Select PubChem

An introduction to SQL is provided in Chapter 3, but with an emphasis on examples relevant to chemical information rather than business information, which is often used in other books. Chapter 4 discusses some of the RDBMS that are available, namely Oracle, MySQL, and PostgreSQL. All of them use SQL to insert, delete, update, and select data. Chapter 5 shows ways in which client programs, including Web-based applications, are used to connect to the database server. Chapter 6 examines ways in which RDBMS are typically used to handle numerical and textual chemical information using relational tables. An example of using data files from the PubChem project is included. 

Notice the use of the Join keyword and the additional table name pubchem.substance in the From clause. This is necessary because data from this table is being selected. The additional columns selected are ext datasource name and substance.ext datasource regid in the Select clause. Any columns of interest in the substance table could be selected. Note that since there is a column named ext datasource id in both tables, it is necessary to specify that the column substance.ext datasource regid is desired. Finally, the clause On nci h23.sid= substance, substance id indicates that these columns are related to each other and must be used in the Join. 

Select From pubchem.compound Where iupac name Like %aldehyde% And heavy atom count < 20 ... 

From the examples in the previous section, it is clear how the substance id relates pubchem.substance to biological assay data and how substance data can be selected using the substance id. How can the compound table be used to select compound data for substances appearing in one of the biological assay data tables In other words, how is the... 

The column pubchem.substance.cid associations is taken directly from the sdf files supplied by PubChem. It has all the necessary information, but it is not in a proper form for a relation between pubchem.substance and pubchem.compounds. This is because too much information has been crammed into this column. For example, the cid associations for substance id 22 contains the data "449653 1449655 2 6540406 2". This means that there are three compound ids associated with this substance id. In other words, there is a many-to-many relationship between compounds and substances. While it would be possible to parse the cid associations column when the compound id is needed, it is better to have a clear relationship between substance ids and compounds ids. It is better because it enforces and preserves the relational integrity (or referential integrity) between these data. It also makes selecting data from all three data sources quicker and easier. 

When the desired data is in two different tables, a join is required. It is often helpful to begin to develop complex SQL statements by considering one table at a time. For example, data from the nci h23 table of pubchem schema was considered earlier in this chapter. The experimental data to be selected from that table was the substance id (called sid in the table), activity outcome, log gi50 M and n.log gi50 ugml. This is accomplished by the simple SQL... 

Figure 12.3 shows the result of searching for the word "aspirin" in Entrez s PubChem Compound database. This default display of multiple records in Entrez is referred to as a document summary (DocSum) report and is common to all Entrez databases. At the top are the common Entrez controls (database selection and search input box) and tabs for other Entrez tools (e.g.. Limits, History, etc.) some of which are described in more detail below. Note that the format of this page evolves over time, but the basic controls remain the same. Moving down the Doc-Sum page, the next section contains controls to change the display type the default is "Summary" (as shown). Each Entrez database has report styles that vary in type and detail of information shown, the overall format is the same—a list of records. 

The filters for each Entrez database may be listed by going to the "Pre-view/lndex" tab in Entrez, opening the menu on the bottom left, selecting "Filters," and pressing the "Index" button. Also, this page provides an interface for adding filters to Entrez queries. A complete list and description of the custom Entrez filters available for the three PubChem databases are detailed in the "Indices and Filters in Entrez" section of the help documentation (http //pubchem. ncbi.nlm.nih.gov/help.html). 

After working with PubChem to achieve a particular subset for a query of inferesf, it is often important for a user to export resulting substance or compound records from PubChem for further local analysis. The structure download tool prepares PubChem Substance or PubChem Compound records as an export from Enfrez in a number of formats. While all PubChem data is available on the PubChem FTP site (via the URL ftp //ftp.ncbi.nlm.nih.gov/pubchem/), being able to interact with a user-selected subset is substantially more convenient. The structure download tool may be directly accessed using the URL ... 

BioActivity summary provides a set of functions that allows one to revise the substance/compound and assay sets. For example, one may focus only on a subset of compounds that are active in one or more of the selected assays using the Compound I Select Active link, or explore additional screen sets where the given compounds were considered active using the Assay I Add Active link. PubChem provides multiple access points for this service. For compounds or substances tested found in Entrez, one can launch this service for each individual record using the direct "BioActivity Analysis" link, or, for all of the records from an Entrez search, through the launching point at the "Tool" area. 

Bayesian and counter propagation neural networks N = 285 from the literature. 3 classes > lOpM, fold cross-validation, N = 58 newly selected compounds used as a test set as well as the PubChem data N = 193 actives, N = 1703 inactives. Used SIBAR Descriptors. 85-88% classification of hERG blockers. 195... 

The PubChem Dataset A randomly selected subset of 1000 measured solubility values selected from a set of 58,000 values that were experimentally determined using chemilumenescent nitrogen detection (CLND) by the Sanford-Bumham Medical Research histimte and deposited in the PubChem database (AID 1996) [23] This dataset is composed primarily of screening compounds from the NIH Molecular Libraries initiative and can be considered representative of the types of compounds typically found in early stage drug discovery programs. Values in this dataset were reported with a qualifier < to indicate whether the values were below,... 

This entire concept was extended by mining [40, 41] public databases such as BindingDB [42], PubChem [43], or ChEMBL [44]. In such a study, all human target protein pairs were extracted, which share at least five active compounds [40]. This selectivity-centric analysis of protein-ligand data unveils more than 200 scaffolds that appear to be selective for certain target families. A subset of these scaffolds refers to highly selective molecules compared to neighboring proteins [40]. 

Go to http //pubchem.ncbi.nlm.nih.gov/summary/summary. cgi dd=5988, dick SDF icon on top right, and select 3D SDF Save. 

Select Open Babel tab under Controls panel and click on the first icon on its toolbar with plus (+) sign on it. Navigate to the Downloads folder and select CID 5988.sdf (sucrose from PubChem). 

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