ever done.

All the technology for this already exists; it just needs some social conventions layering on top.

So, this year of Bio-Ontologies is upon me; I’m sitting in the airport waiting to fly in the wrong direction; although I’ve noticed that the airport signs no longer call this “waiting time” but “shopping time”.

It’s 12 years on now; I can’t remember whether this makes it the oldest SIG at ISMB, but it must be close. Perhaps it is surprising that a small meeting like this has lasted so long, but during it’s time the use of ontologies within biology has blossomed; to some extent, this is true of the outside world also. This year has carried on with the trend. Gone are the days that we used to get enough papers to fill the day, but no more; we’ve stretched the day out, we’ve added a poster session but still we get more. The number of attendees has gone up somewhat also. It’s good to see.

For me, bio-ontologies has also been the centre of my entry into the field; Edmonton was the first ontology paper that I ever presented — perhaps depressingly, still some of my best work. This year has special significance for me. I’m giving a paper myself for the first time since Edmonton; perhaps fitting to end off as I began, because this will also be my last year as conference chair. I’ve been involved now for 6 of the 12 years; while, I’ve enjoyed it and felt privileged to do the work, it’s enough. Organising is hard work, even now when I understand the process well. In the last few years, I’ve tried to push the workshop to be a bit broader than just ontologies, to take in all new forms and technologies for representing and distributing knowledge; I’ve met with some, but limited success. A workshop with a 12 year pedigree takes some time to move. I was heartened to see that it was the first SIG to get a subject on the official conference friendfeed. Web 2.0 is upon us. With luck, this will become a bigger part of the meeting. If so, this will be other peoples achievement, not mine. Did I mention that this is my last year?

I’m looking forward to giving my paper on functions and roles in ontologies. One of the more minor reasons for retiring, is that it’s easier to publish in a workshop which you are not organising. I’m surprisingly nervous about the talk; probably as much so as in Edmonton. I’ve been practicing the talk incessantly, to the point that my back is complaining from too much sitting. It’s my first ever single author paper. I’m hoping that people will like the paper; it’s message is simple and straight-forward. Of course, this doesn’t mean that it’s correct. Last years paper on a similar topic caused quite a fuss (which, let’s be honest, was partly my fault) and I know that some in the audience will be quite vehement in their opposition to mine. Even though I’ve been over it so many times, I have the back-of-my-mind fear that there is a big hole that I’ve missed.

I guess this is good; it means that I’m excited about my own paper in a way that I haven’t been for years. A bit of fuss will mean that other people are too, for good or for ill. In the end, I’ll probably be most disappointed if the paper goes with a whimper not a bang.

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 others. It wasn’t till I noticed the end credits that it finally twigged what it was about the programme that bugged me; it’s a Travel channel co-production; in short, it’s the bastard child of Wildlife on One and the Holiday programme; equals parts documentary and advert.

Still, despite this, something interesting poked through. Archaeology is not something that I know a huge amount about; it was good to hear about the new ideas and new evidence that has discovered in the more recent history. Worth watching, on the whole.

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 decided a partial copy was the way forward; generating both the index and indexed file ensure that they will stay in-sync.

It required a bit of nasty latex hacking; the basic problem was avoiding the limitation of being only able to use legal LaTeX macro characters (that is letters). The system now works like this:

%% This is generated by python which also generates the
%% function_ont.spt file which is a copy of the ontology (with a
%% few new lines gone.

%% This just defines a new macro in what appears to be an
%% unnecessarily complex way.
\expandafter\def\csname OmnEntityHeaderheader\endcsname%
{\lstinputlisting[language=omn,firstline=1,lastline=8]{function_ont.spt}}

%% But the use of \expandafter and \csname means that you can
%% use any character you like, including underscores and numbers
%% in the macro name.
\expandafter\def\csname OmnEntityObjectPropertyhas_role\endcsname%
{\lstinputlisting[language=omn,firstline=206,lastline=219]{function_ont.spt}}

%% We can now define two commands in the style file. Again
%% we use \csname so that we are not bound to characters legal
%% in latex macros.
\newcommand{\omnclass}[2]{\csname OmnEntityClass#1#2\endcsname}
\newcommand{\omnobjprop}[2]{\csname OmnEntityObjectProperty#1#2\endcsname}

%% now in our source, we can do things like this.
\omnobjprop{}{has_role}

Using an index in this way also has another advantage. I’ve had to make a decision whether to go with rdfs:label or the entity name. I can now back out of this; I can just use both in the index file, without too much extra space, so that either would be referencable within the latex.

To me, this feels like the right solution. It’s relatively simple (with a bit of nasty latex, which is nicely hidden), it doesn’t depend on the file system. It needs a bit more work to bring it to completion, but not that much.

Sadly bio-ontologies looms, so next week will be getting ready for that; perhaps I can finish this off on the way back. “Sadly” is perhaps a poor choice of words; I’m greatly looking forward to it, but I’ve kind of had the bit between my teeth with python and latex hacking for the last few weeks.

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 problem; it’s not very modified, so I removed them one by one. For no readily apparent reason the problem appears to be a subdirectory called “images.old”. Surely, not a good reason for a crash.

Weird and wonderful.