BioGuide- Project - Query examples

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Querying process
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A complete user manual is available on this web site, it gives several examples of how to express a query using BioGuide and BioGuideSRS.

The present page briefly gives additional examples considering queries extracted from the list of collected queries.
Below, we give for each query the entities that should be selected in the graph of entities, the filter to use (in BioGuideSRS only), the relationships between entities to select, and possibly the sources to select in the graph of sources-entities (preferences).

It is worth noticing that depending on the goal of the user, a given query/question expressed in natural language can be expressed differently in BioGuide (varying the strategy). Following the BioGuide philosophy, a wide spectrum of strategies can be followed: From a strategy aiming to collect as much information as possible (default strategy: where additional entities are considered, no order is fixed between entities and any source can be visited multiple times) to a strategy aiming to search for precise information (where only the given entities are considered, the order between entities is fixed and a source-entity is only visited once).

Examples of queries

  • What is known about the genetic disease narcolepsy (use at least OMIM), information about proteins are mandatory (they should come from SwissProt)?

    • Entities: Protein, Disease

    • Filter: Narcolepsy (on Disease)

    • Relationships: none

    • Preferences: SwissProt for Protein, Omim for Disease

  • Return the list of genes of EMBL which are nuclear cofactors (function).

    • Entities: Gene, Function

    • Relationships: hasFunction

    • Preferences: EMBL for the genes
  • Where is this gene in the genome (use MapView, fish clones)?

    • Entities: Gene, Chromosome

    • Relationships: none

    • Preferences: MapViewFish for Chromosome

  • What are the related proteins and genes associated with the Narcolepsy disease?

    • Entities: Protein, Gene, Disease

    • Filter: Narcolepsy (on Disease)

    • Relationships: Causes (Gene, Disease), Causes (Protein, Disease), CodesFor(Gene, Protein)

    • Preferences: none

  • Is there a therapeutic target (e.g. phosphatase domains) to be exploited in this group of genes?

    • Entities: Gene, Domain

    • Relationships: none

    • Preferences: none

  • From this gene name, give me its sequence from EMBL, the corresponding transcripts and domains (transcripts from TrEMBL).

    • Entities: Gene, Protein, Domain

    • Relationships: none

    • Preferences: TrEMBL for Protein

Laboratoire de Recherche en Informatique, University of Pennsylvania

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