Discussion

We've been looking into chemistry oriented electronic lab notebooks (ELNs) at Cornell and are now being pleasantly encouraged by what we are seeing available for academic situations, as compared to even a couple years ago. In addition to support for chemical structure and substructure searching (and indexing) within the notebook, we've also been interested in: - ability to import chemically intelligent structure files from external drawing software (via molfiles), - stoichiometric calculation support, - import and view characterization data such as spectra files (and TRC plates, which are treated as images), - ability to export customized text-based outputs (for publication) - ability to export experimental metadata and datafiles in machine-readable form (to be interoperable with other systems, including potential for data repositories) - most notebooks that we've looked at meet legal requires for digital signatures, - access, security and backup considerations Some Chemistry Aware ELNs being marketed for Academic Labs: ~ these are currently all Cloud-based, pricing per user month or year Mbook by Mestralab, <a href="http://mestrelab.com/software/mbook/">http://mestrelab.com/software/mbook/</a> ~ same company that provides Mnova used by many many labs for spectra analysis and links directly between these systems ~ very nice data handling for chemists and for general concerns One-Click Chem ELN from Dotmatics, <a href="http://www.dotmatics.com/one-click-eln/">http://www.dotmatics.com/one-click-eln/</a> ~ this company formerly supported pharma industry so the data handling is excellent ~ one-click option streamlines workflow and pricing for academics, this is being trialled on various campuses ~ also has One-Click Bio ELN in development for cross-disciplinary labs that need a variety of functionality eNovalys Book, <a href="http://www.enovalys.com/book">http://www.enovalys.com/book</a> ~ quite detailed for total synthesis type chemistry, data and metadata fully exportable Elements from Perkin-Elmer, <a href="http://go.perkinelmer.com/Q315-ACSFall-Elements-LP">http://go.perkinelmer.com/Q315-ACSFall-Elements-LP</a> ~ from the makers of ChemDraw, very user-friendly for chemists, a bit lightweight with data handling and getting it back out (HTML) ~ however, they are considering a more robust research version for academic labs based on their successful industry enterprise system ~ review on ChemJobber: <a href="http://chemjobber.blogspot.com/2014/10/product-review-perkin-elmers-elements.html">http://chemjobber.blogspot.com/2014/10/product-review-perkin-elmers-elements.html</a>

As stated, CAS Registry Numbers are proprietary. There are many available out in the world although very few of these are authoritative. Most have been copied from other places, including most of those available through CACTUS. In addition to respecting intellectual property, two things are particularly relevant in the context of using this information: 1- CAS RNs as numeric strings do not contain any encoded information about the chemical entities in these registry records, none. If the number is not associated with additional information about the compound, such as structure or name, there is no way to know anything about the substance. 2- There is not necessarily one CAS RN per one discreet compound or defined substance and it is not a reliable 'identifier' in this way, although it has been forced into that role to meet a community need for a robust identifier (more discussion in next Module). Why there is NOT one CAS per compound is due to several reasons, including: A. The criteria by which CAS assigns chemical entities to records and IDs is not public knowledge and has been primarily driven by what the industry needs to register and what characterization is published in the literature (articles, patents, etc.) B. As more characterization data becomes available for many compounds, overlap occurs between some records and some RNs are determined to be obsolete and deleted. CAS keeps track of these so a CAS database user can find information on any former CAS RN that may have been published. C. How databases, and chemists, and informatics applications, define chemical entities varies and thus the map of CAS to entity will vary depending on which you are using and where the CAS RN data was from Authoritative sources of CAS RNs include: 1. CAS databases, which can be searched (at some cost) via SciFinder and STN, <a href="http://www.cas.org/">www.cas.org/</a> 2. Common Chemistry (from CAS), just under 8k CAS numbers, openly searchable although the associated structures are image only, <a href="http://www.commonchemistry.org/">http://www.commonchemistry.org/</a> 3. Wikipedia, which a version of Common Chemistry by arrangement, look for the green check marks in the ChemBoxes for authoritative numbers

Every chemical structure database is different - you'll reasonably often find compounds that show up in one but not another. Of course, in real life, if you go looking for a compound that isn't showing up as you expect, there's a chance that you're looking for the wrong compound. If one of these compounds isn't showing up in PubChem or ChemSpider, you might think about what you might do next if you were actually sent looking for this compound. An optional extra exercise: can you use these DBs to find closely related compounds, just in case by some miscommunication you were given the wrong structure to start with?

e-Lab Notebooks are becoming more common but are far from ubiquitous. I can think of a handful of universities that even offer them as regular software (eg. my alma mater UW-Madison now offers all researcher LabArchives), but that doesn't mean that every lab on those campuses uses them. Industry is a bit farther ahead on this in terms of e-lab notebook adoption (pharma research being an early adopter). What's unfortunately more common is individual labs/researchers adopting one-off solutions; this can help in the short term but you NEED to make sure that those records are still available in the long term. As far as functionality, it's spotty in chemistry. General e-lab notebooks often fall flat on the features that chemists want, such as structure drawing and structure searching. More relevant to this class may be a digital way to capture the details about how you run code (iPython Notebook is an example), combined with a good version control software (like Git/GitHub). We're at a transition point in this area, so expect adoption to increase going forward. There are still many options for digital notebook technologies available and we're only starting to see some clear winners and losers in this area. That means that until things are settled, your notebook could be at risk in the event that a company folds. So the short answer is yes, you can get a digital lab notebook but you'll want to find ways to minimize the risk of potentially losing all of your notes going forward. And as always, make sure your research advisor is on board before you jump into a new technology.