BdDwC User Guide Bd Dw C
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bdDwC User Guide
Authors: Tomer Gueta and Povilas Gibas
built on2018-11-28 - for bdDwC v0.1.21
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Contents
Introduction 5
1 Installing bdDwC 7
1.1 StableversionfromCRAN ..................................... 7
1.2 Development version from GitHub . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.3 Possibleproblems&solutions.................................... 7
2 The shiny app 9
2.1 Launchingtheapp .......................................... 9
2.2 Appoverview............................................. 9
2.3 Dataupload.............................................. 9
2.4 Dictionaries.............................................. 12
2.5 Darwinizingyourdataset ...................................... 12
2.6 Darwinizerresults .......................................... 12
2.7 Download your Darwinized data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.8 Closingtheapp............................................ 14
2.9 References............................................... 14
3 Command line operations 15
3.1 Loadpackage............................................. 15
3.2 Darwinizingadataset ........................................ 15
3.3 Updating the Darwin Cloud dictionary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4 Examples 17
5 Getting your feedback 19
5.1 Reportabug ............................................. 19
5.2 Contribute............................................... 19
6bdDwC citation 21
7 Learn more about Darwin Core 23
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4CONTENTS
Introduction
bdDwC is a R package that supplies an interactive Shiny app and a set of functions for standardizing eld
names in compliance to the Darwin Core (DwC) format. bdDwC is a key element in the bdverse– a collection
of tools, that form a general framework for facilitating biodiversity science in R.
What is the Darwin Core standard?
Darwin Core (DwC) is a global standard for publishing biodiversity data, whose goal is to facilitate the
sharing of biodiversity information, by providing identiers, labels, and denitions (Wieczorek et al., 2012).
DwC was established as an evolving community-developed standard, by the Biodiversity Information Stan-
dards Working Group (www.tdwg.org). DwC is a library of denitions of common biodiversity data terms,
each of which represents a eld within the database. There are around 200 such elds (not including DwC
extensions); a full set of the DwC terms with their descriptions is available in the Quick Reference Guide
(http://rs.tdwg.org/dwc/terms). For more information see section 6.
Why it’s important to “Darwinize” a dataset
Running the Darwinizer enables you to standardize many eld names in your dataset – and that allows
the bdverse to handle data from various biodiversity portals seamlessly, and lets you enjoy all of bdvers
features, regardless of publishers variation in eld names.
Fundings
• See the GSoC project idea page
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6CONTENTS
Figure 1: bdDwC in the bdverse
Figure 2:
8CHAPTER 1. INSTALLING BDDWC
Chapter 2
The shiny app
2.1 Launching the app
library(bdDwC) # Laod package library
runDwC() # Launch the app
2.2 App overview
In the rst screen, you’ll need to load your biodiversity data; choose dictionary and run the Darwinizer.
There are two options, form a le on your computer, of fetch from a web based data provider.
2.3 Data upload
2.3.1 From a local le
A CSV le or a Darwin Core Archive (DwC-A) zip le can be uploaded.
2.3.2 From an online database
Also, data can be retrieved directly from various online biodiversity databases. You need only to:
• Select the database
• Specify the desired scientic name.
• Specify the number of records (upper limit of 50,000).
• Check the box if records must have coordinates.
• Wait for data to be downloaded.
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10 CHAPTER 2. THE SHINY APP
Figure 2.1: bdDwC App Overview
Figure 2.2: Data upload from a local le
2.3. DATA UPLOAD 11
Figure 2.3: Data upload from online biodiversity databases
12 CHAPTER 2. THE SHINY APP
Figure 2.4: Updating the Darwin Cloud dictionary
2.4 Dictionaries
A dictionary is a key component when Darwinizing a dataset. It’s basically a lookup table that lists a
possible variation of eld name and it corresponding DwC name.
2.4.1 The Darwin Cloud dictionary
The Darwin Cloud dictionary (Wieczorek et al., 2017), is a lookup table that accumulates dierent varia-
tions in DwC eld names from dierent publishers. This valuable and critical dictionary was created and
is maintained by the Kurator project (http://kurator.acis.ufl.edu/kurator-web/), which provides workow
tools for data quality improvement of biodiversity data, via a user-friendly web interface. The development
of bdDwC was inspired by Kurator’s own Darwinizer.
Updating the Darwin Cloud dictionary
It’s recommended to update the Darwin Cloud dictionary le. This can be done easily by clicking the
Update DC button.
2.4.2 Custom dictionary
It’s also possible to add your own dictionary by creating a CSV le with two columns, one for the Field
Names and one for the Standard Names. After uploading the custom disctionary, we need to specify which
eld denotes the ‘User erld names’ and which is the ‘Standard (DwC) eld names’.
2.5 Darwinizing your dataset
Once a dataset is uploaded, the ‘Submit to Darwinizer’ button is activated, Clicking it will begin the
interactive ‘Darwinize the dataset’ process.
2.6 Darwinizer results
2.6.1 Results page overwiew
Manually renaming eld names can be done very easily, just choose the two corresponding elds and click
the Rename button.
Hovering over a DwC standard name will display its description.
2.6. DARWINIZER RESULTS 13
Figure 2.5: Uploading your own dictionary
Figure 2.6: Submit to Darwinizer button
Figure 2.7: Darwinizer results
14 CHAPTER 2. THE SHINY APP
Figure 2.8: Manually renaming elds
2.7 Download your Darwinized data
2.8 Closing the app
Just close the app browser tab, and the R session will be terminated. To reopen it run in the R Console
runDwC().
2.9 References
Chapter 3
Command line operations
3.1 Load package
Load the bdDwC package
library(bdDwC)
3.2 Darwinizing a dataset
bdDwC contains Indian Reptile dataset bdDwC:::dataReptiles.
The function to Darwinize a dataset isdarwinizeNames (replace bdDwC:::dataReptiles with wanted
dataset):
result <- darwinizeNames(dataUser = bdDwC:::dataReptiles,
dataDWC = bdDwC:::dataDarwinCloud$data)
You can replace bdDwC:::dataReptiles with your dataset
Rename your dataset eld names to Darwinized names using renameUserData:
renameUserData(bdDwC:::dataReptiles, result)
3.3 Updating the Darwin Cloud dictionary
To get newest version of Darwin Cloud Data run:
downloadCloudData()
which will download data from the remote repository and extract eld and standard names.
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16 CHAPTER 3. COMMAND LINE OPERATIONS
Chapter 4
Examples
[ TBA ]
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18 CHAPTER 4. EXAMPLES
20 CHAPTER 5. GETTING YOUR FEEDBACK
Chapter 6
bdDwC citation
citation("bdDwC")
##
## To cite package 'bdDwC' in publications use:
##
## Povilas Gibas, Tomer Gueta, Vijay Barve, Thiloshon Nagarajah and
## Yohay Carmel (2018). bdDwC: field names conversion to Darwin
## Core (DwC) format. R package version 0.1.21.
## https://github.com/bd-R/bdDwC
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {bdDwC: field names conversion to Darwin Core (DwC) format},
## author = {Povilas Gibas and Tomer Gueta and Vijay Barve and Thiloshon Nagarajah and Yohay Carmel},
## year = {2018},
## note = {R package version 0.1.21},
## url = {https://github.com/bd-R/bdDwC},
## }
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22 CHAPTER 6. BDDWC CITATION
Chapter 7
Learn more about Darwin Core
•The Darwin Core Questions & Answers Site
•Darwin Core Hour webinar series
•The Darwin Core Questions & Answers wiki
•GBIF: What is Darwin Core, and why does it matter?
•Darwin Core: An Evolving Community-Developed Biodiversity Data Standard (Wiec-
zorek et al., 2012)
References
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24 CHAPTER 7. LEARN MORE ABOUT DARWIN CORE
Bibliography
Wieczorek, J., Bloom, D., Guralnick, R., Blum, S., Döring, M., Giovanni, R., Robertson, T., and Vieglais, D.
(2012). Darwin Core: an evolving community-developed biodiversity data standard. PloS one, 7(1):e29715.
Wieczorek, J., Morris, P. J., Hanken, J., B.Lowery, D., Ludäscher, B., Macklin, J., McPhillips, T., A.Morris,
R., and Zhang, Q. (2017). Darwin cloud: Mapping real-world data to darwin core. Biodiversity Information
Science and Standards, 1:e20486.
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