README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
options(knitr.kable.NA = '')

library(tidyverse)
library(knitr)
```
# ontologics <a href='https://github.com/luckinet/ontologics/'><img src='man/figures/logo.svg' align="right" height="200" /></a>

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## Overview

The `ontologics` package provides tools to build and work with an ontology of [linked (open) data](https://en.wikipedia.org/wiki/Linked_data) in a tidy workflow. In the current workflow, the data are only available at the three-star level in comma-separated values tables or an R-optimized *.rds file of such a table.

The type of ontology is inspired by the [FAO caliper](https://www.fao.org/statistics/caliper/web/) platform and uses the Simple Knowledge Organisation System ([SKOS](https://www.w3.org/TR/skos-reference/)).

An ontology is any data structure that stores the concept of any knowledge field in a linked way. It is typically built on a set of standardized/harmonized terms that have a clear definition and potentially some attributes. According to the SKOS, concepts can have semantic relations or can be mapped to one another. Semantic relations describe how *harmonized concepts* **relate** to one another, and mappings describe which concepts *from different vocabularies* should be **linked**.

The key tasks beyond creating a formally valid ontology are *extracting* concepts and their relation to other concepts and *mapping* new concepts to an existing ontology to capture and set potentially deviating definitions into relation.


## Installation

Install the official version from CRAN:

```{r, eval=FALSE}
install.packages("ontologics")
```

Install the latest development version from github:

```{r, eval=FALSE}
devtools::install_github("luckinet/ontologics")
```

Read the vignettes [Create an ontology](https://luckinet.github.io/ontologics/articles/create_an_ontology.html), [Map new concepts](https://luckinet.github.io/ontologics/articles/map_new_concepts.html) and [Convert Ontology to RDF](https://luckinet.github.io/ontologics/articles/conversion_to_rdf.html).

## Acknowledgement

This work was supported by funding to Carsten Meyer through the Flexpool mechanism of the German Centre for Integrative Biodiversity Research (iDiv) (FZT-118, DFG) and members working on it were additionally supported by Freigeist funding of the Volkswagenstiftung and the BMBF GeoKur project.