bioDBnet 2.1
Release Date: May 6th 2015
Nodes: 205
Edges: 712
Notes:

• New Features
  • New Databases
    • Protein interaction data from STRING and ConsensusPathDB is integrated into bioDBnet. IPI IDs are re-integrated and HGNC ID is now an input identifier, so conversions can be made using HGNC ID's as inputs
• Network
  • Node updates
    • HPRD Protein interactors are now available as output nodes for all input nodes
• Documentation
  • Network Nodes and bioDBnet versions are modified to reflect the changes in the nodes and edges

bioDBnet 2.0
Release Date: Oct 28th 2014
Nodes: 200
Edges: 689
Notes:

• Web Interface
  • bioDBnet
    • The web interface of bioDBnet is modified
• Main Menu
  • dbAnnot
    • A new feature added to bioDBnet. dbAnnot allows conversions based on function for different types of biologial identifiers.
  • Web Services
    • REST APIs for all the main functions in bioDBnet have been added
    • Sample code for the REST calls from different programming languages has been added
• Network
  • Pathways
    • pathway edges have been modified to get detailed information on pathways from several databases including KEGG, Biocarta, NCIPID and Reactome
  • Drugs
    • multiple nodes and edges for obtaining information on drugs from DrugBank and PharmGKB have been added
  • Diseases
    • disease information from PharmGKB has been added
  • Interactions
    • multiple nodes and edges for getting protein interaction information from DIP, MINT, NCIPID etc. have been added
• Documentation
  • Network Graph and Network Nodes
    • modified to reflect the changes in the nodes and edges
  • Examples
    • added example screen shots for dbOrtho, dbAnnot and dbOrg
  • bioDBnet versions
    • versions page has been modified to include all the new version changes

bioDBnet 1.7.1
Release Date: May 23rd 2012
Nodes: 189
Edges: 663
Notes:

• WebServices
  • dbOrtho has been added as a new functionality to the web services. All pages under WebServices have been modified to reflect the update.
• A bug in the download results code that causes problems when input values exceed a certain size has been fixed.
• A bug in the dbOrtho code, that misses ortholog conversions for certain types of biological identifiers has been fixed.
• Documentation
  • bioDBnet versions page has been modified to reflect the changes in download and WebServices code.

bioDBnet 1.7
Release Date: March 7th 2012
Nodes: 189
Edges: 663
Notes:

• Main Menu
  • dbOrtho
    • A new feature added to bioDBnet. dbOrtho provides an easy interface for homolog conversions between any species
• Documentation
  • bioDBnet versions page has been modified to reflect the changes in the nodes and edges

bioDBnet 1.6
Release Date: December 2nd 2011
Nodes: 189
Edges: 663
Notes:

• New Features
  • Web Services
    • A new space for documenting and providing WebServices help has been created
• WebServices
  • SOAP Web Services, SOAP server, WSDL and PHP sample code pages have been rearranged to their new location under WebServices
  • New pages with Java and Python sample implementation code have been added
• Documentation
  • Old documentation page for Web services has been relocated
  • bioDBnet versions page has been modified to reflect the changes in the nodes and edges

bioDBnet 1.5
Release Date: October 16th 2011
Nodes: 189
Edges: 663
Notes:

• New Features
  • New Databases
    • HMDB, NCIPID and KEGG-medicus(Drug, Disease) have been integrated into bioDBnet
• Network
  • New nodes
    • HMDB Metabolite, KEGG Disease ID, KEGG Drug ID and KEGG Drug Name are added as new input nodes to bioDBnet.
    • Allergome Code, COSMIC ID, ChEBI ID, DPD DIN, HMDB Enzyme - Gene Symbol, HMDB Enzyme - UniProt Entry Name, HMDB Metabolite Desc, KEGG Compound ID, KEGG Disease Info, KEGG Drug Info, NCIPID PTM, NCIPID Pathways, NCIPID Protein Complex, NCIPID Protein Interactor, PubChem ID, RefSeq ncRNA Accession, TCDB ID, VectorBase Gene ID
• Deleted nodes
  • Due to changes in the cross reference information in some of the databases nodes BuruList ID, EcoCyc ID, IMGT/LIGM-DB ID, ListiList ID, MypuList ID, Paralog - Ens Protein ID, PhotoList ID, RATMAP ID, RefSeq Genomic Info, SagaList ID, StyGene ID, SubtiList ID, WormPep Transcript ID were deleted from bioDBnet
• Node updates
  • The following node name changes were made for naming consistency: DrugBank ID renamed to DrugBank Drug ID, Drug Info renamed to DrugBank Drug Info, Drug Target renamed to DrugBank Drug Target ID, Drug Enzyme ID renamed to DrugBank Drug Enzyme ID, Non Protein Interactor (HPRD) renamed to HPRD Non Protein Interactor, Protein Complex Interactor (HPRD) renamed to HPRD Protein Complex, Protein Feature (HPRD) renamed to HPRD Protein Feature, Protein Interactor (HPRD) renamed to HPRD Protein Interactor, Protein Modification (HPRD) renamed to HPRD Protein Modification, Xenbase ID renamed to XenBase Gene ID
• Documentation
  • Network Graph, Network Nodes and bioDBnet versions are modified to reflect the changes in the nodes and edges

bioDBnet 1.4
Release Date: September 1st 2010
Nodes: 179
Edges: 625
Notes:

• New Features
  • Web Services
    • All the main conversion features of bioDBnet can now be accessed through web services
  • New Databases
    • DrugBank and HPRD have been integrated into bioDBnet
• Main Menu
  • dbOrg
    • A new feature added to bioDBnet. dbOrg contains downloadable links for Organism wide database identifier conversions.
  • dbReport
    • An additional link to non-B DB is added for 'Gene ID' reports from human or mouse
• Network
  • DrugBank and HPRD
    • DrugBank ID and DrugBank Drug Name are added as new input nodes to bioDBnet.
    • DrugBank Target, DrugBank Enzyme ID, Protein Interactor (HPRD), Non Protein Interactor (HPRD), Protein Complex Interactor (HPRD), Protein Feature (HPRD), Protein Modification (HPRD) are added as new nodes to bioDBnet
• Documentation
  • New documentation pages for Web services and Flexible Database Integrator are added
  • The FAQ page has been modified to include explanation for some annotatoin and visualization links provided for some reports through dbReport
  • Network Graph, Network Nodes and bioDBnet versions are modified to reflect the changes in the nodes and edges

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.