1 / 15

Migrating to DayCart

Migrating to DayCart. Introduction. Thor database concepts. Data (Chemical Structure) hierarchy. Thor data model Daylight/Oracle cartridge data model. Other Considerations. What are the steps. Demo. Thor Database Concepts. Datatrees, Datatypes, Dataitems and Datafields.

arvid
Download Presentation

Migrating to DayCart

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Migrating to DayCart

  2. Introduction • Thor database concepts. • Data (Chemical Structure) hierarchy. • Thor data model • Daylight/Oracle cartridge data model. • Other Considerations. • What are the steps. • Demo.

  3. Thor Database Concepts • Datatrees, Datatypes, Dataitems and Datafields. • These four concepts are closely related. • Datatrees - Is the method for representing chemical information. • Datatypes - A set of definition that indicate the meaning of a dataitems fields. • Dataitems - Tag names a datatype, which in turn defines the meaning of each datafield. • Datafields - A string of characters; the unit of data.

  4. Data (Chemical Structure) hierarchy • Data stored for each chemical entity are organized on a hierarchical basis with each entity expressed in terms of Parent, Version and Preparation(Oracle only). • Parent is the basic structure which is free of salts, solvates and radio labels. • Version is the translation of a Parent into an actual compound, i.e. a free base, salt, solvates, etc... • Preparation being a discrete batch of that Version.

  5. Parent Version 1 Version 2 Version n Prep Prep Prep Prep Prep Prep Prep Prep Prep Data (Chemical Structure) hierarchy Thor Database, with all molecule information

  6. SMILES CC(C)C(O)C1CCCCC1 FP Timestamp 199701291010.03 Graph CC(C)C(O)C1CCCCC1 DB_NO 873 PISM CC(C)[C@@H](O)C1CCCCC1 ATOM_STER 2,1,1,4,1,7,1,10,1 . . DB_NO 97 VISM Cl.CC(C)[C@@H](O)C1CCCCC1 SALT 1,10 Daylight Thor data tree model

  7. Thor data tree in lexical form $SMI<CC(C)C(O)C1CCCCC1> $DB_NO<873> PISM< CC(C)[C@@H](O)C1CCCCC1> ATOM_STER<2,1,1,4,1,7,1,10,1> $DB_NO<750> PISM< CC(C)[C@H](O)C1CCCCC1> ATOM_STER<2,1,1,4,2,7,1,10,1> BOND_STER<1,1,1,5,1,6> ISO<1,0,0> $DB_NO<97> VISM< Cl.CC(C)[C@@H](O)C1CCCCC1> SALT<1,10> . . .

  8. Daylight/Oracle data model(1) Table:R_PARENT Name Null? Type ------------------------------------------------------------------------------------------------- DB_NO NOT NULL NUMBER(7) SMILES NOT NULL VARCHAR(700) ATOM_STER VARCHAR(200) BOND_STER VARCHAR(200) ISO VARCHAR(200) MIXT_INFO VARCHAR(200) CST VARCHAR(200) Table:R_VERSION Name Null? Type ------------------------------------------------------------------------------------------------- DB_NO NOT NULL NUMBER(7) SMILES NOT NULL VARCHAR(700) PARENT_DB_NO NOT NULL NUMBER(7) SALT_INFO VARCHAR(80)

  9. Daylight/Oracle data model(2) Table:R_PARENT Name Null? Type ------------------------------------------------------------------------------------------------- DB_NO NOT NULL NUMBER(7) SMILES NOT NULL VARCHAR(700) Table:R_PARENT_INFO Name Null? Type ------------------------------------------------------------------------------------------------- DB_NO NOT NULL NUMBER(7) DATA_TYPE NOT NULL NUMBER(2) DATA_INFO NOT NULL VARCHAR(200) Table:R_VERSION Name Null? Type ------------------------------------------------------------------------------------------------- DB_NO NOT NULL NUMBER(7) SMILES NOT NULL VARCHAR(700) PARENT_DB_NO NOT NULL NUMBER(7) SALT_INFO VARCHAR(80)

  10. Parent DB_NO SMILES Data Version_1 Version_2 Version_n DB_NO DB_NO DB_NO SMILES SMILES SMILES Parent_DB_NO Parent_DB_NO Parent_DB_NO Data Data Prep_2 Prep_1 Prep_1 Prep_2 Prep_3 Prep_2 Daylight/Oracle Cartridge model Data Data Prep_1 DB_NO Version_DB_NO Data

  11. Other Considerations • 2D coordinates or connection table. • 2D coordinates as in Thor. • Connection table (Molfile, RXNfile, TGFfile … etc) • Data conversion for input/search. • Nitro groups (charge separated, double bond or don’t care). • Parent and salt molecules. • Indexes for normal column data. • Indexes for chemical structure data • i.e. ddexact, ddgraph, ddblob … etc.

  12. Other Considerations • 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.

  13. 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. • Design the database schema. • Export data from Thor (or use SD files). • 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.

  14. DEMO

  15. Thanks • John Bradshaw • Jack Delany • Daylight team • Michael Wainwright (Modgraph)

More Related