Frequently Asked Questions about TOXNET
- Question: What years do TOXLINE and DART cover?
Question: How often are the TOXNET
Answer: We update the TOXNET databases when new information becomes available. We check for new data at least once a week. You can refer to the TOXNET Databases Size Report to see if we’ve updated a specific database.
Question: Where can I get training in
Answer: Visit TOXNET and Beyond Training Class Schedule and Workbook for a class schedule and to download the TOXNET manual.
Question: Can I use TOXNET on my mobile
Answer: You can use TOXNET on you mobile device by going to TOXNET Mobile Access.
The Gallery of Mobile Apps and Sites lists all SIS/NLM resources with mobile versions.
Question: Does TOXNET include information
on prescription and nonprescription drugs?
Answer: CCRIS, DART, GENE-TOX, HSDB, and TOXLINE include prescription and nonprescription drug information. You can search using the chemical, generic or trade name of a drug. ChemIDplus is a good starting point because it links to all NLM databases that have information on a particular drug.
The Drug Information Portal is a gateway to drug information from the National Library of Medicine and other key government agencies. It covers drugs from entry into clinical trials through entry in the market place
Question: What additional drug information
resources are provided by NLM?
- MedlinePlus - information on over 900 diseases and medical conditions. It also provides access to AHFS® Consumer Medication Information from the American Society of Health-System Pharmacists.
- MEDLINE/PubMed - comprehensive coverage of scientific articles on drugs in a database of over 20 million citations to articles in the biomedical literature.
ClinicalTrials.gov - a
database of federally and privately supported clinical
studies on drugs and other treatments under study for
safe and effective treatment of a wide range of
diseases and medical conditions.
Answer: A cookie is information sent by a Web site server to your computer. TOXNET creates session cookies on the your computer. These cookies last for the duration of your connection to TOXNET. The cookie contains information about each search so that previous searches can be displayed. TOXNET itself does not keep track of what searches you have made. It only has files listing the results of those searches. These temporary files are kept for no less than one hour and for no more than two hours. Each time you request a record from a search request, the results file is given a guarantee of one hour to live.
Question: Can an error in a citation be
Answer: Corrections can be made if the error is in the TOXLINE subset PubMed, DART, HSDB, or ChemIDplus, because these databases are produced by NLM. If the error is in other parts of TOXLINE, CCRIS, ITER, TRI, or GENE-TOX, corrections cannot be made because NLM does not produce these databases. You may contact the original producer of the citation to request a change to a citation. The producer for a citation is listed as the "Secondary Source ID" at the bottom of a TOXLINE record. Information on original producers of CCRIS, ITER, TRI, and GENE-TOX can be located on the fact sheets about these databases. You may also send the suggested correction to NLM at email@example.com.
Question: How do I limit my results by
date, age group, language, type of article, etc.?
Answer: TOXNET does not allow limiting retrieval by age or by types of articles. TOXLINE and DART retrieval can be limited by publication year and by language. The other TOXNET databases have limits specific to each database. Visit TOXLINE Help for more information on using limits in TOXLINE.
Question: How do I remove PubMed citations
from TOXLINE or DART searches?
- Beneath the search box on the TOXLINE and DART Basic Search pages, select "No" for "Include PubMed records."
- For a TOXLINE search, add "NOT PubMed [org] NOT
PubDart [org]" to your search box.
Example: benzene NOT PubMed [org] NOT PubDart [org]
- For a DART search, add "NOT PubMed [org]"
in the search box.
Example: benzene NOT PubMed [org]
Question: In what order are the citations
in TOXNET displayed?
Answer: The TOXNET search results are displayed in relevancy ranked order. Relevancy ranking is based on the number of individual search terms in a document, the number of times each search term occurs in a document, the rarity of the search terms within the database, and the nearness of search terms to each other. Records containing combinations of search terms tend to be ranked higher than records with isolated occurrences of search terms.
Question: How do I sort my
Answer: If you want to sort the results in a different order, click on the "Sort" button on the left. For the bibliographic databases, the search results can be sorted by year of publication, title, author, entry month, or relevance. For the chemical databases, the results can be sorted by substance name.
- Question: How do I print my TOXNET search results?
- Question: How do I save my TOXNET search results?
Question: How can I store my TOXNET search
Answer: You cannot store search strategies in TOXNET. You can use the History feature to retrieve searches performed in the last hour. You can also copy and paste your search strategy into a document, save the document, and then later paste the search strategy into the TOXNET search box.
Question: How do I create a canned search
- "dbname" can be: hsdb, iris, genetox, iter, ccris, toxline, dart,
- "query" can be search terms or Boolean queries or search terms in a specified field.
- All spaces must be replaced with a plus sign (+) in the URL.
Example 1: Searching toxicogenomics in TOXLINE
Example 2: Searching by Document Number in TOXLINE
Example 3: Searching vinyl chloride AND hepatocellular carcinoma in CCRIS
Example 4: Finding all records in HSDB that were reviewed in 2004
A relevant field tag should be used following a "@" sign.
Example 5: To learn about creating a link to TOXMAP read the TOXMAP FAQ.
Question: How do I create a link to a
record in a TOXNET database?
To create a link for chemical databases, use the name of chemical, or CAS Registry Number
Example 2: Link to the HSDB vinyl chloride record
Example 3: Link to the CCRIS formaldehyde record by using CAS Registry number 50-00-0
Example 4: For ChemIDplus, use this format: http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=50-00-0 where regno is the CAS Registry Number in the hyphenated format as shown, or the unhyphenated format with leading zeros added to make a total of 9 characters (000050000) or http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?name=formaldehyde where name = chemical name.
Several records can be retrieved by using the vertical bar "|" without spaces to separate values:
Example 5: Link to Haz-Map formaldehyde record
Example 6: Link to Household Products Database formaldehyde record
Example 7: TOXMAP
Link to TOXMAP by CAS Registry Number
Link to TOXMAP by chemical name
Visit TOXMAP for more linking examples.
Example 8: Drug Information Portal
Link to the Drug Information Portal by CAS Registry Number
Link to the Drug Information Portal by drug name
Question: How do I create a link to the
results when I search all the databases in TOXNET?
Add the term you want to send to TOXNET as a parameter in the linkout(' ') function in the HTML code below, enclosed with single quotes. The following example sends the query Formic Acid as a search parameter to TOXNET:
Question: How do I get the full text
version of articles I find in a search?
- If you are affiliated with a hospital or university library, check with that library to find out if they can supply the article.
- If you are not affiliated with a hospital or university library, request a copy from your local library. The library may be able to use Interlibrary Loan (ILL) to get an article.
- If you do not have a local library you can use Loansome Doc, the document ordering feature from the National Library of Medicine.
- Run your search in PubMed and look for free full text articles. Limit your search to the toxicology subset by adding "tox[sb]" to your search strategy (without quotation marks) and select "Free Full Text" from the "Filter your results:" options on the upper right of the page. You can also use the Limits function to restrict retrieval to "Links to full text".
- Check NLM's How to Get the Journal Article for more information.
- You can try one of the sources listed in this resource: Finding Free Full Text Materials
If you are unable to find a copy of an item at a library, it may be possible to purchase a copy. Note: Older materials may no longer be in print.
CRISP Data Base (National Institutes of Health)
- The CRISP citation collection in TOXLINE is old and represents research projects and programs supported by the Department of Health and Human Services from 1994 - 2004
- NIH has replaced CRISP with the RePORT Expenditures and Results (RePORTER) query tool.
- REPORTER has information about a project's results, history, and any sub-projects. Try searching for a CRISP citation by project title and Fiscal Year. The Fiscal Year can be found in the Secondary Source ID in the TOXLINE result.
- You can also search the RePORTER system for more recently funded projects.
Government Reports Announcements & Index (GRA&I)
- You can order GRA&I reports by following the link found in the TOXLINE citation.
International Agency for Research on Cancer (IARC) Monographs
WHO (WORLD HEALTH ORGANIZATION)
- Many materials originate from the International Programme on Chemical Safety.
Question: Why isn't there a link to
the full text for the reference I retrieved?
Answer: There are no links to full text articles in TOXNET because the structure of the databases is not based on journal articles as PubMed is. The information is drawn from a variety of information sources which makes linking to full text difficult. NLM is investigating methods of making the full text available in the future. Note: Full text access may be available for citations in TOXLINE which come from PubMed. Use the link to PubMed within the TOXLINE citation.
Question: How do I cite a reference from a
The citation format preferred by NLM for databases such as HSDB, IRIS, ITER, GENE-TOX, and CCRIS is shown below.
Example: Hazardous Substances Data Bank [Internet]. Bethesda (MD): National Library of Medicine (US), Division of Specialized Information Services. 1986 - [cited 2013 Jan 4]. Available from: http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?HSDB
Question: How do I borrow a book?
To borrow a book from NLM:
- Use the NLM Catalog to verify that NLM carries the book.
- After locating the book, ask your local library to send an Interlibrary Loan (ILL) request to NLM. Contact your library for information on its ILL services and fees.
- For further information, visit Getting Articles and Borrowing Books.
Question: How do I find a library that can
help me with health information?
Answer: The National Library of Medicine maintains the National Network of Libraries of Medicine (NN/LM), a network of health science libraries and information centers throughout the United States. NN/LM can help you locate a public or health library that can assist you in your search. Visit Find a Library to locate a library. Some libraries may charge a fee for photocopies or services.
Question: How do I import references into
my reference management program?
Answer: Only citations from TOXLINE and DART can be imported into reference management programs, such as ProCite, Reference Manager, and EndNote. Results from HSDB, IRIS, ITER, CCRIS, GENE-TOX, and TRI are in formats that cannot be understood by the software.
To import search results from TOXLINE and DART into a reference management program:
- Click on the "Download" button on the left side of the screen.
- A window will pop up, displaying several format options. Highlight the "Tagged" option and click "Download".
- Save the citations using ".txt" as the filename extension.
- When you import the citations, choose the "TOXLINE" filter from the program's list of filters.
Question: How do I find a journal listed
in a reference?
- Many of the journals listed in TOXLINE can be found using the Entrez Journal database.
- NLM's LOCATORplus can also be used to find journals.
- The Library of Congress catalog can also be used.
Question: Where can I get a list of
journals in TOXNET?
Answer: NLM does not maintain a list of journals for references found in TOXLINE or other TOXNET databases. TOXNET resources are drawn from multiple sources that provide data in the format used by each source's producer. There are no title lists for closed subfiles because there is no way to know how those sources gathered their material.
Question: How do I lease/license the TOXNET
Answer: The following TOXNET databases are available for lease: ChemIDplus, DIRLINE, CCRIS, GENE-TOX, HSDB, and TOXLINE. For further information visit Leasing Data from the National Library of Medicine.
Question: I already lease a TOXNET
database(s). Who do I contact if I have questions about the
associated XML data?
Answer: NLM can give only limited support for those acquiring TOXNET data. If you need information about a field or find an error in the data, please email: firstname.lastname@example.org. Since many of the databases are created by other agencies, some problems cannot be corrected immediately.
Attempting to validate the XML data is a common problem. The TOXNET XML files produce well-formed XML data in accordance with W3C specifications. Validating parsers behave differently. Making XML data work for your application may require the services of a professional text programmer.
Question: How often are the TOXNET
databases updated on the FTP site for licensing?
Answer: Updated databases are placed on the FTP site by the close of the 28th of each month, Eastern Standard/Daylight Time. Occasional problems with the data or the coincidence of weekends or holidays may delay the data for 1-2 days.
If there is any change in the data from the previous month, the new version will be placed on the site. Please note that some of these changes may be extremely minor.
Question: What sources do you use to
Answer: ChemIDplus has more than 70 sources. The core sources of substance records correspond to those substances that are cited in one or more of the NLM databases. A list of all the sources can be found at the Alphabetical List of Locators Used in ChemIDplus
Question: How often is ChemIDplus
Answer: ChemIDplus is updated continuously.
Question: What is the difference between
ChemIDplus Lite and Advanced?
Answer: ChemIDplus Lite is designed for simple searching by name or registry number to retrieve basic information about a chemical and provide links to other resources. The Lite version displays structures, but does not allow drawing or searching on structures.
ChemIDplus Advanced is designed for more advanced searching by any combination of name, registry number, molecular formula, classification code, locator code, toxicity, physical property, structure, or molecular weight. Toxicity and physical property data are displayed in tables under Basic Information.
The Advanced version provides links to the same resources as the Lite version. In addition, ChemIDplus Advanced allows users to draw their own structures and perform similarity and substructure searches.
- Question: Why do I get a message about the Marvin Applet when I start ChemIDplus?
Answer: Marvin is a Java applet from ChemAxon that is used to manipulate and edit chemical structures. You will need to register to download Marvin.
When Marvin first loads, you must answer whether to trust it "this time or always". If "always" is selected, it will not ask each session. Marvin is also used to display structures such as PNG (Portable Network Graphics) files in our results page so that a plug in is not needed to view results.
- Question: Why do I get a warning about loading Java when I start ChemIDplus?
Answer: Marvin requires that a JVM (Java Virtual Machine) be loaded. JVM converts and executes byte code for a given platform. If you don't have one, you will be prompted to download it. For security reasons, it is recommended that you get the latest version.
- Question: How do I draw or edit structures with Marvin in ChemIDplus?
Answer: Marvin is the default editor. Clicking on the "Structure" box in ChemIDplus Advanced launches MarvinSketch, the editor. MarvinSketch includes chemical drawing tools and help files. Changes you make in MarvinSketch show up immediately in the ChemIDplus Advanced "Structure" box. You may then select the type of search, add any qualifying data ranges (such as molecular weight), and click on the Search button on the top or bottom of the page.
- Question: How do I draw or edit with Chime and Accelrys Draw?
Answer: Chime is a free chemical display application. Accelrys Draw - No Fee is a companion structure drawing package available from the same site. Both must be downloaded and installed on your machine.
In the "Structure" box, right click > edit > Transfer to Accelrys Draw to automatically start Accelrys Draw (this enables you to draw or edit your own query). Accelrys Draw has a series of chemical drawing tools and help files available. After drawing or editing, click > Transfer mode button in upper left corner to return to the Structure Window for searching.
You will need to register to download Chime and Accelrys Draw - NoFee products. Chime and Draw work best in Internet Explorer. You may have difficulties with the applications in Firefox and Chrome.
- Question: How do I download a single structure Mol file in ChemIDplus?
Answer: If Marvin is loaded in your computer click "Transfer Structure" from a search results page. This moves the structure into the Structure box. Click on the Structure box to start MarvinSketch. Then chose File > Save As > Files of Type > MDL Molfiles (*.mol) format.
- Question: How do I view a structure in ChemIDplus?
Answer: In ChemIDplus Lite click the "Full Record" button. The structure will be at the top of the new page that appears. The ChemIDplus Advanced version automatically displays the structure at the top of the results page. Clicking on the "Enlarge Structure" link opens a window for viewing or manipulating 2D or 3D images of the structure. Use the right mouse button to do this.