changeset 2:9eaf84bf856f draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
author ecology
date Tue, 10 Sep 2024 12:52:44 +0000
parents 06e29cdc08bf
children 36150f04b524
files annotations_template.R raster_template.xml test-data/annotemp/abstract.txt test-data/annotemp/annotations_template.txt test-data/annotemp/annotations_template_2.txt test-data/annotemp/annotations_template_3.txt test-data/annotemp/annotations_template_4.txt test-data/annotemp/attributes_ceamarc_env.txt test-data/annotemp/ceamarc_env.tsv test-data/annotemp/custom_units.txt test-data/annotemp/entities.txt test-data/annotemp/geographic_coverage.txt test-data/annotemp/intellectual_rights.txt test-data/annotemp/keywords.txt test-data/annotemp/methods.txt test-data/annotemp/personnel.txt test-data/annotemp/pivot_wider_jupytool_notebook.ipynb test-data/test_geocov.tsv
diffstat 18 files changed, 410 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotations_template.R	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,81 @@
+#17/07/2024
+#Seguineau Pauline
+
+#Make annotation template
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+args = commandArgs(trailingOnly=TRUE)
+
+if(length(args)>0){
+  prod <- args[1]
+  if (prod == "fr_scratch"){
+      select <- args[2]
+      data_table <- args[3]
+      if(select == "data_table"){
+          data_table <- args[3]
+      }else if(select == "other_entities"){
+          other_entities <- args[3]
+      }else if(select == "both"){
+          data_table <- args[3]
+          other_entities <- args[4]}
+  }else{
+      eml <- args[2]
+  }
+}
+
+#Transform arguments
+
+if(prod =="fr_scratch" && select == "both"){
+     table = strsplit(data_table," ")
+     other = strsplit(other_entities," ")
+
+#Make templates to add annotations from scratch
+
+     template_annotations(
+          path ="data_files/",
+          data.table = table[[1]],
+          other.entity = other[[1]]) 
+          
+}else if (prod == "fr_scratch" && select == "data_table"){
+
+     table = strsplit(data_table," ")
+     template_annotations(
+          path ="data_files/",
+          data.table = table[[1]]) 
+
+}else if (prod == "fr_scratch" && select == "other_entities"){
+
+     other = strsplit(other_entities," ")
+     template_annotations(
+          path ="data_files/",
+          other.entity = other[[1]]) 
+
+#Make templates to add annotations from EML file
+
+}else{
+     template_annotations(
+          path= "data_files/",
+          eml = eml)}
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
--- a/raster_template.xml	Mon Jan 22 14:55:29 2024 +0000
+++ b/raster_template.xml	Tue Sep 10 12:52:44 2024 +0000
@@ -53,4 +53,13 @@
 To use this tool, you need to select, in your history a data collection with your raster data (one or more).To do so, you can select the **Upload file** tool, select the *Collection* tab, upload all your templates, click on the *Start* button to integrate the files to Galaxy and then click on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates.
 You also can upload your files to Galaxy, select them in the history by clicking the *Select items* button, click on the newly appeared box on the right and select *Build dataset list*.
     ]]></help>
+    <citations>
+       <citation type="bibtex">@Manual{,
+       title = {EMLassemblyline: A tool kit for building EML metadata workflows},
+       author = {Colin Smith},
+       year = {2022},
+       note = {https://github.com/EDIorg/EMLassemblyline,
+       https://ediorg.github.io/EMLassemblyline/},
+       }</citation>
+    </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/abstract.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,1 @@
+The Dumont D’Urville sea located off George V and Adélie Land, is one of the better known East-Antarctic marine areas displaying a diversity of abiotic and physical parameters that have been shown to drive the distribution of marine organisms. The dataset presented here contributes to our understanding of these interactions, providing essential information for ongoing research and conservation efforts in this Antarctic ecosystem. This dataset presents a table containing abiotic and physical parameters specific to the Dumont D’Urville Sea and a Jupyter notebook to execute a R script in the ecoregionalization Galaxy workflow. The abiotic and physical parameters were first presented in the research article 'Predicting habitat preferences for Anthometrina adriani (Echinodermata) on the East Antarctic continental shelf' by Hemery et al. (2011). The jupyter notebook is dedicated to the pivot_wider function from the tidyr R package. This notebook is the final part of the data preparation for the ecoregionalization Galaxy workflow. 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/annotations_template.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,95 @@
+id	element	context	subject	predicate_label	predicate_uri	object_label	object_uri
+/dataset	/dataset	eml	dataset	is about	http://purl.obolibrary.org/obo/IAO_0000136		
+/data_blary_al.txt	/dataTable	dataset	data_blary_al.txt	is about	http://purl.obolibrary.org/obo/IAO_0000136		
+/data_blary_al.txt/Id	/dataTable/attribute	data_blary_al.txt	Id	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/dist_field_margin	/dataTable/attribute	data_blary_al.txt	dist_field_margin	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/dist_hedgerow	/dataTable/attribute	data_blary_al.txt	dist_hedgerow	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/dist_forest	/dataTable/attribute	data_blary_al.txt	dist_forest	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/dist_road	/dataTable/attribute	data_blary_al.txt	dist_road	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/dist_water	/dataTable/attribute	data_blary_al.txt	dist_water	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/dist_urban	/dataTable/attribute	data_blary_al.txt	dist_urban	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_field_margins_250m	/dataTable/attribute	data_blary_al.txt	density_field_margins_250m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_field_margins_500m	/dataTable/attribute	data_blary_al.txt	density_field_margins_500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_field_margins_750m	/dataTable/attribute	data_blary_al.txt	density_field_margins_750m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_field_margins_1000m	/dataTable/attribute	data_blary_al.txt	density_field_margins_1000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_field_margins_1500m	/dataTable/attribute	data_blary_al.txt	density_field_margins_1500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_field_margins_2000m	/dataTable/attribute	data_blary_al.txt	density_field_margins_2000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_field_margins_4000m	/dataTable/attribute	data_blary_al.txt	density_field_margins_4000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_roads_250m	/dataTable/attribute	data_blary_al.txt	density_roads_250m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_roads_500m	/dataTable/attribute	data_blary_al.txt	density_roads_500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_roads_750m	/dataTable/attribute	data_blary_al.txt	density_roads_750m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_roads_1000m	/dataTable/attribute	data_blary_al.txt	density_roads_1000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_roads_1500m	/dataTable/attribute	data_blary_al.txt	density_roads_1500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_roads_2000m	/dataTable/attribute	data_blary_al.txt	density_roads_2000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_roads_4000m	/dataTable/attribute	data_blary_al.txt	density_roads_4000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_hedgerows_250m	/dataTable/attribute	data_blary_al.txt	density_hedgerows_250m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_hedgerows_500m	/dataTable/attribute	data_blary_al.txt	density_hedgerows_500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_hedgerows_750m	/dataTable/attribute	data_blary_al.txt	density_hedgerows_750m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_hedgerows_1000m	/dataTable/attribute	data_blary_al.txt	density_hedgerows_1000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_hedgerows_1500m	/dataTable/attribute	data_blary_al.txt	density_hedgerows_1500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_hedgerows_2000m	/dataTable/attribute	data_blary_al.txt	density_hedgerows_2000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/density_hedgerows_4000m	/dataTable/attribute	data_blary_al.txt	density_hedgerows_4000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/shannon_250m	/dataTable/attribute	data_blary_al.txt	shannon_250m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/shannon_500m	/dataTable/attribute	data_blary_al.txt	shannon_500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/shannon_750m	/dataTable/attribute	data_blary_al.txt	shannon_750m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/shannon_1000m	/dataTable/attribute	data_blary_al.txt	shannon_1000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/shannon_1500m	/dataTable/attribute	data_blary_al.txt	shannon_1500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/shannon_2000m	/dataTable/attribute	data_blary_al.txt	shannon_2000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/shannon_4000m	/dataTable/attribute	data_blary_al.txt	shannon_4000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/grassland_250	/dataTable/attribute	data_blary_al.txt	grassland_250	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/forest_250m	/dataTable/attribute	data_blary_al.txt	forest_250m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/urban_250m	/dataTable/attribute	data_blary_al.txt	urban_250m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/grassland_500	/dataTable/attribute	data_blary_al.txt	grassland_500	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/forest_500m	/dataTable/attribute	data_blary_al.txt	forest_500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/urban_500m	/dataTable/attribute	data_blary_al.txt	urban_500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/grassland_750	/dataTable/attribute	data_blary_al.txt	grassland_750	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/forest_750m	/dataTable/attribute	data_blary_al.txt	forest_750m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/urban_750m	/dataTable/attribute	data_blary_al.txt	urban_750m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/grassland_1000	/dataTable/attribute	data_blary_al.txt	grassland_1000	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/forest_1000m	/dataTable/attribute	data_blary_al.txt	forest_1000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/urban_1000m	/dataTable/attribute	data_blary_al.txt	urban_1000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/grassland_1500	/dataTable/attribute	data_blary_al.txt	grassland_1500	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/forest_1500m	/dataTable/attribute	data_blary_al.txt	forest_1500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/urban_1500m	/dataTable/attribute	data_blary_al.txt	urban_1500m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/grassland_2000	/dataTable/attribute	data_blary_al.txt	grassland_2000	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/forest_2000m	/dataTable/attribute	data_blary_al.txt	forest_2000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/urban_2000m	/dataTable/attribute	data_blary_al.txt	urban_2000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/grassland_4000	/dataTable/attribute	data_blary_al.txt	grassland_4000	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/forest_4000m	/dataTable/attribute	data_blary_al.txt	forest_4000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/urban_4000m	/dataTable/attribute	data_blary_al.txt	urban_4000m	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/perc_rapeseed	/dataTable/attribute	data_blary_al.txt	perc_rapeseed	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/nb_crops	/dataTable/attribute	data_blary_al.txt	nb_crops	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/date	/dataTable/attribute	data_blary_al.txt	date	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/X	/dataTable/attribute	data_blary_al.txt	X	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Y	/dataTable/attribute	data_blary_al.txt	Y	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/recorder	/dataTable/attribute	data_blary_al.txt	recorder	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/min_t	/dataTable/attribute	data_blary_al.txt	min_t	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/max_wind	/dataTable/attribute	data_blary_al.txt	max_wind	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/CSI_ER05	/dataTable/attribute	data_blary_al.txt	CSI_ER05	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/CSI_ER01	/dataTable/attribute	data_blary_al.txt	CSI_ER01	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/richness_ER05	/dataTable/attribute	data_blary_al.txt	richness_ER05	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/richness_ER01	/dataTable/attribute	data_blary_al.txt	richness_ER01	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Nyclei_ER05	/dataTable/attribute	data_blary_al.txt	Nyclei_ER05	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Nyclei_ER01	/dataTable/attribute	data_blary_al.txt	Nyclei_ER01	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Pippip_ER05	/dataTable/attribute	data_blary_al.txt	Pippip_ER05	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Pippip_ER01	/dataTable/attribute	data_blary_al.txt	Pippip_ER01	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Eptser_ER05	/dataTable/attribute	data_blary_al.txt	Eptser_ER05	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Eptser_ER01	/dataTable/attribute	data_blary_al.txt	Eptser_ER01	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Nycnoc_ER05	/dataTable/attribute	data_blary_al.txt	Nycnoc_ER05	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Nycnoc_ER01	/dataTable/attribute	data_blary_al.txt	Nycnoc_ER01	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Myo_ER05	/dataTable/attribute	data_blary_al.txt	Myo_ER05	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Myo_ER01	/dataTable/attribute	data_blary_al.txt	Myo_ER01	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Ple_ER05	/dataTable/attribute	data_blary_al.txt	Ple_ER05	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/data_blary_al.txt/Ple_ER01	/dataTable/attribute	data_blary_al.txt	Ple_ER01	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/Blary Constance	/ResponsibleParty	dataset	Blary Constance	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Blary Constance	/ResponsibleParty	dataset	Blary Constance	member of	https://schema.org/memberOf		
+/Barré Kévin	/ResponsibleParty	dataset	Barré Kévin	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Barré Kévin	/ResponsibleParty	dataset	Barré Kévin	member of	https://schema.org/memberOf		
+/Kerbiriou Christian	/ResponsibleParty	dataset	Kerbiriou Christian	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Kerbiriou Christian	/ResponsibleParty	dataset	Kerbiriou Christian	member of	https://schema.org/memberOf		
+/Le Viol Isabelle	/ResponsibleParty	dataset	Le Viol Isabelle	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Le Viol Isabelle	/ResponsibleParty	dataset	Le Viol Isabelle	member of	https://schema.org/memberOf		
+/Blary Constance ""	/ResponsibleParty	dataset	Blary Constance ""	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Blary Constance ""	/ResponsibleParty	dataset	Blary Constance ""	member of	https://schema.org/memberOf		
+/Barré Kévin ""	/ResponsibleParty	dataset	Barré Kévin ""	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Barré Kévin ""	/ResponsibleParty	dataset	Barré Kévin ""	member of	https://schema.org/memberOf		
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/annotations_template_2.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,33 @@
+id	element	context	subject	predicate_label	predicate_uri	object_label	object_uri
+/dataset	/dataset	eml	dataset	is about	http://purl.obolibrary.org/obo/IAO_0000136		
+/ceamarc_env.tsv	/dataTable	dataset	ceamarc_env.tsv	is about	http://purl.obolibrary.org/obo/IAO_0000136		
+/ceamarc_env.tsv/long	/dataTable/attribute	ceamarc_env.tsv	long	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/lat	/dataTable/attribute	ceamarc_env.tsv	lat	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Carbo	/dataTable/attribute	ceamarc_env.tsv	Carbo	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Grav	/dataTable/attribute	ceamarc_env.tsv	Grav	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Maxbearing	/dataTable/attribute	ceamarc_env.tsv	Maxbearing	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Maxmagnit	/dataTable/attribute	ceamarc_env.tsv	Maxmagnit	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Meancurmag	/dataTable/attribute	ceamarc_env.tsv	Meancurmag	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Meansal	/dataTable/attribute	ceamarc_env.tsv	Meansal	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Meantheta	/dataTable/attribute	ceamarc_env.tsv	Meantheta	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Mud	/dataTable/attribute	ceamarc_env.tsv	Mud	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Prof	/dataTable/attribute	ceamarc_env.tsv	Prof	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Rugosity	/dataTable/attribute	ceamarc_env.tsv	Rugosity	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Sand	/dataTable/attribute	ceamarc_env.tsv	Sand	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Seaice_prod	/dataTable/attribute	ceamarc_env.tsv	Seaice_prod	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Sili	/dataTable/attribute	ceamarc_env.tsv	Sili	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Slope	/dataTable/attribute	ceamarc_env.tsv	Slope	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Standcurmag	/dataTable/attribute	ceamarc_env.tsv	Standcurmag	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Standsal	/dataTable/attribute	ceamarc_env.tsv	Standsal	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Standtheta	/dataTable/attribute	ceamarc_env.tsv	Standtheta	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/pivot_wider_jupytool_notebook.ipynb	/otherEntity	dataset	pivot_wider_jupytool_notebook.ipynb	is about	http://purl.obolibrary.org/obo/IAO_0000136		
+/Marc Eléaume	/ResponsibleParty	dataset	Marc Eléaume	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Marc Eléaume	/ResponsibleParty	dataset	Marc Eléaume	member of	https://schema.org/memberOf		
+/Lenaïg G. Hemery	/ResponsibleParty	dataset	Lenaïg G. Hemery	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Lenaïg G. Hemery	/ResponsibleParty	dataset	Lenaïg G. Hemery	member of	https://schema.org/memberOf		
+/Ben Galton-Fenzi	/ResponsibleParty	dataset	Ben Galton-Fenzi	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Ben Galton-Fenzi	/ResponsibleParty	dataset	Ben Galton-Fenzi	member of	https://schema.org/memberOf		
+/Pauline Seguineau	/ResponsibleParty	dataset	Pauline Seguineau	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Pauline Seguineau	/ResponsibleParty	dataset	Pauline Seguineau	member of	https://schema.org/memberOf		
+/Yvan Le Bras	/ResponsibleParty	dataset	Yvan Le Bras	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Yvan Le Bras	/ResponsibleParty	dataset	Yvan Le Bras	member of	https://schema.org/memberOf		
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/annotations_template_3.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,32 @@
+id	element	context	subject	predicate_label	predicate_uri	object_label	object_uri
+/dataset	/dataset	eml	dataset	is about	http://purl.obolibrary.org/obo/IAO_0000136		
+/ceamarc_env.tsv	/dataTable	dataset	ceamarc_env.tsv	is about	http://purl.obolibrary.org/obo/IAO_0000136		
+/ceamarc_env.tsv/long	/dataTable/attribute	ceamarc_env.tsv	long	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/lat	/dataTable/attribute	ceamarc_env.tsv	lat	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Carbo	/dataTable/attribute	ceamarc_env.tsv	Carbo	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Grav	/dataTable/attribute	ceamarc_env.tsv	Grav	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Maxbearing	/dataTable/attribute	ceamarc_env.tsv	Maxbearing	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Maxmagnit	/dataTable/attribute	ceamarc_env.tsv	Maxmagnit	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Meancurmag	/dataTable/attribute	ceamarc_env.tsv	Meancurmag	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Meansal	/dataTable/attribute	ceamarc_env.tsv	Meansal	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Meantheta	/dataTable/attribute	ceamarc_env.tsv	Meantheta	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Mud	/dataTable/attribute	ceamarc_env.tsv	Mud	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Prof	/dataTable/attribute	ceamarc_env.tsv	Prof	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Rugosity	/dataTable/attribute	ceamarc_env.tsv	Rugosity	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Sand	/dataTable/attribute	ceamarc_env.tsv	Sand	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Seaice_prod	/dataTable/attribute	ceamarc_env.tsv	Seaice_prod	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Sili	/dataTable/attribute	ceamarc_env.tsv	Sili	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Slope	/dataTable/attribute	ceamarc_env.tsv	Slope	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Standcurmag	/dataTable/attribute	ceamarc_env.tsv	Standcurmag	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Standsal	/dataTable/attribute	ceamarc_env.tsv	Standsal	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/ceamarc_env.tsv/Standtheta	/dataTable/attribute	ceamarc_env.tsv	Standtheta	contains measurements of type	http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#containsMeasurementsOfType		
+/Marc Eléaume	/ResponsibleParty	dataset	Marc Eléaume	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Marc Eléaume	/ResponsibleParty	dataset	Marc Eléaume	member of	https://schema.org/memberOf		
+/Lenaïg G. Hemery	/ResponsibleParty	dataset	Lenaïg G. Hemery	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Lenaïg G. Hemery	/ResponsibleParty	dataset	Lenaïg G. Hemery	member of	https://schema.org/memberOf		
+/Ben Galton-Fenzi	/ResponsibleParty	dataset	Ben Galton-Fenzi	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Ben Galton-Fenzi	/ResponsibleParty	dataset	Ben Galton-Fenzi	member of	https://schema.org/memberOf		
+/Pauline Seguineau	/ResponsibleParty	dataset	Pauline Seguineau	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Pauline Seguineau	/ResponsibleParty	dataset	Pauline Seguineau	member of	https://schema.org/memberOf		
+/Yvan Le Bras	/ResponsibleParty	dataset	Yvan Le Bras	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Yvan Le Bras	/ResponsibleParty	dataset	Yvan Le Bras	member of	https://schema.org/memberOf		
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/annotations_template_4.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,13 @@
+id	element	context	subject	predicate_label	predicate_uri	object_label	object_uri
+/dataset	/dataset	eml	dataset	is about	http://purl.obolibrary.org/obo/IAO_0000136		
+/pivot_wider_jupytool_notebook.ipynb	/otherEntity	dataset	pivot_wider_jupytool_notebook.ipynb	is about	http://purl.obolibrary.org/obo/IAO_0000136		
+/Marc Eléaume	/ResponsibleParty	dataset	Marc Eléaume	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Marc Eléaume	/ResponsibleParty	dataset	Marc Eléaume	member of	https://schema.org/memberOf		
+/Lenaïg G. Hemery	/ResponsibleParty	dataset	Lenaïg G. Hemery	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Lenaïg G. Hemery	/ResponsibleParty	dataset	Lenaïg G. Hemery	member of	https://schema.org/memberOf		
+/Ben Galton-Fenzi	/ResponsibleParty	dataset	Ben Galton-Fenzi	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Ben Galton-Fenzi	/ResponsibleParty	dataset	Ben Galton-Fenzi	member of	https://schema.org/memberOf		
+/Pauline Seguineau	/ResponsibleParty	dataset	Pauline Seguineau	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Pauline Seguineau	/ResponsibleParty	dataset	Pauline Seguineau	member of	https://schema.org/memberOf		
+/Yvan Le Bras	/ResponsibleParty	dataset	Yvan Le Bras	is a	http://www.w3.org/1999/02/22-rdf-syntax-ns#type	Person	https://schema.org/Person
+/Yvan Le Bras	/ResponsibleParty	dataset	Yvan Le Bras	member of	https://schema.org/memberOf		
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/attributes_ceamarc_env.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,20 @@
+attributeName	attributeDefinition	class	unit	dateTimeFormatString	missingValueCode	missingValueCodeExplanation
+long	Longitude is a geographic coordinate that specifies the east–west position of a point 	numeric	degree	""	-9999	no data available
+lat	Latitude is a geographic coordinate that specifies the north–south position of a point.	numeric	degree	""	-9999	no data available
+Carbo	Percentage of biogenic carbonate	numeric	percent	""	-9999	no data available
+Grav	Percentage of gravel in the seabed	numeric	percent	""	-9999	no data available
+Maxbearing	Maximum current bearing	numeric	radian	""	-9999	no data available
+Maxmagnit	Maximum current magnitude	numeric	meterPerSecond	""	-9999	no data available
+Meancurmag	Mean current magnitude	numeric	meterPerSecond	""	-9999	no data available
+Meansal	Mean salinity of the sea	numeric	PSU	""	-9999	no data available
+Meantheta	Mean temperature of the sea	numeric	degreeCelsius	""	-9999	no data available
+Mud	Percentage of mud in the seabed	numeric	percent	""	-9999	no data available
+Prof	Depth of the sea 	numeric	meter	""	-9999	no data available
+Rugosity	Rugosity of the seabed 	numeric	dimensionless	""	-9999	no data available
+Sand	Percentage of sand in the seabed 	numeric	percent	""	-9999	no data available
+Seaice_prod	Seaice production in meter per year	numeric	meterPerYear	""	-9999	no data available
+Sili	Percentage of biogenic silica in the seabed 	numeric	percent	""	-9999	no data available
+Slope	Slope of the seabed 	numeric	degree	""	-9999	no data available
+Standcurmag	Current magnitude standard deviation 	numeric	meterPerSecond	""	-9999	no data available
+Standsal	Salinity standard deviation	numeric	PSU	""	-9999	no data available
+Standtheta	Temperature standard deviation	numeric	degreeCelsius	""	-9999	no data available
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/ceamarc_env.tsv	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,10 @@
+long	lat	Carbo	Grav	Maxbearing	Maxmagnit	Meancurmag	Meansal	Meantheta	Mud	Prof	Rugosity	Sand	Seaice_prod	Sili	Slope	Standcurmag	Standsal	Standtheta
+139.22	-65.57	0.88	28.59	3.67	0.03	0.03	34.62	-0.13	22.72	-441	-9999	55.76	0.24	3.27	0.28	0.01	0.01	0.18
+139.22	-65.57	0.88	28.61	3.64	0.02	0.03	34.62	-0.13	22.48	-439	-9999	55.74	0.24	3.29	0.27	0.01	0.01	0.18
+139.23	-65.57	0.92	28.62	3.59	0.02	0.03	34.62	-0.14	22.25	-438	-9999	56.28	0.25	3.32	0.22	0.01	0.01	0.19
+139.24	-65.57	0.92	28.63	3.51	0.01	0.03	34.62	-0.14	21.95	-436	-9999	56.57	0.26	3.3	0.08	0.01	0.01	0.19
+139.24	-65.57	0.92	28.64	3.35	0.01	0.03	34.62	-0.14	21.7	-437	-9999	56.58	0.26	3.28	0.05	0.01	0.01	0.19
+139.25	-65.57	0.93	28.65	3	0.0096293305978179	0.03	34.62	-0.15	21.44	-436	-9999	56.63	0.26	3.26	0.29	0.01	0.01	0.19
+139.26	-65.57	0.93	28.63	2.49	0.00871255807578564	0.03	34.62	-0.15	21.11	-432	-9999	56.67	0.26	3.23	0.43	0.01	0.01	0.19
+139.26	-65.57	0.93	28.64	2.01	0.01	0.03	34.62	-0.16	20.83	-429	-9999	56.71	0.26	3.21	0.37	0.01	0.01	0.19
+139.27	-65.57	0.94	28.65	1.71	0.01	0.03	34.62	-0.16	20.55	-427	-9999	56.75	0.26	3.19	0.32	0.01	0.01	0.2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/custom_units.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,4 @@
+id	unitType	parentSI	multiplierToSI	description
+PSU	density	gramPerGram	0.001	"1 PSU = 1g/kg"
+degreeCelsius	temperature	dimensionless	1	"0 °C + 273,15 = 273,15 Kelvin"
+meterPerYear	speed	centimeterPerYear	0.01	"meter per year"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/entities.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,2 @@
+objectName	variable	value
+pivot_wider_jupytool_notebook.ipynb	entityType	executable
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/geographic_coverage.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,2 @@
+geographicDescription	northBoundingCoordinate	southBoundingCoordinate	eastBoundingCoordinate	westBoundingCoordinate
+Dumont D'Urville sea sampling border	-65.57	-67.01	145.53	139.22
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/intellectual_rights.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,1 @@
+This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/keywords.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,9 @@
+keyword	keywordThesaurus
+Antarctica	""
+Southern Ocean	""
+Dumont D'Urville sea	""
+CEAMARC	""
+Abiotic and physical parameters	""
+Ecoregionalization	""
+Jupyter notebook	""
+Pivot wider function	""
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/methods.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,1 @@
+Abiotic and physical parameters in this dataset were taken from oceanographic model and in situ measurements (Hemery et al., 2011). Here we quote the relevant section of the “Materials and methods” part from the study: “Abiotic or physical parameters. Two different categories of abiotic parameters were used (Fig. 2): parameters likely to be subject to daily or seasonal variability (temperature, salinity, current magnitude, general current direction and sea-ice concentration) and parameters with long-term stability (bathymetry, slope, rugosity and seabed sediments). Parameters with short-term variability are taken from an oceanographic model, whereas parameters with long-term stability are derived from in situ measurements. Physical oceanography. Physical oceanographic parameters near the seabed (temperature, salinity, mean current magnitude, standard deviations of these 3 parameters, maximum current magnitude and general current direction) are taken from a climatologically forced ocean circulation model. The model was run for a total of 23 yr. A spinup phase of 20 yr was required for the model to reach quasi-equilibrium. The mean and SD were calculated by using 6-hourly model data for the last 3 yr. Sea ice growth rate was calculated directly from special sensor microwave imager (SSM/I) observations (Tamura et al. 2008). The model is based on the Rutgers/University of California Los Angeles Regional Ocean Model System (ROMS; Shchepetkin & McWilliams 2005) and is identical to the one described by B. K. Galton-Fenzi et al. (unpubl.). The model used here, initially developed for regional modelling studies of the Amery Ice Shelf/Ocean system and has been used in circum-Antarctic modelling studies, is able to simulate ice/ocean interactions at a high level of realism (Galton-Fenzi 2009, 2010). For the region of this study, the model is able to reproduce the circulation patterns and water mass properties when compared with oceanographic measurements taken in the vicinity of the George V and Adélie basins (A. Meijers pers. comm.). The model domain extends from 135.77° E to 158.08° E and from 69.417° S to 62.724° S. The southern boundary of the model is a closed, solid, free slip wall and the eastern and western boundaries are partially open. The horizontal grid resolution is between 2.16 km near the southern boundary to 2.88 km near the northern boundary. There are 31 vertical levels that are concentrated towards the top and bottom of the model domain. The parameters used here were taken from the lowest vertical level in the model that lies immediately adjacent to the seabed. The choice of mixing and advection schemes follows the choices that were successfully used by Dinniman et al. (2003, 2007) for studies of the shelf seas near the Ross Ice Shelf. The melting and freezing formulation uses the full 3-equation formulation and dynamics frazil ice model used in the studies of Galton-Fenzi (2009, 2010). Lateral boundary fields (potential temperature, salinity and currents) on the open boundaries are relaxed to monthly climatologies from ECCO2 (Menemenlis et al. 2008, Wunsch et al. 2009). Ten primary tidal constituents were added as a free-surface forcing. The tidal amplitudes and phase are calculated with a nonstandard ROMS subroutine, based on tidal information from the Proudman Oceanographic Laboratory (Murray 1964) and modified to be included within ROMS, yielding a standard tidal prediction. The bathymetry and the ice-draft information come from a version of R-TOPO (Timmermann et al. 2010) that was modified to include the high-resolution bathymetric data (outlined below, Beaman et al. 2011) and knowledge of the glacial ice drafts in the region (B. Legresy pers.comm.). The open ocean surface fluxes are modified by an imposed climatological sea-ice cover that includes polynyas, derived from SSM/I observations (Tamura et al. 2008). During summer, the Tamura et al. (2008) data are supplemented with open-water heat and salt fluxes by using the monthly climatologies from the NCEP-2 (Kanamitsu et al. 2002). Bathymetry and seabed sediments. A bathymetry model based on multibeam swath sonar and single beam bathymetry data was produced at about 250 m resolution for the study area (Beaman et al. 2011). A raster map of the slope gradient was generated from this bathymetry model by using ESRI ArcGIS 9.2 Spatial Analysis Tools and a raster map of the rugosity was generated by using Benthic Terrain Modeler tools. Sediment grabs provided substratum composition data, such as the percentage of gravel, mud, sand, biogenic carbonate and biogenic silica at sample sites (Beaman & O’Brien 2009). These data are used as a broad-scale representation of the seafloor substratum.” (Hemery et al., 2011). The Jupyter notebook file in this dataset was created with the Interactive JupyTool and the notebook Galaxy tool (https://ecology.usegalaxy.eu/root?tool_id=interactive_tool_jupyter_notebook). This Jupyter notebook script uses the pivot_wider function from the tidyr library to prepare data for the Ecoregionalization workflow.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/personnel.txt	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,7 @@
+givenName	middleInitial	surName	organizationName	electronicMailAddress	userId	role	projectTitle	fundingAgency	fundingNumber
+Marc	""	Eléaume	Muséum National d'Histoire Naturelle	marc.eleaume@mnhn.fr	0000-0003-1999-1177	creator	""	""	""
+Marc	""	Eléaume	Muséum National d'Histoire Naturelle	marc.eleaume@mnhn.fr	0000-0003-1999-1177	contact	""	""	""
+Lenaïg	G.	Hemery	Pacific Northwest National Laboratory Marine Sciences Laboratory	lenaighemery@gmail.com,lenaig.hemery@pnnl.gov	0000-0001-5337-4514	creator	""	""	""
+Ben	""	Galton-Fenzi 	Australian Antarctic Division:Kingston, Tasmania, AU	""	0000-0003-1404-4103	creator	""	""	""
+Pauline	""	Seguineau	Muséum National d'Histoire Naturelle	pauline.seguineau@mnhn.fr	0009-0009-5969-8478	creator	""	""	""
+Yvan	""	Le Bras	Muséum National d'Histoire Naturelle	yvan.le-bras@mnhn.fr	0000-0002-8504-068X	creator	""	""	""
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotemp/pivot_wider_jupytool_notebook.ipynb	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,85 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Pivot wider Jupytool "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This Jupyter notebook is dedicated to the pivot_wider function from the tidyr R package. \n",
+    "This script is the final part of the data preparation for the ecoregionalization Galaxy workflow.   "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 62,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "#Date : 22/05/2024\n",
+    "#Author : Seguineau Pauline & Yvan Le Bras \n",
+    "\n",
+    "#Load libraries\n",
+    "library(tidyr)\n",
+    "\n",
+    "#load file \n",
+    "\n",
+    "input_path = \"galaxy_inputs\"\n",
+    "\n",
+    "for (dir in list.dirs(input_path)){\n",
+    "    for (file in list.files(dir)) {\n",
+    "        file_path = file.path(dir, file)}\n",
+    "}\n",
+    "\n",
+    "file = read.table(file_path,header=T, sep = \"\\t\")\n",
+    "\n",
+    "#Run pivot_wider function\n",
+    "pivot_file = pivot_wider(data = file,\n",
+    "                        names_from = phylum_class_order_family_genus_specificEpithet,\n",
+    "                        values_from = individualCount,\n",
+    "                        values_fill = 0,\n",
+    "                        values_fn = sum)\n",
+    "\n",
+    "#Replace all occurences >= 1 by 1 to have only presence (1) or absence (0) data\n",
+    "for(c in 3:length(pivot_file)){\n",
+    "    pivot_file[c][pivot_file[c]>=1] <- 1}\n",
+    "\n",
+    "\n",
+    "write.table(pivot_file, \"outputs/pivot_file.tabular\", sep = \"\\t\", quote = F, row.names = F)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In this Jupyter notebook, we used the pivot_wider function of the tidyr package to transform our data into a wider format and adapted to subsequent analyses as part of the Galaxy workflow for ecoregionalization. This transformation allowed us to convert our data to a format where each taxon becomes a separate column. We also took care to fill in the missing values with zeros and to sum the individual counts in case of duplications. Then all data >= 1 are replace by 1 to have only presence (1) or abscence (0) data.\n",
+    "\n",
+    "Thus, this notebook is an essential building block of our analysis pipeline, ensuring that the data is properly formatted and ready to be explored and interpreted for ecoregionalization studies."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "R",
+   "language": "R",
+   "name": "ir"
+  },
+  "language_info": {
+   "codemirror_mode": "r",
+   "file_extension": ".r",
+   "mimetype": "text/x-r-source",
+   "name": "R",
+   "pygments_lexer": "r",
+   "version": "4.0.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_geocov.tsv	Tue Sep 10 12:52:44 2024 +0000
@@ -0,0 +1,5 @@
+site	lat	long
+1	-65.999946	142.3360535
+2	-66.394359	140.4840125
+3	-66.023545	142.745584
+4	-66.3379125	144.011634