Release Notes

Next release - 2.5

Scheduled for August 2007
Release 2.4 exhausted our storage space. Biozon is finally expanding and will double in space by mid July, enabling us to update the DB.

2.4

15 August, 2006

Updated Data

  • SwissProt/TrEMBL updated to include data from UniProt release 7.5

2.3

7 October, 2005

Extended Functionality

  • Modified the search graph to include unigene clusters. Unigene may now be incorporated into complex searches using the standard search interface.

New data

  • Refseq has been fully incorporated into Biozon for the first time, adding a number of new protein and nucleic acid sequences in addition to all refseq annotation

Updated Data

  • Unigene has been updated to the most recent version as of September 2005. This is the first complete unigene release incorporated into Biozon. Previously, only human and mouse unigene clusters were uploaded.

2.2

1 September, 2005

New functionality

  • Provenance information is made available for search results that make use of similarity (i.e. fuzzy searches). Clicking on the colored square in the "fuzzy?" column of search results will show a page containing showing exactly how the fuzzy result derived, and where the similarity was applied
  • EST analysis tool: EST sequences can be mapped to their corresponding protein products (if exist) using multiple paths in the Biozon data graph.

Extended Functionality

  • Data sets have been enhanced to allow the public download of Biozon computed alignments and domain predictions. Previously, one had to specifically contact the Biozon administrators to obtain permission for download
  • Materialization of results now supports customization of the download format by allowing the user to specify which attributes for each object type in the query are recorded.

Updated data

  • Swissprot/TrEMBL updated to include data from uniprot release 4.6
  • Genbank updated to include data from release 147
  • BIND updated on 5/1/2005
  • PDB updated on 7/19/2005
  • GO terms updated to reflect new mappings found in Uniprot
  • Protein alignments for new sequences, total alignment count more than doubled

2.1

26 April, 2005

Extended functionality

  • Three types of similarity results may now be independently selected in protein search form when formulating a fuzzy complex query: BLAST alignments, similarity by structural alignment, and similarity by expression profile.
  • Marking of fuzzy results in complex queries has been expanded to indicate the different types of similarity used to deduce search results
  • Expression profile similarity is now accessible from the profile page of any proteins that have such data. A graph of the expression profile comparisons may be viewed for each match

New Data

  • Expression profile similarity for genes expressed by Saccharomyces cerevisiae

2.0 - The first official release (see announcement)

5 January, 2005

New functionality

  • First-of-a-kind biological ranking system which resembles the methods implemented in Google.
  • Fuzzy searches that extend complex searches to include homologous sequences or structures as a search step.
  • Analysis tools such as domain prediction, structure and sequence similarity and analysis of expression data.
  • Account management system that enables users to save queries and materialize data from search results to download for further analysis or include as a step in some other complex query.
  • Graphical visualization of domains, GO terms, protein structures, structural alignments and interaction maps.

Updated data

  • Swissprot/TrEMBL updated
  • Genbank updated
  • BIND updated
  • PDB updated

New data

  • DIP
  • Gene Ontology
  • Structural similarities

1.0 - The beta release

27 January, 2004

New functionality

This release already had many of the basic functions that characterize Biozon
  • Each biological entity can be viewed in its extended biological context, through its relations to other biological entities.
  • Complex searches on the data graph that specify desired interrelationships between types.

New data

  • Swissprot/TrEMBL
  • Genbank
  • BIND
  • PDB
  • KEGG
  • Sequence similarities

The pre-beta times

Biozon was conceived several years ago (2001), as part of our long term plan to develop an infrastructure for the computational analysis of proteins and other related entities. Prior to Biozon our lab developed ProtoMap (a database of protein families) and BioSpace (that combines sequence and structure information, and contains 3D models for more than 160,000 proteins). This type of analysis is faced with special challenges, due to the dynamic nature of the data. Therefore, the further development of these databases was put on hold in order to construct a sustainable infrastructure (a.k.s Biozon) to support this analysis and other research projects. Development of ProtoMap and BioSpace will resume in 2006, where new classification and modeling techniques will be integrated into Biozon, to subsume our previous efforts.

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