1 InstantJChem: a flexible chemical database system G. Marcou, D. Horvath + Laboratoire d’infochimie, Université de Strasbourg, 1, rue Blaise Pascal, Strasbourg

Introduction  The goal is to present InstantJChem for the storage and manipulation of chemical information 1.General presentation 2.Database search 3.Creation of a database from scratch

What is a database?  A database stores data in an ordered form on a precise subject.  A relational database stores information into tables which possess inter-references  A relational database management system (RDBMS) is a software that manages relational databases  InstantJChem is not a database and is not an RDBMS.

What is InstantJChem?  InstantJChem is a friendly interface between a RDBMS, chemical information and the user. User RDBMS Chemical Information

Key concepts of InstantJChem ProjectsSchemaDatabases and TablesEntitiesData TreesViews

Exercise 1 Create a new project names IJCExercises…

Key concept: Project Project contains resources and connections to one or more databases. icon

Exercise 1 …and import the file SC100.SDF in it….

Key concept: Schema Schema/ Database Contains connection to a database and special tables (JChemProperties) icon

Key concept: Database and Tables Table Database and tables are managed by the RDBMS. Actually store information. icon

What can be stored TypeDescription Standard table IntegerLong integer: 232 = TextUser can specify widths of text fields as large as needed. RealReal double-precision DateAllows to store dates. BooleanValue is True or False List (Standard)To store a list of database items JChem table Chemical termsA list of functions evaluated on chemical structures: logD, pKa, tautomers,... StructureChemical structure, automatically created with a Jchem table

Key concept: Entities Entity An entity is a representation of data. icon It is a unique interface to conceptually different types of tables (Standard, Chemical, SQL, Extractions, etc).

Key concept: Data Trees Data Tree A collection of entities and views. icon Organize information using a hierarchy (parent- child relationship between entities).

Exercise 1 ….Customize a browser for it.

Key concept: Views Views An interface to data. icon For simple data, a spreadsheet view is relevant. For complex relational data, a form is mandatory.

Exercise 2 In the SC100 database, search for fluorobenzene and pyridine containing molecules. Use Substructure or Similarity search.

Exercise 2 In the SC100 database, search for fluorobenzene and pyridine containing molecules. Use Substructure or Similarity search. Substructure search: 20 hits Similarity search: 0 hits Substructure search: 14 hits Similarity search: 0 hits Similarity search uses Chemical Hashed Fingerprints defined at database creation.

Chemical Hashed Fingerprints (CHF) Pattern Length: number of bonds of a pattern Fingerprint Length: total number of bits to store the fingerprint Bits per pattern: number of bits a pattern shall set on Efficient annotation to accelerate structure search

Exercise 3 Combine molecule 25 and 89 into a pseudo-molecule to perform a superstructure query.

Exercise 4 Use compound 46 as a Full and Full fragment query to search the database. Repeat after removing the bromide from the query.

Structure Searches

Exercise 5 Search benzene containing compounds, which name contains “pyrimidin” and annotated as “Good” concerning their aqueous solubility.

Exercise 6 Search for compounds with at least one aromatic ring containing at least on Nitrogen atom

Exercise 7 Search for compounds which MolWeight > 200 and not containing a benzene ring

Exercise 8 Search for compounds with MolWeigh > 200, then for compounds without a benzene ring and search for the union of the hit lists.

Execrise 9 Search for compounds possessing more than 4 microspecies at pH=4.0….

Exercise 9 … Export your hit list.

Exercise 10 Import in your project the file ISICCRsm.RDF…

Exercise 10 … Create a Browser for this database

Exercise 11 Search for reactions including an imidazole ring into their reactants then into their products.

Exercise 12 Add to your Schema a new data tree and structure entity named AlkanBoilingPoint…

Exercise 12 … and add a floating point value field named BoilingPoint.

Exercise 13 Add to the AlkanBoilingPoint entity the following data.

Exercise 14 Add to the AlkanBoilingPoint entity a new date field named Date and fill it.

Exercise 15 Add to the AlkanBoilingPoint entity a calculated value of LogP using a Chemicalterm field.

Summary  Create a project and schema  Import data  Search by substructure, superstructure, similarity, and exact match  Search by keyword  Combining queries and result lists  Export query results  Create a new database

Conclusion  InstantJChem is a Chemoinformatics layer above a standard SGDB.  Provides many more Chemoinformatics services (databases overlap, QSPR modeling, plots, enumeration, scripting) SGDB InstantJChem