FAQ

This is a list of Frequently asked questions about this resource, and their answers. If you have a question that is not covered here do not hesitate to contact us.

Contents

  1. General
  2. New Searches
  3. Search History
  4. Details for a Particular Target
  5. Posted Lists
  6. Site Maintenance and Updates

Full text


  1. General

    • 1.1. Who is the target audience of this database, and what can they expect to learn from it?
      The database is meant to be used by anyone with an interest in the development of drugs for treating neglected tropical diseases. It can be used in at least two general ways. If you are interested in a specific gene/protein, the database can provide you with drug discovery-related information on that particular gene/protein. If you are interested in a specific pathogenic organism (or group of organisms), you can generate lists of potential targets in that organism based on criteria you consider important.

    • 1.2. This database seems to include a lot of information. What specific information is available for which organisms?
      Please refer to the "Summary of available data" chart on our home page.

    • 1.3. I'm still confused about what's in the database and how to use it. Is a tutorial available?
      We are developing a user's manual, which includes an overview of datasets available in the database, detailed tips on using the database, and some sample queries and their results. If this manual does not fully meet your needs, please contact us and we will try to provide one-on-one assistance.

    • 1.4. Do I have to register and get a login account in the database to use it?
      No, you do not have to register in order to run queries, view and combine results and export the results. But you may want to register if you want to preserve your work between sessions or if you want to POST or PUBLISH your query results for community-wide access.

    • 1.5. What are the top 10 targets for species X?
      A common misunderstanding is that this site can or should offer a definitive "top 10 list" of the best drug targets for each pathogen. On the contrary, the site's flexible search options enable each user to rank targets according to their own criteria. Browsing the lists posted by other users may offer some insight as to what these users consider to be the best targets. However, unless stated otherwise, information presented on this site should not be considered an endorsement of, or recommendation against, pursuit of a given target.

  2. New Searches

    • 2.1. How do I search for genes that are essential in my favorite organism?
      If your favorite organism is Mycobacterium tuberculosis, then you're in luck; go to the search page, select M. tuberculosis as the pathogen species of interest, and after the Essentiality heading (under Filter Targets Based On...), specify that the gene should be essential in M. tuberculosis. For other species, information is more limited, but within the Curated Targets section you can specify that the Phenotype observed should be a lethal phenotype.

    • 2.2. How do I focus on the data that have been manually curated?
      In the Filter Targets Based On... section, go down to the Curated targets section and enter the desired selection criteria. To see all targets for which any curated data are available, simply check the box next to "Search for targets that have undergone manual curation."

    • 2.3. The search I'm doing is not retrieving the number of records I expect. Gene X should be retrieved by my search!
      This could happen for a variety of reasons (see below). If you are sure this is our fault, do not hesitate to contact us.
      To help you troubleshoot the problem, take into account the following guides:
      Check the version of the datasources we've used when building TDR Targets. Chances are the gene is annotated/present in a new version of the corresponding genome.
      Check the terms of the query that is giving you trouble. Are you specifically requesting this gene (say by its accession or identifier) or are you performing a more indirect query and expect Gene X to show up? If asking for the identifer/accession doesn't work, do contact us. On the other hand, if the target doesn't show up using an indirect query (i.e. genes with PDB structures), it means that we are lagging behind with respect to upstream data providers (PDB, Modbase, PubMed, etc.).

  3. Search History

    • 3.1. What is the 'Upload' function on the history page and how can I use it?
      The Upload function allows users to batch import a list of genes or targets in one step. This list will appear in your history and can then be weighted and combined with other queries. This allows you to work with lists of genes that have been obtained using some filtering criteria that is not available in TDR Targets (e.g. from your own lab research).
      To upload a list of genes prepare a plain text file containing a list of gene identifiers (one per line). Care should be taken to ensure that the gene IDs that are uploaded match the ones that are used in the TDR targets database. In addition to Gene IDs the upload file can optionally contain 'weights' (numerical scores) for each gene. These should be added on the same line as the gene identifier, separated by one or more spaces or TABs.

    • 3.2. How do I download my list of targets?
      Go to the History page to see your query history. Then, under My Queries, find the query you wish to download, click on the word Export, and provide the requested information.

    • 3.3. I have untitled queries in my history. How do I find out about how the query was formulated and RENAME them?
      Under each query, there is a clickable 'Show parameters' link. Clicking on this link will show you the parameters that were used to retrieve the genes. Based on this info the untitled queries can be renamed using the history rename functionality.

    • 3.4. How long will unsaved queries remain in my history? And saved ones?
      All unsaved queries should remain in your 'My queries' section of the history page until you finish your browser session (i.e. you quit your internet browser). If you are registered, you can savee your queries and these will be preserved across browser sessions (you will see them again once you log in back into the site). As it is now, saved queries will remain in your 'Saved queries' until you delete them.

    • 3.5. Why would I want to combine previous queries with weighting rather than simply executing a union or intersection of the previous queries?
      Weighting allows you to rate the relative importance of the many criteria that can be considered in prioritizing targets, such that the targets meeting what you consider to be the most important criteria will receive the highest scores and appear at the top of your list. As an example, if you say that having a druggability index of >0.7 is more important than having 3D structural data, the targets meeting both criteria will score highest, followed by the targets that have a druggability index above 0.7 but lack structural data and then finally the targets with structural data but a druggability index below 0.7.

    • 3.6. Can I combine results from multiple species?
      No. All the history functionalities useful in combining various query results (such as the Union, Intersection and Subtraction functions) work by matching gene IDs and hence cannot be used to combine query results from different pathogens.

  4. Details for a Particular Target

    • 4.1. I'm looking at the information available for target X and I don't see compound Y mentioned. This compound is a known inhibitor of this class of targets. Why it is not listed?
      Most likely, our curation efforts have simply overlooked it. If you contact us with the appropriate information, we will add it to the database.

  5. Posted Lists

    • 5.1. What does it mean to "post" or "publish" a list of targets?
      Website users who have registered and logged in can share the results of their target searches with the public. Again, a given list should not be taken as the author's ironclad ranking of desirable targets. However, researchers and users that are new to the site may find it informative to view searches, search criteria and scoring strategies from others.

  6. Site Maintenance and Updates

    • 6.1. How will the TDR Targets site be updated? For example, as gene products are characterized and validated as drug targets, how will that status change over time on the database?
      Major updates to the database are planned. These are the addition of datasets for recently sequenced genomes. We have been doing minor updates of the information (for example annotation information) to keep in sync with the upstream providers (GeneDB). Manual curation of targets is still not done, and will be an ongoing effort in the next year. As you can imagine, reviewing every KO, RNAi, or drug study ever done in each of these organisms takes time. The site will continue to be maintained after the main annotation effort is complete, but we expect to engage the research community itself in annotating and adding information about targets in the future.

    • 6.2. If a user is an expert or is interested in a specific pathway/target and already has information about it, could that person contribute the information to the site?
      Yes. An effort to survey the community of experts for information on targets is underway for Trypanosoma brucei (see the mention of the Scientific Community Human African Trypanosomiasis Drug Target Survey on our home page). If you have information for other targets, currently you can send us such information via the contact page and our curators will incorporate it into the database. In the future other surveys will be run for other parasites. Also, we hope to have a more direct route to allow the community to contribute and update the information.