focusOnScope

Focus a BE related object on a specific identifier (BEID) scope

An interface for the 'Neo4j' database providing
mapping between different identifiers of biological entities.
This Biological Entity Dictionary (BED)
has been developed to address three main challenges.
The first one is related to the completeness of identifier mappings.
Indeed, direct mapping information provided by the different systems
are not always complete and can be enriched by mappings provided by other
resources.
More interestingly, direct mappings not identified by any of these
resources can be indirectly inferred by using mappings to a third reference.
For example, many human Ensembl gene ID are not directly mapped to any
Entrez gene ID but such mappings can be inferred using respective mappings
to HGNC ID. The second challenge is related to the mapping of deprecated
identifiers. Indeed, entity identifiers can change from one resource
release to another. The identifier history is provided by some resources,
such as Ensembl or the NCBI, but it is generally not used by mapping tools.
The third challenge is related to the automation of the mapping process
according to the relationships between the biological entities of interest.
Indeed, mapping between gene and protein ID scopes should not be done
the same way than between two scopes regarding gene ID.
Also, converting identifiers from different organisms should be possible
using gene orthologs information.
The method has been published by
Godard and van Eyll (2018) <doi:10.12688/f1000research.13925.3>.

Patrice Godard

Biological Entity Dictionary (BED)

focusOnScope function

<dl><dt>x</dt>
<dd>an object representing a collection of BEID (e.g. BEIDList)</dd>
<dt>be</dt>
<dd>the type of biological entity to focus on.
Used if <code>is.null(scope)</code></dd>
<dt>source</dt>
<dd>the source of BEID to focus on.
Used if <code>is.null(scope)</code></dd>
<dt>organism</dt>
<dd>the organism of BEID to focus on.
Used if <code>is.null(scope)</code></dd>
<dt>scope</dt>
<dd>a list with the following element:<ul>
<li>be</li>
<li>source</li>
<li>organism</li>
</ul></dd>
<dt>force</dt>
<dd>if TRUE the conversion is done even between identical scopes
(default: FALSE)</dd>
<dt>restricted</dt>
<dd>if TRUE (default) the BEID are limited to current version
of the source</dd>
<dt>prefFilter</dt>
<dd>if TRUE (default) the BEID are limited to prefered
identifiers when they exist</dd>
<dt>...</dt>
<dd>method specific parameters for BEID conversion</dd></dl>

Arguments

Focus a BE related object on a specific identifier (BEID) scope — focusOnScope

<dl>

<dt>x</dt>
<dd>an object representing a collection of BEID (e.g. BEIDList)</dd>


<dt>be</dt>
<dd>the type of biological entity to focus on.
Used if <code>is.null(scope)</code></dd>


<dt>source</dt>
<dd>the source of BEID to focus on.
Used if <code>is.null(scope)</code></dd>


<dt>organism</dt>
<dd>the organism of BEID to focus on.
Used if <code>is.null(scope)</code></dd>


<dt>scope</dt>
<dd>a list with the following element:<ul>
<li>be</li>
<li>source</li>
<li>organism</li>
</ul></dd>


<dt>force</dt>
<dd>if TRUE the conversion is done even between identical scopes
(default: FALSE)</dd>


<dt>restricted</dt>
<dd>if TRUE (default) the BEID are limited to current version
of the source</dd>


<dt>prefFilter</dt>
<dd>if TRUE (default) the BEID are limited to prefered
identifiers when they exist</dd>


<dt>...</dt>
<dd>method specific parameters for BEID conversion</dd>

</dl>

focusOnScope: Focus a BE related object on a specific identifier (BEID) scope

Description

Usage

Value

Arguments