2. Understanding Chemical Searches

        This section describes various searches that can be performed in PubChem.  Currently PubChem has three different search interfaces:

  1. PubChem homepage (http://pubchem.ncbi.nlm.nih.gov)
  2. PubChem Chemical Structure Search (https://pubchem.ncbi.nlm.nih.gov/search/search.cgi)
  3. PubChem Search (https://pubchem.ncbi.nlm.nih.gov/search/).

The PubChem homepage provides a search interface for all three primary databases (e.g., Substance, Compound, and BioAssay).  However, the search box on the PubChem homepage can accepts textual keywords only, and it is difficult to input non-textual queries (such as chemical structures).  The PubChem Chemical Structure Search allows users to perform various searches using both textual and non-textual queries.  This search interface is integrated with PubChem Sketcher, which enables users to provide the 2-D structure of a molecule as a query for chemical structure search.  While the PubChem Chemical Structure Search is limited to chemical structure searches, the PubChem Search allows users to search for bioassays, bioactivities, patents, and targets as well as chemical structures, but it is still in beta testing.  In this module, we use the PubChem homepage for name/text search and the Chemical Structure Search for others.

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OLCC s12's picture
OLCC s12 | Sun, 10/25/2015 - 22:40
This question is more for any of the chemical search engines, even though this particular sub-section was on PubChem. Chemical search engines are getting extremely complex and this seems to be a great thing for researchers to save time. My question is that when doing my background research on something and later publishing it, should I be keeping really detailed notes on every single option used in my chemical searches to be included into the citations or would this be overdoing things? In the past, it may have only been necessary to include which search engine was used and the keyword, but with replicating an exact search being very complex, it seems there is a big need for this in the science community in regards to publications.

Sunghwan Kim | Mon, 10/26/2015 - 00:01
Actually, it is highly recommendable to keep records on BOTH your search strategy AND search results. In addition to the very complex nature of chemical structure search, data contents in the public chemical databases keep changing, and the search results may also be affected by this change. This often makes things very complicated when you need to re-run your search months later while you are working on a year-long project. Therefore, you need to save your search strategy (query & options/filters and other limits), as well as search results. I strongly suggest that you keep these two things in text files. When you use PubChem Structure search, you can save your query and options so that you can re-run the search later with the same query/options, by simply importing the query/option information from the file. You can find the “save” icon at the bottom of the PubChem Chemical Structure Search page under any tab except for name/text search. The saved file can be imported from the file by using the right-most tab in the PubChem Chemical Structure Search tool.

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