hmdbQuery: working with Human Metabolome Database (hmdb.ca) (original) (raw)
Key utilities of the package
The hmdbQuery package includes a function for querying HMDB directly over HTTP:
library(hmdbQuery)
lk1 = HmdbEntry(prefix = "http://www.hmdb.ca/metabolites/",
id = "HMDB0000001")The result is parsed and encapsulated in an S4 object
## HMDB metabolite metadata for 1-Methylhistidine:
## There are 10 diseases annotated.
## Direct association reported for 4 biospecimens and 1 tissues.
## Use diseases(), biospecimens(), tissues() for more information.The size of the complete import of information about a single metabolite suggests that it would not be too convenient to have comprehensive information about all HMDB constituents in memory. The most effective approach to managing the metadata will depend upon use cases to be developed over the long run.
Note however that this package does provide snapshots of certain direct associations derived from all available information as of Sept. 23 2017. Information about direct associations reported in the database is present in tables hmdb_disease, hmdb_gene, hmdb_protein, hmdb_omim. For example
data(hmdb_disease)
hmdb_disease## DataFrame with 75360 rows and 3 columns
## accession name disease
## <character> <character> <character>
## 1 HMDB0000001 1-Methylhistidine Alzheimer's disease
## 2 HMDB0000001 1-Methylhistidine Diabetes mellitus ty..
## 3 HMDB0000001 1-Methylhistidine Kidney disease
## 4 HMDB0000001 1-Methylhistidine Obesity
## 5 HMDB0000002 1,3-Diaminopropane Perillyl alcohol adm..
## ... ... ... ...
## 75356 HMDB0094706 Serylvaline NA
## 75357 HMDB0094708 Tetraethylene glycol NA
## 75358 HMDB0094712 Serylleucine NA
## 75359 HMDB0100002 TG(i-14:0/17:0/i-13:0) NA
## 75360 HMDB0101657 TG(15:0/i-14:0/a-21:.. NA