The Wall Street Journal article Walked Into a Lamppost? Hurt While Crocheting? Help Is on the Way describes the International Classification of Diseases, 10th Revision that is used to describe medical problems.

“Today, hospitals and doctors use a system of about 18,000 codes to describe medical services in bills they send to insurers. Apparently, that doesn’t allow for quite enough nuance. A new federally mandated version will expand the number to around 140,000—adding codes that describe precisely what bone was broken, or which artery is receiving a stent. It will also have a code for recording that a patient’s injury occurred in a chicken coop.”

We want to see the search engine companies develop and support a Microdata vocabulary for ICD-10. An ICDM-10 OWL DL ontology has already been done, but a Microdata version might add a lot of value. We could use it on our blogs and Facebook posts to catalog those annoying problems we encounter each day, like W59.22XD (Struck by turtle, initial encounter), or Y07.53 (Teacher or instructor, perpetrator of maltreat and neglect).

Humor aside, a description logic representation (e.g., in OWL) makes the coding system seem less ridiculous. Instead of appearing as a catalog of 140K ground tags, it would emphasize that it is a collection of a much smaller number of classes that can be combined in productive ways to produce them or used to create general descriptions (e.g., bitten by an animal).

The Journal of Web Semantics announced two new special issues, one on semantic sensing and another on the semantic and social web. Both will be publshed in 2012 with preprints made freely available online as papers are accepted.

The special issue on semantic sensing will be edited by Harith Alani, Oscar Corcho and Manfred Hauswirth. Papers will be reviewed on a rolling basis and authors are encouraged to submit before the final deadline of 20 December 2011.

The issue on the semantic and social web will be edited by John Breslin and Meena Nagarajan. Papers will be reviewed on a rolling basis and authors are encouraged to submit before the final deadline of 21 January 2012.

See the JWS Guide for Authors for details on the submission process.

The Journal of Web Semantics now has a facebook page and a Twitter account to augment its blog. All three will be used for news and announcements of call for papers, special issues, availability of new papers, etc. As you might expect, the tweets will be terse items, the facebook updates longer notes and the blog posts full of details. Those who are interested can follow @journalWebSem on Twitter, become a fan of the JWS on facebook, and subscribe to the blog’s feed.

Like many newspapers, the New York Times links the first mention of well known entitles in its articles to a reference page. For example, a mention of Barack Obama links to a page which is a collection of basic information on President Obama and links to relevant stories and other resources that the Times has created.

Now the Times is also using RDF to publish some of information as linked open data. Yesterday the Times announced the publication of an LOD collection covering about 5,000 people at http://data.nytimes.com/ under under a Creative Commons 3.0 Attribution License and plan to put their full collection of 30K topics online soon.

“Over the last several months we have manually mapped more than 5,000 person name subject headings onto Freebase and DBPedia. And today we are pleased to announce the launch of http://data.nytimes.com and the release of these 5,000 person name subject headings as Linked Open Data.
…
Over the next several months, we plan to expand http://data.nytimes.com to include each of the nearly 30,000 subject headings we use to power Times Topics pages, a collection that includes locations, organizations and descriptors in addition to person names.”

OWL 2, the new version of the Web Ontology Language, officially became a W3C standard yesterday. From the W3C press release:

“Today W3C announces a new version of a standard for representing knowledge on the Web. OWL 2, part of W3C’s Semantic Web toolkit, allows people to capture their knowledge about a particular domain (say, energy or medicine) and then use tools to manage information, search through it, and learn more from it. Furthermore, as an open standard based on Web technology, it lowers the cost of merging knowledge from multiple domains.”

Wolfram|Alpha is an interesting query answering system developed by Wolfram Research that is a blend of a question answering system and a Semantic Web alternative. It tries to interpret and answer queries expressed as a sequence of words from a large collection of interlinked tables. Oh, and Mathematica is in thrown in for free. A free Web version was released last Spring.

The news today is that Wolfram|Alpha has released an API, as noted in their blog:

“The API allows your application to interact with Wolfram|Alpha much like you do on the web—you send a web request with the same query string you would type into Wolfram|Alpha’s query box and you get back the same computed results. It’s just that both are in a form your application can understand. There are plenty of ways to tweak and control the results, as well.”

The pricing plan runs from $60/month for 1000 (6 cents a query) queries to $220K for up to 10M queries/month (2.2 cents a query). programming language bindings are available for Java, PHP, Perl, Python, Ruby and .NET.

Their original web interface remains free, but the TOS specifies that it “may be used only by a human being using a conventional web browser to manually enter queries one at a time.”

Microsoft has announced an add-in for Word 2007 that lets authors annotate a word or phrase with terms defined in external ontologies.

Addressing this critical challenge for researchers, Microsoft Corp. and Creative Commons announced today, before an industry panel at the O’Reilly Emerging Technology Conference (ETech 2009), the release of the Ontology Add-in for Microsoft Office Word 2007 that will enable authors to easily add scientific hyperlinks as semantic annotations, drawn from ontologies, to their documents and research papers. Ontologies are shared vocabularies created and maintained by different academic domains to model their fields of study. This Add-in will make it easier for scientists to link their documents to the Web in a meaningful way. Deployed on a wide scale, ontology-enabled scientific publishing will provide a Web boost to scientific discovery.

The add-in is available for download from codeplex, Microsoft’s open source project hosting website. Its has support for a number of features, including syntax coloring of informative words, automatic detection of identifiers, and built-in access to ontologies and controlled vocabularies maintained by NCBO as well as biological databases such as Protein Data Bank, UniProtKB, and NCBI GenBank/RefSeq.

The add-in was produced by the UCSD BioLit group, hence the initial connections to bioinformatics ontologies. It would be great if future versions would have builtin awareness of the more popular linked data vocabularies.

The annotation is done using a custom XML schema which can be extracted and mapped to RDF. This example, from the codeplex site, shows the word “disease” being tagged with Human Disease ontology.

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema"
  w:element="biolit-term">
    <w:customXmlPr>
        <w:attr w:name="id" w:val="DOID:4" />
        <w:attr w:name="type" w:val="Human disease" />
        <w:attr w:name="status" w:val="true" />
        <w:attr w:name="OntName" w:val="Human disease" />
        <w:attr w:name="url"
          w:val="http://purl.org/obo/owl/DOID#DOID_4" />
    </w:customXmlPr>
    <w:smartTag w:uri="BioLitTags" w:element="tag1">
        <w:r>
            <w:t>disease</w:t>
        </w:r>
    </w:smartTag>
</w:customXml>

It’s not pretty and more verbose than RDFa, but gets the job done. There are many interesting add-ins for Microsoft Office components but most seem to be available for Office 2007 but not the Mac version, Office 2008.

(h/t Frank van Harmelen)

A two day event, Ontology Summit 2009: Toward Ontology-based Standards, will be held 6-7 April 2009 at NIST in Gaithersburg MD. The Summit is co-organized by NIST and a number of other organizations and is part of NIST’s Interoperability week.

“This summit will address the intersection of two active communities, namely the technical standards world, and the community of ontology and semantic technologies. This intersection is long overdue because each has much to offer the other. Ontologies represent the best efforts of the technical community to unambiguously capture the definitions and interrelationships of concepts in a variety of domains. Standards — specifically information standards — are intended to provide unambiguous specifications of information, for the purpose of error-free access and exchange. If the standards community is indeed serious about specifying such information unambiguously to the best of its ability, then the use of ontologies as the vehicle for such specifications is the logical choice. Conversely, the standards world can provide a large market for the industrial use of ontologies, since ontologies are explicitly focused on the precise representation of information. This will be a boost to worldwide recognition of the utility and power of ontological models. The goal of this Ontology Summit 2009 is to articulate the power of synergizing these two communities in the form of a communique in which a number of concrete challenges can be laid out. These challenges could serve as a roadmap that will galvanize both communities and bring this promising technical area to the attention of others.”

The meeting is free, but advanced registration by March 31 is required. You can also register to participate remotely.

High quality videos of tutorials and talks from the Seventh International Semantic Web Conference are now available on the excellent VideoLectures.net site. It’s a great opportunity to benefit from the conference if you were not able to attend or, even if you were, to see presentations you were not able to attend.

Videolectures captured the slides for most of the presentations (which are available for downloading) and their site shows both the the speaker’s video and slides in synchronization. Videolectures used three camera crews in parallel so were able to capture almost all of the presentations. Here are some highlights from the ~90 videos to whet your appetite.

• Introduction to the Semantic Web: An all-day tutorial featuring ten top researchers covering all aspects of the Semantic Web.
• How to Publish Linked Data on the Web: A three-hour tutorial by five researchers explaining how LOD works and how you can exploit it.
• Freebase: An Open, Writable Database of the World’s Information: A keynote by MetaWeb CTO John Giannandrea on Freebase.
• Semantic Web Challenge & Billion Triple Challenge: The session on the Semantic Web Challenge finalists.
• Semantic Wikis: Fusing the two strands of the Semantic Web: Mark Greaves on Semantic Wikis.
• Requirements Critic: A Tool for Automatically Analyzing Software Requirements Documents: The winner of the best paper award for the In Use track.
• Laconic and Precise Justifications in OWL: Winner of the best paper award for the Research Track.
• An OWL 2 Far?: A panel that takes up the question of whether having standard languages based on formal methods with steadily increasing power is the right way to support the Semantic Web.

Conrad Barski, M.D. will give a talk on “How To Tell Stuff To Your Computer — The Enigmatic Art of Knowledge Representation” at UMBC at 1:00pm on Friday 17 October in Lecture Hall 8 in the ITE building.

Barski maintains an interesting site, Lisperati , that has graphical introductions to a number of topics, including Lisp, Haskell, Emacs, etc. and well as serving as he home of FringeDC an informal group of people interested in “fringe” programming languages.

Here’s the abstract for his talk.

“Have you ever wondered how we take information from the “real world” and put it into our computers? When we do this, do we lose parts of the information? Are some concepts just too hard to turn into ones and zeroes? How is our ability to enter information limited by the data structures we use inside of our computers? These questions enter into a science that is rarely discussed: The science of Knowledge Representation.

My presentation on KR will include some navel gazing, but also some nitty-gritty practical examples of Description Logics, RDF, and other modern approaches to capturing complicated information within a computer. We will also discuss some likely future directions this field may head into.”

Dr. Barski is a Medical Software Developer working on cardiology procedure documentation for Wolters Kluwer Health. He is also currently working on a textbook on the Common Lisp programming language.

You can submit a question either before, during or after the talk here.