Chemistry Resources Mary Markland Southeast Clinical Campus Librarian UND School of Medicine and Health Sciences 701-293-4173 [email_address] March 29, 2008 This project has been funded in whole or in part with federal funds from the National Library of Medicine,National Institutes of Health, under Contract No. NO1-LM-6-3505.
Provide a brief overview of free databases available through the National Institutes of Health.
NLM SIS http://sis.nlm.nih.gov/
Chemical dictionary/directory file
Two versions: “Lite” & Advanced
379,000 + chemical records
257,000 + structural records
In the Advanced file only
Requires JAVA or CHIME software (free)
Search by chemical name or CAS Registry Number
Click on “search” to retrieve results from the “Lite” version
Use the Advanced button to access the Advanced capabilities
Looking for information on ricin
Click here for access to all the Basic Information on a single web page Describe the general category assigned by a given source to a chemical based on toxicity, use and application, pharmacologic and/or therapeutic category, and status on certain chemical lists. Gives a table of toxicity information by organism tested, test type, dose, effect, and source of the given information A description of a compound’s use and utility, often from MeSH controlled vocabulary Nice table of melting & boiling points, water solubility, vapor pressure, and more Names and synonyms associated with this substance
Search for substructures:
Find the drawn structure embedded in other structures
Do similarity searching
Similarity searching Use this box on the results page or Use the Transfer Structure box to move the structure to the initial search page for ChemIDplus Advanced. Both similarity and substructure searches can be done there.
Results of similarity searching
The 1st result in the similarity list will be the substance searched: it is 100% similar to the query structure.
The following substances will be labeled as to how similar they are to the original:
Transfer the structure to the query page
Do a similarity search for molecules 80% similar to this one
Enlarge this structure and provide access to the 3-D model
Advantages of Advanced…
So, what can ChemIDplus Advanced do that the “Lite” version can’t do?
What is PubChem?
A public repository of electronic representations of small molecules and associated bioactivity assay data
A system of four components:
PubChem Structure Search
Part of the NCBI Entrez search and linking system
http://pubchem.ncbi.nlm.nih.gov/search/ Data Analysis Tools: Differential display of data via structure clustering, structure-activity heat maps and customizable result retrieval tables. http://pubchem.ncbi.nlm.nih.gov/assay/assaycluster.cgi
PubChem Databases Primary Databases: records are provided and updated by Submitters. Derivative Database: Records are created and updated by NCBI.
Composed of Experimental data with Background, Protocols and Results for bioactivity screens of chemical substances described in PubChem Substance
Submitters add “Hard” links to PubChem Substance records and outside sources.
Composed of Substances which may be of known or unknown composition and also may contain a discrete compound or mixtures of compounds.
Submitters add “Hard” links to PubChem BioAssay records and outside sources.
Composed of discrete compounds with known chemical structure.
Summary reports about the known chemical compounds described in PubChem Substance.
Addition of Automated “Soft” Links which can be replicated on PubChem Substance & BioAssay records.
PubChem Substance Record Substance ID Compound ID Link to depositor Synonyms supplied by the depositor Identical substances
Redundancy in PC Substance 13 completely identical records for (-)epinephrine! Non-uniformity in PC Substance
Verify Chemical Data
“ Normalize” and Standardize”
Calculate Properties and Links
PubChem Compound Record
Calculated Properties Links for downloading or viewing the full record
Handling Mixtures Asmatane mist CID for the mixture Each standardized component has its own CID
PubChem BioAssay Record
BioAssay Protocol Description of the BioAssay methods Listing of the data fields provided in the BioAssay
TOXNET: Toxicology & Environmental Information http://toxnet.nlm.nih.gov/
What is TOXNET?
System of databases
Information about toxicology, environmental health, hazardous chemicals, and toxic releases
Developed by the Specialized Information Services division (SIS) of the National Library of Medicine (NLM)
TOXNET is freely available on the web. No subscription, no passwords, no registration, no spam, no pop-up ads.
Five Types of Databases
Chemical Information: ChemIDplus
Toxicology Data Files
One record per chemical
Toxicology Literature Files (bibliographic references):
Toxic Releases (chemicals into the environment):
Data files can be searched individually
Select the database to be searched:
Point the cursor at desired database
Search will be conducted only in the chosen database
Or, search all TOXNET databases for information:
Results are hyperlinked. Click a link to see results from that database:
Hazardous Substances Data Bank (HSDB)
Human and animal toxicity
Safety and handling
Human health effects
Emergency medical treatment
Physical & chemical properties
Environmental fate & exposure
Uses: therapeutic, business, etc.
Click here to access this record in PubMed Search terms appear in red Terms in blue are hyperlinks. Click to retrieve more records with those terms.
TRI: Toxics Release Inventory
EPA information regarding the release of certain toxic chemicals
Reporting is mandated by law and does not cover all industries or all businesses
Release years 1987 – 2005 data available in TOXNET
Searching TRI Search by chemical name or CAS Specify release amount and type Select a year or years Search by facility name Search by location Search by SIC code
Searching for Jamestown, ND
This button provides mapping capabilities
Use it to see where the releases in question were located