B-Net schema

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.


Table: activity

This table contains information regarding the activity and its corresponding event (reaction) and ec

activity Structure
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:

 

Index - Schema bnet


Table: activity_protein_state

This table contains information regarding the protein (state) and its corresponding activity

activity_protein_state Structure
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

 

Index - Schema bnet


Table: allnames

This table is general table that stores the name, synonyms for different records in various tables (e.g. genes, compounds, proteins and others)

allnames Structure
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

 

Index - Schema bnet


Table: comment

User added comment are stored in this table

comment Structure
F-Key Name Type Description
comment_id integer PRIMARY KEY
kw_table_id integer
record_id integer
person_id integer
comment text

Index - Schema bnet


Table: complex

This table contains the known complexes and their location

complex Structure
F-Key Name Type Description
complex_id integer PRIMARY KEY
location.location_id location_id integer NOT NULL

 

Index - Schema bnet


Table: complex_member

This table contains the complex members for the complex and their corresponding stoichiometry

complex_member Structure
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

 

Index - Schema bnet


Table: compound

This table contains information about the compounds like their formula and molecular weight. The compound name can be found in the allnames table.

compound Structure
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:

 

Index - Schema bnet


Table: cpd_derivative

This table contains the derivative for a compound. Compound derivatives are generated for purification purposes such as for GC/MS analysis.

cpd_derivative Structure
F-Key Name Type Description
cpd_derivative_id integer PRIMARY KEY
compound.cpd_id cpd_id integer
name character varying(512)

 

Index - Schema bnet


Table: ec

This table contains the enzyme commision number which is stored in the ec_name field.

ec Structure
F-Key Name Type Description
ec_id integer PRIMARY KEY
ec_name character varying(100)

 

Index - Schema bnet


Table: event

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.

event Structure
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:

 

Index - Schema bnet


Table: event_component

This table contains the components for a event. It also stores information like whether the component is a substrate, its stoichiometry, and location

event_component Structure
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

 

Index - Schema bnet


Table: event_ec

This is a linking table between event and ec tables. It links the ec_id with a particular event.

event_ec Structure
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:

 

Index - Schema bnet


Table: event_type

Event can be of different types such as reactions, tranport, etc. So this table contains the type of the event information.

event_type Structure
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:

 

Index - Schema bnet


Table: evidence

This table stores evidence for the information gathered from the literature and other databases

evidence Structure
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:

 

Index - Schema bnet


Table: evidence_code

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.

evidence_code Structure
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

 

Index - Schema bnet


Table: evidence_go_accession

This is a linking table between evidence and go_accession tables.

evidence_go_accession Structure
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

 

Index - Schema bnet


Table: external_database

This table contains information about the external_databases against which data has been linked in this database.

external_database Structure
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)

 

Index - Schema bnet


Table: external_links

This table contains information about what data in this database has been linked with the corresponding data in another database.

external_links Structure
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)

 

Index - Schema bnet


Table: gene

This table contains the list of genes or TCs for a particular species.

gene Structure
F-Key Name Type Description
gene_id integer PRIMARY KEY
specie_id character varying(15)

Tables referencing this one via Foreign Key Constraints:

 

Index - Schema bnet


Table: gene_tf

This table links gene table with protein state stable. This table represents the transcription factor for a gene.

gene_tf Structure
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:

 

Index - Schema bnet


Table: gene_tf_info

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.

gene_tf_info Structure
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

 

Index - Schema bnet


Table: go_accession

This table has information about the GO ids.

go_accession Structure
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:

 

Index - Schema bnet


Table: location

This table contains the list of sub-cellular location.

location Structure
F-Key Name Type Description
location_id integer PRIMARY KEY
location_name character varying(255)

Tables referencing this one via Foreign Key Constraints:

 

Index - Schema bnet


Table: map

This table lists the maps that can be used by BROME to display the expression levels of genes, proteins and metabolites.

map Structure
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

 

Index - Schema bnet


Table: map_component

This table contains the components (genes, compounds and proteins) for each map found in the map table.

map_component Structure
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

 

Index - Schema bnet


Table: map_type

This table describes the type of map such as a pathway map or a neighborhood map.

map_type Structure
F-Key Name Type Description
map_type_id integer NOT NULL
map_type_name character varying(100)

 

Index - Schema bnet


Table: mrna

This is a linking table between gene and protein table. It corresponds to the mrna for a particular species.

mrna Structure
F-Key Name Type Description
protein.protein_id protein_id integer NOT NULL
gene_id integer NOT NULL
mrna_id integer PRIMARY KEY

 

Index - Schema bnet


Table: pathway_class

This table corresponds to the broad pathway class in a biochemical network.

pathway_class Structure
F-Key Name Type Description
pathway_class_id integer PRIMARY KEY
name character varying(256)

 

Index - Schema bnet


Table: pathway_event

This table contains the list of events and their order for a particular pathway.

pathway_event Structure
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

 

Index - Schema bnet


Table: person

person Structure
F-Key Name Type Description
person_id integer PRIMARY KEY
person_name character varying(100) NOT NULL
email 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.

 

Index - Schema bnet


Table: pga_forms

pga_forms Structure
F-Key Name Type Description
formname character varying(64)
formsource text

 

Index - Schema bnet


Table: pga_queries

pga_queries Structure
F-Key Name Type Description
queryname character varying(64)
querytype character(1)
querycommand text
querytables text
querylinks text
queryresults text
querycomments text

 

Index - Schema bnet


Table: pga_reports

pga_reports Structure
F-Key Name Type Description
reportname character varying(64)
reportsource text
reportbody text
reportprocs text
reportoptions text

 

Index - Schema bnet


Table: pga_schema

pga_schema Structure
F-Key Name Type Description
schemaname character varying(64)
schematables text
schemalinks text

 

Index - Schema bnet


Table: pga_scripts

pga_scripts Structure
F-Key Name Type Description
scriptname character varying(64)
scriptsource text

 

Index - Schema bnet


Table: phenotype

This table contains the phenotype information about a particular gene mutant.

phenotype Structure
F-Key Name Type Description
phenotype_id integer PRIMARY KEY
gene.gene_id gene_id integer
phenotype character varying(2000)

 

Index - Schema bnet


Table: protein

This table contains the list of proteins found for a particular species.

protein Structure
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:

 

Index - Schema bnet


Table: protein_state

This table is a linking table between protein and state tables. This table contains information about the state of a particular protein.

protein_state Structure
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:

 

Index - Schema bnet


Table: protein_state_location

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.

protein_state_location Structure
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

 

Index - Schema bnet


Table: ref_kw_table

This table contains the reference ID for the different tables in this schema.

ref_kw_table Structure
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:

 

Index - Schema bnet


Table: reference

This table contains the details about the reference such as title, author, year, etc.

reference Structure
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)

 

Index - Schema bnet


Table: specie_compound

This table contains the list of compound found in a particular species. This data is retrieved from the literature.

specie_compound Structure
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

 

Index - Schema bnet


Table: species

This table contains the different species and their taxonomy ID in NCBI. The database contains information about these species.

species Structure
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:

 

Index - Schema bnet


Table: state

This table refers to the state of the protein. A protein can exist in different states such as phosphorylated, myristylated, etc.

state Structure
F-Key Name Type Description
state_id integer PRIMARY KEY
type character varying(100)

Tables referencing this one via Foreign Key Constraints:

 

Index - Schema bnet


Table: update

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.

update Structure
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)

 

Index - Schema bnet

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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