Q-bank Bacteria

Help on BioloMICSNet

How to search our databases

The BioloMICSNet Software facilitates interogation of the available databases. The Basic search allows you to search on any kind of field.

Should you need to build more complex queries, then the Advanced search ( ) will allow you to customize the query.

The following link : BioloMICS Search will redirects you to the Search page

Similarity based on on-line pair-wise alignments

The BioloMICSNet Software facilitates identifications by the perfomance of on-line pair-wise and probabilistic sequences (DNA and/or Proteins) identifications.

The following link : BioloMICS Sequence Pairwise Alignment will redirects you to the BioloMICS Sequence Pairwise Alignment page

Polyphasic online identification

The BioloMICSNet Software has facilitated perfomance of on-line polyphasic identifications since the first version produced in 1999. Depending on the databases and the criteria that are available, a wide range of characteristics can be entered, combined and analyzed to obtain an identification of an unknown. The more criteria used, the more likely the identification will be reliable. The current on-line version of the software also facilitates for the production of phenetic trees.

For a complete description on fields and algorithms used in the polyphasic identification :

The following link : BioloMICS Polyphasic Identification will redirects you to the BioloMICS Polyphasic Identification page

Deposit of user's data

BioloMICSNet users willing to deposit their data or to order items using the cart system, will have to register. We need to be able to contact the depositor/client For specific information (e.g. BioloMICSNet number, possible points of clarification, for example regarding the name, actual date of publication, etc), and we also need to ensure all entries are genuine.

To register for the first time follow the steps below:

1. Enter your email address (see Register New User), click on the 'Create New Profile' button to receive a provisional password by email (this is to make sure that the provided email is real and that you are the person that can open the given email).

2. Read your email and go to the Register menu again. Enter your email and password (obtained by email). Click on the "Login" button and access the BioloMICSNet profile form where personal information has to be entered. Change the password and personalize it. Click on the "Save profile" button. You will then be registered and ready to deposit new items (strains, species, etc) or to order items on-line via the Cart system.

Link your website

Software developers can connect their website to BioloMICSNet.

Basic address 1:
http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=V2&Descr=V3&Fields=V4&ExactMatch=V5

Basic address 2:
http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=V2&Rec=V6&Fields=V4&ExactMatch=V5

where,

V1: Database Name (see 'Database' block ' below) where to find the wanted record (see table below for more information)

V2: Table Layout Name (see 'Fields Code' block below) where to find the wanted record (see table below for more information)

V3: Name of the wanted record

V4: Fields code (see 'Fields code' below) to be displayed. To display all fields use the 'All' value (ex.: &Fields =All). To display only one field, just paste the code of the field next to the & Fields tag (ex.: &Fields =E1). To display several fields, use several & Fields tag (ex.: &Fields=E1&Fields=T4&Fields=P8). Only the fields that are not empty will be displayed. See table below for more information on fields codes.

V5: Exact match for the queries. Use T for true or F for False (ex.: &ExactMatch =T). Relevant if V3 (Name specified). 'ExactMatch=T' will search for record where Name equals the given value while 'ExactMatch=F' will search for records where Name contains the given value.

V6: Unique ID of a given record (ex.: &Rec =1)

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Information details on Database : Q-bank Bacteria

Fields description for Layout : Names

Field Caption	Field Name	Field Code	Field type
Administration
	Date recorded	E107	H : DateTime (YYYYMMDDHHmmss)
	Date of change	E110	E : Text, administrative field
	Changed by	E111	E : Text, administrative field
General
	Dutch name of the disease	E201	E : Text, administrative field
	English name of the disease	E200	E : Text, administrative field
	EU Quarantine	E195	E : Text, administrative field
	Main hosts	E196	E : Text, administrative field
	Geographical distribution	E198	E : Text, administrative field
	Biology	E197	E : Text, administrative field
	Symptoms	E202	E : Text, administrative field
Pictures
	Picture of symptoms	FLink250	FLink : Link to File
Taxonomy
	Genus	E102	E : Text, administrative field
	Species	E103	E : Text, administrative field
	Subspecies	E105	E : Text, administrative field
	Pathovar	E104	E : Text, administrative field
	Authors	E106	E : Text, administrative field
	Synonym of	RLink117	RLink : Link to one or more records
	Subspecies of	RLink116	RLink : Link to one or more records
	Approved list	T118	T : Discrete data, single state
	Original publication	T119	T : Discrete data, single state
	Status	E125	E : Text, administrative field
	IJSB reference	E109	E : Text, administrative field
	Type strain	E108	E : Text, administrative field
	Remarks	E113	E : Text, administrative field
	Associated strains	RLink121_back	RLink : Link to one or more records

Examples of hyperlinks for Table Names in Database Q-bank Bacteria

Example 1: Record #1 [Acetivibrio], Display all Fields

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Names&Rec=1&Fields=All&ExactMatch=T

Example 2: Record Name is 'Acetivibrio' , Display all Fields, Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Names&Name=Acetivibrio&Fields=All&ExactMatch=T

Example 3: Record Name containing 'Acetivibrio' , Display all Fields, Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Names&Name=Acetivibrio&Fields=All&ExactMatch=F

Example 4: Record Name containing 'Acetobacter' , Display Field 'E107' (Date recorded), Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Names&Name=Acetobacter&Fields=E107&ExactMatch=F

Example 5: Record Name is 'Acetobacter aceti subsp. orleanensis' , Display Field 'E107' (Date recorded) and 'RLink121_back' (Associated strains) , Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Names&Name=Acetobacter aceti subsp. orleanensis&Fields=E107&Fields=RLink121_back&ExactMatch=T

Fields description for Layout : NRC Strains

Field Caption	Field Name	Field Code	Field type
Taxonomy
	Taxon name	RLink121	RLink : Link to one or more records
	Accessed/Deposited as	E13	E : Text, administrative field
	Race	E58	E : Text, administrative field
	Biovar	E59	E : Text, administrative field
	Serovar	E60	E : Text, administrative field
Strain identification numbers
	Culture number Bacteriology	E55	E : Text, administrative field
	NRL sample number	E57	E : Text, administrative field
	Other collections numbers	E123	E : Text, administrative field
Accession data
	Accession date	E29	H : DateTime (YYYYMMDDHHmmss)
	Depositor	E32	E : Text, administrative field
	Reference number depositor	E61	E : Text, administrative field
	Date of deposition	E66	H : DateTime (YYYYMMDDHHmmss)
	Date LY	E74	H : DateTime (YYYYMMDDHHmmss)
	Accession	T11	T : Discrete data, single state
	Recorded by	E77	E : Text, administrative field
	Date of record	E78	H : DateTime (YYYYMMDDHHmmss)
Isolation data
	Isolated from (plant species)	E33	E : Text, administrative field
	Isolated from (plant parts/other)	E54	E : Text, administrative field
	Associated plants	RLink193	RLink : Link to one or more records
	Isolated by	E76	E : Text, administrative field
	Date of isolation	E56	H : DateTime (YYYYMMDDHHmmss)
Identification data
	Identified by	E62	E : Text, administrative field
	Date of identification	E63	H : DateTime (YYYYMMDDHHmmss)
	Re-identified by	E64	E : Text, administrative field
	Date of re-identification	E65	H : DateTime (YYYYMMDDHHmmss)
Lacation of origin
	Location of origin	E67	E : Text, administrative field
Remarks
	Catalogue	E68	E : Text, administrative field
	Serology	E69	E : Text, administrative field
	Biochemistry	E70	E : Text, administrative field
	Genetics	E71	E : Text, administrative field
	Pathogenicity	E72	E : Text, administrative field
	Other	E73	E : Text, administrative field
Status
	Status of the strain	T12	T : Discrete data, single state
	Security	T13	T : Discrete data, single state
	Status NRC	C710	C : Discrete data, multiple state
Pricing
	Price	D191	D : Continuous data, single value

Examples of hyperlinks for Table NRC Strains in Database Q-bank Bacteria

Example 1: Record #1 [PD 2], Display all Fields

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=NRC Strains&Rec=1&Fields=All&ExactMatch=T

Example 2: Record Name is 'PD 2' , Display all Fields, Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=NRC Strains&Name=PD 2&Fields=All&ExactMatch=T

Example 3: Record Name containing 'PD' , Display all Fields, Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=NRC Strains&Name=PD&Fields=All&ExactMatch=F

Example 4: Record Name containing 'PD' , Display Field 'RLink121' (Taxon name), Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=NRC Strains&Name=PD&Fields=RLink121&ExactMatch=F

Example 5: Record Name is 'PD 11' , Display Field 'RLink121' (Taxon name) and 'D191' (Price) , Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=NRC Strains&Name=PD 11&Fields=RLink121&Fields=D191&ExactMatch=T

Fields description for Layout : Organisms included

Field Name	Field Code	Field type
genus	E622	E : Text, administrative field
species	E623	E : Text, administrative field
subspecies	E624	E : Text, administrative field
pathovar	E625	E : Text, administrative field
EPPO data	U626	U : URL
strains	RLink630	RLink : Link to one or more records

Examples of hyperlinks for Table Organisms included in Database Q-bank Bacteria

Example 1: Record #103 [Burkholderia caryophylli], Display all Fields

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Organisms included&Rec=103&Fields=All&ExactMatch=T

Example 2: Record Name is 'Burkholderia caryophylli' , Display all Fields, Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Organisms included&Name=Burkholderia caryophylli&Fields=All&ExactMatch=T

Example 3: Record Name containing 'Burkholderia' , Display all Fields, Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Organisms included&Name=Burkholderia&Fields=All&ExactMatch=F

Example 4: Record Name containing 'Xylella' , Display Field 'E622' (genus), Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Organisms included&Name=Xylella&Fields=E622&ExactMatch=F

Example 5: Record Name is 'Xylella fastidiosa subsp. multiplex' , Display Field 'E622' (genus) and 'RLink630' (strains) , Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Organisms included&Name=Xylella fastidiosa subsp. multiplex&Fields=E622&Fields=RLink630&ExactMatch=T

Fields description for Layout : Q-Bank strains

Field Caption	Field Name	Field Code	Field type
Classification
	Classification	RLink1631	RLink : Link to one or more records
	race	E657	E : Text, administrative field
	biovar	E655	E : Text, administrative field
	phylotype	E656	E : Text, administrative field
General
	Host	RLink1634	RLink : Link to one or more records
	matrix	C635	C : Discrete data, multiple state
Geographical origin
	country	E636	E : Text, administrative field
	state	E637	E : Text, administrative field
	locality	E638	E : Text, administrative field
Strain provider
	Provider	RLink670	RLink : Link to one or more records
Other
	isolation date	H639	H : DateTime (YYYYMMDDHHmmss)
Symptoms
	symptoms associated	C648	C : Discrete data, multiple state
	picture symptoms	FLink647	FLink : Link to File
Virulence and aggressiveness
	description	E649	E : Text, administrative field
Colony phenotype
	colony description	E644	E : Text, administrative field
	picture colonies	FLink646	FLink : Link to File
References to publications with metadata
	genomic profile	E650	E : Text, administrative field
	protein profile	E651	E : Text, administrative field
	malditoff profile	E652	E : Text, administrative field
	fatty acid profile	E653	E : Text, administrative field
Remarks on strain
	comments	E654	E : Text, administrative field
Sequences
	16S rDNA	NLink665	NLink : Link to Sequence
	gyrB	NLink666	NLink : Link to Sequence
	mutS	NLink667	NLink : Link to Sequence
	AvrBs2	NLink707	NLink : Link to Sequence
	23S rDNA	NLink668	NLink : Link to Sequence
	egl	NLink669	NLink : Link to Sequence
	fliC	NLink698	NLink : Link to Sequence
	ftsZ	NLink699	NLink : Link to Sequence
	gltA	NLink700	NLink : Link to Sequence
	groEL	NLink701	NLink : Link to Sequence
	hrpB	NLink702	NLink : Link to Sequence
	16S-23S rDNA	NLink703	NLink : Link to Sequence
	pilU	NLink704	NLink : Link to Sequence
	recA	NLink705	NLink : Link to Sequence
	rpoB	NLink706	NLink : Link to Sequence
	cysG	NLink709	NLink : Link to Sequence

Examples of hyperlinks for Table Q-Bank strains in Database Q-bank Bacteria

Example 1: Record #101 [NCPPB 353], Display all Fields

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank strains&Rec=101&Fields=All&ExactMatch=T

Example 2: Record Name is 'NCPPB 353' , Display all Fields, Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank strains&Name=NCPPB 353&Fields=All&ExactMatch=T

Example 3: Record Name containing 'NCPPB' , Display all Fields, Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank strains&Name=NCPPB&Fields=All&ExactMatch=F

Example 4: Record Name containing 'CFBP' , Display Field 'RLink1631' (Classification), Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank strains&Name=CFBP&Fields=RLink1631&ExactMatch=F

Example 5: Record Name is 'CFBP 6442' , Display Field 'RLink1631' (Classification) and 'NLink709' (cysG) , Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank strains&Name=CFBP 6442&Fields=RLink1631&Fields=NLink709&ExactMatch=T

Fields description for Layout : Q-Bank sequences

Field Name	Field Code	Field type
DNA	N658	N : Sequence (DNA or protein)
Forward primer(s)	E659	E : Text, administrative field
Reverse primer(s)	E660	E : Text, administrative field
Trace files	FLink661	FLink : Link to File
Quality	E662	E : Text, administrative field
Review state	E663	E : Text, administrative field
Remarks	E664	E : Text, administrative field

Examples of hyperlinks for Table Q-Bank sequences in Database Q-bank Bacteria

Example 1: Record #21 [16s rDNA_NCPPB 353], Display all Fields

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank sequences&Rec=21&Fields=All&ExactMatch=T

Example 2: Record Name is '16s rDNA_NCPPB 353' , Display all Fields, Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank sequences&Name=16s rDNA_NCPPB 353&Fields=All&ExactMatch=T

Example 3: Record Name containing '16s' , Display all Fields, Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank sequences&Name=16s&Fields=All&ExactMatch=F

Example 4: Record Name containing '16s' , Display Field 'N658' (DNA), Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank sequences&Name=16s&Fields=N658&ExactMatch=F

Example 5: Record Name is '16s rDNA_CFBP 6442' , Display Field 'N658' (DNA) and 'E664' (Remarks) , Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=Q-Bank sequences&Name=16s rDNA_CFBP 6442&Fields=N658&Fields=E664&ExactMatch=T

Fields description for Layout : EU_EPPO_SPECIES

Field Name	Field Code	Field type
genus	E622	E : Text, administrative field
species	E623	E : Text, administrative field
subspecies	E624	E : Text, administrative field
pathovar	E625	E : Text, administrative field
EPPO data	U626	U : URL
strains	RLink630	RLink : Link to one or more records

Examples of hyperlinks for Table EU_EPPO_SPECIES in Database Q-bank Bacteria

Example 1: Record #103 [Burkholderia caryophylli], Display all Fields

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=EU_EPPO_SPECIES&Rec=103&Fields=All&ExactMatch=T

Example 2: Record Name is 'Burkholderia caryophylli' , Display all Fields, Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=EU_EPPO_SPECIES&Name=Burkholderia caryophylli&Fields=All&ExactMatch=T

Example 3: Record Name containing 'Burkholderia' , Display all Fields, Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=EU_EPPO_SPECIES&Name=Burkholderia&Fields=All&ExactMatch=F

Example 4: Record Name containing 'Xylella' , Display Field 'E622' (genus), Non Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=EU_EPPO_SPECIES&Name=Xylella&Fields=E622&ExactMatch=F

Example 5: Record Name is 'Xylella fastidiosa subsp. multiplex' , Display Field 'E622' (genus) and 'RLink630' (strains) , Exact Match Searching

http://www.q-bank.eu/Bacteria/BioloMICS.aspx?Table=EU_EPPO_SPECIES&Name=Xylella fastidiosa subsp. multiplex&Fields=E622&Fields=RLink630&ExactMatch=T

Contact(s) for Database : Q-bank Bacteria

The following link : BioloMICS Contact information will redirects you to the BioloMICS Contact information page

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