genome/dgi-db

faq:
  title: DGIdb - FAQ
  title_main: FAQ
  title_small: frequently asked questions
  description: > 
    This page provides answers to a wide array of general questions.
  questions:
    - question: What is the goal of DGIdb?
      anchor: goal
      answer: >
        The goal of DGIdb is to help you annotate your genes of interest with respect to known drug-gene interactions and potential druggability.

    - question: How do I cite DGIdb?
      anchor: cite
      answer: >
        Please cite our most recent paper on DGIdb, which can be found on the <a href="/publications">Publications</a> page.

    - question: Is DGIdb open source and open access?
      anchor: source
      answer: >
        The source code for DGIdb is open-source and made available under the MIT license. The license is
        distributed with the source code (<a href="https://github.com/genome/dgi-db/blob/master/LICENSE">DGIdb license</a>).
        The data used in DGIdb is all open access and where possible made available as raw data dumps in the 
        <a href="/downloads">downloads</a> section.

    #- question: How can I learn more about how to use DGIdb?
    #  anchor: learn
    #  answer: > 
    #    You can try reading: the <a href="/getting_started">'Getting Started'</a> section under the help menu,
    #     the <a href="https://doi.org/10.1093/nar/gkx1143">manuscript</a>, and this FAQ.
    #    Some sections also contain a 'Tour' that can be activated by pressing the 'Show Tour' button in the top left.
    #    If all else fails, please <a href="mailto:help@dgidb.org">email us</a> with your questions.

    - question: What types of gene names/symbols should I use as input?
      anchor: types
      answer: >
        The short answer is that you should ideally use official HUGO gene symbols as reported by Entrez Gene. We have developed a gene name grouping
        strategy that attempts to aggregate synonyms for each gene. We start with the official name and alternate names of each Entrez Gene and update
        with additional names from each data source. You should get reasonable results with known synonyms, Ensembl Ids, Uniprot Ids, etc. If you enter a 
        gene name that is ambiguous or unmatched this will be noted in the results. You should attempt to find a more official name for such genes and update
        your gene list.

    - question: How are genes defined in DGIdb?
      anchor: defined
      answer: >
        The gene summary page shows the primary name, alternate names and metadata for each gene locus as provided by each source of data
        imported into DGIdb. Genes in DGIdb are first defined by Entrez but mapped together with gene records from other sources by Entrez ID,
        Ensembl ID, UniProt ID or alternate names/synonyms in that order of preference.

    - question: How are drugs defined in DGIdb?
      anchor: defined
      answer: >
        The drug summary page shows the primary drug name, alternates names, and metadata for each gene as provided by each source of the
        data imported into DGIdb. Drugs are first defined by ChEMBL but mapped together with drug records from other sources.
        
    - question: How are the gene and drug filters defined in DGIdb?
      anchor: filters
      answer: >
        When searching by genes, filters for drug interactions currently include Approved drugs, Antineoplastic drugs, and Immunotherapies.
        Regulatory approval status is extracted from ChEMBL. Anti-neoplastic drugs are defined by inclusion in an anti-neoplastic drug–gene
        interaction source (e.g. My Cancer Genome), or as a drug with an anti-neoplastic attribute from its constituent source. Immunotherapy
        drugs are defined as any drug with an attribute of ‘immunosuppressive agent’, ‘immunomodulatory agent’ or ‘immunostimulant’.
        <br>
        When searching by drugs, filters for gene interactions currently include Clinically Actionable genes, genes included in the Druggable
        Genome definition and Drug Resistant genes. Clinically Actionable genes are genes that constitute the DGIdb ‘clinically actionable’
        gene category, and by definition is used to inform clinical action (e.g. the Foundation One diagnostic gene panels). Similarly,
        druggable genome genes are genes listed in the DGIdb ‘druggable genome’ gene category. Drug resistance genes are defined by the
        Gene Ontology as genes that confer drug resistance or susceptibility (GO identifier 0042493), and are maintained in the DGIdb through the
        ‘drug resistance’ gene category.

    - question: Where can I find the source code for DGIdb?
      anchor: source
      answer: >
        The code for DGIdb is available at <a href="https://github.com/genome/dgi-db">github</a><i class="icon-share"></i>.

    - question: I have a source of druggable genes or drug-gene interactions that I would like to add to DGIdb. How do I do that?
      anchor: add
      answer: >
        This is an open source project and you could therefore create your own instance with your own data. However, if you want that
        source, chances are that we do too. <a href="mailto:help@dgidb.org">Contact us</a> and we will be happy to consider adding your source for you.

    - question: What is the meaning of 'Gene Categories' in DGIdb?
      anchor: categories
      answer: >
        Gene categories in DGIdb refers to a set of genes belonging to a group that is deemed to be 
        <a href="http://en.wikipedia.org/wiki/Druggability">potentially druggable</a>.
        For example, kinases are generally deemed to have high potential value for development of targeted drugs.
        For more details on the sources of druggable gene category definitions, refer to the <a href="/sources">sources</a> 
        and <a href="/about">background reading</a>.

    - question: What is an 'Interaction Type' and "Interaction Type Directionality"?
      anchor: interaction
      answer: >
        An interaction type describes the nature of the association between a particular gene and drug. 
        For example, TTD reports the drug-gene interaction, SUNITINIB-FLT3. The interaction type is reported as 'inhibitor'.
        Interaction type, as used in DGIdb, is very broad. Dozens of interaction types are currently defined.
        Many interaction types describe the mechanism of action between a small molecule and a protein.
        However, other broader types of 'interaction' might also be used. e.g. Gene X mediates 'resistance' or 'sensitivity' to drug Y.
        A full list of interaction types and their definition can be found on the <a href="/interaction_types">Interaction Types & Directionalities</a> page.
        <br>
        Interaction types can be loosely grouped into Activating interaction types and Inhibiting interaction types. Activating interactions
        are those where the drug increases the biological activity or expression of a gene target while Inhibiting interactions are those
        where the drug decreases the biological activity or expression of a gene target. To see which interaction types fall under which
        directionality check out the list of interaction types on the <a href="/interaction_types">Interaction Types & Directionalities</a> page.

    - question: What is the "Interaction Score" and the "Query Score"?
      anchor: score
      answer: >
        Please see the <a href="/score">Interaction Score & Query Score</a> page for a detailed explanation of these terms.

    - question: What is the difference between a drug-gene interaction and druggable gene category?
      anchor: difference
      answer: >
        A drug-gene interaction is a known interaction (e.g. inhibition) between a known drug compound (e.g. lapatinib) and a target gene
        (e.g. EGFR). A druggable gene category is a grouping of genes that are thought to be potentially druggable by various methods of 
        prediction. For example, the 'rule-of-five' analysis described by Hopkins and Groom in 2002 defined lists of genes that were most
        likely to be successfully targeted by small molecule inhibitors. Genes in these categories are *potentially druggable* and 
        may or may not have existing drugs that target them. On the other hand, all of the genes from the drug-gene interaction sources 
        are targeted by specific known compounds.

    - question: What is the difference between a cancer-specific source and a disease-agnostic source?
      anchor: sourcetype
      answer: >
        Cancer-specific sources are sources that only contain information pertaining to cancers while disease-agnostic do not limit their
        data in regards to the disease. While cancer related searches are a major use-case for DGIdb and cancer-specific sources are
        well-represented among all sources, DGIdb is not a cancer-specific resource and is intended to be utilized for non-cancer related
        research as well. In the interaction and category searches the source list in the Source Databases dropdown is grouped by cancer-specific
        and disease-agnostic sources and users may select or deselect all entries in each group by clicking on the respective header in the dropdown.


    - question: How is this application different from DrugBank, TTD or other databases?
      anchor: different
      answer: >
        There are many differences. DGIdb is limited to human genes only. DrugBank and TTD are databases that catalogue drugs and store
        detailed information about those drugs and the genes they target. DGIdb aggregates many such databases into a common framework.
        DGIdb adds considerable functionality for efficiently searching a list of input genes against these sources. DGIdb integrates both
        known drug-gene interactions and potentially druggable gene data. DGIdb allows the user to refine their query to certain gene families,
        types of interactions, etc.  DGIdb is open source and available in a format that would allow you to create your own
        instance. DGIdb incorporates sources of drug-gene interaction data that were previously only available in inaccessible formats (e.g.
        tables in a PDF document). DGIdb is meant to be used in combination with the original sources of raw data. Wherever possible we link
        out to those original sources.

    - question: I found a gene in a category that does not really belong there or a drug-gene interaction that appears false.  Should I report it?
      anchor: belonging
      answer: >  
        We are working on updates to the interface that would allows us to readily capture this kind of information directly from users. In the meantime 
        please feel free to report it to us. The quality of our data is only as good as the sources of raw data. Throughout the results you will
        be able to see if multiple independent sources report the same findings. Using the number of sources, query score, or interaction score as filters may help you disqualify some spurious
        entries and have increased confidence in others.

    - question: Some druggable gene categories seem very inclusive. For example, are there really nearly 2000 human kinases?
      anchor: inclusive
      answer: >
        This is by design. Druggable gene categories are aggregated from multiple sources, some of which are predictive in nature. Predictions based on
        sequence similarity may result in some false positives. More stringent lists can be obtained by limiting to a particular source(s) (e.g. dGene only)
        or by requiring that multiple sources agree.

    - question: How is DGIdb implemented?
      anchor: implementation
      answer: >
        The web interface uses Ruby on Rails and Twitter bootstrap. The backend is a Postgres database. The importers that process data
        from each source and populate this database are written in Ruby with occasional forays into Python.

    - question: How is versioning handled in DGIdb?
      anchor: versioning
      answer: >
        This question has several answers.  The footer of every page in the web interface contains a version stamp that describes versions for various components.
        The interface code itself is meticulously tracked in <a href="https://github.com/genome/dgi-db">dgi-db at github</a>. 
        The source stamp contains a SHA-1 tag that corresponds to the version of code being run.
        Each input source of data we import may have its own version number associated with it. If so, we maintain this info and display it on the <a href="http://dgidb.org/sources">source summary view</a>.
        If an input source does not have concept of versioning, we note the date of import instead.
        Source versions are included in TSV export results for each drug-gene interaction found.

    - question: What does the version stamp at the foot of each view mean?
      anchor: stamp
      answer: >
        It is currently generated whenever we perform a rake task to create a new data snapshot for DGIdb.
        The version number corresponds to a tag in git and eventually the debian package we use to push a development version of DGIdb to the publicly facing server.
        The SHA-1 is the commit id from when the snapshot was generated, as is the datestamp.

    - question: I think I have identified a bug in the DGIdb code. What should I do?
      anchor: bugs
      answer: >
        Please let us know. You may contact us <a href="mailto:help@dgidb.org">by email</a>.
        If your question is more complicated, please ask it publicly on <a href="http://www.biostars.org/">BioStars</a>.
        The <a href="https://github.com/griffithlab/dgi-db">code for DGIdb</a> is open-source, and if you have a GitHub account
        you may post your question directly to the GitHub <a href="https://github.com/genome/dgi-db/issues">issue tracker</a> for our developers to review.
        If you are the curious/ambitious type, feel free to investigate a solution and let us know what you find.