Getting up to Speed With OWL 1.1

Bijan's "Two Interesting Quotes" really got me started on understanding the new features of OWL 1.1. The addition of the RBox (to ABox and TBox), using SROIQ instead of SHOIN, is the obvious one.

The second interesting quote was from, "Describing chemical functional groups in OWL-DL for the classification of chemical compounds" which gives some clear examples using the new features of OWL 1.1 including qualified cardinality, negation and property chains. The first two are analogous to: chemical has two bonds and chemical has exactly one bond.

Property chains are another interesting feature which is highlighted in the above paper, in "The OBO to OWL mapping, GO to OWL 1.1!" and in the first paper Bijan spoke about. In one way this is a bit disappointing because the OBO work replicates what we been doing in the BioMANTA project (I hate duplication in all its forms) - we based it on the Protégé plugin. Our relationships are quite simple, mainly is-a, so OWL DL was enough. We hadn't yet encountered some of the problems such as reflexive and anti-symmetric relationships. It also links to a web page mapping OBO to OWL 1.1 and OWL DL semantics.

As noted in "Igniting the OWL 1.1 Touch Paper: The OWL API" the addition of an object model along with the OWL 1.1 specification makes it obvious what an OWL 1.1 API should look like. I haven't yet used OWL API much, except looking at how it integrates with Pellet and how closely it matched the OWL specification. The use of axioms made the addition of RBox a bit easier to understand (or misunderstand if I've got it wrong). Hopefully, punning will be made clear to me eventually too (I've been too stupid to understand it just based on the explanations and too lazy to look into it). Pellet 1.5 also introduces incremental inferencing which is hopefully as good as it sounds.

The other papers that were of interest: "Representing Phenotypes in OWL" (again making use of qualified cardinality) and "A survey of requirements for automated reasoning services for bio-ontologies in OWL".

And just to round off, I found a very good paper, "Towards a Quantitative, Platform-Independent Analysis of Knowledge Systems", about all the mistakes that can be made during modeling (errors, assumptions, etc.) and other types of failures such as language (under or over expressive), management, learning, reasoning, querying, and others.

And I know I'll need to come back to this, which lists the fragments of OWL 1.1 that can be used to keep things computable in polynomial time.

Bottom Up Semantics

A couple of recent articles on DevX have come up by Rod Coffin exploring how a bit of semantics (and Semantic Web technology) can help improve your applications ability to understand what people are trying to do. The first, Let Semantics Bring Sophistication to Your Applications introduces the concepts of ontologies and querying. The second, Use Semantic Language Tools to Better Understand User Intentions shows how using WordNet you can supplement existing applications to improve search results.

Update: DevX now has a Semantic Web Zone.

0 dollars

SCO's Linux Billions?

For the second quarter of 2007, SCO reported a total of zero dollars of revenue from its SCOsource licensing program. In the first quarter of 2007, SCO reported SCOsource licensing revenue of $34,000, which is somewhat less than the billions McBride had been expecting.

All the Web is a Stage

Google Gears' WorkerPool - Message Passing, Shared Nothing Concurrency

By now, you‘ve probably already seen Google Gears, Google's solution for dragging AJAX applications offline. The one thing that jumped out at me was their WorkerPool component. This is a very nice solution for concurrency in Javascript.
In short: if you have any long running task, you can create a WorkerPool which is basically group of Javascript processes Note: they're not threads! The workers in a WorkerPool share nothing with each other, which makes them like OS processes or Erlang's lightweight processes (actually, they're more like the latter, as they're likely to run in the same address space).

And now guess, how these workers, these processes, communicate? Yep: messages, formatted as strings. Important to remember: if you format objects with as JSON strings, you can even send objects and structures along. The handler that receives messages also gets the ID of the sender, so if the sender implements a handler too, it‘s possible to return results asynchronously.

If you‘re reminded of Erlang or the old Actor concept you‘re right. I wonder what the Google Apps will do with this new concurrency approach (well, new for Javascript… yes I‘m ignoring Javascript Rhino).

I still hope that AJAX will die a quick death, like Java Applets, just for being so damn ugly and horrible to implement. But… things like this tell me that this will probably not happen. Good ideas like Google Gears will help paint over the ugly details of a solution, and it‘s all hip now, so it's easy to ignore many of the problems.

The same idea is also being implemented in Scala with their Actors.

Linked Together

This demo shows what can be achieved with the correct use of metadata from Flickr images. If nothing else, this answers why you would bother with metadata (as if there needs to be a justification these days). By correctly annotating your content you gain an advantage in leveraging a network of data. Via, Semantically-linked Interactive Imagery: Wow! The Emergent Web in Action and the demo Blaise Aguera y Arcas: Photosynth demo.

Update: What? I've edited this entry. Weird, I'm sure it made sense at the time.

JRDF 0.4.1.1 Released

JRDF 0.4.1.1. A bug fix release for an error in the wiring. It was wiring up the join code rather than the union code when it was suppose to do union operations. Both Derby and Hadoop were removed for this release (which reduces the GUI jar by 2 MB).

Why Fahrenheit 451 is not like 1984

Ray Bradbury: Fahrenheit 451 Misinterpreted

Now, Bradbury has decided to make news about the writing of his iconographic work and what he really meant. Fahrenheit 451 is not, he says firmly, a story about government censorship. Nor was it a response to Senator Joseph McCarthy, whose investigations had already instilled fear and stifled the creativity of thousands.

This, despite the fact that reviews, critiques and essays over the decades say that is precisely what it is all about. Even Bradbury’s authorized biographer, Sam Weller, in The Bradbury Chronicles, refers to Fahrenheit 451 as a book about censorship.

Points to Ray Bradbury at Home with movies about many topics including stories and politics.

4:34

I was struck by an interview with Ayaan Hirsi Ali. In it she says a moderate version of Islam cannot exist without disregarding parts of the Koran (and without thinking, questioning and debating). I'd always assumed this was true and thought it wouldn't bother me but I was surprised when it did. About half way through the interview she was prompted to give support for her claim that Islam does promote violence. She says there is a criteria for determining whether something is true and she quoted Sura (4:34). Without dancing around the subject it says when faced with a disobedient wife: shout at her, ignore her, and finally beat her. And as far as I can tell this is not up for dispute. It's a bit hard to describe and I'm sure I'd heard it before but for some reason it finally got to me.

So like, Timothy 2, 12 this is a religious statement, without allegory, that is clearly in conflict with modern laws and morals (assuming that morals can exist outside of religion).

I guess I'd always assumed people ignore bits that don't make sense. But as someone reading Timothy said, "What do you do when you are confronted with a finding in scripture that either goes against what you've always believed or at least contradicts what you would like to believe? There are really only two choices. Understand it, accept it and conform to it or reject it and go on doing whatever you want."

The Road After

D Conference Videos of Bill and Steve. All are from brightcove. The missing intro, complete with MacIntosh dating game is on YouTube (there's also a full transcript).

Oh the Waste

Running the Numbers

This new series looks at contemporary American culture through the austere lens of statistics. Each image portrays a specific quantity of something: fifteen million sheets of office paper (five minutes of paper use); 106,000 aluminum cans (thirty seconds of can consumption) and so on. My hope is that images representing these quantities might have a different effect than the raw numbers alone, such as we find daily in articles and books. Statistics can feel abstract and anesthetizing, making it difficult to connect with and make meaning of 3.6 million SUV sales in one year, for example, or 2.3 million Americans in prison, or 426,000 cell phones retired every day. This project visually examines these vast and bizarre measures of our society, in large intricately detailed prints assembled from thousands of smaller photographs.

It also includes, ".5 feet wide by 10.5 feet tall in three horizontal panels, Depicts 125,000 one-hundred dollar bills ($12.5 million), the amount our government spends every hour on the war in Iraq."

Via, Statistical visualization.

MapReduce SPARQL

Compositional Evaluation of W3C SPARQL Algebra via Reduce/Map "Tested against older DAWG testsuite. Implemented using functional programming idioms: fold (reduce) / unfold (map)

Does that suggest parallelizable execution?"

Thanks to SPARQL's adoption of compositional semantics (algebra) it's possible. From what I can remember, while there is an implicit left to right evaluation of OPTIONAL, which does limit the top level execution, the partial results are parallelizable. Being able to execute order independent OPTIONAL while retaining the correct results for OPTIONAL is still an open question (although feasible I think).

Available from SVN here. More musings, Musings of a Semantic / Rich Web Architect: What's Next?.

One More Pragmatic Language

Pragmatic Haskell

You see, I’ve been talking to the good folks over at Pragmatic Programmers about the possibility of doing a Haskell book. All of my writing effort has been going into that book, and as I didn’t know what the consequences would be of posting potential book content to the net, I elected to keep my mouth shut.

Well, they have agreed.

Via.

Where's the Evil?

I like bats much better than bureaucrats. I live in the Managerial Age, in a world of "Admin." The greatest evil is not now done in those sordid "dens of crime" that Dickens loved to paint. It is not done even in concentration camps and labour camps. In those we see its final result. But it is conceived and ordered (moved, seconded, carried, and minuted) in clean, carpeted, warmed, and well-lighted offices, by quiet men with white collars and cut fingernails and smooth-shaven cheeks who do not need to raise their voice. Hence, naturally enough, my symbol for Hell is something like the bureaucracy of a police state or the offices of a thoroughly nasty business concern.

From, Bullying of Academics in Higher Education. An interesting review, Notes on The Screwtape Letters.

The Health Benefits of the Semantic Web

A page about the HCLS Demo given in Banff at WWW2007 Some interesting demos. Using OpenLink's Virtuoso to store and query about 350 million statements (and many more required). Part of the demo used Armed Bear Common Lisp, which is Lisp for the JVM (compiles Lisp to bytecode).

Defeasible Logic Plus Time

Temporal extensions to Defeasible Logic. Non-monotonic reasoning is about adding more information over time to reach different conclusions. Rather than adding information adding temporal extensions actually removes when this information applies.

Even the Banner Ads are More Interesting

I was reading, Sun Tells Java Plans, of which I got to the second paragraph before noticing an Apple ad (in Flash with sound). Listened to the commercial, closed the tab, I only barely care what the article was about. So who does marketing better (actually yesterday there was one with the PC guy banging his head against the banner which was better)? Of course, I could just be responding in a Pavlovian (hmm dessert) way to the background jingle.

Romulus and Remus - C# and Java

Ted Neward talks about C# and Java. Also mentions the possible .NET backlash, Scala and LINQ. There's also a very impressive demo of LINQ (about 1/4 of the way through the code demo starts) - the struggle from imperative to declarative.

An Efficient Link Store

• Another web of data store that produces a subset of RDF/XML, Astoria, is from an unlikely source, Microsoft. Instead of a proprietary Semantic Web, Danny sees it as going to town with URIs and REST.


• Silverlight was the other surprising Microsoft development, nothing beats running code - except maybe browser-based dynamic code 2000 times faster. Applets are cool again.


• Some ideas for static triple indexing "Most mature triplestores also index a 4th query element ‘graph’ or ‘context’. I intend to support this query type without expanding the index by using a trick: In my triples format the fact that the subjects are auto-generated and local to the graph means I can choose them to be sequential and effectively re-use them as graph indexes..."


• Plugged In/Invisible Worlds/Tucana/Northrop/TKS/TMex/Kowari/Mulgara podcast (links to the Talis page).


• PAGE a distributed triple store using DHT and YARS (the original). It does seem to miss the DELIS work on P2P RDF which scaled up to 64 nodes.


• Haskell and the Faith of Programming Languages Phillip Wadler gives a rather brilliant talk on programming languages. Covers Haskell, Java generics, combining different typed languages (weak, strong, very strong) as well as monads and Links.

YARS Revenge

With little fanfare the folks at DERI have announced YARS2. I know of at least 4 next generation RDF stores (you know who you are) with a few others on the drawing board. Storing data is cool again.

To save disk space for the on-disk indices, we compress the individual blocks using Huffman coding. Depending on the data values and the sorting order of the index, we achieve a compression rate of ≈ 90%. Although compression has a marginal impact on performance, we deem that the benefits of saved disk space for large index files outweighs the slight performance dip.

Figure 4 shows the correspondence between block size and lookup time, and also shows the impact of Huffman coding on the lookup performance; block sizes are measured pre-compression. The average lookup time for a data file with 100k entries (random lookups for all subjects in the index) using a 64k block size is approximately 1.1 ms for the uncompressed and 1.4 ms for the compressed data file. For 90k random lookups over a 7 GB data file with 420 million synthetically generated triples (more on that dataset in Section 7), we achieve an average seek time of 23.5 ms.

I still wonder how the DERI guys can make the claim about it being their indexing scheme especially when Kowari was open sourced before YARS or the original paper came out. Maybe it's who publishes first? See Paul's previous discussion about it in 2005 (under the title "Indexing"). I mind that this hasn't been properly attributed as I'd like Paul and any others to get the attribution they deserve. On the other hand, I'm glad that people are taking this idea and running with it.

It's good to see that text searching on literals now seems like a standard feature too. They used a sparse index to create all 6 indices. They also hint out how reasoning is going to be performed by linking to, "Unifying Reasoning and Search to Web Scale", which suggests a tradeoff over time and trust.

You Are Here, Now

• Mammal rise 'not linked' to dinos Perhaps the best part is the beautifully rendered result of evolution for the last 166 million years. Good global warming? "However, the supertree shows that the placental mammals had already split into these sub-groups by 93 million years ago, long before the space impact and at a time when dinosaurs still ruled the planet."


• Guice Talk by Google Listing all the good ways DI makes your code better - and yes testing is the main one, more OO is another, better than service locater (J2EE) etc. Not much new here, except for no XML, for people who have been doing this for a while.


• Another Google talk by the Cyc people referenced in Priming the Pump and Threshold Conditions . With many examples that will be familiar for Semantic Web proponents.


• Closures for Java JSR Scala gets a mentions as does the BGGA proposal.


• Three reasons that REST is not RPC "Being able to do state transition processing at disparate locations is hugely powerful...A single process can span machines offering differing levels of scalability, reliability and security."


• Six of One, a Half Dozen of the Other "Closures vs. objects should really be a koan". I think this was off a reddit post at some stage. Leads to a purely functional OO system in Scheme.