Friday, May 30, 2008

Stable URIs

Since we published the "Creeps paper", Ben and I have received several queries asking us what we meant when we said "National Center for Biotechnology Information's (NCBI) current use of stable URLs for identifying much of its data". Unfortunately, the reference we gave in the manuscript wasn't very useful - it takes you to the NCBI homepage! Our apologies for that.

So, for anyone who hasn't discovered this on their own, NCBI have made much of their data (and even queries) available through "stable" URIs, as discussed here: Unfortunately, the NCBI's stable links send you to an HTML representation of the record, including all of the various visual paraphernalia on the page, so it isn't particularly suited for automated retrieval/scraping (does anyone know if i'm missing something? Is there a 'switch' I can throw in the URL that gives it back to me as a raw flatfile or as XML or as RDF?). In any case, that's what we were referring to. There is no indication on NCBI's page as to what they mean by "stable", so I can't comment on the actual stability of these URLs, but at least they're there and can be used in semantic-webby type applications to refer in a predictable and "clean" way to NCBI resources.

Since we're on the topic, I'd be amiss if I didn't bring the UniProt efforts into the discussion, since these are (IMO) a model of how we should be approaching the task. The reference for the UniProt work is here (if anyone knows a better, more appropriate reference please let me know). the UniProt data is available in a variety of formats from predictable URLs. e.g. provides the RDF version of the record, while or provides the HTML version of the record and provides an XML version of the record. All nice and predictable.

Anyway, all I wanted to do was put this out on my blog in case anyone is looking for the references and happens to stumble across this page.

Cheers all!

Monday, January 7, 2008

Adventures with a Roomba 540

Okay, Okay, I know this isn't REALLY about semantics, but I just bought a Roomba 540 on the weekend and it has been such a great adventure learning how it "thinks" that I want to share my adventures with everyone!

I have a 650 sqft apartment. This should be a piece of cake for a little vacuum robot that is advertised as being capable of managing four rooms... let's see, shall we?

Day 1: I hit "start". The little robot makes a "the robot is happy!" noise and starts to explore my apartment. It first gets tangled in my television cable wire and spins itself around a few times, but is successful in getting itself untangled - this is as advertised, so well done! It then gets tangled in the speaker wires that are (to my shagrin and frustration) laying across my living room floor because my landlord wont let me cut the carpet to bury them. It, again, untangles itself perfectly and continues on its merry way. It seems that it really does understand what's happening because even after getting twisted and self-rotated in these wires it still "anticipates" walls (if you have never seen these robots work, they clearly have a map of the room in their heads because they will slow-down as they approach a wall such that they nudge it ever-so-gently before turning around. But alas, my Ikea furniture was the death of this little robot... I have two Pella Chairs ( from Ikea. The base of these chairs are, effectively, three wooden planks in a 3/4 square. The robot climbed half-way over the plank, and then was helplessly unbalanced and couldn't get either wheel on the floor to extract itself. It made the "I'm an unhappy little robot" noise, and died. ...Recharge...

Day 2: Same story. Same result. my little robot was helplessly danging on the plank of an Ikea chair. so I lifted it up and moved it 6 inches so that it could get a grip and then restarted it. It made the "happy little robot" sound and ran around cleaning my living room; however somehow it was unable to find its base-station again for charging. It came oh so very close! Within about 6 inches, amusingly... Recharge...

Day 3: This time it seems that it decided to visit the bathroom before fully exploring the living room... and got hung-up on the 2'X3' shag shower mat... unhappy little robot.... Recharge...

Day 4: I decide to tip the Pella chairs over so that the planks are no longer on the floor. THIS time it happily navigates around the chairs and cleans about half of the living room before deciding to wander off and explore the corridor. The corridor leads to my bedroom. It wandered into my bedroom and had a wonderful time in there dashing around under the bed cleaning all sorts of things that I really don't want to know... but it couldn't find it's way out again! Every time it came close to the exit doorway, it hesitated (as if there were a wall there) and turned around and went back in. I watched it do this 7 times!! (my bedroom carpet is now cleaner than it has ever been!). Finally I decided to teach it a lesson and I smaked it's nose every time it turned the wrong way. After a good many smacks (it was absolutely DETERMINED not to go out of the exit!! it would forcefully turn around even when it was half-way out the door!!) I finally got it back into the corridor. Once in the corridor it was happy again, and even anticipated the walls! This surprised me since I must have totally buggered-up it's map my smacking it in the nose so often... nevertheless, it navigated it's way back down the corridor and into the living room. It anticipated the overturned chairs, and then went on to re-program my digital cable box, which is sitting at ground level, and has all of it's buttons exposed to the little robot's bumble-bee-on-a-window bounces as it explores obsticles. I was about to give-up hope when, suddenly, it started to move quite aggressively around a path and directly back to it's charger!! It oriented itself and drove straight into it's charger - perfectly aligned - and stopped for the day!

I suspect that my experience is very similar to what new parents feel when they have to child-proof their apartments... I now know that I have to overturn my chairs (oh, and I have to lift my computer table off of the ground, because it is just a half-centimeter higher than the edges of the robot, and when it hits the underside of the table at full-speed it becomes nicely jammed underneath!)

So I have a half-clean carpet in my living room, a completely clean carpet in my bedroom, and a robot that finally navigated my house without making any "unhappy robot" noises. I think I'm close to having a clean house every day!