Ryan's Blog on NMR Software

Linking to Meaningful Data in an ELN World

In a previous post, I asked the question, why does paper spectra continue to persist in chemistry?

Of course there is the next challenge, as Rich Apodaca points out on his Depth-First Blog in an earlier post:

The previous article in this series, suggested that the same dynamic applied to the compilation, management, and sharing of spectral data by chemists. More to the point:   

... cheminformatics has failed to deliver an inexpensive, robust, and truly usable solution to the problem of compiling, managing, and sharing spectral data for scientists of average computer skills. ...

To be sure, there are tools that address parts of the problem. But no solution addresses them all and that's why scientists and publishers resort to using obviously inferior solutions like PDFs.

Whether or not organizations and groups are resorting to inferior solutions is up for debate because it of course depends on the expectations of the end user. But his comments definitely struck a chord with me.

So the next question is:

"What is the best way to connect my analytical data to my ELN records TODAY?"

By far, the most common way that I have seen organizations connect the analytical data from our software to ELNs is via PDF.

But as Rich mentions in yet another post, for people who are looking to build on experiments or model or compile the results, static PDF images are practically useless.

I couldn't agree more.

So why do organizations choose this route?

The three biggest reasons I have heard are:

1. File size limitations in the ELN
2. The lack of a standard and supported analytical data format that is generic, open, lockable, and widely supported for years to come.
3. Currently,  PDF is more controlled for legacy support than analytical data.

As a result, PDF is the only reasonable approach for many, and it is certainly better than not connecting to a record of the data at all. 

I think the key is for vendors to work horizontally and to combine their strengths to deliver as Rich suggests a:

an inexpensive, robust, and truly usable solution to the problem of compiling, managing, and sharing spectral data for scientists of average computer skills.

But the file format remains an issue.

Work by the ASTM E13.15 Commitee has been ongoing for the past 5-6 years towards a universal analytical data file format. This file format is called AnIML (Analytical Information Markup Language), the developing XML standard for analytical chemistry data. Most vendors support the general directions of the ASTM E13.15 for a universal data format for analytical data.

A final note on the role of MEANINGFUL data in an electronic world. When I refer to meaningful data, I am referring to knowledge gained and stored in an actual data file as opposed to a static PDF. One of the unique features that ACD/Labs has maintained over the years is the ability to electronically assign NMR data to chemical structures to truly capture not only the data but the knowledge gained from the experiment. I think not leveraging this knowledge is an awful shame, especially in an electronic world, but I think it will come.

As of right now, While it is common that NMR Spectroscopists will assign their data electronically, it is very rare to find a group of chemists in the pharmaceutical industry, for example, who routinely use their processing tools to assign their data. Why?

1. They might not have the right software tools
2. It is not required. In fact, in some cases I have learned that it is forbidden. Why spend the time it takes to assign the data if it is not required or permitted?

A static PDF is indeed proof that an experiment was run, but does it contain information that supports a proof of the proposed structure? Where is the knowledge that was gained from this exercise?

I think 1D NMR Assistant significantly reduces the amount of time it takes to electronically assign a spectrum so now it is just a matter of finding an easy way to tie this assigned analytical data to the ELN.

I think there is a real opportunity here.

What are your thoughts?

Would you prefer electronic data over PDFs?

Is simply raw or processed data enough?

How important is maintaining the knowledge gained from the experiment (i.e. assignments)?

Thanks to Rich for the multiple inspirations for this and previous posts.

Let's See your Printed Spectra Do This!- Part 2.

Back to the chemists with their ELN who continue to resort to their paper spectra.

Is it just an old habit?

No. I think it is something else. In fact I think there are two major (and completely understandable) reasons why some chemist continue to resist the complete transition to the electronic world:

1. One of our users who I really enjoy speaking with when I get a chance once told me, "The only way you are going to get chemist to fully adopt these tools is when they can access and interact with the spectra JUST as fast as they can do it on paper." I think it's a great point. For some chemists having to sit in front of a new piece (or old piece) of software to try and get your data out can be a daunting task. But I think significant strides have been made in this regard. With the transition to open access, NMR Spectroscopists have done a nice job (in conjunction with software vendors) to automate processing and create software macros to provide chemists with access to fully processed spectra. In addition, I think that the usability of NMR software for manual processing (See Shortcut Mode for example) has greatly improved over the years, but there is of course still work to do.
2. I think the other reason is that perhaps the benefits associated with electronic handling of NMR data have historically been not convincing enough or educated clearly enough to the user. For example, I have beaten the multiplet report topic to death on here, but I am continually amazed by the number of chemists who have had our software for a long time that aren't aware of this feature.

But perhaps easy access to data from your desk and formatted multiplet reports is not enough for a chemist to let go of the paper and embrace the electronic world. In fact, I am convinced it isn't. After all, an NMR spectrum is a means to an end. Sure, the delivery of the results in a readable form in a convenient place is essential and it has increased producitivity in open access environments, but the bottom line is that there is a reason the chemist ran an NMR experiment. In most cases that reason is to determine if their compound's proposed structure is consistent with their spectrum. Historically, NMR processing software has not provided any assistance in regards to data interpretation. 

I am hoping that ACD/1D NMR Assistant addresses this challenge and finally convinces the chemist to let go of their paper spectra for good and fully embrace the electronic world. To see how 1D NMR Assistant helps chemists interpret and assign their ¹H NMR spectra check out my previous vlog postings (with video) here and here.

Are You Attached to the Paper Printouts of Your Spectra?-Part 1

This is the topic I will be presenting on at our annual ENC Symposium on March 9, 2008. If you happen to be attending this conference in Asilomar, check out the agenda and register here.

I mentioned this before, but I follow the Depth-First Blog authored by Rich Apodaca rather closely and I highly recommend it.

I mention it again because Rich had a very interesting post a few weeks back inspired by a discussion about Electronic Lab Notebooks (ELNs) that took place on Derek Lowe's In the Pipeline Blog (which is another blog I follow frequently and highly recommend!)

Fascinating posts and discussion for sure!

Rich notes:

The wasteful process of entombing valuable scientific data often begins with the paper lab notebook, so the subject of ELNs should be of great interest to anyone involved in creating, using, or reprocessing chemical information.

Why do paper notebooks continue to persist in chemistry?

The issue is complex, but in my view stems from the lack of a truly usable and affordable tool. Although the term "tool" may suggest software, it actually involves a much more complex beast consisting of hardware, software, an ergonomic hardware/software user interface, and a computer network. In chemistry, the problem is compounded by the centrality of chemical structures and the inability of most generic ELN products to capture or use them. Given these constraints, and the costs associated with creating and marketing general-purpose products designed to work within them, it's not surprising that many organizations decide to roll their own ELN. And it's even less surprising that many others decide sticking with paper is a better option - at least for now.

I think this is a good argument, and I want to add to it with the question, "Why does paper spectra continue to persist in chemistry?"

Personally, I am amazed by the number of times I have encountered groups who are already using ELNs, but are still routinely using paper spectra. Sure when the time comes to attach their PDFs (Rich has shared his feelings on this format as well, but that's an entirely different discussion!) to their notebook records, they will extract the electronic file, but until that point many chemists will walk back to the instrument room, pick up their data printout, study it, and then toss it in the recycling bin or toss it on their bench!

For example, I was recently visiting with some chemists in the pharmaceutical industry who were providing me with feedback on our products and discussing their workflow. They mentioned that while they religiously use the desktop NMR processing software for viewing, processing, analysis, interpretation, and reporting to their ELN right on their laptops, in their lab...many chemists from their group still make the walk to the instrument room for their piece of paper instead.

Paperless environment?

Old habits, I guess.

Why use a piece of paper when you can access the data electronically? Meaning you can zoom in and zoom out on regions of the spectra to take a closer look? I guess in most cases, you don't really need to do that but in many labs where the data can be accessed electronically on a laptop in your lab, why make the walk back to the instrument room for that piece of paper?

What are your thoughts? Are you still attached to the paper printout? If so, why?

I'll share my opinion in part 2 of this topic tomorrow.

ACD/1D NMR Assistant Part 1-Processing

So here is my first attempt at showing you some of the features available in ACD/1D NMR Assistant.

The first video will highlight how easy it is to process an NMR spectrum in 1D NMR Assistant.

Make sure to check back early next week and I will post another video showing how the software can help you assign your data.

Enjoy!

If you can't get the above video to work, or if you want a bigger version , click here to watch the demonstration.

A note to people who receive this post via email or RSS feed. If you would like to watch the video, you may need to come to the blog to check it out if you can't see it in your reader:

Electronic Lab Notebook (ELN) Integration

If you have followed ACD/Labs for years you may have come across the following older press releases at one point or another:

http://www.acdlabs.com/clients/pr_cs1002.html

http://chembionews.cambridgesoft.com/Articles/Default.aspx?articleID=269

Over the last few years, it seems that more and more organizations are making the decision to deploy an ELN. The choices are many, and not limited to Cambridge Soft of course (to name a few others). I thought I would take this opportunity however to share with you some of the integration that is possible between Cambridge Soft's E-Notebook and ACD/Labs tools.

While many organizations are busy evaluating different ELN offerings and understanding how it will work in their environment, some are not thinking about how these packages will work with their analytical data. Will a chemist simply be responsible for copy and pasting valuable pieces of a report into their notebooks? Should there be a link to the live or archived data?  Should users be able to access their data right in the ELN interface? Many possibilities and I will highlight one that is available thanks to ACD/Labs SpecX technology and Cambridge Soft's ELN.

For an explanation of what exactly SpecX can do, go here:

http://www.acdlabs.com/products/glob_sol_lab/activex/specx/

As far as demonstrating the integration, I'll just add a couple of screenshots to wet your appetite:

A screenshot of a ¹H NMR and MS spectrum. Note you can freely zoom in or zoom out on different regions of the spectra (click images to enlarge):

By right clicking on the spectrum, you can explore several other options:

For example, you can access all of the data tables available in the ACD/Labs Processor such as tables of assignments, peaks, multiplets, annotations, etc.

Perhaps the coolest feature is if you select the edit option in the drop down menu. This will launch the file in the ACD/1D NMR Processor application so that the user can make modifications to their spectra.

You can also store both the fully processed data as well as the raw data. Of course these can be easily processed and updated in the ACD/1D NMR Processor as well:

Here's a short video (no audio) download of the CS and SpecX integration in action (my japanese readers will be pleased to see the interface is japanese! I apologize to all others, it's all I have at the moment).

Of course there are many other options to tie your analytical data handling in with your ELN practices, I will post more as the months go by. In the meantime, my colleague Andrew Anderson presented at out ENC User Meeting back in April on, "E-Lab Notebook Integration- Leveraging ACD/Labs Tools to Enhance a Paperless Environment". Check it out!

Do you already have a good solution in your organization? Trying to find one?  Feel free to share your stories, challenges, and expectations in the comments section of this post.

Thanks to Arvin and Furuta-san for the images and video!

Where is the Quality? Assumptions vs. Assurance

As I mentioned before in this blog, I have spent the last year and a half visiting with medicinal and process chemists, as well as NMR Spectroscopists who support chemists in an open access environment. I‘ve been trying to understand how NMR software is being used in these environments and how things can be improved in this world.

Of course the convenience of having NMR software at their desk or in their lab is a major bonus. J-Coupler and the ability to produce a multiplet report in journal format for patents and publications is always a huge hit.

A few weeks ago, I blogged about how chemists use NMR and I also questioned the information (or lack thereof) in archived data, and spectra in reports.

I am going to riff a bit about what I have learned about compound registration. In the great majority of medchem groups I have spoken with, a compound is synthesized, an NMR and sometimes an LC-MS is run, and then a registration form is filled out. This registration form consists of a check box where the chemist selects which experiments were run and a statement such as, “the structure is consistent with the data collected”

My question is, what happens with this data? Generally this data will be pasted in a chemist’s lab notebook, or maybe even in their ELN if the organization is that far along. But for the most part this is just data. Whether it’s a printout or an electronic file, it’s generally just the data. Maybe there is a structure attached, and some chemists will diligently assign their spectra to their structure on their printout.

But the issue I see here is that there is no consistency. There is no mandate at the top that is telling the chemists to provide support of a proof of structure. A ¹H NMR and mass value cannot provide a full proof of structure…but how exactly is a simple statement like, “the structure is consistent with the spectrum” validated? Certainly it’s not validated from a paper printout of a spectrum.

I hope people realize that my intention is not to call out chemists. The chemists are not the problem here. Their job at this particular stage is to make compounds and fill out a registration form (forgive me for being overly simplistic). Their job is not to fully assign their data and prove that at least there is nothing in the data that suggests an inconsistency. Again, a ¹H NMR is not going to be a proof of structure. But it was run for a reason, and that reason should be validated.

I’ve talked to many chemists who are very diligent about their handling of NMR data. They will use our software and fully assign their data to a chemical structure and ensure that there is no inconsistency. They do this not because they have to, but for their own piece of mind, and because they believe it is the responsible thing to do. But again, the problem is consistency. For every chemist who is diligent about their NMR data handling, there are several more that don’t do it. In fact, there are perhaps some who run the NMR but don’t look at it. The identity of their compound is confirmed by a mass value, and in the environment they are working that is perfectly acceptable. I personally don’t blame them for not spending the extra couple of minutes to fully assign their data. It’s not their job!

Maybe I am out of place…maybe I am misunderstanding the environment or the reasoning behind not taking this direction. Perhaps this just isn’t the right time to bring this issue up. But in the age of electronic lab notebooks, to me, it seems like a perfect time to discuss and implement this.

But in an industry that is so heavily regulated, it blows my mind that a chemist's decision to register a compound is based on good faith.

Perhaps an expert in this area can clear things up for me and put me in my place. I am simply trying to espouse the benefits of our software. I believe assigning NMR data electronically to structures has major benefits.

P.S. There's another benefit. Imagine chemists in an open access environment fully assigning all of their NMR data and then sending it off to an NMR Spectroscopists. This will create a purgatory database for the NMR spectroscopist to evaluate. Once quality checked the spectroscopists can build a database of all this information and in turn, vastly improve the NMR prediction capabilities within the organization.

Archive This

Maybe this is sufficient:

I disagree. I think this is the way to go:

If you are currently interested in archiving or reporting NMR spectra, I think you should read the following application note. Especially if you have an electronic lab notebook (ELN):

Archiving NMR Data in an Electronic Lab Notebook World