TDR Targets Releases

Current major release: 6 | Current minor release: 1

TDR Targets minor Release 6.1, April 2019
  • Data

  • No major genome or chemical data updates in this minor release.

  • Expression datasets

  • Expression datasets were integrated from a number of select organisms, and new expression queries were developed in this release for these cases.

  • Trypanosoma cruzi (Ribosome Profiling, Smircich P et al)
  • Plasmodium berghei (Gametocyte transcriptomics Yeoh et al, Global transcriptomics Otto T et al)
  • Plasmodium falciparum (Several studies, Zanghi et al, Otto TD et al, Lasonder et al)
  • Plasmodium vivax (Intraerythrocytic Transcriptome, Zhu L et al)
  • Entamoeba histolytica (Transcriptomics of virulent and avirulent strains, Hon CC et al)
  • Trypanosoma brucei (mRNA abundance, Siegel TN et al)
  • Leishmania major (Transcriptome profiling of human-infected macrophages, Fernandes MC et al)
  • Toxoplasma gondii (Several studies, Fritz HM et al, Sibley/Greg et al, Gregory et al)
  • Structural Models

  • Updated structural models for all Tier 1 Organisms in TDR Targets. Thanks to Ben Webb and Andrej Sali for their generous help in computing these!

  • Functionality

  • Precomputed Network-Driven Prioritizations (NDPs) and Network-Derived features (e.g. Druggability Scores) available for all Tier 1 Organisms in TDR Targets. Target NDPs for each organism are linked from the Data Summary page. Also, NDPs for Orphan compounds are available for those organisms for which there is phenotypic screening data in TDR Targets (also linked from the Data Summary page).

  • Bugs

  • As usual, we worked really hard debugging the code and query operations at the history so that everything works smoothly for you all!
    If you happen to find an issue, let us know and we'll have it fixed ASAP

TDR Targets Major Release 6.0, August 2018
    • Data

    • Multiple organisms have been added to the TDR Targets repository. Data for all other existing organisms were accordingly updated

      • Model Organisms
      • Arabidopsis thaliana
      • Caenorhabditis elegans
      • Escherichia coli
      • Drosophila melanogaster
      • Schmidtea mediterranea NEW!
      • Dictyostelium discoideum NEW!
      • Saccharomyces cerevisiae
      • Homo sapiens
      • Mus musculus
      • Pathogens
      • Babesia bovis NEW!
      • Cryptosporidium hominis NEW!
      • Cryptosporidium parvum NEW!
      • Entamoeba histolytica NEW!
      • Giardia lamblia NEW!
      • Leishmania braziliensis NEW!
      • Leishmania donovani NEW!
      • Leishmania infantum NEW!
      • Leishmania major
      • Leishmania mexicana NEW!
      • Mycobacterium leprae
      • Mycobacterium tuberculosis
      • Plasmodium berghei
      • Plasmodium falciparum
      • Plasmodium knowlesi
      • Plasmodium vivax
      • Plasmodium yoelii
      • Theileria parva NEW!
      • Toxoplasma gondii
      • Trichomonas vaginalis NEW!
      • Trypanosoma brucei
      • Trypanosoma cruzi
      • Neospora caninum NEW!
      • Trypanosoma brucei gambiense
      • Trypanosoma congolense
      • Chlamydia trachomatis NEW!
      • Loa Loa NEW!
      • Mycobacterium ulcerans NEW!
      • Wolbachia Brugia malayi
      • Echinococcus granulosus NEW!
      • Echinococcus multilocularis NEW!
      • Schistosoma japonicum NEW!
      • Brugia malayi
      • Schistosoma mansoni
      • Treponema pallidum NEW!
      • Annotations
      • Annotations were either calculated ad hoc using InterProScan v5.3, TMHMM v2.0, GPIPred and KAAS server; or directly extracted from corresponding upstream repositories for each organism.
      • Gene orthology was updated to OMCL v5.0
      • Bioactive compounds
      • Drug repository was updated by implementing ChEMBL 23th release
      • Druggable targets were obtained by semi-automated curation of annotated bioactivities.
      • Essentiality sets
      • Added Toxoplasma gondii and Plasmodium berghei genome wide essentiality data. Also updated E. coli, C. elegans, S. cerevisiae essentiality data.
    • User interface

    • Major changes were made in the user interface to make it easier to use.

    • Priorization lists

    • A set of priorization lists were made for Tier 1 pathogens for users to use a starting point for drug discovery projects.

    • A set of priorization lists were made for orphan compound sets from pathogen boxes for drug repositioning endeavors.

    • Functionality
    • JME chemical drawing applet was replaced for Chemaxons Marvin JS application
    • The History section, which allows for query complex operations, has been refurbished and provides clearer clues on how the queries are going to be processed
    • The user may now peek into the network by visualizing targets and their neighbouring elements (wether this are annotations or compounds, or even related targets)
    • Predicted gene-drug interactions now rely ALSO in associations made through the network (view (2016) A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. Berenstein AJ, Magariños MP, Chernomoretz A, Agüero F. PLOS Neglected Tropical Diseases 10(1): e0004300.)
    • Bug fixes
    • We worked really hard to deliver a bug free version to life. If you happen to find an issue, let us know and we'll have it fixed ASAP
TDR Targets Release 5, September 2011
  • Functionality
  • Get lists of compounds associated with targets (and viceversa). From the targets page, after querying the database and obtaining a list of genes/targets it is now possible to obtain the list of all/curated/predicted compounds. The mirror operation is also available (from the compound search, get all/curated/predicted targets).
  • Get orthologs (in a species of interest) from any list of targets. For any query that retrieves a list of targets (e.g. those with loss of fitness phenotypes in T. brucei) it is now possible to get the corresponding list of orthologs (e.g. in T. cruzi). This 'ortholog transformation' operation is available from the history page.
  • Data
  • Genome-wide essentiality data for T. brucei now available in TDR Targets. Data from the paper by Alsford S et al (2011) was integrated into TDR Targets, and is available for searches either as phenotype descriptions (loss of fitness, gain of fitness), or through the 'essentiality' searches (using inference by orthology, and therefore allowing users to look for e.g. 'T. cruzi genes with loss of fitness phenotypes in T. brucei'. Data covers ~ 80% of the protein coding genes and resulted in > 30,000 phenotype descriptions (including normal phenotypes)
  • Phenotype curation data is now available for T. cruzi. The TDR Targets curation team completed an initial round of curation for T. cruzi. Manually curated data is now available for 105 T. cruzi genes, including the associations with 1174 compounds.
  • Additional information is now available for 3D Models. Additional data contributed to TDR Targets by the Modbase team at UCSF (Ursula Pieper, Andrej Sali) is now available for evaluating the available structural models for each modelled target.
  • Bug fixes:
  • As usual there have been a number of bug fixes, the majority of which were trivial or cosmetic. One important bug causing problems with operations using prioritized lists at the history page was fixed.
  • Warning! as for other releases, remember that items saved in your history (saved queries) might now return a different number of genes/compounds because of data updates. For this release, expect all saved queries depending on T. brucei phenotypes to be outdated. Please re-run these queries to catch up with the new data.
TDR Targets Release 4, June 2010
  • Data
  • Chemical Compounds are now an integral part of the TDR Targets database. Bioactive compounds from different upstream sources (ChEMBL, DrugBank, PubChem) have been integrated into the database. Their activities and targets are shown. More information about these new data can be found in the Acknowledgements and Datasources page.
  • Orthology relationships between all gene products, and also against protein targets in the ChEMBL database are now derived from the OrthoMCL v4 database.
  • Genome data (gene models, annotation) have been updated and synced to their corresponding upstream sources: Tuberculist (http://tuberculist.epfl.ch, v2.3), Leprosy (http://mycobrowser.epfl.ch, v2.1), GeneDB/TriTrypDB (http://tritrypdb.org, v2.0), PlasmoDB (http://plasmodb.org, v6.3), ToxoDB (http://toxodb.org, v6.0), GeneDB/SchistoDB (http://genedb.org, http://schistodb.net).
  • Pfam domains, and automated GO assignments (from InterPro); and EC numbers and metabolic pathways (from KEGG), have been updated
  • New species have been added to the menu of species that are available for phylogenetic queries: Apicomplexa: Babesia bovis, several species of Cryptosporidium (hominis, muris, neoformans, parvum), several additional species of Plasmodium (berghei, chabaudi, knowlesi, yoelii), and Neospora caninum; Kinetoplastida: several species of Leishmania (braziliensis, infantum, mexicana), and several species of Trypanosoma (brucei congolense, brucei gambiense, vivax).
  • Curated phenotypes and drugs are now available for S. mansoni, from the TDR Targets curation effort.
  • Functionality
  • New functionality allows searches on chemical compounds. This functionality allows both text based queries, as well as queries that are started from molecules that are drawn by the user
  • [Behind the scenes] Improved and faster management of queries in the user session (intersections, unions, re-weighting strategies)
  • Warnings: user data!
  • If you're a registered user of the database, and you have stored (auto-saved or permanently saved) queries, in some cases, these queries may display an incorrect number of genes; and some queries may not work at all. These issues are caused by data updates in TDR Targets, and can be easily solved by re-running these queries again. Some affected queries are those returning targets that belong to an ortholog group (using an old OrthoMCL identifier, the query would fail to retrieve targets in v4); and phylogenetic queries (due to the update of the ortholog mappings queries may now return a different number of genes).
TDR Targets Release 3, March 2009
    • Data
    • 3D models are now available at Modbase and have been integrated for searching in TDR Targets for Schistosoma, Brugia malayi, and its endosymbiont Wolbachia and M. leprae. Contributed by Ursula Pieper and Andrej Sali (UCSF).
    • Pathways (1089 genes), EC numbers (637 genes) and updated literature references for Brugia malayi.
    • Curated data on assays, and production of recombinant proteins from BRENDA
    • Arabidopsis thaliana is now available in phylogenetic queries as a representative of the Viridiplantae phylum. This now allows searching for targets with/without orthologs in plants.
    • Survey entries and references updated based on user input (Paul Michels)
    • Functionality
    • it's now easier to revise the weighting/scoring strategy of a ranked UNION.
    • it's now possible to run a prioritization session (multi-step search) from the search page, without having to see the results of each intermediate search query
    • support for user roles has been added (moderator, admin), and an initial set of user input forms has been layed out (comments associated with genes/targets, which moderators have to approve).
    • Links out to Tuberculist now go to their new site.
    • Lots of minor bugfixes and some other major (but too technical) changes.
TDR Targets Release 2, June 2008
    • Data & Features
    • Schistosoma mansoni. A new helminth genome has been incorporated into TDR Targets. Version 4.0 of the S. mansoni genome is now in TDR Targets.
    • New slideshow tutorials. Starting with this release we will be providing short slideshow tutorials on different aspects of the site functionality and/or usage.
    • Drug Targets Survey. In this release we have integrated the data from the Human African Trypanosomiasis survey on drug targets. All entries have been incorporated and linked to the corresponding targets and bibliographic references.
    • New functional classification. genes have been classified in three main categories (enzymes, receptors, transporters). This manual classification (described in the documentation) complements the other classification schemes available (metabolic pathways, GO slims), providing more search options.
    • Query history page. You can now export smarter spreadsheets that will allow you to re-prioritize datasets on the fly by changing weights to each criteria. There is also a new interface for easier subtraction between queries, and other minor changes to the history UI we expect will make your life easier.
    • More PDB structures for Mycobacterium tuberculosis. We have updated the list of PDB structures available for M. tuberculosis. All these structures are also available for M. leprae.
    • Curated target information for M. tuberculosis and M. leprae. As part of the ongoing curation effort, we have loaded curated information for M. tuberculosis.
    • Result tables. You can now re-sort the results of queries, and also specify the number of records that should be displayed per page.
    • Bugfixes. Lots of bugfixes are included in this release. Keep sending your bug reports!
TDR Targets Release 1, April 2007
    • Data & Features
    • Presentation of TDR Targets. TDR Targets was unveiled on April 16th in Geneva at a meeting of TDR's Drug Discovery committee.
    • First genomes. The first genomes included in TDR Targets are those of: Plasmodium falciparum, Mycobacterium tuberculosis, Trypanosoma brucei, Leishmania major and Trypanosoma cruzi.