bioDBnet 1.3.2 (bug fix)
Release Date: October 15th 2009
Nodes: 170
Edges: 612
Notes:

• A bug in the java script code that causes the form fields to disappear in some versions of IE has been fixed

bioDBnet 1.3.1 (bug fix)
Release Date: October 5th 2009
Nodes: 170
Edges: 612
Notes:

• A bug in the code for appending results from multiple queries for the same edge has been fixed.

bioDBnet 1.3
Release Date: September 15th 2009
Nodes: 170
Edges: 612
Notes:

• Network
  • UniProt Protein Name
    • UniProt Protein Name was added as a new input node to bioDBnet.
• Main Menu
  • db2db, dbFind, dbReport and dbWalk
    • A new radio button to check if the input values have a comma has been added to facilitate the queries with 'UniProt Protein Name' as input. If the value for this new parameter is 'no' then bioDBnet treats only the 'new line' as a delimiter otherwise by default both commma and new line will be treated as delimiters.
    • New hyperlink to the orgTaxon tool has been added to all the forms
• Documentation
  • Network Graph, Network Nodes and bioDBnet versions
    • modified to reflect the changes in the nodes and edges

bioDBnet 1.2
Release Date: September 2nd 2009
Nodes: 169
Edges: 608
Notes:

• Network
  • MGC,XGC,ZGC
    • connections to the Mammalian, Xenopus and Zebrafish Genome Collections from NCBI Gene IDs have been added.
• Back end code
  • A bug in the code for merging results, which was causing bioDBnet to miss some results, has been fixed
  • The drawChr program has been modified so that only the data on chromosomal locations is represented. In the previous version extra bands were being printed when the bands were extra-chromosomal or unknown

bioDBnet 1.1.1
Release Date: August 3rd 2009
Nodes: 166
Edges: 605
Notes:

• The back end databases of bioDBnet have been migrated to Oracle 11g

bioDBnet 1.1
Release Date: June 1st 2009
Nodes: 166
Edges: 605
Notes:

• Network
  • Homolog information from Ensembl
    • added edges for getting homolog information from the Ensembl database in addition to the already existing information from HomoloGene
    • added edges for getting paralog information from the Ensembl database
  • dbSNP database
    • The underlying schema for the dbSNP database has been modified. These modifications allowed for addition of more connections for dbSNP to Gene and RefSeq identifiers
  • miRBase
    • connections to and from miRBase ID to Ensembl IDs have been added
  • GO
    • GO IDs are now split into the 3 underlying categories: biological process, molecular function and cellular component
    • The output format is now GO_ID[Name: ] instead of the previous GO_ID[Type: ][Name: ]
• Main Menu
  • db2db and dbReport
    • In the previous version if a Taxon ID is entered in the optional organism field results were returned even for input identifiers not belonging to the Taxon ID. This issue has been fixed so that even if a mixture of identifiers from different species is submitted and a taxon id is entered only the inputs belonging to this taxon id will have results. Note: If a Taxon ID is not given and the inputs are a mixture of identifiers from different species then the results for all the identifiers can be obtained.
  • dbReport
    • The results page for dbReport has been modified to include links for both the PNG and SVG versions of the chromosome maps
• Documentation
  • Network Graph and Network Nodes
    • modified to reflect the changes in the nodes and edges
  • bioDBnet versions
    • a new versions page has been added to record changes in bioDBnet
• Tools
  • orgTaxon
    • a query tip has been added to the description
  • chrView
    • The chrView script has been modified to produce both PNG and SVG images. The result page displays the PNG image and provides a link for the SVG image for more interactive use.
    • The description has also been modified to reflect these changes
• Contact
  • feedback form has been added to get user feedback on bioDBnet

bioDBnet 1.0
Release Date: Nov 23rd 2008
Nodes: 153
Edges: 554
Notes:

• The first release of bioDBnet.
• Details have been published in the journal Bioinformatics.
  bioDBnet: the biological database network
  Mudunuri U, Che A, Yi M, Stephens RM.
  Bioinformatics 2009 Feb 15;25(4):555-6.