B-Net is a reference database of biochemistry and molecular biology. B-Net is part of the DOME system, but it can also be implemented as a stand-alone database.
A pictorial view of the B-Net schema is as follows:
This schema was created by Bharat Mehrotra, Xing jing Li, Aejaaz Kamal, Olga Brazhnik, Stefan Hoops, and Pedro Mendes.
This table contains information regarding the activity and its corresponding event (reaction) and ec
F-Key | Name | Type | Description |
---|---|---|---|
activity_id | integer |
PRIMARY KEY
Unique activity_id |
|
event_ec.event_ec_id | event_ec_id | integer |
Event and EC information corresponding to this activity |
Tables referencing this one via Foreign Key Constraints:
This table contains information regarding the protein (state) and its corresponding activity
F-Key | Name | Type | Description |
---|---|---|---|
activity_protein_state_id | integer |
PRIMARY KEY
Unique activity_protien_state_id |
|
activity.activity_id | activity_id | integer |
Link to activity table |
protein_state.protein_state_id | protein_state_id | integer |
Link to protein_state table |
This table is general table that stores the name, synonyms for different records in various tables (e.g. genes, compounds, proteins and others)
F-Key | Name | Type | Description |
---|---|---|---|
name_id | integer | PRIMARY KEY | |
aname | character varying(1000) | ||
kw_table_id | integer | ||
record_id | integer | ||
is_primary | character(1) | ||
search_name | character varying(1000) | ||
unikey | character varying(1000) |
Unique identification key for each entity. This cannot change for the entity. This key will be used to coordinate data between different copies of bnet |
User added comment are stored in this table
F-Key | Name | Type | Description |
---|---|---|---|
comment_id | integer | PRIMARY KEY | |
kw_table_id | integer | ||
record_id | integer | ||
person_id | integer | ||
comment | text |
This table contains the known complexes and their location
F-Key | Name | Type | Description |
---|---|---|---|
complex_id | integer | PRIMARY KEY | |
location.location_id | location_id | integer | NOT NULL |
This table contains the complex members for the complex and their corresponding stoichiometry
F-Key | Name | Type | Description |
---|---|---|---|
complex_member_id | integer | NOT NULL | |
complex_id | integer | NOT NULL | |
record_id | integer | NOT NULL | |
ref_kw_table.kw_table_id | kw_table_id | integer | NOT NULL |
stoichiometry | real |
This table contains information about the compounds like their formula and molecular weight. The compound name can be found in the allnames table.
F-Key | Name | Type | Description |
---|---|---|---|
cpd_id | integer | PRIMARY KEY | |
cpd_formula | character varying(500) | ||
mol_wt | real | ||
inChi | character varying(1000) |
InChi representation |
Tables referencing this one via Foreign Key Constraints:
This table contains the derivative for a compound. Compound derivatives are generated for purification purposes such as for GC/MS analysis.
F-Key | Name | Type | Description |
---|---|---|---|
cpd_derivative_id | integer | PRIMARY KEY | |
compound.cpd_id | cpd_id | integer | |
name | character varying(512) |
This table contains the enzyme commision number which is stored in the ec_name field.
F-Key | Name | Type | Description |
---|---|---|---|
ec_id | integer | PRIMARY KEY | |
ec_name | character varying(100) |
This table contains the event that take place in the cell. An example is a reaction between different compounds. The type of event is stored in the event_type table.
F-Key | Name | Type | Description |
---|---|---|---|
event_id | integer | PRIMARY KEY | |
event_type.event_type_id | event_type_id | integer |
Tables referencing this one via Foreign Key Constraints:
This table contains the components for a event. It also stores information like whether the component is a substrate, its stoichiometry, and location
F-Key | Name | Type | Description |
---|---|---|---|
event_component_id | integer | PRIMARY KEY | |
record_id | integer | NOT NULL | |
ref_kw_table.kw_table_id | kw_table_id | integer | NOT NULL |
is_substrate | character(1) | NOT NULL | |
location.location_id | location_id | integer | NOT NULL |
stoichiometry | real | ||
event.event_id | event_id | integer |
This is a linking table between event and ec tables. It links the ec_id with a particular event.
F-Key | Name | Type | Description |
---|---|---|---|
event_ec_id | integer | PRIMARY KEY | |
event_id | integer | ||
ec_id | integer |
Tables referencing this one via Foreign Key Constraints:
Event can be of different types such as reactions, tranport, etc. So this table contains the type of the event information.
F-Key | Name | Type | Description |
---|---|---|---|
event_type_id | integer | PRIMARY KEY | |
event_type_name | character varying(255) |
Tables referencing this one via Foreign Key Constraints:
This table stores evidence for the information gathered from the literature and other databases
F-Key | Name | Type | Description |
---|---|---|---|
evidence_id | integer | PRIMARY KEY | |
reference_id | integer | ||
evidence_code_id | integer | ||
record_id | integer | ||
ref_kw_table.kw_table_id | kw_table_id | integer |
Tables referencing this one via Foreign Key Constraints:
This table refers to the evidence code for each evidence. It is similar to Gene Ontology and has been expanded so as to cover all posible encountered evidences.
F-Key | Name | Type | Description |
---|---|---|---|
evidence_code_id | integer | PRIMARY KEY | |
evidence_code | character varying(8) | ||
ref_kw_table.kw_table_id | kw_table_id | integer | |
technique | character varying(512) | ||
strength | real |
This is a linking table between evidence and go_accession tables.
F-Key | Name | Type | Description |
---|---|---|---|
evidence_go_acc_id | integer | ||
evidence.evidence_id | evidence_id | integer | |
go_accession.go_accession_id | go_accession_id | integer |
This table contains information about the external_databases against which data has been linked in this database.
F-Key | Name | Type | Description |
---|---|---|---|
external_database_id | integer | PRIMARY KEY | |
database_name | character varying(255) | ||
full_db_name | character varying(255) | ||
url | character varying(255) |
This table contains information about what data in this database has been linked with the corresponding data in another database.
F-Key | Name | Type | Description |
---|---|---|---|
external_links_id | integer | PRIMARY KEY | |
external_database_id | integer | ||
external_table_name | character varying(50) | ||
ref_kw_table.kw_table_id | kw_table_id | integer | |
external_field_name | character varying(50) | ||
internal_field_name | character varying(50) | ||
record_id | integer | ||
external_id | character varying(20) |
This table contains the list of genes or TCs for a particular species.
F-Key | Name | Type | Description |
---|---|---|---|
gene_id | integer | PRIMARY KEY | |
specie_id | character varying(15) |
Tables referencing this one via Foreign Key Constraints:
This table links gene table with protein state stable. This table represents the transcription factor for a gene.
F-Key | Name | Type | Description |
---|---|---|---|
gene_tf_id | integer | PRIMARY KEY | |
gene.gene_id | gene_id | integer | |
protein_state.protein_state_id | protein_state_id | integer |
Tables referencing this one via Foreign Key Constraints:
This table has information from the chIP-chIP experiment about the level of binding of transcription factor to the promotor region of the corresponding gene.
F-Key | Name | Type | Description |
---|---|---|---|
gene_tf_info_id | integer | PRIMARY KEY | |
gene_tf.gene_tf_id | gene_tf_id | integer | |
ratio | real | ||
p_value | real |
This table has information about the GO ids.
F-Key | Name | Type | Description |
---|---|---|---|
go_accession_id | integer | PRIMARY KEY | |
go_id | character varying(50) | ||
go_name | character varying(500) | ||
ec_number | character varying(200) | ||
go_type | character varying(500) |
Tables referencing this one via Foreign Key Constraints:
This table contains the list of sub-cellular location.
F-Key | Name | Type | Description |
---|---|---|---|
location_id | integer | PRIMARY KEY | |
location_name | character varying(255) |
Tables referencing this one via Foreign Key Constraints:
This table lists the maps that can be used by BROME to display the expression levels of genes, proteins and metabolites.
F-Key | Name | Type | Description |
---|---|---|---|
map_id | integer | NOT NULL | |
map_name | character varying(500) | ||
map_type_id | integer | ||
map_number | character varying(25) | NOT NULL |
This table contains the components (genes, compounds and proteins) for each map found in the map table.
F-Key | Name | Type | Description |
---|---|---|---|
map_component_id | integer | NOT NULL | |
map_id | integer | ||
kw_table_id | integer | ||
record_id | integer | ||
component_name | character varying(256) | ||
brome_id | character varying(256) | ||
specie_id | integer |
Link to the species |
This table describes the type of map such as a pathway map or a neighborhood map.
F-Key | Name | Type | Description |
---|---|---|---|
map_type_id | integer | NOT NULL | |
map_type_name | character varying(100) |
This is a linking table between gene and protein table. It corresponds to the mrna for a particular species.
F-Key | Name | Type | Description |
---|---|---|---|
protein.protein_id | protein_id | integer | NOT NULL |
gene_id | integer | NOT NULL | |
mrna_id | integer | PRIMARY KEY |
This table corresponds to the broad pathway class in a biochemical network.
F-Key | Name | Type | Description |
---|---|---|---|
pathway_class_id | integer | PRIMARY KEY | |
name | character varying(256) |
This table contains the list of events and their order for a particular pathway.
F-Key | Name | Type | Description |
---|---|---|---|
pathway_event_id | integer | PRIMARY KEY | |
pathway_id | integer | NOT NULL | |
event.event_id | event_id | integer | NOT NULL |
event_order | integer |
F-Key | Name | Type | Description |
---|---|---|---|
person_id | integer | PRIMARY KEY | |
person_name | character varying(100) | NOT NULL | |
character varying(40) | |||
phone | character varying(20) | ||
url | character varying(80) | ||
position | character varying(40) | ||
group | character varying(20) | ||
role | character varying(40) | ||
affiliation | character varying(40) | ||
login | character varying(20) | ||
passwd | character varying(20) | ||
access_to_schemas | character varying(200) |
Please enter which schemas (projects) does this person has access to. |
F-Key | Name | Type | Description |
---|---|---|---|
formname | character varying(64) | ||
formsource | text |
F-Key | Name | Type | Description |
---|---|---|---|
queryname | character varying(64) | ||
querytype | character(1) | ||
querycommand | text | ||
querytables | text | ||
querylinks | text | ||
queryresults | text | ||
querycomments | text |
F-Key | Name | Type | Description |
---|---|---|---|
reportname | character varying(64) | ||
reportsource | text | ||
reportbody | text | ||
reportprocs | text | ||
reportoptions | text |
F-Key | Name | Type | Description |
---|---|---|---|
schemaname | character varying(64) | ||
schematables | text | ||
schemalinks | text |
F-Key | Name | Type | Description |
---|---|---|---|
scriptname | character varying(64) | ||
scriptsource | text |
This table contains the phenotype information about a particular gene mutant.
F-Key | Name | Type | Description |
---|---|---|---|
phenotype_id | integer | PRIMARY KEY | |
gene.gene_id | gene_id | integer | |
phenotype | character varying(2000) |
This table contains the list of proteins found for a particular species.
F-Key | Name | Type | Description |
---|---|---|---|
protein_id | integer | PRIMARY KEY | |
species.specie_id | specie_id | character varying(15) |
Tables referencing this one via Foreign Key Constraints:
This table is a linking table between protein and state tables. This table contains information about the state of a particular protein.
F-Key | Name | Type | Description |
---|---|---|---|
protein_state_id | integer | PRIMARY KEY | |
protein.protein_id | protein_id | integer | |
state.state_id | state_id | integer | |
description | character varying(100) |
Tables referencing this one via Foreign Key Constraints:
This is a linking table between protein_state and location tables. This table contains information about the sub-cellular location for the proteins in particular states.
F-Key | Name | Type | Description |
---|---|---|---|
protein_state_location_id | integer | PRIMARY KEY | |
protein_state.protein_state_id | protein_state_id | integer | NOT NULL |
location.location_id | location_id | integer | NOT NULL |
This table contains the reference ID for the different tables in this schema.
F-Key | Name | Type | Description |
---|---|---|---|
kw_table_id | integer | PRIMARY KEY | |
kw_table | character varying(50) | NOT NULL | |
in_bnet | boolean |
Whether the table is from bnet schema or project schema |
Tables referencing this one via Foreign Key Constraints:
This table contains the details about the reference such as title, author, year, etc.
F-Key | Name | Type | Description |
---|---|---|---|
reference_id | integer | PRIMARY KEY | |
authors | character varying(250) | ||
year | smallint | ||
title | character varying(500) | ||
locator | character varying(250) | ||
pubmed_accession | character varying(50) |
This table contains the list of compound found in a particular species. This data is retrieved from the literature.
F-Key | Name | Type | Description |
---|---|---|---|
compound.cpd_id | cpd_id | integer | NOT NULL |
species.specie_id | specie_id | integer | NOT NULL |
specie_cpd_id | integer | PRIMARY KEY |
This table contains the different species and their taxonomy ID in NCBI. The database contains information about these species.
F-Key | Name | Type | Description |
---|---|---|---|
specie_id | integer | PRIMARY KEY | |
taxon_ncbi_accession | character varying(15) | NOT NULL |
Tables referencing this one via Foreign Key Constraints:
This table refers to the state of the protein. A protein can exist in different states such as phosphorylated, myristylated, etc.
F-Key | Name | Type | Description |
---|---|---|---|
state_id | integer | PRIMARY KEY | |
type | character varying(100) |
Tables referencing this one via Foreign Key Constraints:
This is a update table which stores all the changes that take place in different tables. This information is later used to synchronize different versions of bnet.
F-Key | Name | Type | Description |
---|---|---|---|
update_id | integer | PRIMARY KEY | |
kw_table_id | integer | ||
record_id | integer | ||
operation | character(1) | ||
time | timestamp with time zone | DEFAULT now() | |
identifier | character varying(5000) |
Generated by PostgreSQL Autodoc
DOME and B-Net were created in the Biochemical Networks Modeling Group at the Virginia Bioinformatics Institute. Copyright 2001-2006, VTIP
This material is based upon work supported by the National Science Foundation under Grant No. 0109732. Any opinions findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation