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CHEM 115: Chemical Structure and Bonding with Inquiry Lab (HC) Fall 2017

Chemistry 115: Chemical Structure and Bonding with Inquiry Lab (Stuart)

Using SciFinder

Quick Start: How to search by topic (3 min)

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Why SciFinder?

SciFinder is the largest chemical information database for professional chemistry needs. It is an intuitive front-end capable of searching using keywords or structures. See a summary of the content searchable through the SciFinder interface at the CAS-At-a-Glance website.

How to search SciFinder

CAS (Chemical Abstracts Service) has developed a series of concise videos (Need-to-Know Series) on how to search effectively:

How to connect to SciFinder from Haverford campus

 

N.B. If you're away from campus, you can either use the EZProxy method or VPN method to appear to be accessing it from campus. Many resources only recognize campus connections to be authorized users.

Searching for a synthesis

In addition to using a structure search as substance or a reaction, you can also use CAS Registry No. or a chemical name or trade name. This kind of searching is especially convenient for drug synthesis search. For example, I am searching for the laboratory synthesis of arteminisin.

 

Since there are 416 reactions, it is useful to make use of the SORT options

as well as GROUPING options

You can Analyze by a number of parameters

 

and Refine, even by drawing a reaction substructure

Topic Search 

Here is a possible strategy for finding how the structure of drugs affect the mechanism of action. 

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Saving Results

See this video on how to save results and merge results sets.

 

 

Using PubMed

Why PubMed?

A very useful database for researching biological chemistry topics is MedLine (which is searched through PubMed) because it covers biology (molecular and macrobiology), biochemistry, clinical medicine and more.  

PubMed is a search interface for retrieving bibliographic citation and abstracts from MEDLINE, the premier bibliographic database of biomedical literature (basic biology and clinical medicine) indexing more than 5,665 biomedical journals from around the world. The time coverage is from 1946 and ongoing. There are now over 24 million journal articles and is the largest biomedical database in the world.

Keyword searches in PubMed

Keywords can be connected by Boolean operators AND, OR, NOT. PubMed requires that you capitalize them. The default operator is AND.
Pubmed has built-in artificial intelligence that parses your search statement made up of keywords. For example, I wanted to know about the metabolism of ritalin. 

ritalin AND metabolism

Note: PubMed search terms are not case-sensitive, but look how the intelligent engine treats the query. Look in the "Search Detail" all the way down on the right ladder.

Notice how PubMed automatically looks for the medical subject headings (MESH) that match my keywords and searched for them.  It also finds the correct medical subject heading (MeSH) for "ritalin" (methylphenidate)  and "metabolism" (as a subheading, and as a main heading "metabolic networks and pathways") while still searching for my keywords as  individual words co-occurring in the same record in all fields. If I had entered two adjacent words, PubMed would have searched for them separately as individual words, and also as a phrase.

This is the automapping function in PubMed that broadens the search and maximizes retrieval of answers. Sort a very large results set using Relevance to get a different perspective than Newest first (default sorting order in PubMed). Look through the first 50 titles that come up to get a sense of the kind of information it fetches. For anything that is on-point, click on the title to read the abstract. For very relevant articles, look at the MeSH heading within and make a note of them. Mark it and save to the Clipboard. Restrict the time period to 5 or 10 years, and look at the Reviews. 

Subject Heading search in PubMed

Medical subject headings (MeSH) describe the concepts in the MEDLINE database to give it uniformity and consistency. Users reliably retrieve relevant articles when they use MeSH without having to hit on all the correct keywords and their synonyms or foreign language spellings.

For example, you wanted to explore further  methylphenidate as Medical Subject Heading.

Using the dropdown menu next to the search box, you select MeSH and enter methylphenidate 

You see the definition of the term and the entry terms that would map to this heading. 

Subheadings in PubMed

There is also the ability to fine tune your search by specifying whether a heading should be a major focus (major heading), and whether the terms that are below the current subject heading within the MESH tree (i.e. narrower in scope) should also be searched (a.k.a. “exploding” a term).

For example, I wanted to intersect the idea of chemistry of ritalin AND metabolism of ritalin, I need to check each subheading and add to the search builder with the AND connector.

PubMed's default is to "explode" the term if there are any narrower terms in the hierarchy unless you check the box to not explode. In the above example, it is fine to include the narrower term dexmethylphenidate (the d-isomer).

 

To get more info on how to use PubMed's MeSH efficiently - check out the 3-min YouTube Tutorial under the Search Builder box.

Discovering is not optimizing

Constructing search statements is an iterative process. Once you get an initial set, it is appropriate to scan your answers to learn the information landscape of your topic. Go into each one that looks on target to find more subject headings for your subsequent searches, and look at related articles listed on the right side. PubMed's automapping feature provides a useful way to discover subject headings so that searches can be adjusted by searching specific MESH along with suitable subheadings.

N.B. If you use wildcard symbol * or put words in quotes, the automapping no longer works.

Wildcards and phrase searching are profitably searched in specific fields such as title and abstracts (this is also called a fielded search). If there are exact phrases (enclose your phrase in " ")and word stems (use wildcard * for any number of characters) you want to use, by all means use them in your fielded search to gain more precision in your results.

The best searches take advantage of the MeSH advantage of precision and relevance and the flexibility of keyword searches.

For example, I wanted to find articles that mention actual enzymes to show me the catalytic mechanism, so I add the keyword enymes

"Methylphenidate/metabolism"[Majr]) AND "Methylphenidate/chemistry"[Mesh] AND enzymes

And I found this article 

Methylphenidate is stereoselectively hydrolyzed by human carboxylesterase CES1A1.

Sun Z, Murry DJ, Sanghani SP, Davis WI, Kedishvili NY, Zou Q, Hurley TD, Bosron WF.

J Pharmacol Exp Ther. 2004 Aug;310(2):469-76. Epub 2004 Apr 13.

PMID:15082749
 
[PubMed - indexed for MEDLINE] 
Free Article
From this article by Sun, I found that "Human liver carboxylesterases (E.C.3.1.1.1) play an im- portant role in metabolism and detoxification of ester drugs" including methylphenidate. Knowing the enzyme classification number 3.1.1.1 allows me to take this information to BRENDA enzyme database to find the article that reveals the mechanism.

Advanced Searching

Accessing the Advanced Search page by clicking the link below the search box. On the Advanced Search page is your search history, with all the searches you have conducted during the session. You can combine different searches with boolean operators for more relevant answers. It is also convenient to enter terms to search in specific fields.


Refine and Filter

  • Since research is an iterative process, after each set of answers are displayed, evaluate whether their relevance and refine the search statement accordingly.

  • Click on the article title to read the abstract, keywords, MeSH and other descriptors. Look at the Related Citations for each article. These are often very helpful. Also look for newer articles that cite the parent article. This carries your line of inquiry forward in time to get to the latest developments. This process of tracking citations backwards and forwards in time is called citation chaining.

  • The default sort order is reverse chronological order – newest first.  You can also sort by relevance. If too many results appear, you can refine by using filters. 

  • Filter types are on the left side. Some useful filters are “Article Type”, “Publication Dates” etc. Within each type of filter, you can see more choices by clicking on “More…”

  • To display more filter types, click on “Show additional filters.” Check the filter items to apply.  Click again to uncheck.

  • Article Type filter – the most useful ones are “reviews” which gives a review of the literature, an overview, on your topic.

    Publication Date filter – popular options are the 5-years and 10-year brackets. When more than 1,000 hits are found, you can see a histogram of publications by year. Click on any year to limit.

Saving results

  • To save answers from your searches, click on the double arrows next to the Send to widget. You can email, print, or export your clipboard items.

  • To export, check the Citation Manager radio button. The saved file will have the filename citations.nbib.

  • If your citation manager is Endnote Basic (Endnote Web) you can import this file using either the Refman RIS or PubMed(NLM) import filter.
  • As you find yourself using PubMed more often, you may want to create your own workspace with it. Create a free account in MyNCBI. You can save your answers in different folders (Collections), save your fine-tuned search strategies that are just-so, and create alerts so your search can run periodically. I love MyNCBI. Maybe you will too.

About review articles

Literature review articles decribe the historical development of concepts, theories and experiments in a research area to establish context. Often the review will include discussions of seminal studies and how they influenced the development of the field. These could be discoveries of structures, neural circuits, endogenous chemicals such as neurotransmitters, peptides and the molecular mechanisms they use to interact. New techniques and methodologies pushes the frontier of neuroscience forward - they have an important place in a review paper as well.

By reading recent authoritative review articles, one can select and focus on particular aspects of the topic and  acquire useful vocabulary to use as keywords for searching.

Literature review articles have a robust reference list that is most convenient for more in-depth study of particular aspects - enclose the article title in quotes to bring up the article in PubMed. Use the button to link to full text (if we subscribe) or get a pre-filled interlibary loan form (ILL form).

But Google Scholar often finds PDFs in the wild so try that first before going the ILL route!