R Usage

All the R commands that perform search return data frames. The query parameter that can be passed as an argument is the one that can be copied from the search page.

Connection

# Load library
library(micar)

# Open connection
m <- mica.login(url="https://mica-demo.obiba.org")

# Make queries
# ...

# Close connection
mica.logout(m)

Search

A unified search service allows to get any kind of document type, the search criteria can be applied to same or other document types. Only the published documents can be searched.

Networks

Search for published networks.

mica.networks(m)
mica.networks(m, query="network(in(Mica_network.studyIds,clsa))")
mica.networks(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))", locale="en", from=0, limit=10)

Studies

Search for studies, populations and data collection events.

mica.studies(m)
mica.studies(m, query="study(in(Mica_study.methods-design,cohort_study))")
mica.studies(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))", locale="en", from=0, limit=10)
mica.study.populations(m)
mica.study.dces(m)

Datasets

Search for datasets.

mica.datasets(m)
mica.datasets(m, query="dataset(in(Mica_dataset.className,HarmonizationDataset))")
mica.datasets(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))")

Variables

Search for variables.

mica.variables(m)
mica.variables(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))")
mica.variables(m, query="dataset(in(Mica_dataset.className,HarmonizationDataset))")

Taxonomies

The taxonomies describe the variable annotations and are also used to build the search criteria.

# Get taxonomies, vocabularies, terms
mica.taxonomies(m,target="variable")
mica.taxonomies(m,target="variable", query="sex", locale="en", taxonomies = list("Mlstr_area", "Mlstr_additional"))
mica.taxonomies(m,target="study")
mica.vocabularies(m,target="variable", query="cancer", locale = "en")