Category Archives: Chemical Information issues

Quality Data for Safer Experiments CHAS Chat

On March 11, 2021, Leah McEwen, chemistry librarian at Cornell University and Ralph Stuart, Chemical Hygiene Officer at Keene State College led a discussion on “Quality Data for Safer Experiments”.

We will talk about about finding and assessing the quality and relevance of chemical safety information sources. We will also discuss supporting researchers and educators with the emerging publication requirements for safety information.

Three take-aways we see from this discussion are:

  1. Safety considerations are part of your experimental method.
  2. You need quality data for risk assessment.
  3. Safety precautions should be described in your publications, both research and educational.

Key Web Sites mentioned:

In the video:

In the discussion:

Chat Comments during the discussion:

From Dave Finster: Love the video. A quick reference to PubChem in the video?
From Ralph Stuart: PubChem = National Library of Medicine
From Rob Toreki: I have an interesting insight about DMSO we did not know and only found out about AFTER the accident
From Rob Toreki: Exactly on stability decomp

From Samuella Sigmann: https://www.rxlist.com/dmso_dimethylsulfoxide/supplements.htm
From Ralph Stuart: DMSO is popular as a home remedy
From Ralph Stuart: https://www.thefrugallife.com/dmso.html

From Rob Toreki: Last I heard Brethericks is no longer being updated.
From Rob Toreki: They were searching for a new editor a couple years back
From Ralph Stuart: Yes, Brethericks is a historical document at this point with still useful information
From Rob Toreki: Agreed

From Neal Langerman: OPRD was the first ACS journal to require safety information along w/ a manuscript. The requirement preceded the ACS requirement and was used to develop the ACS requirement.

From Ralph Stuart: It occurs to me that DMSO is a good example of the impact of context on risk assessment. What level of students should be exposed to research? General chemistry, organic chemistry, research chemists?
From Ralph Stuart: In my remark, research = literature research. i.e. SDS vs LCSS vs process safety literature references

From Rob Toreki: Hah saw that firsthand 25 years ago now
From Rob Toreki: Took out the hotplate but nothing else in the hood luckily and blast shield was in place

From Grace Baysinger: https://safescience.cas.org/ – Pistoia Alliance Chemical Safety Library (CSL) which is hosted by CAS is a crowd-resourced tool for users to report hazardous reactions. Recent post: https://www.ccdc.cam.ac.uk/Community/blog/safety-and-community/
From Samuella Sigmann: Pubs has made the chapter freely available as a pdf
From Ralph Stuart: The URL to the chapter is http://pubsapp.acs.org/paragonplus/submission/ACS_Guide_to_Scholarly_Communication_1.3_Communicating_Safety_Information.pdf

From Neal Langerman: Ralph, Leah – the title of today includes the word “quality” In the context of the mass of information Leah just discussed, will you address “quality assessment”?
From Ralph Stuart: Thanks for the question Neal, that’s part of why we wanted to do today’s session – to start that discussion

From Samuella Sigmann: Still requires presenting data and information in the educational setting where you can teach this.

From Grace Baysinger: https://guides.library.stanford.edu/lab-safety – This is a guide that I’ve been working on for Stanford users. Contains a combination of licensed and free resources. I’m still working on the search strategy page. Tried to group resources using RAMP for part of this guide.
From a very minimal use of vivid color with respect to the acronyms – good reinforcer of what everything stands for
From Ralph Stuart: Color is coming to the video in the final version

From M Sabolefski: Please explain the FAIR acronym again
From Ralph Stuart: FAIR = FAIR data are data which meet principles of findability, accessibility, interoperability, and reusability
From Ralph Stuart: https://en.wikipedia.org/wiki/FAIR_data

From Rob Toreki: Question about data and provenance we can think about
From Rob Toreki: The purple book is the UN GHS model standard
From Rob Toreki: The GHS is only a model and implementation across the world varies significantly
From Ralph Stuart: GHS breaks Leah’s first rule of considering the situation first before gathering data
From Ralph Stuart: It is a hazard banding system rather than a risk or control banding system, although there are controls suggested in the system

From Samuella Sigmann: I would add the wayback machine for broken links.

From Ralph Stuart: Leah and Sammye are leading a 4 hour workshop on meeting the ACS safety publication requirement on April 2. See http://dchas.org/2021/01/22/spring-2021-professional-workshops/ for more information

From Neal Langerman: Leah and Ralph, – as always you are an amazing team. Thank you for this.
From M Sabolefski: thank you, this has been a worthwhile seminar/chat
From mwilhelm: This was so very helpful. Thank you for offering this topic.
From CJakober: Many thanks Leah, Ralph, et al!
From James Wright: Thanks Ralph and Leah!
From Pat Ceas: Great information, thank you!
From rossy: Thank you very much to Leah and Ralph
From Glenda Pons: Thank you!
From Marta Gmurczyk: Thank you. Great sessions.

Update on Chemical Safety Information in PubChem

PubChem LCSS Update – March 2017

The PubChem database, hosted by the US National Library of Medicine, includes a wide variety of data on over 90 million chemical compounds. PubChem’s  goal  is to make this data accessible to chemists, chemical safety professionals, chemical educators and others working with laboratory chemicals. Data are reported from multiple sources, allowing users to compare and determine the best use of this data in their work. The data are also organized to facilitate downloading in a variety of formats as well via programmatic access for reuse in local software applications.

In addition to structural, physical and toxicological raw data, the PubChem collection includes chemical safety information from national and international agencies. For human browsers, this chemical safety information in PubChem is organized into a data view based on the Laboratory Chemical Safety Summary (LCSS) format described in “Prudent Practices in the Laboratory“.  This LCSS view chemical and physical properties and safety information for compounds that have Globally Harmonized System designations publicly available. The number of records with this chemical safety information has increased from 3000 in 2015 to more than 103,000 today. LCSS data provided by PubChem are intended to support, but not replacelaboratory risk assessments, Safety Data Sheets and institutional guidance for safe laboratory practices and procedures.

Notably, the data compiled by PubChem includes safety information beyond that generally provided by Safety Data Sheets. This additional information is found in sources such as the NIOSH Pocket Guide, CAMEO and European Chemicals Agency, among others. There are also specific incompatible reactions reported from the  Hazardous Substances Data Bank (HSDB), sourced from Sigma Aldrich Safety Center notes, the National Fire Protection Association Fire Protection Guide to Hazardous Materials, Sax’s Dangerous Properties of Industrial Materials, Bretherick’s Handbook of Reactive Chemical Hazards and others.

LCSS data can be viewed online, or downloaded either by individual compound or in bulk.  In this way, PubChem information can be used to support electronic safety tools such as institutional chemical inventory management systems or laboratory-specific personal protective equipment guidelines. More information about this feature can be found here.

Traffic to the safety information in PubChem has increased over 80% in the past year. The PubChem staff are interested in continuing to improve the usability and accessibility of this information to the laboratory community. To this end, representatives of the ACS Divisions of Chemical Information (CINF) and Chemical Health and Safety (CHAS) are working with the PubChem staff to identify additional sources and uses for health and safety data. Efforts are also underway to improve annotation of the data and enable more specific data retrieval options.  We welcome  ideas for organization and presentation of the data. To participate or provide comments, contact the CINF safety representative, Leah McEwen at lrm1@cornell.edu or the CHAS secretary, Ralph Stuart at ralph.stuart@keene.edu.

Using Public Information to Support Chemical Safety

Laboratory use cases for chemical safety information
Ralph Stuart

Risk assessment and crisis management in the research laboratory using online resources: A EH&S perspective
Neelam Bharti

UCal Chemicals: An overview of growing challenges
Chris Jakober, Russell Vernon, Phillip Painter

Chemical Safety and Hazard Information in PubChem
Jian Zhang

Semantic annotation of the LCSS in PubChem
Gang Fu

GHS and NFPA diamonds: How they can be useful
Roger Sayle

iRAMP & PubChem
L
eah McEwen

Chemical Classification ClassyFire Applications in EHS
Yannick Feunang

Surveying the chem safety landscape
Ralph Stuart

Related CHED and CINF presentations:

Co-developing lab safety and chemical information skills
Ralph Stuart and Leah McEwen