Showing posts with label Pharma. Show all posts
Showing posts with label Pharma. Show all posts

Thought on the Electronic Lab Notebook

This topic is becoming more interesting to me every day as we see the technologies and the processes evolve. A simple definition of an Electronic Lab Notebook (ELN) is becoming almost impossible to agree on as can be seen in a recent discussion group I am a member of over on LinkedIn that points to the LimsWiki definition.

An electronic laboratory notebook (also known as electronic lab notebook or ELN) is a software program or package designed to replace more traditional paper laboratory notebooks. Laboratory notebooks in general are used by scientists and technicians to document, store, retrieve, and share fully electronic laboratory records in ways that meet all legal, regulatory, technical and scientific requirements.[1] A laboratory notebook is often maintained to be a legal document and may be used in a court of law as evidence. Similar to an inventor's notebook, the lab notebook is also often referred to in patent prosecution and intellectual property litigation. Modern electronic lab notebooks have the advantage of being easier to search upon, support collaboration amongst many users, and can be made more secure than their paper counterparts.

A mouthful and it scrapes the surface of what may be meant when speaking of an investment in an ELN. I gave a talk at an informatics conference in London a couple of years back and showed a chart with overlapping functionality intersecting the role of traditional LIMS systems and the growing ELN segment. That chart has moved forward to the point where now you find markets where they are almost one and the same.

This brings up a couple of interesting discussion points

  • Do we need both, or should we blend the systems to make it one experience?
  • What is the value of a lab notebook? (GxP / Exploratory / Other – context is a big part of this but I am thinking beyond those aspects to the scientific thought process)
  • Does the act of capturing free thought in a (paper?) notebook encourage a different type of thinking than the act of capturing data in a structured system that allows encourages free text or unstructured input as a part of the structure?

Clearly there is room for a discourse on all these topics, and many more that dive deep into the specifics, but as we look at the tools, I can’t help but come back to the question of what are we really trying to do? The technology is not the barrier to capturing data, or even in most cases, information. But are we making the technology a barrier to the process of creative thinking?

LIMS are by design typically built to capture structured information and results sets, manage samples and lifecycles and other common analytical workflow. Paper lab notebooks have for centuries been used to record everything from wild ideas that need to be formed into hypothesis and examined before even approached as a test, to being used as evidence of test execution or development. Now, in the litigious world of drug research and development, they hold a very high burden depending on where in the lifecycle they sit, acting in some cases as patent defense platforms!

I wonder how much we have moved away from creative thinking and free capture of those ideas in our pursuit of the right toolset to capture our data. I know a common theme I have heard from my scientific associates over the years is that there is less and less time for thinking, and more and more effort devoted to execution. Looking at the innovation cycle and the pharma pipeline as a whole, I wonder sometimes how much of the hollow sound in that pipe is regulatory pressure, or external pressure, and how much is a shifting in innovation and creative thinking.

Chemistry Add-in for Word

So as promised, here is the blurb on the Chemistry add in for Word. Very cool idea and I hope they include it in PowerPoint as well since so much of the work ends up there for presentation.

The Chemistry Add-in for Word makes it easier for students, chemists, and researchers to insert and modify chemical information, such as labels, formulas and 2-D depictions, from within Microsoft Office Word. In addition to authoring functionality, Chem4Word enables user denotation of inline “chemical zones,” the rendering of high-quality and print-ready visual depictions of chemical structures, and the ability to store and expose semantic-rich chemical information in a semantically rich manner.

You can head over to the MSR site and grab it here.

BioCoder - code for Biologists

While trolling through some Microsoft research projects recently I ran across two of particular interest in my current area - BioCoder, described below, and Chemistry for Word which I will cover in a later post. The BioCode concept applies programming constructs to the protocol definition process. The idea is interesting and worth exploring. The blurb below from the site summarizes it nicely and you can read more by downloading the package here.

BioCoder is a high-level programming language that enables standardization and automation of biology protocols. Our vision is to change the way that experimental methods are communicated: rather than publishing a written account of the protocols used, researchers will simply publish the code. The code can be automatically converted to human-readable steps for manual execution in the laboratory. When written as a computer program, biology protocols can be parameterized to facilitate reuse in different contexts. They can also be mapped automatically to the setup of a given laboratory, taking into account the equipment and reagents that are available.

ELN Talk this summer / fall

I'm scheduled to give a talk in Amsterdam billed as "The leading conference for ELNs and Data Management strategies" at the end of the summer. The details are online at the conference website.

My talk is: Keynote Presentation: The Role Of ELNs: A Chapter In A Much Larger Story

  • How do you strategically select an ELN to fit in with your company requirements?
  • Outlining the importance of creating the enterprise strategy to create a seamless informatics platform
  • Delving deeper into the Wyeth/Pfizer GLP ELN deployment: why was it a success and what lessons were leaned along the way

I enjoy these events as I almost never leave without great contacts and networking. Any thoughts to contribute are welcome, so feel free to get in touch with me.

iPads and ELN's

It seems the iPad is everywhere lately, even popping up on a LinkedIn discussion on Lab Notebooks.

My opinion on this topic is essentially the same as the tablet-pc form factor. The tech is not there yet to get any real advantage in most cases, though there may be a few isolated edge cases. What I think we are waiting for is the next disruptive way of recording lab observations and tying the information flow together in a more seamless fashion. I do not see anything the iPad will make easier yet, except the type of task already relegated to the iPaq, or similar form factor which is essentially basic, situation specific, observational recordings. Now - don't get me wrong, I think it's very cool and would like to have one dropped in my lap to play with, but from a business value in the labs perspective, I think we are waiting on the killer app. (Let's just hope it's not Flash based)

Pleased with the results

We had a good meeting with Pfizer today. The team was good and seemed genuinely interested in fully understanding the landscape at Wyeth. The repeatedly stated concern was that they capture sufficient detail to not leave any business users in the lurch when things went down. All in all, despite the building and meeting room shuffle, it was a productive visit. I am sure there will be many more, across many more areas, to get things fully sorted out but the process seems to be on track so far.

The announcements on organization today were also an interesting step – it looks like the executive level will get some Wyeth participation in the new organization. While the roles named were all key business folks, I think they reflect a desire to maintain the talent that lead to the acquisition in the first place. Perhaps that’s my eternal optimism surfacing again, but either way, I am feeling upbeat about the process.

The looming specter of the 20,000 projected layoffs is certainly on most everyone's mind as we go into this process, but the best way through is to focus on the solutions and while planning for the worst, look for the best. The drain of worry can become a self fulfilling prophecy if you allow it. - no extra charge for that bit of advice ;)

Ontology based data & semantic relationships

Working through a data architecture and strategy for clients recently, I had to compile some information regarding development of the landscape. This information is reflected below.

The primary components to reference are detailed in the included diagram. In this case, the ontology is clearly a piece of the stack, but not the “data” or the single UI.

The ontology is best thought of as a view of an established information set that uses concepts to define relationship. The data is then mapped onto ontology to provide a specific high value view of the data, aiding in the generation of information and knowledge. Clearly there is an assumption that as a precursor to the use of the selected ontology, significant work has gone into the process of cleaning the target data through direct manipulation or a meta data based transformation layer to manage synonym matching, etc. across sources.

Another definition, more succinct is, “Ontologies are computable conceptualisations of a knowledge domain” as defined by Nico Adams, emphasizing the transformation from data to information that can then be further acted upon.

The OWL Web Ontology Language is designed for use by applications that need to process the content of information instead of just presenting information to humans. OWL facilitates greater machine interpretability of Web content than that supported by XML, RDF, and RDF Schema (RDF-S) by providing additional vocabulary along with a formal semantics. OWL has three increasingly-expressive sublanguages: OWL Lite, OWL DL, and OWL Full. Source: http://www.w3.org/TR/owl-features/

The semantic layer-cake.: (Copyright © 2008 World Wide Web Consortium, (Massachusetts Institute of Technology, European Research Consortium for Informatics and Mathematics, Keio University). All Rights Reserved. http://www.w3.org/Consortium/Legal

Useful links :

  1. W3 OWL Reference a) http://www.w3.org/TR/owl-features/
  2. Good article on Ontology implementation a) http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T64-4GMB0F0-F&_user=358874&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000017638&_version=1&_urlVersion=0&_userid=358874&md5=4b5c6decc4b2f01fad8183b00aec72b1
  3. 3) DDI - An Ontology for Drug Discovery Investigations a) http://users.aber.ac.uk/ddq/ddi/wiki/index.php?title=Main_Page
  4. Open BioMedical Ontologies a) http://www.obofoundry.org/crit.shtml
  5. OWL ontology browser a) http://pellet.owldl.com/ontology-browser/
  6. OBO Ontology Download Matrix a) http://www.berkeleybop.org/ontologies/
  7. Semantic Chemistry a) http://www.semanticuniverse.com/articles-semantic-chemistry.html

Reference:Stephen P. Gardner, Ontologies and semantic data integration, Drug Discovery Today, Volume 10, Issue 14, 15 July 2005, Pages 1001-1007, ISSN 1359-6446, DOI: 10.1016/S1359-6446(05)03504-X.(http://www.sciencedirect.com/science/article/B6T64-4GMB0F0-F/2/f296f93f44347cfd561668ede72ac5f9)

Nico Adams, Semantic Chemistry http://www.semanticuniverse.com/articles-semantic-chemistry.html

More to come...