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Toxicology - In-depth Research Guide: Database Details

This guide is designed to assist patrons who need to do an in-depth search of the detailed toxicology of a particular substance or make an extensive review of a topic related to toxicology such as endocrine disrupters.
Last Updated: Apr 4, 2022 9:54 AM

Databases Details

Database Search Details

SciFinder [Search Details]

If MEDLINE information has already been searched via TOXLINE, PubMed, UB's MEDLINE via OVID, or MEDLINE via Web of Science, then the MEDLINE portion of SciFinder can be turned off by clicking on the Preferences Button, then the Databases Tab, and then deselecting MEDLINE. This must be done before starting the search. However, SciFinder's powerful natural language query system may retrieve MEDLINE records missed by the other MEDLINE search interfaces.

Two basic approaches, compound or subject, can be used to find toxicological information in SciFinder Web.

a) Starting with a specific compound

If the user has a particular substance of interest, click on the Locate button, then on the Locate Substances: Substance Identifier button. Enter a CAS registry number or chemical name. A brief record with the chemical structure will display. Click on the Get References button at the bottom of the page. Activate the References Associated With radio button; then check the Adverse Effect, including Toxicology box. Click the OK button to retrieve the references.

All the Chemical Abstracts records are displayed first, then all the MEDLINE records, each group in reverse chronological order. Clicking on the Microscope icon for any record will display the full record including abstract and indexing. Clicking on the Full-text icon (looks like a page of paper) will lead to the full-text of the item.

If another version of MEDLINE has already been searched, MEDLINE citations can be eliminated from retrieved sets by clicking on the Analyze/Refine button, then the Refine button, the Database button, and then checking only the CAPLUS box. MEDLINE records duplicated by CAPlus records can be removed by clicking on the Remove Duplicates button.

It is also possible to retrieve substance records by molecular formula, exact structure, or substructure searching using the Explore option. The process for retrieving the toxicology literature references remains the same regardless of how the substance record(s) are retrieved.

Note that SciFinder Web has an extensive database of regulatory information based on various state, US, and international lists created by various agencies. This information can be accessed by retrieving any substance record and clicking on the small gray icon that looks like a building with 3 columns. See the Regulated Chemicals (CHEMLIST) Database Information Page for further details.

b) Subject/Topic search

From the main search screen, click on the Explore button, and then the Research Topic button. It is important to phrase the search query naturally using prepositions to separate search concepts. For example, the query 'mutations in salmonella by ultraviolet light' would retrieve a group of very relevant citations on that topic. Simply putting in a list of individual words with spaces in between (as in Google) should NOT be done. The system first presents a candidate list of hit sets based on various combinations of the concepts in the query. Choose whatever hit sets are desired based on the description of each and click on the Get References button.

If the results are unsatisfactory or too small, use the Back button and rephrase the query. If there are a large number of hits, one can rephrase the query or limit the retrieval set by use of the Analyze/Refine button. Refine options include date, document type, language, and availability of full-text. Another option under Refine is Research Topic which permits limiting the query using additional keyword(s). Analyze/Refine options can be used reiteratively as many times as needed to narrow the search results. When doing keyword searches, keep in mind that SciFinder Web covers all aspects of chemistry and chemistry-related topics, not just toxicology.

Chemical Abstracts Service provides a set of excellent downloadable, interactive tutorials for those needing additional help in using the system.

BIOSIS Citation Index (Web of Science Platform) [Search Details]

In BIOSIS Citation Index a simple keyword search will search all fields containing text including title, abstract, indexing and concept & taxonomic names. The BIOSIS Citation Index Quick Reference Card outlines search syntax and describes how to search various fields. An in-depth description of the Web of Science search interface is beyond the scope of this guide. Web of Science Quick Reference Guide provides a brief introduction to the search platform.

Searching specific index/code fields can greatly enhance the retrieval or limit a large results list to a much more focused set. Individual fields can be searched by clicking on the drop down menu boxes to the right of the search term boxes on the main search query screen. Search examples below the query term text boxes change to show sample format(s) for the chosen field. For many of the search fields, a magnifying glass icon appears to the right that allows one to browse the field in an alphabetical or hierarchical fashion. A brief review of some of the key index fields follows.

Concept Codes: This field contains five-digit codes representing broad biological concepts mentioned in the document. Codes can be searched at the broader three-digit or the narrower five-digit level. The table below lists key codes for toxicology-related fields.

  • Toxicology - 225
  • Air, Water, and Soil Pollution - 37015
  • Ecology - 075
  • Neoplasms and Neoplastic Agents - 240
  • Occupational Health - 37013
  • Pharmacology - 220

Chemical & Biochemical : This search option searches the chemical and biochemical indexing including chemical names and Chemical Abstracts Service Registry Numbers, which are assigned to chemicals mentioned in the article. The Registry Number defines a unique substance independent of nomenclature. Two hyphens appear in every Registry Number, which separate the number into three parts.

Taxonomic Data: This search option searches taxonomic names & notes, super taxa, organism classifiers & names, and variants.

 

MEDLINE (Ovid) [Search Details]

In MEDLINE, a simple keyword search using the text entry box under Enter Keyword or phrase will search all fields containing text including title, abstract, and subject headings. Be sure to retain the default checkmark in the box Map Term to Subject Heading on the main search page and then click on the Perform Search button. A pick list of subject headings related to the query keyword will be presented. The user can pick as many items as desired to be searched in the database. Clicking on underlined subject headings will display the hierarchical context of that particular term within the overall MeSH thesaurus.

Note the three columns after each term on the pick list. Checking the Explode option will retrieve that subject heading plus all narrower terms as defined by the MeSH thesaurus. Checking the Focus option will retrieve only those records where that particular subject heading is identified as a major concept in the article. The third column, Scope , having icons with the letter I inside a circle provides helpful scope notes about the term. Note the very last item on the pick list will be a simple keyword search in all text fields.

An in-depth description of the Ovid search interface is beyond the scope of this guide. See Ovid's Tutorials & Short Demos to learn more about search syntax and interface features. More extensive information can be reviewed by clicking on the blue Help button in the upper right hand corner of most Ovid web pages.

Searching certain index/subject heading fields can greatly enhance the retrieval and/or limit a large results list to a much more focused set. Individual fields can be searched by clicking on the Search Fields icon at the top of the Ovid search page. A detailed discussion of each search field is provided in Ovid's MEDLINE Database Guide. A brief review of key index fields follows.

Floating Subheadings: The Floating Subheadings ( FS ) field contains standard 2-letter codes used to subdivide MeSH subject headings. Useful subheading codes for toxicology-related areas include TO for toxicity , AE for adverse effects, PO for poisoning, DE for drug effects, ME for metabolism, and PK for pharmacokinetics. To link (relate) a subheading to a particular term or substance, one should search the full MeSH subject heading, if known, in the Subject Heading field ( SH ). If the desired MeSH subject heading is not known, follow the keyword search procedure described in the first two paragraphs of this section.

MeSH Subject Headings: In general, these can be most conveniently searched simply by entering likely keywords in the general keyword search box while making sure to retain the default checkmark in the box Map Term to Subject Heading. This is described in the first two paragraphs of this section. However, if MeSH subject headings are already known, they can be searched directly in the SH field.

Biological Sciences Librarian

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Fred Stoss
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