fetchNode: Query for an entity or list of entities from grinn internal...
In kwanjeeraw/grinn: graph database and R package for omics data integration

Description Usage Arguments Value Author(s) Examples

from the list of keywords, query for entities from the grinn internal database. Quried results include entity information and relationship information. The keywords can be any of these node types: metabolite, protein, gene and pathway. Relationship information includes information of adjacent nodes, name and additional attributes of relationships.

1	fetchNode(txtInput, nodetype, searchField, exactMatch, returnAs, dbXref)

`txtInput`	list of keywords, can be one of grinn id, name, synonym, database xref, inchi e.g. txtInput = list('name1', 'name2'). The type of keywords needs to be provided in the argument `searchField`, see `searchField`. Default is grinn id e.g. G371.
`nodetype`	string of entity type. It can be one of "metabolite","protein","gene","pathway".
`searchField`	string of keyword property to search for, see `txtInput`. It can be one of "grinn","name","synonym","xref","inchi". Default is "grinn". If `searchField = "xref"`, the argument `dbXref` is required, see `dbXref`. If `searchField = "name" or "synonym"`, the argument `exactMatch` is required, see `exactMatch`.
`exactMatch`	boolean value. The argument is required if `searchField = "name" or "synonym"`, see `searchField`. Default is TRUE.
`returnAs`	string of output type. It can be one of "list","json", default is "list".
`dbXref`	string of database name. Specify the database name used for the txtInput when the argument `searchField = "xref"`, see `txtInput` and `searchField`. It can be one of "grinn",chebi","kegg","pubchem","hmdb","smpdb","reactome","uniprot","ensembl","entrezgene". Default is "grinn". If pubchem is used, it has to be pubchem SID (substance ID).

list of nodes and first neighborhoods. Return empty list if found nothing.

Kwanjeera W kwanich@ucdavis.edu

# Query metabolites by grinn ids
txtInput <- list('G371','G783')
result <- fetchNode(txtInput, nodetype="metabolite")
# Query genes by KEGG ids
txtInput <- list('hsa:4514','hsa:4537')
result <- fetchNode(txtInput, nodetype="gene", searchField="xref", dbXref="kegg", returnAs="list")
# Query proteins by names
txtInput <- list('14-3-3 protein beta/alpha','ARL14 effector protein-like','6-phosphogluconolactonase')
result <- fetchNode(txtInput, nodetype="protein", searchField="name", returnAs="list")