Daybase (DayCart) Introduction What is ‘Daybase’ ? Oracle Schema Objects. Oracle Datatypes. Simple Example. Demo.

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Presentation transcript:

Daybase (DayCart)

Introduction What is ‘Daybase’ ? Oracle Schema Objects. Oracle Datatypes. Simple Example. Demo.

Oracle Schema Objects Tables. –Tables are the basic unit of data storage. Data is stored in rows and columns. Views. –View is a tailored presentation of the data contained in one or more tables (or other views). Indexes. –Indexes are optional structures associated with tables. You can create indexes explicitly to speed SQL statement execution on a table.

Oracle Schema Objects Sequences. –Please read the Oracle Server Concept manual. Synonyms. –Please read the Oracle Server Concept manual. Clusters. –Please read the Oracle Server Concept manual. Hash Clusters. –Please read the Oracle Server Concept manual.

Oracle Datatypes CHAR. –The CHAR datatype stores fixed-length character strings. VARCHAR2 (VARCHAR). –The VARCHAR2 datatype stores variable-length character strings. NUMBER. –The NUMBER datatype stores fixed and floating-point numbers. You can optionally specify a precision (total number of digits) and scale (number of digits to the right of decimal point).

Oracle Datatypes DATE. –The DATE datatype stores point-in-time values (dates and time) in a table. LONG –Stores variable-length character data, up to two gigabytes of information. RAW and LONG RAW. –Stores variable-length character and binary data. ROWID. –Please read the Oracle Datatypes Concept manual.

Simple Supplier Schema STRUCTURE Data SMILES Supplier Data SUPPLIER

Oracle Table Definitions Table:STRUCTURE NameNull?Type STR_IDNOT NULLNUMBER(7) SMILESNOT NULLVARCHAR(700) MFVARCHAR(200) MWTNUMBER(12,6) CLOGPNUMBER(12,6) Table:SUPPLIER NameNull?Type STR_ID NOT NULLNUMBER(7) SUP_IDNOT NULLVARCHAR(80) SUP_NAMENOT NULLNUMBER(200) COSTNOT NULLNUMBER(10,5)

The STRUCTURE Table SMILESSTR_IDMFMWTCLOGP CC(=O)N C12H16N OCn1c2ccc… 2345 C10H12N3… O=C1N(C(… 2873 C18H28N2O… Cc1(=O)n… 2693 C16H12N… Rows Columns Column names Column NOT allowing nulls Column allowing nulls

The Structure/Supplier Table SMILESSTR_IDMFMWTCLOGP CC(=O)N C12H16N OCn1c2ccc… 2345 C10H12N3… O=C1N(C(… 2873 C18H28N2O… Cc1(=O)n… 2693 C16H12N… STR_IDSUP_IDSUP_NAMECOST 2482ID-2211 ChemBridge Corp ID ChemBridge Corp Tocris LT Lab-Tech Tocris LT-2376Lab-Tech ID-23467ChemBridge Corp ID-23466ChemBridge Corp Tocris Structure Table Supplier Table

What are the steps Design the data model. –Consider input, access and modification of your data. –Consider how chemical data is going to be searched. –2D coordinates. –Connection table (Molfile, RXNfile, TGFfile … etc). –SMILES column size (what to use?). 700 bytes or less, Oracle will allow you to put unique indexes and blob-based index. This may or may-not be important to you. greater than 700 bytes you can use blob-based index. Design the database schema.

What are the steps Indexes for normal column data. Indexes for chemical structure data –i.e. ddexact, ddgraph, ddblob … etc. Create PL/SQL program to load the data. If the data is formatted you may be able to use ‘sqlldr’ command to load the tables. For data from SD files use mol2smi procedure. Application/tools for the user to search and display of this data.

Thanks Daylight team Bernd Rohde (Novartis) Michael Wainwright (Modgraph)

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