Services

Here is a list of services that are provided at GENODESY.

BED database

BED (Biological Entity Dictionary) is an R package to get and explore mapping between identifiers of biological entities (BE). It relies on a Neo4j database in which the relationships between the identifiers from different sources are recorded.

An instance of the BED database (docker image) is running at GENODESY. The following code shows how to connect to it.

library(BED)
connectToBed(url="https://genodesy.org/BED/", remember=TRUE, useCache=TRUE)

mapt <- convBeIds(
   "MAPT", from="Gene", from.source="Symbol", from.org="human",
   to.source="Ens_gene", restricted=TRUE, prefFilter=TRUE
)
exploreBe(
   mapt$to, source="Ens_gene", be="Gene", showProbes=TRUE
)

For performance purpose, it is recommended to instantiate the BED database close to the computing environment used to run the analyses.

DODO database

DODO (Dictionary of Disease Ontologies) is an R package to interact and explore disease ontologies and their identifiers. It also relies on a Neo4j database in which the relationships between the identifiers from different sources are recorded.

An instance of the DODO database (docker image) is running at GENODESY. The following code shows how to connect to it.

library(DODO)
connect_to_dodo(url="https://genodesy.org/DODO/", remember=TRUE)

disNet <- build_disNet(
  term="focal cortical dysplasia", 
  fields=c("label", "synonym")
)
extendedDisNet <- extend_disNet(
  disNet,
  relations=c("xref", "child"),
  intransitive.ambiguity=1
)
plot(extendedDisNet)

Plotting 113 nodes

For performance purpose, it is also recommended to instantiate the DODO database close to the computing environment used to run the analyses.

Shiny apps

A portfolio of Shiny apps is displayed on this page.