bonus edition: knowledge management...eral manager, informatics at perkinelmer, who estimates the...

Cambridge Healthtech Media Group

BONUS EDITION: Knowledge Management

www.bio-itworld.com

[2] BIO•IT WORLD: KNOWLEDGE MANAGEMENT EDITION www.bio-itworld.com

BON

US

EDIT

ION

: KN

OW

LED

GE

MA

NA

GEM

ENT

Subscriptions: Address inquires to Bio•IT World, 250 First Avenue, Suite 300, Needham, MA 02494 888-999-6288 or e-mail [email protected]

Reprints: Copyright © 2011 byBio•IT World, All rights reserved. Reproduction of material printed in Bio•IT World is forbidden without written permission. For reprints and/or copyright permission, please contact Jay Mulhern, (781) 972-1359, [email protected].

This index is provided as an additional service. The publisher does not assume any liability for errors or omissions.

Bonus Edition: Knowledge Management

3 Thomson Reuters Releases APIs for Cortellis Life Sciences Platform

4 ELN Excellence: The New Lab Notebooks

6 Driving Innovation from Within

7 Pharma Lit: Elsevier Serves Pharma with Acquisitions of Ariadne, Quosa

8 Making Semantic Sense of Unstructured Data

10 Wingu Makes Science Simple

Insight Pharma Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

InsightPharmaReports.com

Advertiser IndexAdvertiser Page #

Follow us on Twitter, LinkedIn, and Facebook Google Plus, You Tube and Xing

®

EDITORIAL DIRECTOR

Allison Proffitt (617) 233-8280 [email protected]

ACCOUNT MANAGER, MEDIA

Jay Mulhern (781) [email protected]

LEAD GENERATION ACCOUNT MANAGER, COMPANIES A-K

Katelin Fitzgerald (781) [email protected]

LEAD GENERATION ACCOUNT MANAGER, COMPANIES L-Z

Tim McLucas (781) [email protected]

CORPORATE MARKETING COMMUNICATIONS DIRECTOR

Lisa Scimemi (781) [email protected]

MARKETING ASSISTANT

Lisa Hecht (781) [email protected]

Contributing EditorsDeborah Janssen

John Russell Ann Neuer

Cambridge Healthtech InstitutePRESIDENT

Phillips Kuhl

Contact Informationeditor@healthtech .com

250 First Avenue, Suite 300 Needham, MA 02494

BIO•IT WORLD: KNOWLEDGE MANAGEMENT EDITION [3]

Thomson Reuters Releases APIs for Cortellis Life Sciences PlatformBY ALLISON PROFFITT | ORIGINALLY PUBLISHED FEBRUARY 28, 2012

Thomson Reuters announced a series of APIs (application pro-gramming interfaces) for its Cortellis life sciences platform this morning called Cortellis for Informatics. The APIs will

give customers direct access to the Cortellis content.

The product grew out of an exchange with Thomson Reuters customer Biogen Idec. William Hayes, director of decision support at Biogen, explains that data wasn’t the problem. “We have plenty of information,” he says. “More information than we could possibly use!” Biogen Idec initially ap-proached Thomson Reuters asking about ways to cull specific data from the Thom-son Reuters databases and deliver them to teams internally.

“We wanted [to pull] selected segments of the Thomson data into our system for cus-tomized competitive intelligence,” explains Hayes. Biogen’s initial plan was to Web scrape the Thomson data—“With permis-sion!” he says—but it was tedious and not very effective. “It was very problematic, trying to pull 200 different compounds, it would take either a long time or fail and required lots of care and maintenance.”

An API was the natural solution. “From the beginning we said [APIs] would be a lot easier,” says Hayes. “But it takes time to build a decent API… An API on top of content allows us to customize what we’re pulling out and deliver internally [by email or RSS] bits of information someone can quickly review and decide if they want to follow up.”

The idea aligned with Thomson Reuter’s aims as well. One of Thomson Reuter’s goals is to enable analytics against content rather than just publishing it, says Wendy Hamilton, senior vice president at Thomson Reuters.

Thomson Reuters Cortellis is a brand new platform that integrates data that previ-ously existed in several legacy databases that didn’t talk to each other—including drug monographs, company records, pat-ent reports, deal reports, and more—she says. The Cortellis platform includes a Web portal, but the Cortellis for Informatics APIs are a “significant step” toward “push-ing content into user workflows,” says Hamilton. She echoes Hayes’ concerns. Researchers are busy; they don’t always want a lot of Web portals. They need in-formation at their point of need, she says.

The Cortellis for Informatics APIs have been developed around areas of content in the Cortellis platform including investi-gational drugs, targets, patents, analytics, and ontologies. An API on clinical trials is expected by the end of March, and more will be released by the end of the year. APIs will be offered as more data and databases are integrated into Cortellis. Hamilton mentioned offerings for PK data, omics data, pharmacology data and molecular data as likely areas of expansion.

Cortellis access is a subscription-based service that is hosted by Thomson Reuters and that enables people and companies to access rich content either through a Web interface or programmatically via Cortellis for Informatics.

If a client chooses the API route, an API “key” gives the client’s developer team access to both SOAP and RESTful web services, allowing them to query Cortellis content programmatically. Developer sites provide documentation as well as “tips and tricks” to get people started. Clients also have the option of choosing from a selection of add-ons readymade for the popular components including Microsoft SharePoint and Accelrys Pipeline Pilot, or to make use of Thomson Reuters’ profes-sional implementation service.

It’s, “a very comprehensive, excellent prod-uct,” says Hayes. “But it requires a lot of expertise to use. The more we can extract and simplify, the wider the audience can use the information.” Since their first foray into Web scraping, Hayes and Biogen have converted to the APIs and, “It works much better!” It’s being used by both research scientists and marketing and sales staff.

“The more we can deliver what our end users within the company need, the more attached we are to their system,” Hayes says. “Divorce gets harder and harder.”

BON

US ED

ITION

: KNO

WLED

GE M

AN

AG

EMEN

T


BON

US

EDIT

ION

: KN

OW

LED

GE

MA

NA

GEM

ENT

ELN Excellence: The New Lab NotebooksElectronic lab notebooks are no longer just replacing paper, but enabling collaboration, global research, and IP protection. BY ALLISON PROFFITT | ORIGINALLY PUBLISHED FEBRUARY 22, 2012

Of all the life science software that has sprung up in the past ten years or so, electronic lab notebooks (ELNs) are the only platforms that have emerged as strategic players

across the market. That’s the opinion of Michael Stapleton, Gen-eral Manager, Informatics at PerkinElmer, who estimates the mar-ket penetration is still only 30% to 40%—leaving massive growth opportunities for companies including Sapio Sciences, Agilent, Rescentris, Accelrys and IDBS in the space.

Of course PerkinElmer isn’t the only company to have identified the niche. The ELN vendor landscape has narrowed significantly in the past few years thanks to mergers and acquisitions, but there are still many players vying to penetrate the marketplace.

“If you ask five people what ‘electronic lab notebook’ means, you’ll get five re-sponses,” says Kevin Cramer, Sapio’s VP of sales. The sentiment has been repeated for many concepts in life sciences research (and beyond) but it still holds true for ELNs. Sapio entered the ELN market in 2008, when ELNs were primarily a chemistry-focused, paper-replacement product. ELNs are now commonly used in chemistry, biology, and beyond, and the watchword is collaboration.

“There’s really been a maturing of the industry,” says Jeff Spitzner, chief scien-tific officer for Rescentris, a division of ELN Technologies. ELN used to be thought of as only a paper replacement option, but Spitzner sees a movement toward enabling collaboration and flexibility.

“The goal of the ELN is going beyond just the replacement of a paper notebook, and starting to support process efficiency,” says Dominic John, Accelrys’ product marketing director. “People are thinking of more than just the notebook replacing paper, but how can I use this information and turn it from information into knowledge? In other

words, create a knowledge base combin-ing the thoughts and intellectual property (IP) from multiple different researchers and partners.”

Many ELN products include some nifty new collaboration features. For example, Agilent’s most recent version of the Open-LAB ELN allows multiple scientists to col-laborate on a single experiment, and enter data and results from various techniques on multiple samples. Audit trails are main-tained in an environment that delivers stringent IP protection.

The collaborative nature of research is ex-panding the ELN’s role globally as well. In-stead of having a platform installed in one of pharma’s big US sites, says Stapleton, companies need a platform to be securely deployable to external as well as internal collaborators across the globe. Internal and external collaborations need to be

carefully tracked wherever the research is being done.

Accelrys’ John is seeing a dramatic expan-sion of the market in Asia Pacific, espe-cially China, and notes that with increasing contract work and outsourcing, secure connections between partners will only become more crucial. Accelrys recently partnered with Scynexis to provide access to the cloud-based HEOS platform for data sharing and collaboration (see “Accelrys’ Cheminformatics Solution in the Cloud” Bio-IT World, Jan 2012).

ELNs vs LIMS

Lines have been blurring between ELNs and LIMS (laboratory information manage-ment system) for some time. In general, the strength of ELNs lies is the paper replace-ment functionality and its ability to support collaboration, workflows, and discovery. LIMS have historically enabled manufactur-ing, sample tracking, and more regulated environments. The two approach the mar-ket from different directions but appear to be converging. It makes sense to link the two, because they both follow the sample, says Sapio’s Cramer.

As recently reported in Bio-IT World (see, “PerkinElmer Targets Holistic Data Solutions” Bio-IT World, Nov 2011), PerkinElmer has taken big steps into the software space lately, acquiring Cam-bridgeSoft, a leading chemistry ELN; Lab-tronics, maker of the LIMS Link product to link LIMS and ELNs, and Artis Labs (data visualization and data mining). Along with the company’s existing LabWorks LIMS product, the four-pillar PerkinElmer Infor-matics stable is intended to cover the full spectrum of ELN/LIMS needs.

Most of PerkinElmer’s customers are large pharma and diversified companies, says Stapleton, where the combination of ELN

“People are thinking of more than just the

notebook replacing paper, but how can I use this information and turn it from information into

knowledge?”

Dominic JohnAccelrys’ product marketing director


and LIMS makes perfect sense. These com-panies need to ”derive knowledge from data, [know] where the data resides, how much of it there is, and how diverse it is in terms of bioinformatics, biology, chemistry, toxicology studies, all the way into clinical and the market,” he says.

Accelrys has also made acquisitions in the space. Following the Symyx merger in June 2010, bringing the Symyx Notebook under the Accelrys’ umbrella, last May, Accelrys acquired Contur, a Swedish company pro-viding an online or on-premises ELN with a “keep-it-simple” approach. The large customers are moving toward a “conver-gent lab,” employing ELNs further into

development toward LIMS, says John. But John adds that Accelrys fully recognizes that much of market opportunity exists in smaller customers that may not need the LIMS capacity.

“Systems like LIMS are very expensive to implement in resources, time, services, etc. There’s a very large segment of the market that hasn’t adopted yet,” says John. “The challenge there is these guys aren’t after heavy, expensive, high investment. They want lighter systems just to replace the paper notebook.” Contour could conceiv-ably meet that need. It’s scalable—recently deployed to 5,000 users at the Karolinska Institute—and easy and inexpensive to deploy.

Rescentris’ CERF product (two-time win-ner of a Bio-IT World Best of Show award), started as a biology ELN, but as the market matures, Rescentris’ offerings and cus-tomers are becoming more diverse, says

Rescentris’ Spitzner. Rescentris now offers chemistry modules, and the semantic-based product has ontologies for many dif-ferent disciplines. The firm is also building a LIMS-like module to give scientists some structured input forms.

Rescentris’ customers are a mix of non-profit research institutions, companies, biotechs, and national labs. They tend to be focused more on basic research than manufacturing and about 60% are biology-based. Rescentris sees a lot of growth in academic labs, in part, Spitzner believes, due to the product’s full compat-ibility with Mac and PC operating systems and the ability to share data easily across

both platforms with native installations, not Web-apps. That flexibility and focus on user experience is crucial, says Rob Day, director of sales for Rescentris.

Flexibility is a common request. Sapio’s ELN Workflow Engine exists as a component of its LIMS and includes standard operating procedures beyond chemistry into biology and regulatory compliance standards like CLIA and Part 11.

Many of Sapio’s customers are working in the next-generation sequencing space and Sapio has found that many customers need scalable solutions to seamlessly manage data from a number of instruments. Cra-mer stressed that a key feature of Sapio’s product is a really well-designed API. As ELNs expand into myriad different areas and workflows, great APIs save the user work and cost to be able to quickly and ef-fectively build what is needed and upgrade automatically.

Notebook Futures

Recent changes to US patent legislation (see, “Patent Reform’s Brave New World,” Bio-IT World, September 2011) only confirm the need for ELNs. IP protection has always been a driving force behind ELN adoption. But now that patents will be awarded to “first to file” rather than “first to invent” researchers, the time-to-filing is even more crucial for IP protection, says Stapleton. The new standard “redefines the essential na-ture of having an electronic record and the speed with which you can act on it,” he says.

Spitzner agrees. Now, more than ever, re-searchers need to good records, but for dif-ferent reasons. They no longer have to simply defend their timing, but they must be able to build and file a patent application quickly.

But for ELNs to truly replace paper, the next frontier is mobility. A keyboard and a mouse aren’t really replacing paper, points out Stapleton, but an iPad can be a true paper replacement. Mobile solutions that accompany the researcher promote inter-action with both collaborators and instru-ments. The notebook should be where the researcher is, which means both a portable user interface and likely a cloud back end as well. “We see the iPad and the portable form factor in general as being a very im-portant part of the future of our company,” says Rescentris’ Day. The CERF 4.5 product has an “email to CERF” feature that allows researchers to send themselves (or oth-ers) email notes within the framework of the ELN—time stamped, with appropriate metadata—from any mobile device during a meeting, for instance. But they’ve also re-leased version 1 of the Rescentris iPad app and versions 2 and 3 are underway.

“This is a native app, the real thing!” says Res-centris’ Spitzner. Gone are the days when the notebook needed to stay in the lab. “Scien-tists should have access to their science 24/7.”

“Systems like LIMS are very expensive to implement in resources, time, services, etc. There’s a very large segment

of the market that hasn’t adopted yet.”

Dominic JohnAccelrys’ product marketing director

BON

US ED

ITION

: KNO

WLED

GE M

AN

AG

EMEN

T


BON

US

EDIT

ION

: KN

OW

LED

GE

MA

NA

GEM

ENT

Driving Innovation from WithinBY ALLISON PROFFITT | ORIGINALLY PUBLISHED MAY 17, 2012

“It’s survival of the fittest,” explains Ulrich Betz, department head of Merck Serono’s Innovation & Entrepreneurship In-cubator, of Merck’s innospire program, winner of the 2012

Bio-IT World Best Practices award for Knowledge Management. Only the best ideas win. “We wanted to make sure we were really leveraging the innovation potential of all the Merck employees via crowd sourcing ideas across hierarchical boundaries and divisional and organizational boundaries,” says Betz. The innospire program spans the Merck enterprise and seeks to give intrapreneurs—people within the com-pany with entrepreneurial skills and aspira-tions—an opportunity to launch new ideas in a highly transparent and open process.

This isn’t your classical idea competition, Betz stresses. “A big problem with most of the old-style idea competitions is that management asks employees, ‘Please send us your best ideas,’ then some people hand something in, then a committee looks at it, selects the best, then a prize is given out and nothing happens anymore.”

innospire is designed to refine ideas throughout a yearlong process and de-velop the strongest candidates into mar-ket-ready products or processes. Ideas are solicited from anyone in the company via an online portal. The initial pool of ideas is screened by a team of experts, and highly promising concepts are presented and dis-cussed at innovation marketplaces—open poster sessions held at Merck’s R&D hubs globally. Posters are presented by the “idea champion” and team members who sup-port and are helping develop the idea.

Later, concepts are presented to all em-ployees worldwide in a one-week online

event and feedback is solicited in chat rooms and discussion group. The field is narrowed again, and leading concepts are invited to an “innovation bootcamp” and receive legal coaching and further devel-opment direction. Finally a management grand jury selects the concepts that will be funded by Merck.

Unique to the program is the dynamic nature of the process. “The idea as it is handed in does not stay the same through-out the process but it is constantly further

optimized in multiple cycles,” says Betz. “People talk about it at the innovation mar-ketplaces, they discuss the ideas in online forums and rate it in prediction markets.”

The project teams don’t stay static either. Until the grand jury selection process, the innospire concepts are developed in employees’ spare time, with the idea cham-pion recruiting aid and expertise to further refine the project. The leadership and skills of the team are crucial, says Betz. “When management decides which projects to fund, as important as the quality of the idea

is the commitment and drive of the team.” If no one wants to put in the effort to work on an idea, Betz says this is a bad sign. “Either something’s wrong with the idea or with the idea champion and in either case the company should not invest in it.”

Once the winning concepts have been chosen by the grand jury, development goes “on the books” so to speak, and projects are either taken up immediately by a Merck business unit, or, for special projects, moved into a Merck incubator for two to three years. Incubator projects are funded by a specific cross-divisional budget to allow them to rapidly move to market readiness.

The result is global and cross-discipline collaborations between Merck groups. For

example, one innospire project is seek-ing to develop a new formula for poorly soluble drugs which uses technology that was in place in the chemicals division and is now being applied to a pharmaceutical problem.

innospire has contributed 14 new projects for the product pipeline since 2009 with a total sales potential of several hundred mil-lion dollars. The first innospire-fed product is planned for launch in 2012, and Betz expects the next idea call to go out in 2013.

“We wanted to make sure we were really leveraging the innovation potential of all the Merck employees via crowd

sourcing ideas across hierarchical boundaries and divisional and organizational boundaries.”

Ulrich BetzDepartment head, Merck Serono’s Innovation & Entrepreneurship Incubator


Pharma Lit: Elsevier Serves Pharma with Acquisitions of Ariadne, QuosaBY KEVIN DAVIES | ORIGINALLY PUBLISHED FEBRUARY 16, 2012

“We have a history of servicing life sciences and drug discovery/drug development in the pharma indus-try,” says Alexander van Boetzelaer, managing direc-

tor of corporate markets for the Dutch publishing giant Elsevier.

But while that history is based largely on serving up traditional scientific literature—Elsevier currently publishes some 2,000 academic titles, or what van Boetzelaer modestly calls “a sizeable business”—the needs of the pharma industry are chang-ing. The volume of the medical literature is so vast and unwieldy that there is a pre-mium on software tools that can navigate and digest the archives.

“We’ve seen demands from pharma grow as the complexity of science and the amount of data available increases. Our customers are coming to us looking for more than just access to scientific literature.”

Elsevier has made headlines lately with the acquisitions of pathway analysis firm Ariadne and Quosa, a text-mining software company, but the decision to broaden beyond journals dates back at least 5-6 years. “This did not happen overnight,” says van Boetzelaer, noting that Elsevier staff conducts hundreds of interviews with customers annually to gauge their satisfac-tion, needs, and pain points.

For example, in 2007 Elsevier bought the famous Beilstein Database. Now known as Reaxys, it has expanded from a purely inorganic chemistry database to a resource that helps researchers designing and syn-thesizing compounds to draw reactions in a much more interactive manner.

Elsevier also operates PharmaPendium, which provides electronic access to the FDA database, helping pharma view a host of preclinical and clinical safety data, pro-viding valuable intelligence in designing early trials and avoiding mistakes.

Another key product is Embase, a data-

base that sits above Medline and Elsevier’s proprietary content, providing in-depth in-formation on drug discovery. And in 2010, Elsevier bought Collexis, with the goal of adding more value for customers.

More than Content

Elsevier management acknowledges that it needs to provide better access to all of its sizeable content, and one way of doing that is by incorporating visualization tools. Van Boetzelaer talks about a “Content/Technology/Platform” triangle to provide customer solutions. “They don’t need to wade through thousands of reactions or articles but get to the information relatively

quickly and have a sense the search is rela-tively complete,” he says.

The goal of adding a visualization ca-pability, particular in the area of biology and disease progression, was the prime reason behind the purchase of Ariadne. “They have a state-of-the-art text mining capability, fine-tuned for biology,” says van Boetzelaer. Together with Elsevier’s content, “there is an opportunity for a new solution.” Ariadne is best known for its flag-ship product Pathway Studio and its allied semantic technologies.

It was a similar proposition with text-mining company Quosa, providing another tool to help customers mine the scientific literature. “Our customers struggle with publishers’ proprietary content. They’re looking for ways to store and search and manage that content. We believe that’s a natural exten-sion of our offering. Quosa provides a state-of-the-art software system, and combined with our own content, we can provide a truly value-added service.”

In particular, van Boetzelaer believes cus-tomers will be able to store and search their content and keep it accessible in a “copy-right–compliant way.” That will be particu-larly important in pharma, where there are regulatory obligations and a strong incen-tive to search for adverse effects.

“We are committed to the Quosa and Ari-adne products and will continue to invest in those areas. Existing customers should

see improvements. We’re not stripping these assets. This is a direction we are com-mitted to,” says van Boetzelaer. He adds that Elsevier will consider “any attractive opportunity,” but the immediate priorities are on integration.

The immediate priority is pharma. “We see an immediate need we can satisfy and monetize,” says van Boetzelaer. “But there’s a big use case in academia. Pharma companies are outsourcing fundamental research. To be successful, we need to bridge both.”

“Our customers struggle with publishers’ proprietary content. They’re looking for ways to store and search and

manage that content. We believe that’s a natural extension of our offering. Quosa provides a state-of-the-art software

system, and combined with our own content, we can provide a truly value-added service.”

Alexander van BoetzelaerManaging director of corporate markets, Elsevier.

BON

US ED

ITION

: KNO

WLED

GE M

AN

AG

EMEN

T


BON

US

EDIT

ION

: KN

OW

LED

GE

MA

NA

GEM

ENT

Making Semantic Sense of Unstructured DataSophia’s Digital Librarian software relates documents without taxonomies.

BY KEVIN DAVIES | ORIGINALLY PUBLISHED NOVEMBER 15, 2011

A somewhat stifling aspect of many sophisticated semantic search tools is the need to build ontologies and taxonomies to organize the data. Nonsense, says David Patterson, the

co-founder and CEO of Sophia Search, who believes in freedom from taxonomies or ontologies.

“People are so attuned to building taxono-mies and ontologies because they think they need to,” says the Northern Irishman. “Our message is, that just isn’t true! We understand the purpose they serve, but one of our long-term goals has been to build a search tool that doesn’t rely on background knowledge structures. Let’s free people up from the overheads and expense of these knowledge structures.”

The Sophia Digital Librarian search tool thrives on finding relationships between documents without the need for any kind of taxonomy. Just set the software loose on a collection of unstructured data, and it does the rest.

Patterson co-founded Sophia with Vladimir Dobrynin, a professor at St. Petersburg State University and Sophia’s chief sci-ence officer. Patterson’s background is in artificial intelligence. He was director of an artificial intelligence R&D lab at the Univer-sity of Ulster, working on data mining, ma-chine learning, and information retrieval. Patterson has collaborated with Dobrynin since 2003. After some five years of R&D, the researchers came up with a prototype version of Sophia. The Sophia product engineering team is based in Belfast, while the R&D team is based in St. Petersburg, Russia and sales in Silicon Valley, California.

Semantic Searching

“The Sophia Digital Librarian is all about content enrichment within organizations or repositories,” says Patterson. “It helps organizations improve the findability of the content they have in their organiza-

tion or external repositories.” Interest is high among pharma companies, life science organizations and the scientific publishing community.

The Digital Librarian is built on Sophia’s patented contextual discovery engine,” says Patterson. “We’re empowering orga-nizations to become more innovative and

creative through discovery. Search should not just be about retrieving information you expect to find but also about uncover-ing and discovering new things you weren’t aware of.”

Taxonomies can stifle innovation, says Patterson, by constraining staff to all think conventionally and uniformly. “You’re not allowing your employees to think freely… If we are constrained by the boundaries of conventional thinking, we limit creativ-ity and our ability to discover new things. Sophia removes these constraints and enables users to discover unknown rela-tionships and knowledge from within their content—that’s the real power behind what we do.”

After reading through documents in an or-ganization’s repository, the Sophia Librar-

ian gets to work. “It extracts the meaning, organizes them into topics, understands what they’re about, captures metadata de-scribing their topic and subtopics, and at-taches tags to the document to make them more findable,” says Patterson. Tags can be extracted from the document, but the tool also creates semantic tags—relevant words or phrases that do not actually crop up in the source document.

“We also identify the most similar docu-ments among all the documents in the corpus,” says Patterson. “Then we rank the “nearest neighbors”—the most semanti-cally similar documents. This quickly brings

to the user a list of related documents and helps users focus and find information rel-evant to their needs.”

The metadata—Sophia calls it the “seman-tic profile”—are exposed as XML, through a series of web services to make the infor-mation available to any search or content management tool. The goal, says Patter-son, is to augment current search tools and make them smart.

In a quick demo, Patterson uses Sophia to automatically create a semantic profile for a document taken from the Web using knowledge extracted from a corpus of 1.8 million news stories spanning 20 years. The articles have been automatically indexed by Sophia and semantic profiles created for each document. “Sophia uses knowledge extracted from these documents to come

“We’re empowering organizations to become more innovative and creative through discovery. Search should

not just be about retrieving information you expect to find but also about uncovering and discovering new things

you weren’t aware of.”David Patterson

Co-founder and CEO of Sophia Search


up with a semantic profile—topic, tags and nearest neighbors—for the new docu-ment,” he says. It uses knowledge extracted from the news corpus to intelligently assign metadata to the new document.

A similar search can be done using an abstract from PubMed on Alzheimer’s disease, for example, retrieving tags re-lated to dementia, amyloid protein, and neurodegenerative diseases among others. The numerical score offers a gauge of the “distance” between the source document and any retrieved article. “Our capabilities relate topics and documents together that wouldn’t have been otherwise known,” says Patterson. “We’re able to make con-nections years ahead of [traditional means of] discovery.”

In time, it will be possible to filter those results by source or date, for example selecting just PDFs or documents within a specific date range. The functionality is there, says Patterson, it just requires using a web services user interface.

Customer Stories

Sophia’s sales director Jeff Bierach says the company has a number of customers in the U.S. already, and is targeting many more in the life sciences community and publishing sectors. As discussed in a recent

Bio•IT World guest commentary (see, “Re-evaluating the Role of Research Librarian in Pharma R&D,” Bio•IT World, Sept 2011), many pharma companies have been down-sizing their librarian staff for some time.

“Look at what’s been happening in pharma companies over the last 3-5 years,” says Bierach. “Genentech used to have a staff of over 20 librarians—researchers finding information. They have zero now. That’s really a big play for us, to automate a lot of this capability around discovery and docu-ment classification. Those are really time consuming tasks that we can automate.”

One big pharma company had spent three man-years building custom queries for PubMed to extract information on over 30 different topics they track. “Based on the last two years of MEDLINE abstracts which we have indexed, our client was able to reproduce those queries in Sophia in less than one week,” says Bierach. “We essen-tially solved his entire job that took three years to get to where he is now. There’s a huge amount of value there.

“We’re starting to create semantic pro-files for content of a pharma company in San Francisco,” adds Patterson. “They use Microsoft FAST [search tool] and want to add semantic profiles to the content.” With stagnant drug discovery pipelines,

Patterson also sees an opportunity in drug repositioning, helping to find correlations at significant cost savings.

While most content search applications focus on bespoke internal datasets rather than the web, Patterson says Sophia is looking to work with partners, including a Google reseller in Chicago. “We’ll supply a layer between the Google search appliance and Sophia.”

Another promising target segment is the publishing sector, which could leverage Sophia to ‘up-sell’ related journal articles to customers. Another early project involved helping a publishing company sift through 20 years of legacy content. “Within three days, we were able to see what information was evergreen. The client said that saved him 9 man-months of effort,” says Patterson.

Version 1.2 of the Sophia Digital Librarian is now in full commercial release, but Pat-terson stresses that his team is still build-ing functionality. Because the company is relatively small, “we can move very quickly,” says Bierach.

This article also appeared in the November-December 2011 issue of Bio-IT World maga-zine. Subscribe today!

BON

US ED

ITION

: KNO

WLED

GE M

AN

AG

EMEN

T


BON

US

EDIT

ION

: KN

OW

LED

GE

MA

NA

GEM

ENT

Wingu Makes Science Simple‘Google for research’ organizes info in one place.

BY KEVIN DAVIES | ORIGINALLY PUBLISHED MARCH 29, 2011

What happens if you cross expertise in social network-ing and bioinformatics with semantic medical search and Cloud computing? The answer is Wingu, the boot-

strapped brainchild of Brian Gilman and Nick Encina, which emerg-es from hibernation this spring after two years in stealth mode.

“Wingu is a next-generation platform for scientific data management,” says Gilman, who previously founded Panther Informatics and SciLink (see, “SciLink Scours the Web for Connections,” Bio•IT World, Oct 2007).

“We’re a data company. We like to think of ourselves as Google for research—think Google apps or Google docs. Wingu allows you to capture and organize all your infor-mation in one place.”

Gilman and Encina chose the name Wingu, which means “cloud” in Swahili, because as Gilman says, “we’re launching in the Cloud and have a commitment to lowering boundaries for research.”

Functionality on the Platform

But Wingu also borrows the concept of an Apple App Store. Gilman and Encina were fed up having to buy software piecemeal that served a limited number of user needs.

“We were often sold software that promised the application would take care of user re-quirements in our businesses or consultan-cies, but that was always a fib! If those apps needed to be changed in some manner, there was typically a large professional ser-vices model attached to that engagement, and it was very expensive,” says Gilman.

The goal was to dispense with those giant professional services teams and instead, “empower our customers and the informat-ics community to put new functionality on the platform and either share functionality with the scientific community or sell it if you’re a vendor.”

Encina’s background is in cell biology and

computer science. He helped launch a com-pany called Transform, which was acquired by Johnson & Johnson. He was also an early employee at Infinity Pharmaceuticals (see, “Conquering Infinity with Chemical Genet-ics,” Bio•IT World, Feb 2003) and a founder of Praxeon.

“The initial concept was this: Brian was in so-cial networks for science, and I did semantic medical search. So how do we bring Web 2.0 technology into life sciences? Most plat-forms used by pharma are just so outdated, 10-15 years old,” says Encina.

“We wanted to take a much more evolution-ary approach to helping scientists. We want-ed to come up with smaller applications that satisfy specific needs, so in concert you can create more sophisticated applications. We could align ourselves with the workflow of how scientists work by providing much more granular applications.

“At a high level,” he continues, “we’re a data company. We want to make it easy to get data in but then provide analytics to tell you something about your data that you may or may not know, e.g. what experiments in your organization are similar to yours, or

what patents are related or what vendors can assist in your work.”

All of Wingu’s services run on the Amazon Cloud. “We’re not tied to any one vendor, but Amazon is pretty awesome,” says Gil-man. Clients don’t purchase or run a data-center, and can use the Wingu service on a pay-per-use method. “But we can run on private clouds, there’s a lot being produced in pharma companies. We don’t have a pref-erence,” says Gilman.

Wingu is primarily a platform shop, but the manifestation of the platform is a multidis-ciplinary electronic lab notebook (ELN). Dur-ing the past two years, Wingu has quietly enrolled a handful of customers, including a “top 6 pharma” and several academic users, including groups at Boston University, Har-vard and the Broad Institute using the ELN app on a daily basis.

Gilman says the strength of Wingu’s ELN is simplicity: “We’ve architected the system and interacted with users, we thought hard about what the user experience should be in science. Users are finding it extremely easy to do their work on a daily basis.”

“They don’t think of it as an ELN but as an entire workflow, like a scientific desktop,” says Gilman. “They can just do it in one place.” There is an aspect of Wingu’s ELN app that resembles PipelinePilot, but Encina says, “we cover everything from the design to the execution of an experiment to the analysis of the data. In pharma and biotch,

“We wanted to take a much more evolutionary approach to helping scientists. We wanted to come up with smaller applications that satisfy specific needs, so in concert you

can create more sophisticated applications. We could align ourselves with the workflow of how scientists work

by providing much more granular applications.

Nick EncinaWingu


research groups are becoming much more heterogeneous. Project teams need differ-ent hats. We’re trying to allow biologists and chemists and clinicians to have a discussion on the platform. It’s very social; we allow people to see the information that makes sense to them, all the while having a con-versation online.”

Science as a Service

The interface is visually appealing and ro-bust, and becomes more intuitive with time, like an Apple app. “We want to make science a little bit more fun,” says Encina. “We don’t believe in blocking customers from their data. An open platform will force them to be more innovative. Although people can leave the platform, hopefully they won’t want to.”

Robert Azad, a graduate student at Boston University and early Wingu user, praised the interface, saying he could leave the software open for “days at a time... so that I can eas-ily update my experiments as needed” and noted that his experiments are easy to share with his colleagues and searchable. He even credited Wingu with organized documenta-tion that will make his experiments success-fully repeatable in the future.

Gilman sees Wingu as a very data-centric company. “Not only can you produce apps

that augment the platform for your own needs, but you’ll be able to deploy analytics onto the platform to allow yourself or oth-ers to analyze the data. That’s how we see ourselves supporting science around the world in the future.”

“Our platform will tell you things whereas before, you needed people like us on staff! We’re trying to help informaticians do stuff that is more interesting and eliminate some of the tedium.” And from pharma’s point of view, Wingu will try to help make the IT/IS staff’s work less burdensome.

The user experience is “just like using Gmail. You just log in, working on our platform, the experience is just seamless. People can sign off from one computer and hop on another. It’s all delivered through a browser.”

Security is, of course, a major concern, but Encina says, “In some ways you’re more protected on our platform.” With traditional methods of sharing data—using email or PDFs—Encina says there is no way to know where they might end up. “On our system, we have full audit trails. All information is captured, so there’s no way for someone to look at something without people knowing about it.”

From an early focus on the discovery pipe-

line, Gilman says Wingu will likely move closer to the translational and clinical infor-matics side of pharma. Eventually the plat-form could handle many other data types. Users could be able to see if a particular compound was efficacious, or a clinician could feed information back to the program team about a compound’s efficacy in Phase I. “That’d be the kind of thing we’d love to see enabled,” says Gilman.

Wingu is not doing next-gen sequencing, but companies like DNAnexus could be a partner. “We’re not going to do everything, we’re not trying to boil the ocean here,” says Gilman. “We’d love to partner with the DNAnexus’ of the world to augment some of our own functionality.”

Users will contribute apps to the platform. “A major inflexion point will occur when some-one has built a small business on top of our business. We’ve built our own apps on the platform, and certain well-known vendors are building apps on the platform.” Expect some announcements over the next year.

This article also appeared in the March-April 2011 issue of Bio-IT World Magazine. Sub-scriptions are free for qualifying individuals. Apply today.

For more information on our reports go to InsightPharmaReports.com or contact:Kerri Simpson

Marketing Manager, Insight Pharma ReportsPhone: 781.972.1347 l Email: [email protected] l Web: www.insightpharmareports.com

Insight Pharma Reports: Follow us on Twitter and LinkedIn

l Cloud Computing Usage in Biotech & Pharma Market Study

l Cloud Computing in Life Sciences R&Dl Bioinformatics and Computational Biology:

Bottlenecks and Options

l Bioinformatics Partnering Terms and Agreementsl Healthcare IT Market to 2016 - Demand for

Integration of Advanced Clinical Applications to Drive the Market

l US Healthcare IT Market Forecast to 2014

BON

US ED

ITION

: KNO

WLED

GE M

AN

AG

EMEN

T

www.bio-itworld.com

250 First Avenue, Suite 300

Needham, MA 02494

bonus edition: knowledge management...eral manager, informatics at perkinelmer, who estimates the...

Documents