instantjchem: a flexible chemical database system
DESCRIPTION
InstantJChem: a flexible chemical database system. G. Marcou, D. Horvath + Laboratoire d ’ infochimie, Université de Strasbourg, 1, rue Blaise Pascal, 67000 Strasbourg. Introduction. The goal is to present InstantJChem for the storage and manipulation of chemical information - PowerPoint PPT PresentationTRANSCRIPT
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1
InstantJChem: a flexible chemical database system
G. Marcou, D. Horvath+Laboratoire d’infochimie, Université de Strasbourg, 1, rue
Blaise Pascal, 67000 Strasbourg
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Introduction The goal is to present InstantJChem for the
storage and manipulation of chemical information
1. General presentation2. Database search3. Creation of a database from scratch
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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.
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What is InstantJChem? InstantJChem is a friendly interface between a
RDBMS, chemical information and the user.
User
RDBMS
Chemical Information
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Key concepts of InstantJChem
ProjectsSchemaDatabases and TablesEntitiesData TreesViews
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Exercise 1Create a new project names IJCExercises…
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Key concept: Project
Project
contains resources and connections to one or more databases.
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Exercise 1
…and import the file SC100.SDF in it….
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Key concept: Schema
Schema/Database
Contains connection to a database and special tables (JChemProperties)
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Key concept: Database and Tables
Table
Database and tables are managed by the RDBMS.
Actually store information.
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What can be storedType Description
Standard tableInteger Long integer: 232 = 4294967296
Text User can specify widths of text fields as large as needed.
Real Real double-precision
Date Allows to store dates.
Boolean Value is True or False
List (Standard) To store a list of database items
JChem table
Chemical terms A list of functions evaluated on chemical structures: logD, pKa, tautomers,...
Structure Chemical structure, automatically created with a Jchem table
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Key concept: Entities
Entity
An entity is a representation of data.
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It is a unique interface to conceptually different types of tables (Standard, Chemical, SQL, Extractions, etc).
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Key concept: Data Trees
Data Tree
A collection of entities and views.
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Organize information using a hierarchy (parent-child relationship between entities).
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Exercise 1….Customize a browser for it.
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Key concept: Views
Views
An interface to data.
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For simple data, a spreadsheet view is relevant. For complex relational data, a form is mandatory.
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Exercise 2In the SC100 database, search for fluorobenzene and pyridine containing molecules. Use Substructure or Similarity search.
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Exercise 2In the SC100 database, search for fluorobenzene and pyridine containing molecules. Use Substructure or Similarity search.
Substructure search: 20 hitsSimilarity search: 0 hits
Substructure search: 14 hitsSimilarity search: 0 hits
Similarity search uses Chemical Hashed Fingerprints defined at database creation.
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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
www.chemaxon.com
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Exercise 3Combine molecule 25 and 89 into a pseudo-molecule to perform a superstructure query.
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Exercise 4Use compound 46 as a Full and Full fragment query to search the database. Repeat after removing the bromide from the query.
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Structure Searches
www.chemaxon.com
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Exercise 5Search benzene containing compounds, which name contains “pyrimidin” and annotated as “Good” concerning their aqueous solubility.
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Exercise 6Search for compounds with at least one aromatic ring containing at least on Nitrogen atom
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Exercise 7Search for compounds which MolWeight > 200 and not containing a benzene ring
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Exercise 8Search for compounds with MolWeigh > 200, then for compounds without a benzene ring and search for the union of the hit lists.
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Execrise 9Search for compounds possessing more than 4 microspecies at pH=4.0….
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Exercise 9… Export your hit list.
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Exercise 10Import in your project the file ISICCRsm.RDF…
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Exercise 10… Create a Browser for this database
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Exercise 11Search for reactions including an imidazole ring into their reactants then into their products.
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Exercise 12Add to your Schema a new data tree and structure entity named AlkanBoilingPoint…
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Exercise 12… and add a floating point value field named BoilingPoint.
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Exercise 13Add to the AlkanBoilingPoint entity the following data.
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Exercise 14Add to the AlkanBoilingPoint entity a new date field named Date and fill it.
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Exercise 15Add to the AlkanBoilingPoint entity a calculated value of LogP using a Chemicalterm field.
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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
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Conclusion InstantJChem is a Chemoinformatics layer above a
standard SGDB. Provides many more Chemoinformatics services
(databases overlap, QSPR modeling, plots, enumeration, scripting)
SGDBSGDB InstantJChemInstantJChem