The human metabolomics database (HMDB, http://www.hmdb.ca) includes XML documents describing 114000 metabolites. We will show how to manipulate the metadata on metabolites fairly flexibly.
The hmdbQuery package includes a function for querying HMDB directly over HTTP:
The result is parsed and encapsulated in an S4 object
## HMDB metabolite metadata for 1-Methylhistidine:
## There are 4 diseases annotated.
## Direct association reported for 5 biospecimens and 2 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
## DataFrame with 75360 rows and 3 columns
## accession name
## <character> <character>
## 1 HMDB0000001 1-Methylhistidine
## 2 HMDB0000001 1-Methylhistidine
## 3 HMDB0000001 1-Methylhistidine
## 4 HMDB0000001 1-Methylhistidine
## 5 HMDB0000002 1,3-Diaminopropane
## ... ... ...
## 75356 HMDB0094706 Serylvaline
## 75357 HMDB0094708 Tetraethylene glycol
## 75358 HMDB0094712 Serylleucine
## 75359 HMDB0100002 TG(i-14:0/17:0/i-13:0)
## 75360 HMDB0101657 TG(15:0/i-14:0/a-21:0)[rac]
## disease
## <character>
## 1 Alzheimer's disease
## 2 Diabetes mellitus type 2
## 3 Kidney disease
## 4 Obesity
## 5 Perillyl alcohol administration for cancer treatment
## ... ...
## 75356 NA
## 75357 NA
## 75358 NA
## 75359 NA
## 75360 NASome HMDB metabolites have been mapped to diseases.
## DataFrame with 4 rows and 4 columns
## metabolite disease
## <character> <character>
## 1 1-Methylhistidine Alzheimer's disease
## 2 1-Methylhistidine Diabetes mellitus type 2
## 3 1-Methylhistidine Kidney disease
## 4 1-Methylhistidine Obesity
## pmids accession
## <CharacterList> <character>
## 1 9693263,10494443,15465626,... HMDB0000001
## 2 15899597,15982426,6321058,... HMDB0000001
## 3 11573638,12032193,11380830,... HMDB0000001
## 4 15899597,17264178,16253646,... HMDB0000001pmids = unlist(diseases(lk1)[1,]$pmids)
library(annotate)
pm = pubmed(pmids[1])
ab = buildPubMedAbst(xmlRoot(pm)[[1]])
ab## An object of class 'pubMedAbst':
## Title: Abnormal substrate levels that depend upon mitochondrial
## function in cerebrospinal fluid from Alzheimer patients.
## PMID: 9693263
## Authors: N Redjems-Bennani, C Jeandel, E Lefebvre, H Blain, M
## Vidailhet, JL Guéant
## Journal: Gerontology
## Date: Month 1998Note that pre HMDB v 4.0, biospecimens were called biofluids.
There are arbitrarily many biospecimen and tissue associations provided for each HMDB entry. We have direct accessors, and by default we capture all metadata, available through the store method.
## [1] "Blood" "Cerebrospinal Fluid (CSF)"
## [3] "Feces" "Saliva"
## [5] "Urine"## [1] "Muscle" "Skeletal Muscle"## [1] "version" "creation_date" "update_date"
## [4] "accession" "status" "secondary_accessions"## [1] 51## protein
## "Beta-Ala-His dipeptidase"
## protein
## "Protein arginine N-methyltransferase 3"## protein protein
## "CNDP1" "PRMT3"