Description Usage Arguments Details Value Author(s) See Also Examples
query networks containing a specific relationship type between the given from
and/or to
nodes using grinn id (gid), see details.
1 | fetchNetworkByGID(from, to, fromtype, totype, reltype, returnas)
|
from |
a character vector of start nodes e.g. from = c('id1', 'id2'). Given |
to |
a character vector of end nodes e.g. to = c('id1', 'id2'). Given |
fromtype |
a string specifying the type of the start node. It can be one of compound, protein, gene, pathway, rna, dna, phenotype. The node types correspond to node labels of the database. |
totype |
a string specifying the type of end nodes, see |
reltype |
a string specifying a relationship type. It can be one of annotation, biochemical_reaction, catalysis, control, conversion, genetic_association, molecular_binding. |
returnas |
a string specifying output type. It can be one of dataframe, list, json. Default is dataframe. |
The function is specifically used to query one type of relationship. Use fetchHetNetworkByGID
to query networks containing one or more relationship types (heterogeneous network).
The database uses two id systems. The neo4j id is a numeric, internal id automatically generated by the database system. The grinn id (gid) is an id system of Grinn database that uses main ids of standard resources i.e. ENSEMBL for genes (e.g.ENSG00000139618), UniProt for proteins (e.g.P0C9J6), PubChem CID for compounds (e.g.5793), KEGG for pathways (e.g.hsa00010).
list of network information with the following components:
nodes:
id
= node neo4j id
gid
= node grinn id
nodename
= node name
nodelabel
= node type
nodexref
= node cross references
edges:
source, target
= node neo4j id
type
= relationship type
datasource
= relationship resource
properties
= relationship properties
Return empty list if error or found nothing.
Kwanjeera W kwanich@ucdavis.edu
convertId
, fetchHetNetworkByGID
For database structure see http://grinnhomepage
1 2 3 4 5 6 7 | # Query the network of (from:Compound)-BIOCHEMICAL_REACTION->(to:Compound)
#from = list('1060','284','760') #By default, PubChem ids can be used as grinn ids for compounds
#to = list('222656','107689','5950','71080') #By default, PubChem ids can be used as grinn ids for compounds
#result = fetchNetworkByGID(from=from, to=to, fromtype="compound", totype="compound", reltype="biochemical_reaction")
# Query the network of (:Protein)-CATALYSIS->(to:Compound)
#to = c('222656','107689','5950','71080') #By default, PubChem ids can be used as grinn ids for compounds
#result = fetchNetworkByGID(from=NULL, to=to, fromtype="protein", totype="compound", reltype="catalysis")
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