In TIBHannover/BacDiveR: Programmatic Interface For The Bacterial Diversity Metadatabase by DSMZ

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Context

The BacDive Web Service accepts 4 types of requests and replies in 3 different ways:

request type | unambiguous? | JSON-reply -------------|:------------:|-------- taxon | no | URL(s) of matching strain(s) sequence | yes | URL of matching strain culturecollectionno | yes | URL of matching strain bacdive_id | yes | dataset of that strain

The advanced search has an option called "Download list of BacDive Ids", which returns a text file with one bacdive_id per line.

Decision

Because:

a) we assume that most users want to analyse the strain datasets, not lists of URLs or IDs, and a) the request types seem to form a funnel from search to URL/ID to dataset,

we will ensure that all main functions return full dataset(s) by default.

Status: Removed in v0.9.0

Consequences

A uniform data structure was needed and implemented, see #31. In case IDs need to be retrieved, retrieve_data() and retrieve_search_results() either need an extra parameter for that, or a retrieve_IDs() function needs to be added (see #54)

TIBHannover/BacDiveR documentation built on June 2, 2022, 2:51 p.m.