You may understand the process better by reading this file. Here is a practical exercise designed to give participants hands-on experience with the PLAZI workflow, specifically focusing on the extraction and annotation of taxonomic treatments using GoldenGATE Imagine.
Practical Exercise: Extracting and
Annotating a Taxonomic Treatment
Objective:
To practice the process of extracting and annotating a taxonomic treatment from
a digitized taxonomic paper using GoldenGATE Imagine and to prepare the data
for upload to TreatmentBank.
Materials Needed:
•
A computer with internet
access.
•
GoldenGATE Imagine software
installed.
•
A sample taxonomic paper
provided in PDF format (preferably one that has been OCR-processed).
•
Access to TreatmentBank for
uploading the final annotated treatment.
Instructions:
1. Preparation:
•
Review the GoldenGATE Imagine
user guide to familiarize yourself with the interface and features.
•
Open the sample taxonomic paper
in GoldenGATE Imagine.
2. Identification:
•
Skim through the sample paper
to locate the taxonomic treatment section. This may include the description of
a new species, revision of a genus, or other taxonomic changes.
•
Use the guidelines provided in
the training to identify the start and end of the treatment.
3. Extraction:
•
Use GoldenGATE Imagine selecting
the text and images that make up the taxonomic treatment
•
Follow the steps to the
selected treatment into a new document within GoldenGATE Imagine.
4. Editing:
•
Carefully read through the
extracted treatment to correct any OCR errors.
•
Format the treatment according
to the standards provided, ensuring that headings, taxon names, descriptions,
and other elements are correctly presented.
5. Annotation:
•
Annotate the treatment with
semantic tags using the tools in GoldenGATE Imagine. This may include tagging
taxon names, morphological descriptions, geographic locations, etc.
•
Ensure that all annotations are
accurate and that the semantic tags used are consistent with the Plazi
guidelines.
6. Quality
Control:
•
Review the annotated treatment
to ensure that all information is correctly extracted and annotated.
•
Check for completeness and
accuracy and make any necessary adjustments.
7. Exporting:
•
Once the treatment is fully
annotated, export the data from GoldenGATE Imagine in the format required for
TreatmentBank.
•
Save the exported file to your
computer.
8. Uploading
to TreatmentBank:
•
Log in to TreatmentBank with
the credentials provided.
•
Upload the exported file
following the instructions provided in the training.
•
Fill in any required metadata
for the treatment such as the bibliographic reference, authors, and publication
date.
9. Reflection:
•
Write a brief reflection on the
process, noting any challenges faced and how you overcame them.
•
Consider the importance of each
step in the context of the PLAZI workflow and biodiversity data sharing.
Deliverables:
•
The extracted and annotated
treatment in the format ready for TreatmentBank.
•
A reflection document
discussing the process and learning outcomes.
•
Assessment:
Your work will be assessed on the following
criteria:
•
Accuracy of the extracted
treatment text and images.
•
Quality and precision of the
OCR error corrections.
•
Correa use of semantic
annotations.
•
Adherence to the PLAZI
standards and guidelines.
•
Completeness of the metadata
provided during the upload to TreatmentBank.
This exercise will help participants
understand the intricacies of the Plazi workflow and the importance of each
step in contributing to the global effort of digitizing taxonomic literature.
It also emphasizes the attention to detail required to ensure the data is
accurate and usable for scientific research and biodiversity studies.Last modified: Thursday, 16 November 2023, 8:40 PM