Searching for Chemicals
Searching for Chemicals in MEDLARS® Databases
The publication Medical Subject Headings -Supplementary Chemical Records has been discontinued. This tool contained the listings for chemicals which are not MeSH headings and have been mentioned in a significant way in journals indexed in MEDLINE. These chemical names may be found online in the Name of Substance (NM) field. The NM field is searchable. However, the NM exists only in the dictionary files, MEDLINE, the MEDLINE Backfiles, and the MEDLINE-derived portions of the following composite files: AIDSLINE, CANCERLIT, HealthSTAR and in the MEDLINE-derived portion and DART subfile in TOXLINE.
MeSH, ChemID, and CHEMLINE
Chemicals are listed in three dictionary files online: MeSH, ChemID, and CHEMLINE. The MeSH file is updated several times each week, throughout the year. It is the most current of all the online files listing chemicals. ChemID and CHEMLINE are updated several times a year and therefore may not have an entry for a chemical that does have a record in MeSH (which means that there are citations present in MEDLINE and/or the MEDLINE Backfiles).
See Figure 1 for an example of locating the same chemical in the MeSH, ChemID and CHEMLINE files. Note that File MeSH does not indicate which MEDLINE files contain postings for any chemical. Files ChemID and CHEMLINE both contain a Locator (LO) field which indicates the files in which a particular chemical appears. Keep in mind that these Locator listings may be several months out-of-date, depending on when you are conducting your search. Also note that searching MeSH and ChemID are roughly comparable in price; for example, it costs about $0.11 to find and download the information for fluoromethane. It costs $1.79 to retrieve this same information in CHEMLINE (a file containing Chemical Abstracts Service (CAS®) royalty data).
Which Chemical Dictionary File Should You Use?
You might want to consider restricting your search for a chemical to MeSH if you were only interested in citations appearing in MEDLINE or the MEDLINE Backfiles and you wanted the most current information available. You would use ChemID in place of or in addition to MeSH, when you were interested in citations from the full range of MEDLARS files (including TOXNET files) and you want the convenience of seeing the Locator files (realizing that they are not completely current). You would use CHEMLINE last, in addition to or in place of MeSH and ChemID, if you couldn't find a chemical in the first two files. There are chemicals which are only listed in CHEMLINE; generally, the citations for these chemicals appear only in TOXLIT and the TOXLIT backfile which are also CAS royalty files.
Searching the non-Dictionary Databases for non-MeSH Chemicals
Once you have found your chemical in MeSH, ChemID or CHEMLINE, in most MEDLARS files it is easiest to retrieve citations about that chemical by searching on the Registry Number. The Registry Number may be entered in all MEDLARS files (including TOXNET files) qualified by (rn) or without qualification. In MEDLINE, MEDLINE Backfiles, and MEDLINE-derived files, you may choose to substitute the Name of Substance qualified by (nm) for the Registry Number. In TOXNET files, searching on the registry number is easiest and yields consistent results because all records contain an RN field. In the composite file TOXLINE, not all records contain a Registry Number, so it is best to search on the Registry Number ORed together with the chemical name as a Text Word.
To display the Name of Substance field (in those files where it exists), you need to print the Registry Number (RN) field. If you give the command PRINT NM, you will see the following response online: 'NM' IS NOT A VALID PRINT PARAMETER. COMMAND IGNORED. This situation is analogous to the one for displaying subheadings. You can search on the subheading field, but you cannot give the command PRT SH; subheadings display only as part of the MeSH heading field. Similarly NMs display only as part of the Registry Number field.
See Figure 2 for an example of retrieving on the registry number for fluoromethane in MEDLINE and displaying the Registry Number field containing the Name of Substance. See Figure 3 for an example of retrieving information on fluoromethane in TOXLINE.
SS 1 /C? USER: file mesh PROG: YOU ARE NOW CONNECTED TO THE MESH VOCABULARY (1997) FILE. SS 1 /C? USER: fluoromethane (nm) PROG: SS (1) PSTG (1) SS 2 /C? USER: prt dl PROG: 1 NM - fluoromethane RN - 593-53-3 RR - 59122-96-2 (ion(1+)) RR - 20666-44-8 (13C-labeled cpd) RR - 3832-44-8 (18F-labeled cpd) RR - 20666-45-9 (14C-labeled cpd) SY - methyl fluoride HM - *HYDROCARBONS, FLUORINATED DA - 810626 MR - 830801 RO - O:RLS RO - C:NLM RO - M:ACS SO - Arch Phys Med Rehabil 1981;62(3):100 TH - Merck Index, 9th ed, #4060 FR - 24 * Indicates the frequency of postings in MEDLINE and the Backfiles, but not the specific file locations. NO - RN given refers to parent cpd RY - C UI - C029999 SS 2 /C? USER: show cost PROG: THE ESTIMATED TOTAL ONLINE COST FOR THIS 0 MINUTE MESH VOCABULARY SESSION IS $ 0.11. SS 1 /C? USER: file chemid PROG: YOU ARE NOW CONNECTED TO THE CHEMID (NON-ROYALTY) FILE. SS 1 /C? USER: fluoromethane (nm) PROG: SS (1) PSTG (1) SS 2 /C? USER: prt dl PROG: 1 RN - 593-53-3 MF - C-H3-F [EINECS:TSCAINV] N1 - Fluoromethane [EINECS] N1 - Methane, fluoro- (8CI)(9CI) [TSCAINV] NM - Fluoromethane [MESH] NM - [LIST] Methyl fluoride [UN2454] [Flammable gas] [DOT] NM - [LIST] UN2454 [DOT] SY - EINECS 209-796-6 [EINECS] SY - Fluoromethane [NLM] SY - Fluorure de methyle [French] [NLM] SY - Fluoruro de metilo [Spanish] [NLM] LLO - DOT LO - CANCERLIT ; EINECS ; HSTAR ; * Shows the files where citations on fluoromethane can be found. MEDLINE ; MED80 ;MED85 ; MED90 ; MESH ; TOXLINE ; TOXLINE65 ; TOXLIT ; TOXLIT65 ; TSCAINV ; SUPERLIST EM - 9701 SS 2 /C? USER: show cost PROG: THE ESTIMATED TOTAL ONLINE COST FOR THIS 0 MINUTE CHEMID SESSION IS $ 0.11. SS 1 /C? USER: file chemline PROG: YOU ARE NOW CONNECTED TO THE CHEMLINE (ROYALTY) FILE. SS 1 /C? USER: fluoromethane (nm) PROG: SS (1) PSTG (1) SS 2 /C? USER: prt dl PROG: 1 RN - 593-53-3 MF - C-H3-F N1 - Methane, fluoro- (8CI)(9CI) NM - Fluoromethane [MESH] SY - Fluoromethane [NLM] SY - Fluorure de methyle [French] [NLM] SY - Fluoruro de metilo [Spanish] [NLM] SY - Methyl fluoride [CAS:MESH] LO - CANCERLIT * Shows the files where citations on fluoromethane can be found. LO - EINECS LO - HSTAR LO - MEDLINE LO - MED80 LO - MED85 LO - MED90 LO - MESH LO - TOXLINE LO - TOXLINE65 LO - TOXLIT LO - TOXLIT65 LO - TSCAINV EM - 9502 SS 2 /C? USER: show cost PROG: THE ESTIMATED TOTAL ONLINE COST FOR THIS 0 MINUTE CHEMLINE SESSION IS $1.79.
YOU ARE NOW CONNECTED TO THE MEDLINE (1994 - 97) FILE. SS 1 /C? USER: 593-53-3 * The Registry Number for fluoromethane. PROG: SS (1) PSTG (1) SS 2 /C? USER: prt include nm * PRINT commands may not be used with NM. PROG: 'NM' IS NOT A VALID PRINT PARAMETER. COMMAND IGNORED. SS 2 /C? USER: prt include rn * The NM will display in the RN field in MEDLINE, MEDLINE Backfiles, MEDLINE-derived files, and the DART subfile in TOXLINE. PROG: 1 UI - 94368117 AU - Hyman MR AU - Page CL AU - Arp DJ TI - Oxidation of methyl fluoride and dimethyl ether by ammoniamonooxygenase in Nitrosomonas europaea. RN - EC 1. (Oxidoreductases) RN - EC 1.7.3.- (ammonia monooxygenase) RN - 0 (Hydrocarbons, Fluorinated) RN - 0 (Methyl Ethers) RN - 115-10-6 (dimethyl ether) RN - 50-00-0 (Formaldehyde) RN - 593-53-3 (fluoromethane) * The NM is displayed here. RN - 67-56-1 (Alcohol, Methyl) SO - Appl Environ Microbiol 1994 Aug;60(8):3033-5
file toxline PROG: YOU ARE NOW CONNECTED TO THE TOXLINE (1981 FORWARD, NON-ROYALTY) FILE. SS 1 /C? USER: 593-53-3 * RN for fluoromethane. PROG: SS (1) PSTG (16) SS 2 /C? USER: 1 or fluoromethane (tw) PROG: SS (2) PSTG (18) SS 3 /C? USER: 1 and fluoromethane (nm) PROG: SS (3) PSTG (1) * Only one of the eighteen citations retrieved contains fluoromethane in the Name of Substance (NM) field. SS 4 /C? USER: prt include rn PROG: 1 AU - Green T TI - The metabolic activation of dichloromethane and chlorofluoromethane in a bacterial mutation assay using Salmonella typhimurium. SI - TOXBIB/84/013878 * TOXBIB is the MEDLINE-derived subfile in TOXLINE. SO - Mutat Res; VOL 118, ISS 4, 1983, P277-88 RN - 0 (Hydrocarbons, Chlorinated) RN - 0 (Hydrocarbons, Fluorinated) RN - 0 (Hydrocarbons, Halogenated) RN - 0 (Mutagens) RN - 593-53-3 (fluoromethane) * The NM is displayed in the RN field. RN - 593-70-4 (chlorofluoromethane) RN - 75-09-2 (Methylene Chloride) SS 4 /C? USER: 2 and not 3 PROG: SS (4) PSTG (17) SS 5 /C? USER: prt 1 include rn * In TOXLINE, only MEDLINE-derived records and DART subfile records have a Name of Substance (NM) field. PROG: 1 CN - UNIV COLLEGE DUBLIN TI - KINETICS AND MECHANISMS FOR THE REACTIONS OF HALOGENATED ORGANIC COMPOUNDS IN THE TROPOSPHERE - STEP-HALOCSIDE/AFEAS WORKSHOP, WITH COVER LETTER DATED 032494 SI - TSCATS/442284 * This record comes from the TSCATS subfile of TOXLINE. SO - EPA/OTS; Doc #86940000219 RN - 56-23-5; 71-55-6; 74-84-0; 74-98-6; 75-10-5; 75-28-5; 75-37-6; 75-43-4; 75-44-5; 75-45-6; 75-46-7; 75-68-3; 75-73-0; 75-87-6; 75-89-8; 76-02-8; 76-05-1; 100-42-5; 110-83-8; 306-83-2; 334-99-6; 353-36-6; 353-49-1;353-50-4; 354-32-5; 354-33-6; 354-34-7; 359-35-3; 377-36-6; 421-14-7; 422-56-0; 425-82-1; 431-89-0; 507-55-1; 556-82-1; 593-53-3; * RN for fluoromethane without NM. TSCATS records do not have NMs. 593-70-4; 679-86-7; 690-22-2; 763-32-6; 811-97-2; 927-84-4; 1493-02-3; 1674-10-8; 1691-17-4; 1717-00-6; 1885-48-9; 2551-62-4; 2837-89-0; 3822-68-2; 6117-91-5; 6185-26-8; 7631-99-4; 7722-84-1; 7727-37-9; 7732-18-5; 7782-44-7; 7782-50-5; 10028-15-6; 10102-43-9; 10102-44-0; 16413-86-8; 21811-29-0; 69884-58-8; 70490-95-8; 73761-32-7; 108083-11-0; 118986-32-6; 119437-62-6; 119437-63-7; 134469-96-8; 134469-97-9; 134469-98-0; 134469-99-1; 138495-42-8; 139702-33-3; 143645-30-1; 144109-03-5; 145252-03-5; 147703-38-6; 147703-39-7 SS 5 /C? USER: prt si * This displays the Secondary Source ID (SI) fields, indicating the subfile sources for the other records retrieved in a search on the RN associated with fluromethane. PROG: 1 SI - TSCATS/442284 . . . 16 SI - BIOSIS/89/05815 17 SI - HEEP/83/04303