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).
-
Where is this gene in the genome (use
MapView,
fish clones)?
-
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).
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