CBS Database

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.cbs.knaw.nl/collections/BioloMICS.aspx?Table=V2&Descr=V3&Fields=V4&ExactMatch=V5

Basic address 2:
http://www.cbs.knaw.nl/collections/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 : CBS Database

Fields description for Layout : Growth media

Field Name	Field Code	Field type
Full name of medium	E1	E : Text, administrative field
Other name	E2	E : Text, administrative field
Method-recipe	E3	E : Text, administrative field
pH	E4	E : Text, administrative field
Sterilization conditions	E5	E : Text, administrative field
Remarks	E6	E : Text, administrative field
Ingredients	E7	E : Text, administrative field
References	E8	E : Text, administrative field

Examples of hyperlinks for Table Growth media in Database CBS Database

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

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Growth media&Rec=1&Fields=All&ExactMatch=T

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

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Growth media&Name=AAA&Fields=All&ExactMatch=T

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

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Growth media&Name=AAA&Fields=All&ExactMatch=F

Example 4: Record Name containing 'BARN' , Display Field 'E1' (Full name of medium), Non Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Growth media&Name=BARN&Fields=E1&ExactMatch=F

Example 5: Record Name is 'BARN' , Display Field 'E1' (Full name of medium) and 'E8' (References) , Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Growth media&Name=BARN&Fields=E1&Fields=E8&ExactMatch=T

Fields description for Layout : Bibliography

Field Name	Field Code	Field type
Authors	E1	E : Text, administrative field
Authors_BK	E2	E : Text, administrative field
Editors	E3	E : Text, administrative field
Year	H1	H : DateTime (YYYYMMDDHHmmss)
Page	E4	E : Text, administrative field
Collection	E5	E : Text, administrative field
ISBN	E6	E : Text, administrative field
Num_	E7	E : Text, administrative field
NumB	E8	E : Text, administrative field
ISSN	E9	E : Text, administrative field
Volume	E10	E : Text, administrative field
Keywords	E11	E : Text, administrative field
Edit_Ref	E12	E : Text, administrative field
Revue	E13	E : Text, administrative field
Remarks	E14	E : Text, administrative field
Url	E15	E : Text, administrative field
Journal	RLink523	RLink : Link to multiple records
Pubmed	U804	U : URL

Examples of hyperlinks for Table Bibliography in Database CBS Database

Example 1: Record #1 [Intérêt systématique de la recherche de l'uréase chez les levures et organismes levuriformes], Display all Fields

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Bibliography&Rec=1&Fields=All&ExactMatch=T

Example 2: Record Name is 'Intérêt systématique de la recherche de l'uréase chez les levures et organismes levuriformes' , Display all Fields, Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Bibliography&Name=Intérêt systématique de la recherche de l'uréase chez les levures et organismes levuriformes&Fields=All&ExactMatch=T

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

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Bibliography&Name=Intérêt&Fields=All&ExactMatch=F

Example 4: Record Name containing 'The' , Display Field 'E1' (Authors), Non Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Bibliography&Name=The&Fields=E1&ExactMatch=F

Example 5: Record Name is 'The use of stored frozen yeast starter in wine production' , Display Field 'E1' (Authors) and 'U804' (Pubmed) , Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Bibliography&Name=The use of stored frozen yeast starter in wine production&Fields=E1&Fields=U804&ExactMatch=T

Fields description for Layout : Yeasts species

Field Caption	Field Name	Field Code	Field type
General information
	Remarks	E1	E : Text, administrative field
	Taxonomic information	E6	RLink : Link to multiple records
Sexuality
	Number of ascospores per ascus	S1	S : Continuous data range (Min,LP,HP,Max)
	Asci evanescence	T4	T : Discrete data, single state
	Asci shape	T5	T : Discrete data, single state
	Ascospores with gelatinous sheath	T6	T : Discrete data, single state
	Ascospores with a groove	T7	T : Discrete data, single state
	Basidia septation	T8	T : Discrete data, single state
	Basidia shape	T9	T : Discrete data, single state
	Basidia catenate-solitary	T11	T : Discrete data, single state
	Teliospores	T12	T : Discrete data, single state
	Sexual reproduction	T43	T : Discrete data, single state
	Ascospores shape	C6	C : Discrete data, multiple state
	Conjugation	C7	C : Discrete data, multiple state
	Conditions for sporulation	E43	E : Text, administrative field
Morphology
Macro-morphology
	Reddish diffusing pigment	T1	T : Discrete data, single state
	Colony margin	T2	T : Discrete data, single state
	Colony colour	C1	C : Discrete data, multiple state
	Colony appearance	C2	C : Discrete data, multiple state
	Colony texture	C3	C : Discrete data, multiple state
	Conditions for growth (on solid media)	E63	E : Text, administrative field
Micro-mophology
	Filaments	T3	T : Discrete data, single state
	Asexual reproduction	C4	C : Discrete data, multiple state
	Cell shape	C5	C : Discrete data, multiple state
Physiology
Fermentation
	D-Glucose (F1)	T21	T : Discrete data, single state
	D-Galactose (F2)	T22	T : Discrete data, single state
	Maltose (F3)	T23	T : Discrete data, single state
	Me a-D-Glucoside (F4)	T24	T : Discrete data, single state
	Sucrose (F5)	T25	T : Discrete data, single state
	a,a-Trehalose (F6)	T26	T : Discrete data, single state
	Melibiose (F7)	T27	T : Discrete data, single state
	Lactose (F8)	T28	T : Discrete data, single state
	Cellobiose (F9)	T29	T : Discrete data, single state
	Melezitose (F10)	T30	T : Discrete data, single state
	Raffinose (F11)	T31	T : Discrete data, single state
	Inulin (F12)	T32	T : Discrete data, single state
	Starch (F13)	T33	T : Discrete data, single state
	D-Xylose (F14)	T34	T : Discrete data, single state
Assimilation-Growth
	50% D-Glucose (O4)	T35	T : Discrete data, single state
	60% D-Glucose (O5)	T36	T : Discrete data, single state
	Starch formation (M1)	T37	T : Discrete data, single state
	Acid acetic production (M2)	T38	T : Discrete data, single state
	Urea hydrolysis (M3)	T39	T : Discrete data, single state
	Diazonium Blue B reaction (M4)	T40	T : Discrete data, single state
	Methanol (C41)	T41	T : Discrete data, single state
	Ethanol (C42)	T42	T : Discrete data, single state
	Yeasts physiological data	A1	A : Array of discrete data
	Absorbance values from yeast microplate	M1	M : Vector of S fields
	Physiology classical method	A2	A : Array of discrete data
CoQ
	Coenzyme Q system	D1	D : Continuous data, single value
Temperatures
	Temperature, pH, Salinity & Ethanol information	E39	E : Text, administrative field
	Temperatures growths tests	C8	C : Discrete data, multiple state
Bibliography
	Other bibliographic data	E17	E : Text, administrative field
	Bibliography	B1	RLink : Link to multiple records
DNA
Other information
	GC Data	E28	E : Text, administrative field
	Plasmids	E35	E : Text, administrative field
Sequences
	rDNA sequences 26S	N1	NLink : Link to Sequence
	rDNA sequences 18S	N2	NLink : Link to Sequence
	rDNA sequences ITS	N3	NLink : Link to Sequence
	Miscellaneous sequences	N4	NLink : Link to Sequence
	Original sequence files_Link	P2_Link	FLink : Link to File
	Sequences URLs_Url	P4_Url	U : URL
	Actin	N5	NLink : Link to Sequence
	RPB1	N6	NLink : Link to Sequence
	RPB2	N7	NLink : Link to Sequence
	Elongation Factor 1	N8	NLink : Link to Sequence
	Beta tubuline	N9	NLink : Link to Sequence
Electrophoresis
	GACA electrophoresis gels	G1	GLink : Link to Gel
	FITR	G2	GLink : Link to Gel
Pictures
	Pictures_Link	P1_Link	FLink : Link to File

Examples of hyperlinks for Table Yeasts species in Database CBS Database

Example 1: Record #1 [Aciculoconidium aculeatum], Display all Fields

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Yeasts species&Rec=1&Fields=All&ExactMatch=T

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

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Yeasts species&Name=Aciculoconidium aculeatum&Fields=All&ExactMatch=T

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

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Yeasts species&Name=Aciculoconidium&Fields=All&ExactMatch=F

Example 4: Record Name containing 'Arxula' , Display Field 'E1' (Remarks), Non Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Yeasts species&Name=Arxula&Fields=E1&ExactMatch=F

Example 5: Record Name is 'Arxula adeninivorans' , Display Field 'E1' (Remarks) and 'P1_Link' (Pictures_Link) , Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=Yeasts species&Name=Arxula adeninivorans&Fields=E1&Fields=P1_Link&ExactMatch=T

Fields description for Layout : CBS strain database

Field Caption	Field Name	Field Code	Field type
General information
Taxonomy
	Taxon name	E6_Mycobank	U : URL
	Name confidence	T558	T : Discrete data, single state
	Name changes	E24	E : Text, administrative field
	Type of organism	T1122	T : Discrete data, single state
	Status of the strain	E13	E : Text, administrative field
Collections
	Other collections	E12	E : Text, administrative field
	Other strain numbers (personal numbers)	E560	E : Text, administrative field
	History	E23	E : Text, administrative field
	Herbarium number	E561	E : Text, administrative field
Biosafety and restrictions
	Biological Safety Level	T1389	T : Discrete data, single state
	Human pathogenicity code	T728	T : Discrete data, single state
	Pathogenicity	E731	E : Text, administrative field
	Plant pathogenicity code	T729	T : Discrete data, single state
	Remarks pathogenicity	E732	E : Text, administrative field
	Code toxicity	T730	T : Discrete data, single state
	GMO	T1700	T : Discrete data, single state
	Precautions and restrictions	E7	E : Text, administrative field
Origin
	Substrate of isolation	E15	E : Text, administrative field
	Category of substrate	E16	E : Text, administrative field
	Habitat	E719	E : Text, administrative field
	Country	RLink564	RLink : Link to multiple records
	Locality	E18	E : Text, administrative field
	Latitude, longitude coordinates where collected	L1	L : GIS Location (latitude, longitude, altitude, precision)
	Collected by	E566	E : Text, administrative field
	Collectors number	E720	E : Text, administrative field
	Isolated by	E19	E : Text, administrative field
	Identified by	E21	E : Text, administrative field
	Deposited by	E22	E : Text, administrative field
	Substrate (including host)	E562	E : Text, administrative field
Miscellaneous information
	Public remarks	E1388	E : Text, administrative field
	Miscellaneous information	E38	E : Text, administrative field
	Miscellaneous properties	E735	E : Text, administrative field
	Chemistry	E734	E : Text, administrative field
	Applications	E733	E : Text, administrative field
	Vegetative compatibility	E726	E : Text, administrative field
	Hybrid	E725	E : Text, administrative field
	Mutant	E723	E : Text, administrative field
	Mutation method	E724	E : Text, administrative field
	Price per culture	D1126	D : Continuous data, single value
	Predicted taxon name by ITS sequences	E2941	E : Text, administrative field
	LSU barcode information	T1871	T : Discrete data, single state
	ITS barcode information	T1872	T : Discrete data, single state
	Taxon names	TRLink1634	TRLink : Link to Taxon Name record
Media and growth conditions
	Medium for growth	RLink355	RLink : Link to multiple records
	Conditions for growth (on solid media)	E63	E : Text, administrative field
	Temperatures growths tests	C8	C : Discrete data, multiple state
	Temperature, pH, Salinity & Ethanol information	E39	E : Text, administrative field
Morphology
Macro-morphology
	Reddish diffusing pigment	T1	T : Discrete data, single state
	Colony margin	T2	T : Discrete data, single state
	Colony colour	C1	C : Discrete data, multiple state
	Colony appearance	C2	C : Discrete data, multiple state
	Colony texture	C3	C : Discrete data, multiple state
Micro-mophology
	Filaments	T3	T : Discrete data, single state
	Asexual reproduction	C4	C : Discrete data, multiple state
	Cell shape	C5	C : Discrete data, multiple state
Sexuality
	Number of ascospores per ascus	S1	S : Continuous data range (Min,LP,HP,Max)
	Asci evanescence	T4	T : Discrete data, single state
	Asci shape	T5	T : Discrete data, single state
	Ascospores with gelatinous sheath	T6	T : Discrete data, single state
	Ascospores with a groove	T7	T : Discrete data, single state
	Basidia septation	T8	T : Discrete data, single state
	Basidia shape	T9	T : Discrete data, single state
	Basidia catenate-solitary	T11	T : Discrete data, single state
	Teliospores	T12	T : Discrete data, single state
	Sexual reproduction	T43	T : Discrete data, single state
	Ascospores shape	C6	C : Discrete data, multiple state
	Conjugation	C7	C : Discrete data, multiple state
	Conditions for sporulation	E43	E : Text, administrative field
	Medium for sporulation	RLink570	RLink : Link to multiple records
	Race	E559	E : Text, administrative field
Physiology
Fermentation
	D-Glucose (F1)	T21	T : Discrete data, single state
	D-Galactose (F2)	T22	T : Discrete data, single state
	Maltose (F3)	T23	T : Discrete data, single state
	Me a-D-Glucoside (F4)	T24	T : Discrete data, single state
	Sucrose (F5)	T25	T : Discrete data, single state
	a,a-Trehalose (F6)	T26	T : Discrete data, single state
	Melibiose (F7)	T27	T : Discrete data, single state
	Lactose (F8)	T28	T : Discrete data, single state
	Cellobiose (F9)	T29	T : Discrete data, single state
	Melezitose (F10)	T30	T : Discrete data, single state
	Raffinose (F11)	T31	T : Discrete data, single state
	Inulin (F12)	T32	T : Discrete data, single state
	Starch (F13)	T33	T : Discrete data, single state
	D-Xylose (F14)	T34	T : Discrete data, single state
Assimilation-Growth
	50% D-Glucose (O4)	T35	T : Discrete data, single state
	60% D-Glucose (O5)	T36	T : Discrete data, single state
	Starch formation (M1)	T37	T : Discrete data, single state
	Acid acetic production (M2)	T38	T : Discrete data, single state
	Urea hydrolysis (M3)	T39	T : Discrete data, single state
	Diazonium Blue B reaction (M4)	T40	T : Discrete data, single state
	Methanol (C41)	T41	T : Discrete data, single state
	Ethanol (C42)	T42	T : Discrete data, single state
	Yeasts physiological data	A1	A : Array of discrete data
CoQ
	Coenzyme Q system	D1	D : Continuous data, single value
Bibliography
	Other bibliographic data	E17	E : Text, administrative field
	Bibliography	B1	RLink : Link to multiple records
	Provisional bibliography	E530	E : Text, administrative field
DNA
Other information
	GC Data	E28	E : Text, administrative field
	Plasmids	E35	E : Text, administrative field
Sequences
	rDNA sequences 26S	N1	NLink : Link to Sequence
	rDNA sequences 18S	N2	NLink : Link to Sequence
	rDNA sequences ITS	N3	NLink : Link to Sequence
	Miscellaneous sequences	N4	NLink : Link to Sequence
	Actin	N5	NLink : Link to Sequence
	RPB1	N6	NLink : Link to Sequence
	RPB2	N7	NLink : Link to Sequence
	Elongation Factor 1	N8	NLink : Link to Sequence
	Beta tubuline	N9	NLink : Link to Sequence
	Calmodulin	NLink2508	NLink : Link to Sequence
Pictures
	Pictures_Link	P1_Link	FLink : Link to File
	Pictures from Linda Barnett_Link	P5_Link	FLink : Link to File
	Link to pictures of Linda Barnett (NCYC website)_Url	P6_Url	U : URL

Examples of hyperlinks for Table CBS strain database in Database CBS Database

Example 1: Record #1 [CBS 14], Display all Fields

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=CBS strain database&Rec=1&Fields=All&ExactMatch=T

Example 2: Record Name is 'CBS 14' , Display all Fields, Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=CBS strain database&Name=CBS 14&Fields=All&ExactMatch=T

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

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=CBS strain database&Name=CBS&Fields=All&ExactMatch=F

Example 4: Record Name containing 'CBS' , Display Field 'E6_Mycobank' (Taxon name), Non Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=CBS strain database&Name=CBS&Fields=E6_Mycobank&ExactMatch=F

Example 5: Record Name is 'CBS 74' , Display Field 'E6_Mycobank' (Taxon name) and 'P6_Url' (Link to pictures of Linda Barnett (NCYC website)_Url) , Exact Match Searching

http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=CBS strain database&Name=CBS 74&Fields=E6_Mycobank&Fields=P6_Url&ExactMatch=T

Contact(s) for Database : CBS Database

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

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