neuromorpho_literature_search: Make a custom literature search to the neuromorpho.org...

In jefferislab/neuromorphr: R client utilities for interacting with the NeuroMorpho online repository for neuron morphology data

Make a custom literature search to the neuromorpho.org repository

Description

Search for literature in the neuromorpho.org repository. The returned data frame can be used to get article IDs and neuron names, that can be fed to neuromorpho_get_article, in order to get information on studies that have submitted reconstructions to neuromorpho.org. Searches are made by looking at the meta data for items of literature in the repository, i.e. querying for certain field entries for certain literature fields.

Usage

neuromorpho_literature_search(
  search_terms = c("species:Drosophila melanogaster"),
  neuromorpho_url = "http://neuromorpho.org",
  ...
)

Arguments

search_terms	a vector of search terms, with each term formatted as "field:field entry". All valid neuron fields can be seen by calling neuromorpho_fields, and all the entries for certain fields can be seen using neuromorpho_fields_entries. Only meta data for neurons that have the entries described for all given search terms will be returned.
neuromorpho_url	the base URL for querying the neuromorpho database, defaults to http://neuromorpho.org
...	methods passed to neuromorpho_async_req, or in some cases, neuromorphr:::neuromorpho_fetch

Details

Beware, that these terms are different from the equivalent fields and field entries for neurons, e.g. the cell type literature field is cellType rather than cell_type, as it is for neurons. Articles can also be searched in a web browser at http://neuromorpho.org/LS.jsp.

See Also

Other literature functions: neuromorpho_get_article(), neuromorpho_literature_field_counts(), neuromorpho_literature_field_entries(), neuromorpho_literature_fields()

Examples

## Not run: 
# Let's search for some literature that has contributed reconstructions to neuromorpho.org

## let's have a look at articles that have worked on Drosophila melanogaster
lit.search = neuromorpho_literature_search(field="species:Drosophila melanogaster")

## We have found this many papers
print(nrow(lit.search))

## Note this is a little different from what we get when we pull this information for neurons
neuron.fields = neuromorpho_field_entries(field="species")
print(neuron.fields)

## End(Not run)

jefferislab/neuromorphr documentation built on April 25, 2023, 9:07 p.m.