|April 24, 2000 [posted]|
|ChemIDplus: A Web-Based Chemical Search System|
hemIDplus (http://chem.sis.nlm.nih.gov/chemidplus/) is a Web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. The core of ChemIDplus is the MeSH Category D descriptors and the Supplementary Concepts for chemicals as extracted from MeSH, NLM's Medical Subject Headings. ChemIDplus also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. The database contains over 351,000 chemical records, of which over 58,000 include chemical structures. ChemIDplus is searchable by Name/Synonym, CAS Registry Number, Molecular Formula, Classification Code, Locator Code, and Structure. To use ChemIDplus, you will need:
Once Chime is installed, right click with the mouse on the Structure Input Box on the Search Input Page. A menu of options for structure drawing and manipulation will be shown. Without the Chime plug-in, ChemIDplus will not display the structure but will still search and display all text data (e.g., Name/Synonym, CAS Registry Number, Molecular Formula, Classification Code, Note, and Locator Code) as well as search all the Locator sites from the query output.
Search Input Page
Figure 1: Search Input Page.
There are four drop-down menus in the Search Input Page (see Figure 1):
Data Queries (or Searching for Chemical Information)
Figure 2: Search for Dioxin.
To perform a query on a chemical, the data search type and the appropriate logic operator are selected from the drop-down menus on the left side of the Search Input Page before the query term is entered. Click the Search button or hit the Enter key to initiate the search. The Input Page showing a search for the substance dioxin is given in Figure 2.
The search above retrieves the dioxin record and displays the result in the format shown in Figure 3. The complete record is displayed because there was only one match to the search entered. If more than one record matched the search, the Query Results Page would display a short record of the first 10 matches. Each record displayed in the Query Results Page shows an ID number, the Structure (if available), CAS Registry Number, Molecule Name, and the Molecular Formula. Without the Chime plug-in, only the text data will be displayed.
Three blue button options are available in the bottom frame of the Entire Record Display. Enlarge Structure is a display option that allows the user to open the structure in a larger window for easier viewing. Use Structure For Query and Use Structure for Similarity are search options that eliminate the need to draw structure queries and therefore facilitate structure searching (see Structure Queries).
The Full Record button, that only appears on the short record format, retrieves the entire record from the database, including text and structure, if available. Figure 3 shows the full dioxin record. The fields include the following:
Locator Codes Page
Figure 4: Locator Codes Page - Dioxin.
The Locator Codes Page provides a list of resources with additional chemical information beyond that found in ChemIDplus. Figure 4 shows the Locator Codes Page for the dioxin record. This is displayed by clicking on the Locator Codes button in the top frame of the Full Record Page. You may click on the information icon (i) next to a particular locator to get a description of that database and the scope of the search. Figure 5 shows information on the MEDLINE locator. Click on one of the hyperlinked locators (e.g., MEDLINE) to directly search this resource for information on dioxin by CAS Registry Number. Figure 6 shows the MEDLINE output on the right screen (see the flag marker on the left screen).
Once you are in a database you can customize your search to meet your needs. Note the flag icon on the left screen marking the active locator (next to MEDLINE in Figure 6). Navigating to a different database is accomplished by simply clicking on another hyperlinked locator on the left screen of the Locator Codes page. The previous output would then be replaced with output from the new locator. Ease of navigation from the Locator Display Page to the other web sites and vice versa is a characteristic feature of ChemIDplus.
Figure 5: Locator Codes Page - Locator and Search Information.
Figure 6: Locator Codes Page - MEDLINE Output.
Enlarging the Structure
The Enlarge Structure option, found on the Entire Record or Full Record page, opens the structure in a larger window for easier viewing. Some structures are large and the structure displayed in the Query Results Page may be cramped and unclear (see Figure 7). The Enlarge Structure option provides a better and clearer view of the structure (see Figure 8). In addition, the 3D display button (below the enlarged structure) allows for the display of the 3D model if this is available in the database.
Figure 7: Query Results Page - Vancomycin.
Figure 8: Enlarged Structure of Vancomycin.
ChemIDplus gives you the option of using Chime and ISIS/Draw to draw your structure for use in a query or using one of the structure query options available on the Query Results Page. The two options are described below.
Using Chime and ISIS/Draw:
Figure 9: Chime menu.
Figure 10: ISIS/Draw - Dibenzodioxin Structure.
Figure 11: Substructure Search Query for Dibenzodioxin.
Select one of the Structure Search Types (Substructure Search in this example) and click the Search button. Figure 12 shows two of the 89 hits obtained from this search for the dibenzodioxin substructure in the database.
Figure 12: Dibenzodioxin Substructure Query Results Page.
Use Structure From Query Results Page for Searching:
For example, given the results shown in Figure 12, select the second record (RN = 1746-01-6) and click on the Use Structure for Similarity button. You will be prompted to enter a percent similarity ranging from 50% to 100% (default is 80%). The higher the percentage entered, the more similar the resulting compounds. After entering the percent similarity and clicking on OK, the system searches for similar structures. Figure 13 shows the percent similarity prompt and Figure 14 shows the Similarity Query Results Page.
Figure 13: Percent Similarity Prompt.
The Query Results Page in Figure 14 shows two of the 79 hits from the similarity search for the compound with CAS Registry Number 1746-01-6. The output is in CAS Registry Number/ID order.
Figure 14: Similarity Query Results Page.
The following are examples of information that can be obtained by searching ChemIDplus.
Example #1: Which NLM databases carry information on MTBE (methyl tert-butyl ether)? Is it on the U.S. E.P.A. Clean Air List (CAA1)? Try to search MEDLINE from the Locator Codes Page.
Example #2: Does acrylamide have a TWA (Time Weighted Average)? If so, what is it?
Example #3: How many chemicals exhibit antipsychotic activity? How many are phenothiazines?
Example #3a: Alternate Search Using Phenothiazine Substructure. This will retrieve all phenothiazines with known antipsychotic activity including records not specifically assigned the Classification Code "Antipsychotic agent, phenothiazines." Compare your results here with the previous search.
Example #4: Give a list of chemicals evaluated for carcinogenic risk by the International Agency for Research on Cancer (IARC)?
Example #5: Identify chemicals similar to saccharin. (Use 80% similarity.)
By Perlita M. Liwanag,
Liwanag PM, Hudson VW, Hazard GF Jr, ChemIDplus: A Web-Based Chemical Search System. NLM Tech Bull. 2000 Mar-Apr;(313):e3.