ege-kaya / dtbank

A unified drug-target database with a web-based user interface.

DTBank

A unified drug-target database with a web-based user interface.

DTBank contains the following information:

1. User includes the following attributes; username, institute name, and password. There exists only one user with a specific username and institute. There can be an unlimited number of users. Passwords are encrypted using the SHA256 algorithm and stored in the database accordingly.
2. Database manager consists of the following attributes: username and password. There exists only one database manager with a specific username. There can be at most 5 database managers registered to the system. Passwords are encrypted using the SHA256 algorithm and stored in the database accordingly.
3. DrugBank includes DrugBank ID, drug name, description, and interaction with other drugs. By definition, each DrugBank ID is unique.
4. SIDER includes UMLS CUI (side effect IDs), DrugBank ID, and side effect name. By definition, each UMLS CUI is unique.
5. BindingDB includes Reaction ID, DrugBank ID, UniProt ID, target (protein) name, SMILES (chemical notation of drug), affinity in nM (the strength of the binding interaction between drugs and targets), the measure of the interaction (Ki, Kd, IC50), DOI (link on the web to identify the article or document that mentions the drug-target interaction. E.g., https://doi.org/10.1093/bioinformatics/bty593), authors of the article or document, usernames of the corresponding authors, and institutions of the authors. Authors are considered as contributors. Each contribution makes an impact on the institute. By definition, each Reaction ID is unique and contributors are users of DTBank.
6. UniProt includes UniProt ID and amino acid sequence of the corresponding protein. By definition, each UniProt ID is unique.

Two types of people can use DTBank: users and database managers. Both types can log in to the system. Users are able to perform only the operations that are defined for their roles. DTBank users can be contributors to the papers/documents stored in BindingDB. Each institute has a score based on the number of publications and number of the contributors to these publications. Institutes get 5 points for each publication and get 2 points for each contributor of the corresponding publication.

The UI supports the following operations:

1. Database managers are able to log in to the system with their credentials.
2. Database managers are able to add new users to the system.
3. Database managers are able to update affinity values of drugs using Reaction IDs and delete drugs using DrugBank IDs.
4. Database managers are able to delete proteins using UniProt IDs.
5. Database managers are able to update contributors of papers=documents using Reaction IDs.
6. Database managers are able to separately view all drugs listed in DrugBank, all proteins listed in UniProt, all side effects listed in SIDER, all drug-target interactions, all papers and their contributors listed in BindingDB, and all users in DTBank.
7. Users are able to log in to the system with their credentials.
8. Users are able to separately view the names, DrugBank IDs, SMILES strings, descriptions, target names, and side effect names of all drugs.
9. Users are able to view all interactions of a specific drug.
10. Users are able to view all side effects of a specific drug.
11. Users are able to view all interacting targets of a specific drug.
12. Users are able to view interacting drugs of a specific protein.
13. Users are able to view drugs that affect the same protein.
14. Users are able to view proteins that bind the same drug.
15. Users are able to view drugs that have a specific side effect.
16. Users are able to search a keyword and view the drugs that contain this keyword in their descriptions.
17. Users are able to view the drug(s) with the least amount of side effects that interact with a specific protein.
18. Users are able to view the DOI of papers and contributors of the corresponding paper.
19. Users are able to rank institutes according to their total scores (Decreasing order).
20. Users are able to filter interacting targets of a specific drug considering the selected measurement type and the range of the affinity values.
21. The system has three triggers:

• When a drug is deleted, it is removed from the the list of the interacting drugs of other drugs, and its corresponding entries from SIDER and BindingDB.

• When a protein is deleted, its corresponding entries from BindingDB are removed.

• When a new publication is added to the system, the corresponding institute gets 5 points for a new publication and gets 2 points for each individual who contributed to it. Also, when there is an update on the publication that changes the number of contributors, update the corresponding institute's score accordingly.