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.

Goals Chemisty ChemID plus PubChem Toxnet HSDB Toxline TRI Others Provide a brief overview of free databases available through the National Institutes of Health.

Chemisty

ChemID plus

PubChem

Toxnet

HSDB

Toxline

TRI

Others

NLM SIS http://sis.nlm.nih.gov/

Chemical Information http://sis.nlm.nih.gov/chemical.html

http://sis.nlm.nih.gov/chemical.html

ChemIDplus 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)

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)

Searching ChemIDplus 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

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

Molecular formula

ChemIDplus Advanced

Structure Searching! Draw structures Search for substructures: Find the drawn structure embedded in other structures Do similarity searching

Draw structures

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:

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:

Added functionality 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

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? 3-D structures Structure-based searching Similarity searching

So, what can ChemIDplus Advanced do that the “Lite” version can’t do?

3-D structures

Structure-based searching

Similarity searching

http://pubchem.ncbi.nlm.nih.gov

What is PubChem? A public repository of electronic representations of small molecules and associated bioactivity assay data A system of four components: PubChem Substance PubChem Compound PubChem BioAssay PubChem Structure Search Part of the NCBI Entrez search and linking system

A public repository of electronic representations of small molecules and associated bioactivity assay data

A system of four components:

PubChem Substance

PubChem Compound

PubChem BioAssay

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.

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 Links

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

PubChem Compound Standardize Structures Verify Chemical Data “ Normalize” and Standardize” Calculate Properties and Links

Standardize Structures

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.

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 HSDB CCRIS GENE-TOX IRIS ITER LactMed Toxicology Literature Files (bibliographic references): TOXLINE DART Toxic Releases (chemicals into the environment): TRI TOXMAP Other Databases: Haz-Map Household Products ToxTown

Chemical Information: ChemIDplus

Toxicology Data Files

One record per chemical

HSDB

CCRIS

GENE-TOX

IRIS

ITER

LactMed

Toxicology Literature Files (bibliographic references):

TOXLINE

DART

Toxic Releases (chemicals into the environment):

TRI

TOXMAP

Other Databases:

Haz-Map

Household Products

ToxTown

Data files can be searched individually Select the database to be searched: Point the cursor at desired database Click

Select the database to be searched:

Point the cursor at desired database

Click

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 Antidotes Physical & chemical properties Interactions Environmental fate & exposure Manufacturers Uses: therapeutic, business, etc.

Human and animal toxicity

Safety and handling

Human health effects

Emergency medical treatment

Antidotes

Physical & chemical properties

Interactions

Environmental fate & exposure

Manufacturers

Uses: therapeutic, business, etc.

Using TOXLINE

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

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

Mapping results This button provides mapping capabilities Use it to see where the releases in question were located

This button provides mapping capabilities

Use it to see where the releases in question were located

ToxSeek http://toxseek.nlm.nih.gov

Household Products Database http://hpd.nlm.nih.gov/