Parasite Programmatic Access WormBase Workshop International Worm Meeting 2017

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This document discusses programmatic access to WormBase ParaSite data through R. It describes how to install the biomaRt package to access the database directly from R with syntax similar to Ensembl. An example is provided to retrieve all Schistosoma mansoni genes that have a C. elegans ortholog using the WormBase ParaSite mart. The document also notes the database can be queried through a REST API from any programming language.

Science

Access using R
• Access our database directly from R, via the biomaRt
package
• Syntax almost identical to Ensembl
• Very quick access to large amounts of multi-species
data
• Ideal for downloading a large dataset once, for further
offline processing

WormBase ParaSite in R
• Install the biomaRt package:
source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
• Include the biomaRt package:
library(biomaRt)

WormBase ParaSite in R
• Establish a connection to WormBase ParaSite
mart <- useMart("parasite_mart”,
dataset = "wbps_gene",
host = "parasite.wormbase.org")

WormBase ParaSite in R
• Example: get all the Schistosoma mansoni genes with a C. elegans
orthologue:
genes <- getBM(mart = mart,
filters = c("species_id_1010",
"with_celegans_homologue"),
value = list("prjea36577", TRUE),
attributes = c(”wbps_gene_id",
"celegans_gene”))
head(genes)
wbps_gene_id celegans_gene
1 Smp_078570 WBGene00009448
2 Smp_063300 WBGene00004450
3 Smp_210640 WBGene00009305
4 Smp_049930 WBGene00010465
5 Smp_132740 WBGene00001395
6 Smp_132740 WBGene00001396

Language neutral queries
• REST API allows access using any programming
language
• For processing large amounts of data: consider
whether making one query to BioMart may be more
suitable
• Examples provided in Perl, Python, Ruby, Java, Curl
and Wget

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Parasite Programmatic Access WormBase Workshop International Worm Meeting 2017

1. Programmatic access to WormBase ParaSite

2. Access using R • Access our database directly from R, via the biomaRt package • Syntax almost identical to Ensembl • Very quick access to large amounts of multi-species data • Ideal for downloading a large dataset once, for further offline processing

3. WormBase ParaSite in R • Install the biomaRt package: source("http://bioconductor.org/biocLite.R") biocLite("biomaRt") • Include the biomaRt package: library(biomaRt)

4. WormBase ParaSite in R • Establish a connection to WormBase ParaSite mart <- useMart("parasite_mart”, dataset = "wbps_gene", host = "parasite.wormbase.org")

5. WormBase ParaSite in R • Example: get all the Schistosoma mansoni genes with a C. elegans orthologue: genes <- getBM(mart = mart, filters = c("species_id_1010", "with_celegans_homologue"), value = list("prjea36577", TRUE), attributes = c(”wbps_gene_id", "celegans_gene”)) head(genes) wbps_gene_id celegans_gene 1 Smp_078570 WBGene00009448 2 Smp_063300 WBGene00004450 3 Smp_210640 WBGene00009305 4 Smp_049930 WBGene00010465 5 Smp_132740 WBGene00001395 6 Smp_132740 WBGene00001396

6. Language neutral queries • REST API allows access using any programming language • For processing large amounts of data: consider whether making one query to BioMart may be more suitable • Examples provided in Perl, Python, Ruby, Java, Curl and Wget

7. Endpoint Catalogue

8. Endpoint Specifics

9. Endpoint Examples

10. Code Examples

Editor's Notes

Syntax is the same as Ensembl, so there is plenty of guidance available online at sites like BioStars

Parasite Programmatic Access WormBase Workshop International Worm Meeting 2017

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