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- Journal citations from Medline on toxicology: TOXBIB
- Non-Medline, specialist sources on toxicology: TOXNET
ToxFile presents information on the toxicological, pharmacological,
biochemical and physiological effects of drugs, pesticides and other
chemicals. Adverse drug reactions, chemically induced diseases,
carcinogenesis, mutagenesis, teratogenesis, environmental pollution,
waste disposal, radiation, and food contamination are typical areas
of coverage.
DataStar creates the ToxFile database by merging data from two
sources: first, the toxicology records within Medline are copied
into ToxFile; secondly, the NLM's specialised, non-Medline material
is added. These are known as TOXBIB and TOXNET respectively.
TOXNET is derived from an assortment of specialised journals and
other sources published by government departments and international
organisations. There are 15 TOXNET datasets, as listed in 'sources'
below. TOXNET forms about 20% of the total database.
The TOXBIB part of ToxFile can be searched in the same way as
Medline: subjects are easily accessed by means of the NLM's
Medical Subject Headings, and DataStar offers an online thesaurus
to take full advantage of these.
Some TOXNET documents are also indexed with MeSH headings,
but most are indexed with keywords supplied by the individual
source organisation.
Use ToxFile to answer questions like:
- what is the toxicology of metaldehyde?
- what is the occupational neurotoxicity of ethylene oxide?
- what is the nephrotoxicity of the gasoline-component
2,2,4-trimethylpentane?
Sources
ToxFile is composed of TOXBIB, the toxicology-related journal
citations from Medline, and TOXNET, the specialist, non-Medline
material on toxicology supplied by the NLM.
The TOXNET files are as follows:
Special journal and other research literature:
Developmental and Reproductive Toxicology (DART)
International Labour Office (CIS)
Swedish National Chemicals Inspectorate (RISKLINE)
Technical reports and research projects:
Federal Research in Progress (FEDRIP)
Toxic Substances Control Act Test Submissions (TSCATS)
Toxicology Document and Data Depository (NTIS)
Toxicology Research Projects (CRISP)
Archival collection (no longer updated through NLM):
Aneuploidy (ANEUPL)
Environmental Mutagen Information Center File (EMIC)
Environmental Teratology Information Center File (ETIC)
Epidemiology Information System (EPIDEM)
Hazardous Materials Technical Center (HMTC)
Health Aspects of Pesticides Abstract Bulletin (HAPAB)
Pesticides Abstracts (PESTAB)
Poisonous Plants Bibliography (PPBIB)
AN - Accession number & update
14561078 TOXBIB Completed 20050101.
TI - Title
Arsenic hazards to humans, plants, and animals from gold mining.
SO - Source
Reviews of environmental contamination and toxicology, {Rev-Envi
Contam-Toxicol}, 2004, vol. 180, p. 133-65, 99 refs, ISSN: 0179-5
953.
AU - Author(s)
Eisler-Ronald.
IN - Author affiliation
U.S. Geological Survey, Patuxent Wildlife Research Center, 11510
American Holly Drive, Laurel, MD 20708-4019, USA.
AB - Abstract
Arsenic sources to the biosphere associated with gold mining
include waste soil and rocks, residual water from ore
concentrations, roasting of some types of gold-containing ores to
remove sulfur and sulfur oxides, and bacterially enhanced
leaching. Arsenic concentrations near gold mining operations are
elevated in abiotic materials and biota: maximum total arsenic
concentrations measured were 560 microg/L in surfce waters,
5.16 mg/l in sediment pore waters, 5.6 mg/kg DW in bird liver,
27 mg/kg DW in terrestrial grasses, 50 mg/kg DW in soils, 79 mg/
kg DW in aquatic plants, 103 mg/kg DW in bird diets, 225 mg/kg
DW in soft parts of bivalve molluscs, 324 mg/L in mine drainage
waters, 625 mg/kg DW in aquatic insects, 7,700 mg/kg DW in
sediments, and 21,000 mg/kg DW in tailings. Single oral doses of
arsenicals that were fatal to 50% of tested species ranged from
17 to 48 mg/kg BW in birds and from 2.5 to 33 mg/kg BW in
mammals. Suscepticle species of mammals were adversely
affected at chronic doses of 1-10 mg As/kg BW or 50 mg As/kg
diet. Sensistive aquatic sepcies were damaged at water...
DE - MeSH headings
ARSENIC/AN (analysis), *TO (toxicity);
ARSENIC-POISONING/*;
ENVIRONMENTAL-POLLUTANTS/AN (analysis), *TO (toxicity);
GOLD/*;
PUBLIC-HEALTH/*.
ANIMALS;
ANIMALS-WILD;
ENVIRONMENTAL-MONITORING;
HUMAN;
INVERTEBRATES;
MINING;
PLANTS;
RISK-ASSESSMENT;
TOXICITY-TESTS.
RN - CAS Registry numbers
0 (Environmental-Pollutants);
7440-38-2 (Arsenic);
7440-57-5 (Gold).
LG - Language
English.
PT - Publication type
Journal-Article, Review, Review-Tutorial.
SB - Journal subset
IM.
CP - Country of publisher
United-States.
JC - Journal code
0008703602.
IP - Information provider
NLM
NT - Notes
Publication model: Print.
YR - Publication year
2001.
DT - Publication date
20040000.
ED - Entry date
Date created: 20031016
Date completed: 20031028
Date revised: 20041117.
Sample document - TOXNET:
AN - NLM accession number
DART-TER-2001561 TOXNET 20050101.
TI - Title
Chronic maternal ethanol ingestion decreased lung glutathione
availability and altered pulmonary function.
SO - Source
Pediatr-Res, Apr 2002, vol. 51, no. 4 Pt 2, p. 471A
ISSN: 0031-3998.
AU - Author(s)
Brown-L-A, Gauthier-T-W, Harris-F-L.
IN - Author affiliation
Pediatrics, Emory University, Atlanta, GA.
AB - Abstract
BACKGROUND: In the premature child, lung injury during
oxygen therapy is inversely related to availability of the
antioxidant glutathione (GSH). Life style studies showed that
chronic alcohol abuse during pregnancy is a significant
health problem. Since alcohol freely crosses the placenta,
it results in maternal and fetal chronic oxidative stress.
In adults, alcohol abuse results in decreased lung GSH, chronic
oxidative stress, altered type II cell function and increased
risk of acute lung injury. The effects of maternal alcohol abuse
(...)
DE - MeSH headings
MeSH Headings:
PREGNANCY;
GUINEA-PIGS;
ANIMAL;
FEMALE;
SUPPORT-NON-U-S-GOVT;
ETHANOL/*TO (TOXICITY);
GLUTATHIONE/*ME (METABOLISM);
LUNG/*DE (DRUG EFFECTS);
LUNG/*ME (METABOLISM);
LUNG/*PH (PHYSIOLOGY);
RESPIRATORY-FUNCTION-TESTS;
OXIDATIVE-STRESS;
PHOSPHOLIPIDS/ME (METABOLISM).
RN - CAS Registry numbers
64-17-5
Ethanol
70-18-8
Glutathione
NO CAS RN
Phospholipids.
SI - Secondary source
DART-TER-2001561.
LG - Language
English.
PT - Publication type
MEETING-ABSTRACT.
YR - Publication year
2002.
DT - Publication date
20020000.
ED - Entry date
200210
Date revised: 20021003.
Label/description Example
AN Accession number 1_: 11344715.AN.
& update 2_: 20050101.AN.
TOXBIB documents (those 3_: TOXBIB.AN.
extracted from Medline)
TOXNET documents (non-Medline 4_: TOXNET.AN.
material)
TI Title 5_: UVEITIS WITH
ANTIMETABOLITES.TI.
TT Title in original language 6_: UVEITES WITH ALKYLANTS.TT.
SO Source
Any word(s) of journal name 7_: BELGE WITH
OPHTALMOLOGIE.SO.
Abbreviated journal name 8_: BULL-SOC-BELGE-OPHTALMOL
A list of similar names 9_: ..ROOT BELGE.SO.
ISSN 10_: 0081-0746
Volume number 11_: VOLUME=279
Issue number 12_: ISSUE=17
Page number 13_: PAGE=133-65
AU Author(s)
Family name 14_: CASPERS.AU.
Family name and initials 15_: CASPERS-VELU-L-E.AU.
A list of similar names 16_: ..ROOT CASPERS.AU.
FA First author 17_: JONES-M-J.FA.
IN Author affiliation 18_: PIERRE WITH BRUGMAN.IN.
CA Corporate author(s) 19_: PRODUCT ADJ SAFETY.CA.
AB Abstract 20_: CORTICOSTEROIDS WITH BONES
Documents with abstracts 21_: ABSTRACT=YES
DE MeSH descriptors - single word 22_: AZATHIOPRINE.DE.
Multi-word term 23_: MYCOPHENOLIC-ACID
24_: MYCOPHENOLIC ADJ ACID.DE.
MeSH with subheading 25_: AZATHIOPRINE WITH AE
- hyphens for faster retrieval 26_: AZATHIOPRINE-AE
Exploded term 27_: ANTIMETABOLITES#
Find appropriate MeSH terms 28_: ..MESH ANTINEOPLASTIC
See a term in its TREE
structure(s) 29_: ..TREE UVEITIS
NOTE: many TOXNET documents do not have MeSH headings
MJ Major emphasis of descriptor 30_: UVEITIS.MJ.
PN Named persons 31_: HAYNES-R$.PN.
A list of similar names 32_: ..ROOT HAYNES.PN.
RN CAS Registry numbers 33_: 59-05-2.RN.
GS Gene Symbol 34_: FOS.GS.
SI Secondary source 35_: SI=DART
LG Language of publication 36_: LG=FRENCH
A list of languages 37_: ..ROOT LG=
Note: many TOXNET documents do not have language of publication
PT Publication type 38_: PT=PUBLICATION-TYPE
A list of publication types 39_: ..ROOT PT=
CM Comment 40_: TOXICOL ADJ PATHOL.CM.
SB Journal subset 41_: IM.SB.
A list of subsets 42_: ..ROOT SB=
CP Country of publisher 43_: BELGIUM.CP.
JC Journal code 44_: BYO.JC.
IP Information provider 45_: NASA.IP.
NT Notes 46_: 160.NT.
YR Publication year 46_: YEAR=2001
DT Publication date _: DATE=20010615
ED Entry date 48_: 20010628.ED.
1_: LAURYL ADJ SULFATE
YEAR Publication year (YYYY) 2_: ..L 1 YEAR>1999
UMONTH DS Update month (YYYYMM) 3_: ..L 1 UMONTH WL 200403,
200406
UDATE DS Update date (YYYYMMDD) 4_: ..L 1 UDATE>20050925
EDATE NLM Entry date (YYYYMMDD) 5_: ..L 1 EDATE>20040531
Tags - HUMAN, ANIMAL, FEMALE, MALE,6_: ..L 1 HUMAN=Y
ADULT, CHILD, REVIEW, PRIORITY
AB Abstract 7_: ..L 1 AB=Y
LG Language 8_: ..L 1 LG=FR
By paragraph - title, author _: ..P TI, AU ALL
SHORT AN, AU, IN, TI, TT, SO, CM, DO, YR
MEDIUM AN, AU, IN, TI, TT, SO, CM, AB, DO, YR
LONG AN, AU, IN, TI, TT, SO, CM, PT, DE, PN, RN, GS, SI, AB, JC, IP, CC,
DO, YR
FREE AN, TI, TT, CA, LG, PT, DE, RN, NT, DO, YR, DT, ED.
_: ..P LONG 1-5,12.
TOXNET data is the non-Medline (and largely non-journal) material
supplied by the NLM, and sourced from government departments and
international organisations. To restrict your search to TOXNET
data only, use TOXNET.AN.
To search each TOXNET file use the SI= quick code:
SI=ANEUPL
SI=CIS
SI=CRISP
SI=DART
SI=EMIC
SI=EMICBACK (The backfile for EMIC)
SI=ETICBACK (The backfile for ETIC)
SI=EPIDEM
SI=FEDRIP
SI=HAPAB
SI=HMTC
SI=PESTAB
SI=PPBIB
SI=RISKLINE
SI=TSCATS
Many TOXNET documents do not have MeSH headings or some of the other
standard Medline indexing such as language of publication, human/
animal/male/female indicators. Searching these will mostly
restrict your results to TOXBIB documents.
ToxFile and Medline:
All TOXBIB documents in ToxFile are displayed and searched
exactly as in Medline. Each document has MeSH headings describing
the subject content of the article. The following notes on their use
may be useful. But bear in mind that TOXNET documents frequently do
not contain MeSH headings, human/animal/male/femal/child/adult tags,
language of publication and other standard features of Medline.
Using these features will restrict your results to largely TOXBIB
documents.
DE - Descriptors: Medical Subject Main Headings
(MeSH Terms):
The DE paragraph contains descriptors from the Medline Thesaurus,
which consists of about 24,000 controlled Medical Subject Headings
(MeSH). MeSH is available online (..MESH, ..THES, ..TREE, ..EXPL)
and in the MVOC database.
Use the MeSH descriptors to produce the most accurate search
results.
The descriptor terms are double-posted. For example, GENES.DE. will
retrieve not only articles indexed to GENES, but also those on
GENES-BACTERIAL, GENES-FUNGAL, GENES-VIRAL etc.
If you wish to restrict your search to the single MeSH term GENES,
qualify to .W.:
1_: GENES.DE.
2_: 1.W.
Use the online MeSH to check search terms:
3_: ..MESH GENES
THES GENES$
R1 # GENES
R2 GENES-ABL
R3 2 GENES-APC
R4 2 GENES-ARAC
R5 ART-TRS-GENES -->
R6 # GENES-BACTERIAL
R7 BACTERIAL-STRUCTURAL-GENES -->
GENES-STRUCTURAL-BA+
(...)
then select appropriate R number.
Use hyphens or the ADJ and WITH operators, and qualify to .DE. when
searching multi-word MeSH terms:
4_: GENES-BACTERIAL
5_: GENES ADJ BACTERIAL.DE.
Major emphasis descriptors are displayed with an asterisk (*).
Qualify MeSH terms to .MJ. when you want them to be the major
descriptors, or .MN. for minor descriptors:
6_: GENES-BACTERIAL.MJ.
7_: BREAST-IMPLANTS.MN.
Use the hash mark (#) to explode MeSH terms, i.e. to retrieve all
terms in the hierarchy, for example:
8_: GENES#
Or use the online MeSH and select terms with the hash (#) mark:
9_: ..MESH GENES
THES GENES$
R1 # GENES '65
R2 GENES-ABL '91
R3 2 GENES-APC '93
R4 2 GENES-ARAC '88
R5 ART-TRS-GENES --> GENES-REV '90
R6 # GENES-BACTERIAL '82
(...)
10_: R1#
MeSH Subheadings:
An additional strength of the Medline indexing system is the use of
Subheadings which put the MeSH Main Heading into a more specific
context.
The Subheadings appear in the DE paragraph after the Main Heading,
as a two-letter abbreviation and full word(s):
DE BONE-DENSITY/*DE (drug effects);
CROHN-DISEASE/CO (complications);
DENTAL-CARE-FOR-DISABLED/*;
DENTAL-IMPLANTATION-ENDOSSEOUS/*CT (contraindications);
GLUCOCORTICOIDS/*AE (adverse effects);
HUMAN;
OSTEONECROSIS/CI (chemically induced);
OSTEOPOROSIS/CI (chemically induced);
PERIODONTIUM/DE (drug effects);
SUBSTANCE-DEPENDENCE/CO (complications).
The subheadings must be searched as abbreviations:
11_: GLUCOCORTICOIDS WITH AE
To check which Subheadings are available for the Main Headings, use
the online MeSH and the command ..D SH (..DISPLAY SUBHEADING):
12_: ..MESH GLUCOCORTICOID
THES GLUCOCORTICOID$
R1 GLUCOCORTICOID-ANALOGS -->
R2 2 RECEPTORS-GLUCOCORTICOID
R3 # GLUCOCORTICOIDS
R4 # GLUCOCORTICOIDS-SYNTHETIC
R5 # 4 GLUCOCORTICOIDS-TOPICAL
END OF THES
13_: ..D SH R3
ALLOWABLE SUBHEADINGS FOR
R3 GLUCOCORTICOIDS
AD ADMINISTRATION & DOSAGE
AE ADVERSE EFFECTS
AI ANTAGONISTS & INHIBITORS
AN ANALYSIS
BI BIOSYNTHESIS
BL BLOOD
CF CEREBROSPINAL FLUID
CH CHEMISTRY
CS CLASSIFICATION SYNTHESIS
CT CONTRAINDICATIONS
DF DEFICIENCY
DU DIAGNOSTIC USE
EC ECONOMICS
GE GENETICS
(...)
Pre-exploded Subheadings:
MEDLINE has some pre-exploded subheadings which allow fast retrieval
of some important subheading groups:
QT - Quick therapy. Contains the subheadings TH (therapy), DT
(drug therapy), RT (radiotherapy), DH (diet therapy) and SU
(surgery).
QD - Quick diagnosis. Contains the subheadings DI (diagnosis), RA
(radiology), RI (radionuclide imaging) and US
(ultra-sonography).
QX - Quick toxicology. Contains the subheadings AE (adverse
effects), PO (poisoning), TO (toxicology) and CT
(contra-indications).
14_: INTESTINAL-NEOPLASMS# WITH QT
This gives the same result as, but is faster than:
15_: INTESTINAL-NEOPLASMS# WITH (TH DT SU RT DH)
Some new quick-subheading groups were introduced in 2003. The full
list is as follows:
QA - Quick anatomy (AH BS CY PA UL EM AB IR)
QB - Quick embryology (EM AB)
QC - Quick chemistry (CH AG AA AI CS)
QD - Quick diagnosis (DI PA RA RI US)
QE - Quick etiology (ET CI CO SC CN EM GE IM MI VI PS TM)
QG - Quick surgery (SU TR)
QK - Quick microbiology (MI VI)
QL - Quick complications (CO SC)
QM - Quick metabolism (ME BI BL CF DF EN PK UR)
QN - Quick analysis (AN BL CF IP UR)
QO - Quick organization (OG EC LJ MA ST SD TD UT)
QP - Quick pharmacology (PD AD AE PO TO AG AI CT DU PK)
QS - Quick statistics (SN EP EH MO SD UT)
QT - Quick therapy (TH DH DT NU PC RT RH SU TR)
QU - Quick therapeutic use (TU AD AE CT PO)
QW - Quick epidemiology (EP EH MO)
QX - Quick toxicology (PO TO AE CT)
QY - Quick physiology (PH GE GD IM ME BI BL CF DF EN PK UR PP SE)
QZ - Quick cytology (CY PA UL)
Quick-Search:
Quick-Search is a fast and easy method of retrieving Subheadings
linked to MeSH terms and pre-exploded Subheadings. The Subheadings
can only be Quick-Searched as abbreviations. Precede your search
with QS:
16_: QS CORONARY-DISEASE# WITH (PP CI DT)
17_: QS ARRHYTHMIA WITH QD
Quick-Search also works very well in combination with the online
MESH and TREE, which saves time and typing:
20_: ..MESH ARRHYTH
THES ARRHYTH$
R1 # ARRHYTHMIA
R2 # ANTI-ARRHYTHMIA-AGENTS
R3 ARRHYTHMIA-SINUS
22_: ..TREE R1
T1 # CARDIOVASCULAR-DISEASES
T2 # HEART-DISEASES
T3 # ARRHYTHMIA
T4 ATRIAL-FIBRILLATION
T5 ATRIAL-FLUTTER
T6 BRADYCARDIA
T7 EXTRASYSTOLE
T8 HEART-BLOCK
T9 ADAMS-STOKES-SYNDROME
(...)
23_: QS (R1 R3 T4 T5) WITH (PP CI DT)
Search statements containing Quick-Search may be saved in Alerts and
for later re-execution.
..RANK and ..MAP are available in the AU, SO, DE and RN paragraphs.
Search aids:
At the end of 2003 NLM ceased publication of the three print MeSH
tools - the Annotated Alphabetic MeSH, the MeSH Tree Structures and
the Permuted MeSH. Similarly, the publication of the
Medical Subject Headings Supplement to Index Medicus (familiarly
known as the 'Black and White' MeSH) ceased with the 2007 edition.
The MeSH terms can be browsed online in ..MESH, in MVOC, in Medline
on DataStarWeb and in the MeSH Browser on the NLM's website.
ToxFile is the mark used by Dialog/DataStar for a collection of
toxicology-related material provided by the National Library of
Medicine.
For The Dialog Corporation's Electronic Redistribution and Archive
Policy, enter HELP ERA online. The following terms and conditions
also apply.
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The duplication, resale, or redistribution of data obtained under
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Unless otherwise prohibited, organizations or institutions may
download small amounts of NLM-produced citations for redistribution.
For ToxFile, this is about 1,000 per month or 12,000 records for
each year of coverage. Since NLM makes corrections and enhancements
to and performs maintenance on these records at least annually,
users should plan to replace or correct the records once a year to
ensure that they are still correct and searchable as a group.
NLM databases are produced by a U.S. government agency and as such
the contents are not covered by copyright domestically. They may be
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