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DataModelDescription.md

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User [msb_user]

Necessary user data for login.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
nick VARCHAR(180) UNIQUE, NOT NULL Name for login
roles JSON NOT NULL Application roles, ROLE_ADMIN can edit the visibility of containers and assign users to containers
password VARCHAR(255) NOT NULL Password stored as hash
mail VARCHAR(255) Email for reset password
api_token VARCHAR(255) UNIQUE Token authentication
conditions TINYINT(1) NOT NULL If user agree with terms and conditions
chem_spider_token VARCHAR(255) Apikey from ChemSpider to perform queries against it
last_activity DATETIME Time with last user activity, used for logout user when is inactive

Container [msb_container]

Users can create containers with sequences, blocks, etc.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
container_name VARCHAR(255) NOT NULL Name of container
visibility VARCHAR(10) NOT NULL Visibility values: 'PRIVATE', 'PUBLIC'

U2C [msb_u2c]

Relational table between User and Container M:N relationship. Users can view/edit many Containers and Container may be view/edited by many users.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
user_id INT FOREIGN KEY, NOT NULL Reference to User
container_id INT FOREIGN KEY, NOT NULL Reference to Container
mode VARCHAR(10) NOT NULL User rights to container, values: 'R', 'RW'

Sequence [msb_sequence]

The sequence consists of many Blocks and Modifications (Up to 3 - n, c, b). The sequence is in the given Container and may have a SequenceFamily tag.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
n_modification_id INT FOREIGN KEY Reference to n terminal Modification
b_modification_id INT FOREIGN KEY Reference to branch terminal Modification
c_modification_id INT FOREIGN KEY Reference to c terminal Modification
container_id INT FOREIGN KEY, NOT NULL Reference to Container
sequence_type VARCHAR(255) NOT NULL, DEFAULT 'other' Values: linear, cyclic, branched, branch-cyclic, linear-polyketide, cyclic-polyketide, other
sequene VARCHAR(500) Comptuted sequence of block acronnyms
sequence_original VARCHAR(500) Sequence with numbers not acronyms, used for deleting acronyms from sequence
sequence_name VARCHAR(255) NOT NULL Name of sequence ex.: Cyclosporin A
sequence_formula VARCHAR(255) NOT NULL Chemical formmula ex.: C62H111N11O12
sequence_mass DOUBLE Mass of molecule ex.: 1201.841368
sequence_smiles VARCHAR(4000) Description of molecula by SMILES format ex.: CCC1C(=O)N(CC(=O)N(C(C(=O)NC(C(=O)N(C(C(=O)NC(C(=O)NC(C(=O)N(C(C(=O)N(C(C(=O)N(C(C(=O)N(C(C(=O)N1)C(C(C)CC=CC)O)C)C(C)C)C)CC(C)C)C)CC(C)C)C)C)C)CC(C)C)C)C(C)C)CC(C)C)C)C
usmiles VARCHAR(4000) Unique SMILES representation
source SMALLINT Reference to other databases (can be extended), defined: PUBCHEM = 0, CHEMSPIDER = 1, NORINE = 2, const PDB = 3, CHEBI = 4, MSB = 5, DOI = 6, SIDEROPHORE_BASE = 7, LIPID_MAPS = 8, COCONUT = 9, NP_ATLAS = 10
identifier VARCHAR(255) Unique identifier of molecula in another database
decays VARCHAR(255) Auxiliary variable for coloring decay points
unique_block_count INT NOT NULL, DEFAULT 0 Unique number of blocks used in sequence, used for similarity search
block_count INT NOT NULL, DEFAULT 0 Number of blocks used in sequence (duplicit blocks are count in), used for similarity search

UNIQUE INDEX on sequence_name and container_id columns.

Modification [msb_modification]

name Type Properties Description
id INT PRIMARY KEY Unique identifier
container_id INT FOREIGN KEY, NOT NULL Reference to Container
modification_name VARCHAR(255) NOT NULL Name of modification ex.: Acetyl
modification_formula VARCHAR(255) NOT NULL Chemical formmula ex.: H2C2O
modification_mass DOUBLE Mass of molecule ex.: 42.0105646863
n_terminal BOOLEAN NOT NULL, DEFAULT 0 is n terminal?
c_terminal BOOLEAN NOT NULL, DEFAULT 0 is c terminal?

UNIQUE INDEX on modification_name and container_id columns.

Block [msb_block]

name Type Properties Description
id INT PRIMARY KEY Unique identifier
container_id INT FOREIGN KEY, NOT NULL Reference to Container
block_name VARCHAR(255) NOT NULL Name of modification ex.: Valine
acronym VARCHAR(30) NOT NULL Name of modification ex.: Val
residue VARCHAR(255) NOT NULL Chemical formmula ex.: C5H9NO
block_mass DOUBLE Mass of molecule ex.: 99.068414
losses VARCHAR(255) Potencional losses ex.: NH3;CONH
block_smiles VARCHAR(255) Description of molecula by SMILES format ex.: CC(C)C(C(=O)O)N
usmiles VARCHAR(255) Description of molecula by SMILES format but in unique format
source SMALLINT Reference to other databases (can be extended), defined: PUBCHEM = 0, CHEMSPIDER = 1, NORINE = 2, const PDB = 3, CHEBI = 4, MSB = 5, DOI = 6, SIDEROPHORE_BASE = 7, LIPID_MAPS = 8, COCONUT = 9, NP_ATLAS = 10 (same as values in Sequence)
identifier VARCHAR(255) Unique identifier of molecula in another database
is_polyketide TINYINT(1) NOT NULL, DEFAULT 0 Flag if block is polyketide or not, when block is polyketide, his name should starts with (-2H)

UNIQUE INDEX on block_name and container_id columns.

B2S [msb_b2s]

Relational table between Sequence and Block M:N relationship. The sequence can consist of many Blocks and Block can be in many Sequences.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
sequence_id INT FOREIGN KEY Reference to Sequence
block_id INT FOREIGN KEY Reference to Block
next_block_id INT FOREIGN KEY Reference to next block in sequence
branch_reference_id INT FOREIGN KEY Reference to next block in branch
is_branch TINYINT(1) NOT NULL, DEFAULT 0 Flag if block is on branch
block_original_id INT NOT NULL Original id from SmilesDrawer
sort INT NOT NULL Order of blocks in Sequence

Block Family [msb_block_family]

name Type Properties Description
id INT PRIMARY KEY Unique identifier
container_id INT FOREIGN KEY, NOT NULL Reference to Container
block_family_name VARCHAR(255) NOT NULL Name of block family tag

UNIQUE INDEX on block_family_name and container_id columns.

B2F [msb_b2f]

Relational table between Block and BlockFamily M:N relationship. Block can have many BlockFamily tags and BlockFamily tags can be used on many Blocks.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
block_id INT FOREIGN KEY, NOT NULL Reference to Block
family_id INT FOREIGN KEY, NOT NULL Reference to BlockFamily

Sequence Family [msb_sequence_family]

name Type Properties Description
id INT PRIMARY KEY Unique identifier
container_id INT FOREIGN KEY, NOT NULL Reference to Container
sequence_family_name VARCHAR(255) NOT NULL Name of sequence family tag

UNIQUE INDEX on sequence_family_name and container_id columns.

S2F [msb_s2f]

Relational table between Sequence and SequenceFamily M:N relationship. The sequence can have many SequenceFamily tags and the SequenceFamily tags can be used on many Sequences.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
sequence_id INT FOREIGN KEY, NOT NULL Reference to Sequence
family_id INT FOREIGN KEY, NOT NULL Reference to SequenceFamily

Organism [msb_organism]

name Type Properties Description
id INT PRIMARY KEY Unique identifier
container_id INT FOREIGN KEY, NOT NULL Reference to Container
organism VARCHAR(255) NOT NULL Name of organism

UNIQUE INDEX on the organism and container_id columns.

S2O [msb_s2o]

Relational table between Sequence and Organism M:N relationship. The sequence can have many Organism tags and the Organism tags can be used on many Sequences.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
organism_id INT FOREIGN KEY, NOT NULL Reference to Organism
sequence_id INT FOREIGN KEY, NOT NULL Reference to Sequence

Setup [msb_setup]

Independent table for application setup. Should have only one row forever.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
similarity VARCHAR(10) NOT NULL, DEFAULT 'name' Values (name, tanimoto) tells which similarity search to use

Condition [msb_condition]

Independent table for terms and conditions as a blob text. In Application is used terms with the highest id.

name Type Properties Description
id INT PRIMARY KEY Unique identifier
text TEXT NOT NULL Terms and conditions text