12 Matching Annotations
  1. Mar 2017
    1. In 2-D similarity methods, structural similarity between two molecules is estimated by comparing their molecular fingerprints. 

      So, will each structure on PubChem have a fingerprint and a molfile? lyndsie

    2. targets

      what is a target? lyndsie

    3. In substructure search, one provides an input substructure as a query to find molecules that contain the query substructure

      My question is if I were trying to find a large superstructure with more than one substructure, can I input more than one substructure to search? i.e. If I want to find compounds that contain and aldehyde and an alcohol. Lyndise

    1. substance is a contributed chemical substance sample description from a particular PubChem data provider.  A compound is a normalized chemical structure representation found in one or more contributed substance

      On module 4 #4, it states that databases often share information with each other. Does PubChem share information from the substance database to an outsid data base or do they go through the process to be linked to PubChem compound first? Lyndsie

    1. Unique Ingredient Identifiers (UNIIs) and pharmacological classifications were added from the U.S. Food and Drug Administration (FDA).

      "Ingredient indentifiers". Are these similar to InCHi Keys or in a leauge of its own? Lyndsie

    1. Therefore, it is very common that database groups exchange their information with each other. 

      Does this mean PubChem is sharin information between BioAssay and Compound databases or PubChem is sharing information with ChemSpider, etc.? Lyndsie

    2. Although the data provenance information is critical in the reliability of a data source (and its data), this information is not easy to manage. 

      How do we determine the reliability of a source? Like, I've gone through and looked at the data provenance, how do I say this peice of info is reliable, but this conflicting information on a different database is not based on their data provenance?


    3. In turn, users should always pay attention to the data provenance issue when using a database.

      Since we are focusing on PubChem and this sentence tell us, as users, to pay attention to the sources, how do we find the source on PubChem? Furthermore, say that source leads to another souce, how far do we go back?


    1. The BioAssay database (https://www.ncbi.nlm.nih.gov/pcassay)

      I followed the link here to find out more. I do not know what BioAssay means. Googling gives bio screening programs, but can anyone give me the gist of what this is? Lyndsie

  2. Feb 2017
    1. Are connection tables not used for inorganic compounds? Is there a different program used to analyze these?

    2. Our atom table will consist of two fields: one an index number identifying the atom we’re talking about, one indicating atom type (i.e. C, H, O, N, etc.). Our bond table will consist of three fields: two indicating the two atoms that the bond connects, and one indicating the bond order (1=single, 2=double, 3=triple).

      Are the atoms numbered by a set of governing rules or does it matter which atom is numbered what?

      Even given the following examples, I still do not understand how to read or create a bond table. I would like to see an example worked in steps so that I can follow the process.

    1. WIREs Computational Molecular Science Representation of chemical structuresFIGURE 3|A redundant connection table

      Just a comment here. This table is much easier for me to follow than the examples in module 2 part 2.