A series of high profile laboratory accidents over the last 7 years has increased the academic community’s awareness of the importance of risk assessment in laboratories, both teaching and research. Because of the many different chemicals used in laboratory work, these risk assessments require ready access to safety information for a large number of chemicals. In order to provide researchers, educators and students with electronic access to chemical health and safety information, PubChem provides a “Laboratory Chemical Safety Summary” (LCSS) data view for more than three thousand chemicals commonly encountered in laboratories (https://pubchem.ncbi.nlm.nih.gov/lcss/).
The LCSS contains pertinent chemical health and safety data for a given PubChem Compound record, based on the format described by the National Research Council in “Prudent Practices in the Laboratory: Handling and Management of Chemical Hazards”. Information contained in the LCSS is a subset of the PubChem Compound Summary page content, and includes information on flammability, toxicity, exposure limits, exposure symptoms, first aid, handling, clean up and more. These data are provided by various data contributors, including authoritative agencies such as the U.S. National Institute for Occupational Safety and Health (NIOSH), the Occupational Safety and Health Administration (OSHA), and the International Labor Organization (ILO). Of special interest in this collection is specific “Stability and Reactivity” information, which lists known chemical reactions between the chemical of interest and other chemicals and chemical classes. This information often extends beyond that found on Safety Data Sheets for the chemical of interest.
LCSSs are available for PubChem Compound records which have GHS (Globally Harmonized System of Classification and Labeling of Chemicals) hazard classification information from PubChem’s data contributors. PubChem is actively recruiting this GHS information from additional contributors in order to expand its LCSS coverage. If a PubChem Compound record has an LCSS, the link to view it is provided at the top of the Compound Summary page of that compound under the heading “Safety Summary”. In addition, one can get the complete list of chemicals with an LCSS by visiting the PubChem LCSS project webpage (https://pubchem.ncbi.nlm.nih.gov/lcss/) or by using the PubChem Classification Browser (https://pubchem.ncbi.nlm.nih.gov/classification/). If desired, LCSS data can be downloaded from the LCSS page for each compound, or in bulk from the PubChem LCSS project webpage.
Introduction
A series of high profile laboratory accidents over the last seven years has increased the academic community’s awareness of the importance of chemical risk assessment in laboratories, both teaching and research. These accidents are described in two reports from the US Chemical Safety Board1,2 addressing chemical safety in education settings and research labs. Approaches to laboratory chemical risk assessment have been suggested by the American Chemical Society’s Committee on Chemical Safety.3 Many different chemicals are used in laboratory work and these risk assessments require ready access to safety information for a large number of chemicals.
In order to support this risk assessment process by providing researchers, educators and students with electronic access to chemical health and safety information, PubChem4-8 (https://pubchem.ncbi.nlm.nih.gov) provides a “Laboratory Chemical Safety Summary” (LCSS) data view (Figure 1) for thousands of chemicals (https://pubchem.ncbi.nlm.nih.gov/lcss/). This format is intended to supplement the more traditional MSDS by providing a concise view of data types most relevant to use of chemicals as described in the OSHA lab standard.9
This conference paper describes PubChem’s LCSS data view, including compound coverage, data contents, web accessibility, and download-ability. This paper also describes ongoing community efforts to apply the LCSS to build chemical safety information systems at academic institutions.
PubChem LCSS Coverage and Content
LCSSs are available for PubChem Compound records that have hazard classification information based on the Globally Harmonized System of Classification and Labeling of Chemicals (GHS)10. This system is an international standard that establishes technical criteria for classifying chemicals according to their health, physical, and environmental hazards (Figure 2). In addition, GHS defines hazard communication requirements for product labels and safety data sheets. Thus, the GHS provides a global basis for the harmonization of rules and regulations on hazardous chemicals, thereby improving regulatory efficiency and facilitating international trade. The GHS is still in the “roll-out” stage in the U.S. and thus some chemical suppliers have not fully updated their information to meet GHS requirements.
Figure 2. GHS pictograms and hazard classes (provided by Ralph Stuart)
Click Image for Higher Resolution
As of October 2015, PubChem has collected GHS hazard classification information for more than three thousand compounds, primarily from two data sources: (1) the International Chemical Safety Cards (ICSC) database11 at the International Labour Organization (ILO) and (2) Regulation (EC) No. 1272/200812,13 (a European Union regulation for classification, labelling and packaging of substances and mixtures). A third source of GHS classification information from the National Institute of Technology and Evaluation in Japan is being processed at the time of this writing.
When a PubChem Compound record has an LCSS, the link to view it is provided at the top of the Compound Summary page of that compound under the heading “Safety Summary” (Figure 3). One can obtain the complete list of chemicals with an LCSS by visiting the PubChem LCSS project webpage (https://pubchem.ncbi.nlm.nih.gov/lcss/) or by using the PubChem Classification Browser (https://pubchem.ncbi.nlm.nih.gov/classification/) (Figure 4).
Figure 4. A partial screenshot of the classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/). The complete list of compounds with an LCSS page can be obtained by choosing the following options: PubChem Compound Table of Contents (ToC) ® Compound ® Safety and Hazards ® Hazards Identification ® GHS Classifications.
Click Image for Higher Resolution
The LCSS contains chemical-specific health and safety data for a given PubChem Compound record, based on the format described by the National Research Council in “Prudent Practices in the Laboratory: Handling and Management of Chemical Hazards”.14 Figure 5 shows information contained in the LCSS and its data sources. The LCSS includes information on flammability, toxicity, exposure limits, exposure symptoms, first aid, handling, clean up and more. These data are provided by various data contributors, including authoritative agencies such as the U.S. National Institute for Occupational Safety and Health (NIOSH), the Occupational Safety and Health Administration (OSHA), the Environmental Protection Agency (EPA), the National Oceanic and Atmospheric Administration (NOAA), and the ILO.
Figure 5. Data contents included in the PubChem Laboratory Chemical Safety Summary (LCSS) at the time of writing.
Click Image for Higher Resolution
Of special interest in the PubChem LCSS collection is specific “Stability and Reactivity” information. These entries list hazardous chemical reactions that have been reported between the main chemical in the record and other chemicals and chemical classes. This information is of varied specificity, but often extends beyond that found on Safety Data Sheets (SDS) for the chemical of interest.
Viewing and Using Data in PubChem LCSS
No one source contains all relevant safety data reported for a chemical and the compiled view of data from several sources provided by the LCSS is convenient and reduces time searching. However, there are many caveats to working with chemical data from any source, especially in an aggregated system where the information is usually cited as in the original source. It is important for the user to verify that the data they are viewing pertains to the form of the chemical that they care about. They may need to review multiple sources to ascertain the extent of data variability.
Chemical information notation varies among sources, which complicates further validation and analysis of the data. For example with names or name-structure associations: general entries on acetic acid may be further specified in some sources as the tri-hydrate form; the structure for formaldehyde may retrieve data about the gas form as well as the saturated water solution, formalin, which may or may not also contain methanol as a stabilizer. Units, conversions and conditions for measurement also vary widely, such as boiling points reported in deg C, or ºF, at mmHg or atm, etc. All of these variables impact the utility of the data for any purpose.
Direct access to the source of each data entry in the PubChem LCSS is provided by a link next to the data presented. This makes establishing the credibility of the data easy. This feature is important because PubChem only aggregates and reports the information from its sources and does not check accuracy of most properties. For example, for some chemicals, different flashpoints are reported from different sources. These differences may represent different protocols for determining the property at hand, or they may represent errors in the data collection, or perhaps just a typo in the original source. It is the responsibility of the user of the data to make an assessment of whether the data presented is of sufficient accuracy and appropriate for their purpose.
LCSS data can also be downloaded helping to enable additional annotation of the data to specific procedures in place at an institution. Pilot projects for using LCSS data to improve local chemical inventory systems are underway at several campuses in the U.S. There are many options for accessing the data, including downloading records from the LCSS page for each compound in several formats (JSON, XML, etc.), or in bulk as an ftp from the PubChem LCSS project webpage. Additional relevant information contained in the PubChem Compound database, such as molecular weight, molecular formula, etc., can be accessed programmatically through a Representational State Transfer (REST)-like interface called PUG-REST15, allowing one to automate the local LCSS annotation process with additional data from PubChem.
FUTURE Directions
The most immediate priority for improving the PubChem LCSS collection is increasing the number of chemicals covered. This will be driven by identifying sources of GHS classification data for chemicals. The most likely sources for such data are chemical suppliers, particularly for those chemical suppliers who specialize in laboratory chemicals. Supplier generated safety sheets may not cover all data types relevant to laboratory use as part of the routine process of bringing a chemical to market. For this reason, it will also be important to continue expanding the number and diversity of additional authoritative public data sources (for example, government agencies and professional organizations similar to those currently represented in the database) to further enrich the LCSS data view.
A second area of development is looking into opportunities to improve the annotation and classification of the health and safety data in PubChem LCSS. Currently much of the information valuable for risk assessments is locked in strings of text from the original sources. Efforts are underway to develop vocabularies for richer indexing of entries by relevant safety concepts, such as exposure routes and incompatible storage conditions. Chemical structure classifications are in development to support reactivity fingerprinting and predicted incompatibilities.
The third area for improving PubChem LCSS usability is the development of documentation and materials that describe how to most effectively use the information available. Supporting these services is an ongoing collaborative effort among academic librarians, educators, health and safety professionals and information scientists. Such collaborations are actively underway in the work of several professional organizations, particularly the technical divisions of the American Chemical Society that represent those stakeholders. The collaboration of these professional communities can help make the PubChem LCSS data an important asset to support laboratory safety in the 21st Century.
Disclaimer
The LCSS provided by PubChem is intended to augment, not replace, safe laboratory practices and procedures for chemical information, such as those found in chemical inventory management systems or laboratory-specific personal protective equipment information. It is the responsibility of PubChem users to determine applicability of or gaps in the LCSS information to support safe use of a chemical. In addition, laboratory risks can arise not only from the specific chemicals used, but also from 1) changes in the concentrations and quantities of those chemicals, 2) new chemicals that are produced, 3) energy sources that occur during a laboratory process, among other variables.
Although we are not aware of any limitations or restrictions on the reuse of PubChem LCSS data, we are not able to give unconditional permission for reuse and advise consultation with intellectual property experts when reusing this data. For more information, please see the disclaimer available at https://www.ncbi.nlm.nih.gov/home/about/policies.shtml.
AUTHOR INFORMATION
Corresponding Author: Sunghwan Kim
*E-mail: kimsungh@ncbi.nlm.nih.gov
Acknowledgments
This work was supported in part by the Intramural Research Program of the National Library of Medicine, National Institutes of Health, U.S. Department of Health and Human Services.
REFERENCES
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2. United States Chemical Safety Board. Texas Tech University Laboratory Explasion. Washington, DC, 2011. http://www.csb.gov/assets/1/19/CSB_Study_TTU_.pdf (accessed Oct. 21, 2015).
3. American Chemical Society, Committee on Chemical Safety, Hazard Identification and Evaluation Task Force. Identifying and Evaluating Hazards in Research Laboratories. Washington, DC, 2015. http://www.acs.org/content/dam/acsorg/about/governance/committees/chemicalsafety/publications/identifying-and-evaluating-hazards-in-research-laboratories.pdf (accessed Oct. 21, 2015).
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8. Bolton, E. E.; Wang, Y.; Thiessen, P. A.; Bryant, S. H. PubChem: integrated platform of small molecules and biological activities. In Annual Reports in Computational Chemistry, Wheeler, R. A.; Spellmeyer, D. C., Eds.; Elsevier: 2008; Vol. 4, Chapter 12, pp 217-241.
9. Toxic and Hazardous Substances: National Research Council Recommendations Concerning Chemical Hygiene in Laboratories (Non-Mandatory). 29 CFR $1910.1450 Appendix A. Occupational Safety and Health Administration, Washington, DC, 2012. https://www.osha.gov/pls/oshaweb/owadisp.show_document?p_table=STANDARDS&p_id=10107 (accessed Oct. 21, 2015).
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Comments
Educators, LCSS and PubChem
Hi Sunghwan and All,
I am going to ask two sort of different but related questions, with the first not directly related to the article, but to PubChem.
I suspect there are people on this list who are not familiar with PubChem. Not a single student in my Cheminformatics OLCC class was exposed to it in their studies, although several had discovered it on their own. Would it be possible to give a brief description of what PubChem is, what its mission is, and without writing a book, what educators should know about it?
My second question, which you may not be able to answer, deals with the NRC, the National Academy and LCSS. I understand the National Academy was founded by congressional charter. When I look at Prudent Practices I see Appendix B: LCSS for many compounds, but also in Appendix A: The OSHA Laboratory Standard 29 CFR1910.1450. My question is hard to articulate, but are the NRC LCSS legal documents in any way? Or should I say, more "authoritative", then say a commercial companies MSDS or SDS? And if so, is this transferred to PubChem LCSS.
These questions are actually related, and it is easy to see how students and teachers may think that anything in PubChem (LCSS and otherwise), which is posted in a website that ends with *.gov, has the endorsement of the government. Can you comment on this?
Thank you for sharing this rich and powerful resource with us.
Cheers,
Bob
Legal status of Chemical Safety Information
>are the NRC LCSS legal documents in any way? Or should I say, more "authoritative", then say a commercial companies MSDS or SDS? And if so, is this transferred to PubChem LCSS.
Unfortunately, there isn't an easy "common sense" reasoning to answer this important question, but the short answer is no, there is no legal standing to the LCSSs, either those from the National Research Council or from PubChem.
My reason for this answer is based on 20 years of experience, including being part of 3 or 4 OSHA inspections, 4 or 5 EPA inspections, and other assorted regulatory interactions. The legal requirement, as established by OSHA's lab standard with a variety of nuances, rests on the employer to provide appropriate information and training to its employees when they work with hazardous chemicals in labs. (Determining the employee status of many academic lab workers, including students, teaching assistants and research assistants can be complicated, so I'll skip over that.)
The supplier of the chemical provides Safety Data Sheets to assist with the employer's duty, but there is no legal requirement that the SDS's be correct or useful. That's one reason that the GHS and the PubChem LCSS's based on it are so important - they collect the data that an employer should use to determine whether the SDS information is correct and appropriate for a particular use of a chemical. PubChem also includes data for a much wider range of chemicals that the NRC was able to. Because PubChem is simply collecting and transmitting data from well-identified sources and not interpreting its meaning, there is no new legal responsibility associated with its work.
I would note that in addition to Prudent Practices referring to the OSHA Lab Standard, as Dr. Belford points out, the OSHA Lab Standard refers to Prudent Practices in an optional Appendix to the Lab Standard; it's kind of a mutual admiration relationship, but OSHA is the organization with the legal authority to establish and enforce regulations related to workplace use of chemicals. The National Research Council is simply an scientific advisory organization to the government and other paying customers.
>These questions are actually related, and it is easy to see how students and teachers may think that anything in PubChem (LCSS and otherwise), which is posted in a website that ends with *.gov, has the endorsement of the government. Can you comment on this?
I understand this point and the challenges it raises. This mistaken understanding is based on two factors:
1)the information literacy challenge of understanding the context of the information being presented (this challenge applies to all web sites, but is heightened with government sources), and
2) a general ignorance of the legal responsibilities that an organization assumes when it buys a hazardous chemical. Just because someone will sell you a chemical doesn't mean that you know how to use it legally.
The recent sequence of methanol demonstration fires is making misunderstanding of the legal issues associated with lab chemical use more problematic. See the C&EN Safety Zone Blog for information about last week's fire and previous fires and their regulatory impacts.
Let me know if you have any questions about this.
- Ralph
Ralph Stuart, CIH, CCHO
Chemical Hygiene Officer
Keene State College
ralph.stuart@keene.edu
Post of response from Rob Toreki
MSDS's were fairly notorious for inaccurate and incomplete information, primarily because the HazCom Standard (29 CFR 1910.1200) had few mandatory elements that defined what kinds of resources the author of the sheet should consult. Other than listing authoritative sources for carcinogenicity determination, it merely had a requirement for "hazard determination" that relied on the author somehow stumbling upon the information
The recent update to the HCS (2012) which took us from MSDS to SDS has a number of mandatory elements that define how the hazard *classification* process is done. In fact, Appendix A says at A.0.1.2 says "For many hazard classes, the criteria are semi quantitative or qualitative and expert judgment is required to interpret the data for classification purposes." In short, OSHA has kicked the process of searching for and reporting the data up a couple of notches. For example, compare the in HCS 1994 Hazard Determination was one appendix with 4 short paragraphs:
http://www.ilpi.com/msds/osha/preGHS/1910_1200_APP_B.html
versus HCS 2012, in which it's two mandatory and one non-mandatory appendices, all of which are long and rigorous:
http://www.ilpi.com/msds/osha/1910_1200_APP_A.html
http://www.ilpi.com/msds/osha/1910_1200_APP_B.html
http://www.ilpi.com/msds/osha/1910_1200_APP_F.html
While MSDS's were always required to be "correct", the issue was that "correct" was in the eye of the beholder. I'm unaware of any OSHA citations for an inaccurate sheet, but I am aware of at least two lawsuits that had at their crux the accuracy of the information on the MSDS. In contrast, the current regulation establishes very hard criteria for "correct", and inaccurate information is indeed listed as a citable offense under CPL 02-0-079 ("Inspection Procedures for the Hazard Communication Standard", in short, the OSHA field inspector's manual). See http://www.ilpi.com/msds/osha/cpl0202079.html#sds_g , in particular, paragraph (1)(o) which includes:
"The information supplied on the SDS must be accurate. The company preparing the SDS must accurately report their classifications which must be based on valid scientific data."
CPL-02-0-79 also has an Appendix H which inspectors can use to determine completeness of an SDS, although it does not deal with accuracy: http://www.ilpi.com/msds/osha/cpl0202079_apph.html
That said, I'm not holding my breath for the accuracy of SDS's to improve dramatically over MSDS's, but the regulatory switch to a hazard classification system definitely encourages it, particularly as we move farther into the modern information age and resources like the LCSS's become available to SDS authors.
Rob Toreki
PubChem is a chemical information resource at the U.S. NIH
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical information resource developed and maintained by the U.S. National Institutes of Health (NIH). It collects chemical information from more than 360 data contributors in more than 30 countries, including university labs, government agencies, pharmaceutical companies, chemical vendors, journal publishers, and other database groups. The collected information is provided to the public free of charge.
PubChem contains a broad range of information on more than 60 million unique compounds, including chemical and physical properties, biological activities determined in in vitro or in vivo assay experiments, toxicological data, safety and hazards information, biological pathways (and proteins and genes) involved, relevant scientific articles and patent documents, and many others. Arguably, PubChem is the most popular “public” database with the “largest” corpus of chemical information. (For comparison, The ACS Chemical Abstract Service (CAS) registry contains 102 million unique chemicals).
For this reason, PubChem plays a key information resource that serves biomedical research communities in many areas, including cheminformatics, chemical biology, and medicinal chemistry. Currently, PubChem routinely receives more than 150 thousand users a day. According to the most recent statistics, we had 289 thousand users a day on average in October 2015. PubChem is the 5th most popular chemistry website (following the American Chemical Society, SigmaAldrich, Royal Society of Chemistry, and chemistry.about.com), although it is not well known to those who are in traditional chemistry fields (that is, physical, organic, inorganic, and analytical chemistry) (see this website: http://www.alexa.com/topsites/category/Top/Science/Chemistry).
Abstracts?
Since I have never tried this resource, I decided to look up something at random. I looked up Glyphosate since it is in a lot of public media these days and the state of California has recently reclassified it.
I must have missed something since no abstract came up for the first article. The only thing which I could bring up in that area was just citation information. There were links to other resources on this topic and some of them were pretty good. Is there any requirement for the abstract?
I teach online only these days and do not have as much library access as I would like.
Thanks
Would you please clarify your question?
I am not sure what you mean by “no abstract” for “the first article”, so would you please clarify your comment/question? By the way, if you need general information on the PubChem project, I recommend you to read our recent paper published in Nucleic Acids Research (https://doi.org/10.1093/nar/gkv951). This paper and all other papers published by PubChem are open-access, because we comply with the NIH’s public access policy.
By first article, I am
By first article, I am referring to the first article pulled up in a search for "Glyphosate". By "no abstract" I mean that no abstract came up for that article. Is that common? I know that there are journals without abstracts. Are there requirements for this in the database?
Thanks
Richard
Chemical information beyond literature information
Thank you for your clarification. I think I understand what you mean. It seems to me that you are thinking PubChem is a (sort of) literature database, similar to SciFinder, WebOfKnowledge, or Scopus, which one can search for scientific articles of interest. However, PubChem provides “comprehensive” information on chemicals, including chemical and physical properties, biological activities, toxicology, safety and hazards information, patent, and many others, as well as relevant scientific articles. That is, the scope of data contained in PubChem is beyond typical literature/abstract databases.
When you search PubChem for “glycosate” as a query, the search will return a list of “compounds”, not “scientific papers”, that are relevant to the query. That is the reason why you don't see any abstracts (or articles). For each compound returned, we provide a Document Summary (or DocSum) which displays the compound’s 2-D image with some relevant data (e.g., chemical name, molecular formula, and so on).
Please let me know if you have any other questions/comments about my explanation. Thank you.