| DOCUMENTATION |
- Introduction
- Architecture of BIAdb
- Definition of the scope of the database
- Data Source
- Web server
- Criteria for data collection
- Data submission and updates
i. Architecture of BIAdb
ii. Definition of the scope of the database
The 'BIAdb' database contains the following data for each benzyl isoquinoline alkaloid:
- Name: It represents the name of the benzyl isoquinoline alkaloid being queried
- ID: This is the ID number given by us to all the entries of the databasePubchem ID: This is the PubchemID of that particular entry
- KEGG ID: This is the KEGG ID of that particular entry
- Source: This is the source of that particular Benzylisoquinoline(BIA) compound
- Type: This is the type of that particular BIA compound
- Function: This is the function of that particular BIA compound
- Molecular formula: This represents the molecular formula of the entry
- Molecular weight: This depicts the molecular weight of the entry
- Exact mass: This is the exact mass of that particular BIA compound
- XLogP: It is the XLogP value of the specific entry
- Topological Polar Surface Area: gives the value of TPSA of particular compound
- H-Bond Donor: gives number of H-Bond donors in the compound
- H-Bond Acceptor:gives number of H-Bond acceptors in compound
- Rotational Bond Count: gives number of rotatable bonds in the compound
- IUPAC Name: gives the IUPAC name of the benzyl isoquinoline alkaloid
- 2-D & 3-D Structure: represents the 2-D & 3-D structures of the entries
- Canonical SMILES: Canonical SMILE for the given benzyl isoquinoline alkaloid
- Isomeric SMILES: Isomeric SMILE for the given benzyl isoquinoline alkaloid
- Drugpedia: This is the external link to the drugpedia developed by our group where the detailed information of the entries in the database can be accessed easily. User can also add or edit the information on pages of particular entries.
- References: External link to PubMed references
Our belief is that the BIAdb can be useful to the people working with alkaloids and it can be helpful in the studies of theraupeutic efficacy of the natural alkaloids.
iii. Data Source
The main sources of the data in the BIAdb are:
| Data Source | Number of Entries |
|---|---|
| KEGG (COMPOUNDS & DRUGS) | 196 |
| CTD | 145 |
| PubChem | 171 |
| Other Sources (literature search) | 334 |
The database is up-to-date and is regularly updated to add new entries.
Information regarding the benzyl isoquinoline alkaloids can be retrived through the web server using the:
- Text Search
- Advance Search
- Open the ADVANCE SEARCH page by clicking the link on the HOME page.
- User can query the database by
entering the appropriate name e.g. : "morphine"
Or
specifying molecular weight, XLogP and TPSA ranges. - Then click the search button below.
- If you want to reset the values then click on Reset button adjacent to Search button
- What is BIAdb ?
- Why search BIAdb ?
- How does BIAdb assign identifiers ?
- How does BIAdb process my deposited compounds ?
- How do I process a text search with BIAdb
databases ?
Q: What is BIAdb ?
A: The Benzylisoquinoline Alkaloid Database is an attempt to gather the scattered information related to the Benzylisoquinoline Alkaloids.
Q: Why search BIAdb ?
A: It is useful to search BIAdb when one is looking for information regarding the benzyl isoquinolines, and/or when one is looking for information on compounds such as natural products which may have associated theraupeutic properties. These special cases aside, it is generally most useful to search for chemical names or structures of benzyl isoquinoline Alkaloids in BIAdb. This provides a concise view, combining information derived from multiple Substance records that specified the same structure.
Q: How does BIAdb assign identifiers ?
A: A BIAdb ID is assigned to each unique entry provided by a BIAdb data source.
Q: How does BIAdb process my deposited compounds ?
A: The conversion of the deposited information goes through a series of validation steps (to confirm the compound is "valid") and then a series of standardization steps to remove redundancy.
Q: How do I process a text search with BIAdb database ?
A: You can process any name, or ID search through the BIAdb homepage or you may go to advance search for specific queries.
How to search database:
Benzylisoquinoline alkaloids
Alkaloids are naturally occurring secondary metabolites containing nitrogen atoms. Benzylisoquinoline alkaloids are catergory of alkaloids having isoquinoline ring in their structure.
This definition of Benzylisoquinoline alkaloids was kept in mind during collection of entries.Collection of Benzylisoquinoline alkaloids
We searched various databases like PubChem, KEGG Compounds, KEGG Drug, CTD etc. A total of 846 BIA's were collected. The following table depicts the data types and their source of collection for Benzylisoquinoline alkaloids:| Data Types | Source |
| ID | Unique |
| PubChem ID | PubChem |
| Name | PubChem, KEGG |
| Source | KnapSack, Literature |
| Type | KnapSack, Literature |
| Function | KnapSack, Literature |
| Molecular Weight | PubChem, KEGG |
| Molecular Formula | PubChem, KEGG |
| Exact Mass | PubChem, KEGG |
| H-Bond Donor | KEGG |
| H-Bond Acceptor | KEGG |
| Rotational Bond Count | PubChem |
| IUPAC Name | PubChem, KEGG |
| Canonical Smiles | PubChem, KEGG |
| Isomeric Smiles | PubChem |
| XLogP | PubChem, KEGG |
| TPSA | PubChem |
| Drugpedia ID | Link to DrugPedia by Name |
| References | PubMed |
The web server allows user to submit their BIA related data online by sumitting a HTML form with all mandatory fields filled correctly. However, before including in BIAdb we will validate the supplied data, in order to maintain the quality. Our team is also searching and adding more BIA's into the database from published literature.
BIAdb will be updated regularly to add new enyries into the database. The success of this database is highly dependent on contributors, please enter the new BIAs in BIAdb or inform our team so that we can include more and more BIAs in the database.
| BIAdb FAQ |
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