searchId

DEPRECATED: use searchBeid and geneIDsToAllScopes instead.
This function is meant to be used with getRelevantIds in order
to implement a dictonary of identifiers of interest. First
the searchId function is used to search a term.
Then the getRelevantIds function
is used to find the corresponding ID in a context of interest.

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)

searchId function

<dl><dt>searched</dt>
<dd>the searched term. Identifiers are searched by exact match.
Symbols and names are also searched for partial match when searched is
greater than ncharSymb and ncharName respectively.</dd>
<dt>be</dt>
<dd>optional. If provided the search is focused on provided BEs.</dd>
<dt>organism</dt>
<dd>optional. If provided the search is focused on provided
organisms.</dd>
<dt>ncharSymb</dt>
<dd>The minimum number of characters in searched to consider
incomplete symbol matches.</dd>
<dt>ncharName</dt>
<dd>The minimum number of characters in searched to consider
incomplete name matches.</dd>
<dt>verbose</dt>
<dd>boolean indicating if the CQL queries should be displayed</dd></dl>

Arguments

Search identifier, symbol or name information — searchId

<dl>

<dt>searched</dt>
<dd>the searched term. Identifiers are searched by exact match.
Symbols and names are also searched for partial match when searched is
greater than ncharSymb and ncharName respectively.</dd>


<dt>be</dt>
<dd>optional. If provided the search is focused on provided BEs.</dd>


<dt>organism</dt>
<dd>optional. If provided the search is focused on provided
organisms.</dd>


<dt>ncharSymb</dt>
<dd>The minimum number of characters in searched to consider
incomplete symbol matches.</dd>


<dt>ncharName</dt>
<dd>The minimum number of characters in searched to consider
incomplete name matches.</dd>


<dt>verbose</dt>
<dd>boolean indicating if the CQL queries should be displayed</dd>

</dl>

searchId: Search identifier, symbol or name information

Description

Usage

Value

Arguments

See Also