BIODEGRADATIVE
    STRAIN
        DATABASE

How to use this site


Go to:
Individual Strain and Substrate Data Pages
Accessing Individual Data Pages
Searching the Database
User Input

Individual Strain and Substrate Data Pages

      BSD data is centered around three linked and required, core data types: 1) a strain, 2) a substrate that it degrades or transforms, and 3) the reference supporting 1 & 2. Data from any one of these fields is not included unless the corresponding data from the other two fields are also available.

      Each strain and each compound (substrate) represented in the BSD has an individual data page that displays detailed strain or substrate information and links to additional information elsewhere on the web. To give database users an idea of future development goals, these pages display both currently functional data fields, as well as, data fields still under development. When available, data related to non-functional data fields are currently displayed in the "Comments" section of each strain or substrate page (for example: strain G4 and benzene). The strain and substrate pages are linked to each other through their corresponding substrate or strain tables. The table of substrates for any given strain should not be considered an exhaustive list, only the data we have so far compiled for that strain. Unlike the other two core data types, references do not have individual pages. However, when available, references are displayed as links to their PubMed abstracts.

Table 1. Functional data fields (bold typeface indicates searchable fields).

Strain Data

Substrate Data

Reference Data

strain designation

CAS number

BSD short ID

genus

table of strains that degrade it

links to PubMed abstracts

species

link to UM-BBD data

 PubMed ID numbers

phylogenetic affiliation

link to Chemfinder data

  

table of substrates degraded

link to health and safety data

  
culture collection accessions chemical synonyms  

16S rRNA accessions

    

source of isolation

    

associated patents

    

link to UM-BBD

    

taxonomic basonymes

    


Accessing Individual Data Pages

      The individual data pages can be accessed via three major avenues.

1. Data Lists
      A series of strain, substrate or reference lists are available from the BSD frontpage. There are three strain lists, each containing the same data in a different order: 1) alphabetical by strain designation, 2) alphabetical by latin name (genus) and 3) phylogenetically ordered. In the substrate and reference lists, only strain designations, not genus and species, are displayed to reduce complexity of the tables and downloading time. However, placing your cursor over a strain designation in those tables will display that strain's latin name in the status bar at the bottom of your browser (right).

 

2. The Phylogenetic Tree
      A list of degradatave strains belonging to a particular phylogenetic group can be generated using the phylogenetic tree interface (left).

 

3. BSD Search
      Specific strain, substrate and reference data can be used to access the database using the search engine on the BSD frontpage (see details below).


Searching the Database

      BSD data can be searched by any of the criteria listed in Table 1 above. The search engine is not case sensitive and full or partial words can be used. An asterisk is not needed and will not work. Boolean strings are not yet functional. All searches result in a list of strains relevant to the search criteria - even when searching by substrate or reference data. The search engine, as developed so far, allows reference data to be searched using only the information provided in the BSD short IDs i.e. only by first author or year (See the BSD Reference List). An exception is two author publications, which can be searched by both authors.

Some examples: Some special search criteria:
User Input

      One of the goals of the BSD is to provide a forum for researchers and database users to contribute to suggestions and new or corrected data to the database. To facilitate user contributions, a Data Submission Form is accessible from the individual strain pages and from the BSD frontpage. A User Survey Form is also available on the BSD frontpage.

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Contact us with any comments or suggestions.