New Life for Semantic Technologies

Cambridge Semantics provides flexible solutions for the data deluge.

By Kevin Davies

February 4, 2011 | A small software company formed by a group of former IBM staffers is breathing new life into semantic technologies. But don’t look for Cambridge Semantics to harp on the term.

“The world of people well versed in semantic technology is still quite small,” says co-founder Lee Feigenbaum. “It’s important that anyone working with our software should not be IT. You won’t see the word ‘semantics’ anywhere in our software. It’s an enabler for us. We can’t build our software without these technologies, but now we’ve built them, we’ve no interest in preaching that you’re using semantics.” (see, “Masters of the Semantic Web,” Bio•IT World, Oct 2005)

“We don’t lead with ‘Semantic Web’ as a marketing term,” adds senior product manager Rob Gonzalez. “We’d like to see more companies like us trying to solve real-world problems. For us it’s about the problems we’re solving.”

Along with CTO Sean Martin, Feigenbaum was one of a group of about 20 people in an advanced technology group at IBM dating back to 1995. The group’s mission was to research new Internet technologies (including semantic technologies) and potential applications for IBM. An early client was a group of cancer researchers at the Massachusetts General Hospital (the Center for the Development of a Virtual Tumor), for which the IBM team helped to deploy semantic technologies for building and sharing models, data, and literature.

In 2007, Martin and Feigenbaum, together with Simon Martin and Emmett Eldred, established Cambridge Semantics and spent a couple of years building up the engineering team and testing early products before launching its first commercial product in late 2009. Luckily, much of the IBM group’s technology was open source. “People have been [saying] that they can’t build libraries or services that are really reusable or discoverable. We think with semantics, you get these benefits,” says Feigenbaum.

Early customers include Johnson & Johnson, Merck, and Biogen Idec, although Cambridge Semantics’ client base includes Fortune 500 companies in advertizing and the oil industry. “This technology can be used in many industries, but is particularly geared toward life sciences,” says Gonzalez. “The data bonanza isn’t comparable to other industries. Life scientists simply need this flexibility.”

Semantic Sidestep

There’s a saying that Feigenbaum admits is neither new nor particularly funny, but it makes a point: If you put ten Semantic Web advocates in a room, you’ll get 15 different explanations of what the Semantic Web is. “You have a loosely coupled set of technologies that people can use for a million different things. People will latch onto something and say this is the real semantic technology.”

Indeed, Feigenbaum is blunt in his criticism of vendors and users alike who proclaim the magical properties of the Semantic Web. “I’ve seen pharma talk about semantics as the ultimate data integration/analysis tool. That’s all well and good and we might get there in the next 10-15 years, but it’s never been what we’ve seen in semantics.”

For Feigenbaum, the interesting bit of semantic technology is the notion of rebranding data in a flexible and agile way. “The underlying properties of semantic technologies let you build very agile, adaptive software systems as data sources changes. It happens in all industries but especially in life sciences.”

Semantics is about flexibility and having a common data model upon which one can take information from a variety of sources—XML, relational databases, or public clinical trial database—and “map them to a common format not constrained by any a priori database schema or XML structure. We saw this flexibility in 2001, and proved it out at IBM. That’s what we wanted to leverage.”

Cambridge Semantics released its first three products in 2009. “There’s no magic to the software,” says Feigenbaum. Just an easy-to-use interface and set of tools that allows users to point to a particular area in a spreadsheet, for example, and ascribe a meaning, e.g. adverse event, assay result. “You have these common vocabularies and data models, and the system takes care of finding values that match and links them together, without having necessarily considered that way of linking things when you set up the system.”

The Anzo Data Collaboration Server, which sits on the user’s server, is semantic middleware, the plumbing that runs and connects everything else. Says Feigenbaum: “It invokes Web services. It has data services and server services that let you build flexible applications.”

Anzo on the Web is a Web 2.0-style application for self-service reporting of any data connected to the data collaboration server. Typically, when users want to use a new data source, Gonzalez explains, they have to change the database, then the application code, then the web tier. “With Anzo on the Web, you can bring the new data source easily into the data collaboration server, and it propagates throughout the system without requiring a lot of manual changes, so it’s resilient to new types of information being added.” The application is designed for scientists who aren’t necessarily IT experts. “They don’t have to go to IT to build new views; they can do it,” says Feigenbaum.

Anzo for Excel is a plug-in to Microsoft Excel that lets people use spreadsheets more effectively. It makes the collection of ad hoc data trivial, says Feigenbaum. “It turns Excel into a data collection application and lets it serve as a user interface for all this data integrated on the server. Now you can consume the data.” A recently-released second version adds an unnamed component that allows users to collect and integrate data from relational databases.

The company announced in mid-January an agreement with Cray to collectively develop and market solutions, including the Cray XMT system and the Anzo product suite. But Feigenbaum is also using the Amazon Cloud, particularly with new prospects. “The data integration paradigm we’re preaching is anathema to a lot of traditional IT,” says Feigenbaum, particularly in regard to procuring hardware, which can sometimes take months. “Many customers run a proof-of-concept in the Cloud with hosted versions of the software. That lets them prove out the technology and work on the procurement to deploy inside their firewall.”

One of the chief benefits of Cambridge Semantics, says Feigenbaum, is that it affords pharma customers the ability not only to pull in and analyze the data from a traditional database but also “the last 10-15% of their data that might be lurking in a desktop spreadsheet or a public resource such as NCBI. They don’t want to spend millions of dollars and 18 months only to get 90% of the way. They need to handle the heterogeneity of Excel and public data. [The missing data] might only be a small part of the total information but it’s a deal breaker.”

Early users span applications from manufacturing quality control to budgeting, allowing customers such as Biogen Idec to compare their actual spend with budget projections. Merck is using Cambridge Semantics applications to procure time on lab equipment.

Cambridge Semantics is still learning from its early customers where its technology can be leveraged. One promising area is in clinical trial data management. Says Feigenbaum: “When you’ve brought together data that don’t normally talk to each other, there’s a bunch of things you can do, such as looking at data for a drug across trials/phases. But some [historical] trials might have used SAS or Oracle Clinical. This is a good way to bring data together,” perhaps to identify reporting discrepancies for regulatory purposes.

An alternative term for semantic technologies that is growing in popularity is “linked data.” “It’s fine,” shrugs Feigenbaum. “It’s just another name. It’s had some success in life sciences, but I don’t care what it’s called.” •

An Immortal Lesson in Design

The Mac's Inventor's Deathbed Gift: An Immortal Lesson in Design For His Son

The man who created the Mac interface gives his son Aza Raskin a final gift that that testifies to the beauty and power of simplicity.

Twenty five days before my father Jef died, on my birthday exactly six years ago, he gave me a present. He had the sparkle back in his eye -- the one that had been reduced by pancreatic cancer to an ashen ember -- when he gave it to me. It was a small package, rectangular in shape, in crisp brown-paper wrapping. Twine neatly wrapped around the corners, crisscrossing back and forth arriving at a bow crafted by the sure hands of a man who built his first model airplane at age seven.
This small brown package was to be the final gift my father ever gave me.
My family does gifts strangely. For instance, we have our own mangled interpretation of Hanukkah, where each person of the family has a night to give out presents. If we have five people home for Hanukkah, we celebrate only five of the eight nights. The joy of gifts are in the giving, not receiving, so before opening your present you must first guess what’s inside. This tradition is "plenty questions," a more forgiving version than the standard twenty questions.
“Animal, vegetable, or mineral?”, I ask.

I stare at the package. In it is my father. The man who invented the Mac.

We are in it for the game of teasing the gift out of the gifter. It's like extracting a ball of yarn from a kitten. The tugs, pulls, and misdirections are the fun. The question must answerable by a simple "yes" or "no." Naturally, the later into the questions we get, the more liberal this rule becomes. We don't break the rule exactly, but answers become a series of "not-exactly"s and "yes-but"s. In past years, the givers have often spent hours creating elaborate disguises for the gifts. I've shaped styrofoam into a fantastic reptilian shape to disguise a pair of earrings for my mother. She guessed them perfectly anyway. There may be collusion going on.
"Mineral," my father says.
We often waste questions on silly asides. We ask about refrigerators and ostrich eggs when the gift is clearly book shaped. But my father is sick. Where there was once the thought that a cure might be found, only fleeting misplaced hope remains like a high school summer fling dissipating in the face of college. We know there isn't much time. Still I ask.
I stare at the package in my hands. In it is my father. The man who invented the Macintosh and misnamed what should be "typefaces" as the "fonts" menu. He never forgave himself for his incorrect usage of English. He groomed me to use language exactingly and considered that mistake a failure of being young and reckless with semantics. The man who invented click-and-drag was now the man who could hardly keep his gaze focused on his son. The box is, of course, smaller than a bread box. It's a question we always ask. My family smiles only out of habit.
"No," my father says. A long pause. "No," he says again, "it is smaller than a bread box. Smaller and sharper." He speeds the guessing game along. Time.

The gift was a message about an entire way of thought.

"Sharper?" I ask. A knife? The box is too small for a typical kitchen knife. It could be a Swiss Army knife. Jef always carries one. The big blade is for food, the little blade for everything else. He gets a bit indignant if you borrow it and use the wrong blade. I have a Swiss Army knife, but I haven't carried it since airport security theater ramped up after 9/11. It probably isn't a knife. Maybe a razor? One can't just ask outright, that doesn't give enough information when you are wrong. Something sharp could be many things. Seeking something more strategic I ask, "Can it be found in a bathroom?"
Long pause.
"Yes."
Three days before he passed, Jef had an accident. He needed to use the restroom, so -- stooped under his arm -- I supported his weight as he hobble to his business. There was something quietly unsettling about escorting my father to a toilet that had been taller than me when we first moved into the house twenty years earlier. I sat him down, walked out, and closed the door. Moments later, a crash jolted the house. I slammed the door open. The metallic smell of water fresh from a pipe whipped my nose and water flooded the floor. The toilet was dislocated from its base like an arm from its socket, and lodged between the toilet and the wall was my father. Despite his size, he looked small and meager. He stared up at me with eyes full of innocent surprise. Why am I on the floor, they asked? Why am I wet? The shocked curiosity in his wide-open eyes is the single most haunting image I have of my father. In the dark space between closing my eyes and falling asleep, that image sometimes steals in and taints me. When it does, there is no help for it. I have to get out of bed and go for a run. Otherwise, sleep will be overshadowed by those confused, guileless eyes.
"It must be a razor?" I ask. He nods his assent with a satisfied smile. He gestures for me to open it. Carefully undoing the knot, the twine, and the paper reveals a cardboard box on which he has written "For Pogonotomy." Of course there is a word for beard trimming, and of course my father knows and uses it. In high school, I played a trick on my teachers: in every essay I used my own made-up word. I used "indelic" to mean something between "endemic" and "inextricably entwined." No matter how many times I trotted it out, not one of my teachers caught me. I used it once in passing with my father and he immediately but gently pointed it out as a non-word. Some men spend time meticulously trimming their beard. My father trimmed his vocabulary. Language is communication, and my father was fastidious about it. Often when we got into particularly deep conversations, he'd pause and continue the rest of the discussion in written form where he could distill his thoughts into a sharp crystalline relief.
The razor itself was a vintage safety razor. Looking at it, I understood the allure. It is an inventive and simple design. The razor takes a flat blade and arches it under a metal shield, giving the blade both greater mechanical strength as well as a protective sheath that keeps you safe. It's the kind of clear insight for which all designers and inventors strive: beauty in turning constraints into advantages.
That razor is a message, rendered in steel and wood, about an incorporeal way of thought. That was my father's final gift to me: A way of looking at the world through the lens of playful questioning, which reveals more than just an answer.Twenty five days later, the razor remained but my father did not.
Jef, I miss you.