diff --git a/.gitignore b/.gitignore
index a547bf3..094c172 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,7 @@ dist-ssr
*.njsproj
*.sln
*.sw?
+
+# project configuration
+config.yml
+!examples/config.yml
diff --git a/.somesy.toml b/.somesy.toml
index 8bf901d..2b92a17 100644
--- a/.somesy.toml
+++ b/.somesy.toml
@@ -1,34 +1,31 @@
[project]
-name = "beamer-gui"
-version = "0.0.1"
-description = "A GUI for creating a Beamer presentation using LaTeX."
-keywords = ["beamer", "latex"]
+name = "rdf-graph-visualization"
+version = "0.1.0"
+description = "Visualization of RDF graphs in Turtle format in 3D on the web."
+keywords = ["rdf", "graph", "turtle", "visualization"]
license = "MIT"
-repository = "https://github.com/Materials-Data-Science-and-Informatics/beamer-gui"
+repository = "https://github.com/Materials-Data-Science-and-Informatics/rdf-graph-visualization"
+homepage = "https://github.com/Materials-Data-Science-and-Informatics/rdf-graph-visualization"
[[project.people]]
family-names = "Soylu"
given-names = "Mustafa"
email = "m.soylu@fz-juelich.de"
orcid = "https://orcid.org/0000-0003-2637-0432"
-
-contribution = "Main developer and project manager."
-contribution_types = ["maintenance", "code", "test", "review", "doc"]
-
+contribution = "The main author, maintainer and tester."
+contribution_begin = "2023-03-01"
+contribution_types = ["ideas", "code", "design", "test"]
author = true
maintainer = true
[[project.people]]
-family-names = "D'Mello"
-given-names = "Fiona"
-orcid = "https://orcid.org/0000-0002-0465-1009"
-email = "f.dmello@fz-juelich.de"
-
-contribution = "Main developer."
-contribution_types = ["ideas", "code", "test", "review", "doc"]
-
-author = true
+family-names = "Fathalla"
+given-names = "Said"
+email = "s.fathalla@fz-juelich.de"
+orcid = "https://orcid.org/0000-0002-2818-5890"
+contribution_begin = "2023-03-01"
+contribution_types = ["ideas", "userTesting"]
[[project.people]]
family-names = "Hofmann"
@@ -36,6 +33,10 @@ given-names = "Volker"
email = "v.hofmann@fz-juelich.de"
orcid = "https://orcid.org/0000-0002-5149-603X"
+contribution = "Discussions and suggestions concerning tool scope and usability."
+contribution_begin = "2023-06-01"
+contribution_end = "2023-06-30"
+contribution_types = ["ideas", "userTesting"]
publication_author = true
[[project.people]]
@@ -44,7 +45,5 @@ given-names = "Stefan"
email = "s.sandfeld@fz-juelich.de"
orcid = "https://orcid.org/0000-0001-9560-4728"
-contribution_types = ["ideas", "fundingFinding"]
-
+contribution_types = ["fundingFinding"]
publication_author = true
-
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000..5e9ae95
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,34 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it using these metadata.
+type: software
+title: rdf-graph-visualization
+abstract: Visualization of RDF graphs in Turtle format in 3D on the web.
+version: 0.1.0
+keywords:
+- rdf
+- graph
+- turtle
+- visualization
+authors:
+- family-names: Soylu
+ given-names: Mustafa
+ orcid: https://orcid.org/0000-0003-2637-0432
+ email: m.soylu@fz-juelich.de
+- family-names: Hofmann
+ given-names: Volker
+ orcid: https://orcid.org/0000-0002-5149-603X
+ email: v.hofmann@fz-juelich.de
+- family-names: Sandfeld
+ given-names: Stefan
+ orcid: https://orcid.org/0000-0001-9560-4728
+ email: s.sandfeld@fz-juelich.de
+contact:
+- family-names: Soylu
+ given-names: Mustafa
+ orcid: https://orcid.org/0000-0003-2637-0432
+ email: m.soylu@fz-juelich.de
+license: MIT
+repository-code:
+ https://github.com/Materials-Data-Science-and-Informatics/rdf-graph-visualization
+url:
+ https://github.com/Materials-Data-Science-and-Informatics/rdf-graph-visualization
diff --git a/README.md b/README.md
index 74872fd..1f88184 100644
--- a/README.md
+++ b/README.md
@@ -1,50 +1,90 @@
-# React + TypeScript + Vite
+# RDF Graph Visualization
-This template provides a minimal setup to get React working in Vite with HMR and some ESLint rules.
+## Description
+This project is a TypeScript/JavaScript application that processes RDF data to create a graph representation. It uses React for the frontend and Chakra UI for styling.
-Currently, two official plugins are available:
+We strongly suggest users to use `turtle` format for RDF data and `schema.org` vocabulary for the properties. The application is designed to work with the `schema.org` vocabulary, since we developed it for a specific use case. However, it can be easily modified to work with other vocabularies.
-- [@vitejs/plugin-react](https://github.com/vitejs/vite-plugin-react/blob/main/packages/plugin-react/README.md) uses [Babel](https://babeljs.io/) for Fast Refresh
-- [@vitejs/plugin-react-swc](https://github.com/vitejs/vite-plugin-react-swc) uses [SWC](https://swc.rs/) for Fast Refresh
+## Features
+- Parses RDF data and filters relevant properties.
+- Creates nodes and edges for a graph representation.
+- Filters and displays nodes based on user-selected criteria.
-## Expanding the ESLint configuration
+## Installation
+1. Clone the repository.
-If you are developing a production application, we recommend updating the configuration to enable type aware lint rules:
+```bash
+git clone https://github.com/Materials-Data-Science-and-Informatics/rdf-graph-visualization.git
+```
+2. Install dependencies:
+
+```bash
+npm install
+```
+
+3. Create the `config.yml` file in the root directory and set it according to next section.
+4. You can run the application with:
-- Configure the top-level `parserOptions` property like this:
+```bash
+npm run dev
+```
+
+5. Or you can build the application with below command and serve it with a web server.
-```js
-export default tseslint.config({
- languageOptions: {
- // other options...
- parserOptions: {
- project: ['./tsconfig.node.json', './tsconfig.app.json'],
- tsconfigRootDir: import.meta.dirname,
- },
- },
-})
+```bash
+npm run build
```
-- Replace `tseslint.configs.recommended` to `tseslint.configs.recommendedTypeChecked` or `tseslint.configs.strictTypeChecked`
-- Optionally add `...tseslint.configs.stylisticTypeChecked`
-- Install [eslint-plugin-react](https://github.com/jsx-eslint/eslint-plugin-react) and update the config:
-
-```js
-// eslint.config.js
-import react from 'eslint-plugin-react'
-
-export default tseslint.config({
- // Set the react version
- settings: { react: { version: '18.3' } },
- plugins: {
- // Add the react plugin
- react,
- },
- rules: {
- // other rules...
- // Enable its recommended rules
- ...react.configs.recommended.rules,
- ...react.configs['jsx-runtime'].rules,
- },
-})
+## Configuration
+Configuration file has the necessary information to show nodes and links in the graph. Since a 3D graph on the browser consumes a lot of resources, it is important to filter the data to show only the necessary information. Properties that are not in the yaml file will be ignored. You can check [example config file](examples/config.yml) for more information.
+You can also check example RDF files in the examples folder to see how the data should be formatted.
+
+The configuration file is a YAML file that has the following properties:
+```yaml
+# links will be created from these properties
+relationProperties:
+ - "http://schema.org/affiliation"
+
+# labels will be created from these properties
+labelProperties:
+ - "http://schema.org/name"
+
+# groups will be created from these properties
+groups:
+ - name: 'Organization'
+ types:
+ - 'http://schema.org/Organization'
+ properties:
+ - 'http://schema.org/affiliation'
+ color: '#FF0000'
```
+
+- `relationProperties`: List of properties that will be used to create links between nodes.
+- `labelProperties`: List of properties that will be used to create labels for nodes.
+- `groups`: List of groups that will be created based on the properties. Each group has the following properties:
+ - `name`: Name of the group.
+ - `types`: List of types that will be included in the group.
+ - `properties`: List of properties that will be used to filter the data. **Can be empty.**
+ - `color`: Color of the group. Please use HEX color codes.
+
+## How to Cite
+
+If you want to cite this project in your scientific work,
+please use the [citation file](https://citation-file-format.github.io/)
+in the [repository](https://github.com/Materials-Data-Science-and-Informatics/rdf-graph-visualization/blob/main/CITATION.cff).
+
+## Acknowledgements
+
+We kindly thank all authors and contributors.
+
+
+

+
+

+
+
+
+This project was developed at the Institute for Materials Data Science and Informatics
+(IAS-9) of the Jülich Research Center and funded by the Helmholtz Metadata Collaboration
+(HMC), an incubator-platform of the Helmholtz Association within the framework of the
+Information and Data Science strategic initiative.
\ No newline at end of file
diff --git a/codemeta.json b/codemeta.json
new file mode 100644
index 0000000..c733586
--- /dev/null
+++ b/codemeta.json
@@ -0,0 +1,66 @@
+{
+ "@context": [
+ "https://doi.org/10.5063/schema/codemeta-2.0",
+ "https://w3id.org/software-iodata",
+ "https://raw.githubusercontent.com/jantman/repostatus.org/master/badges/latest/ontology.jsonld",
+ "https://schema.org",
+ "https://w3id.org/software-types"
+ ],
+ "@type": "SoftwareSourceCode",
+ "author": [
+ {
+ "@type": "Person",
+ "givenName": "Mustafa",
+ "familyName": "Soylu",
+ "email": "m.soylu@fz-juelich.de",
+ "@id": "https://orcid.org/0000-0003-2637-0432"
+ }
+ ],
+ "name": "rdf-graph-visualization",
+ "description": "Visualization of RDF graphs in Turtle format in 3D on the web.",
+ "version": "0.1.0",
+ "keywords": [
+ "rdf",
+ "graph",
+ "turtle",
+ "visualization"
+ ],
+ "maintainer": [
+ {
+ "@type": "Person",
+ "givenName": "Mustafa",
+ "familyName": "Soylu",
+ "email": "m.soylu@fz-juelich.de",
+ "@id": "https://orcid.org/0000-0003-2637-0432"
+ }
+ ],
+ "license": [
+ "https://spdx.org/licenses/MIT"
+ ],
+ "softwareHelp": "https://github.com/Materials-Data-Science-and-Informatics/rdf-graph-visualization",
+ "codeRepository": "https://github.com/Materials-Data-Science-and-Informatics/rdf-graph-visualization",
+ "contributor": [
+ {
+ "@type": "Person",
+ "givenName": "Said",
+ "familyName": "Fathalla",
+ "email": "s.fathalla@fz-juelich.de",
+ "@id": "https://orcid.org/0000-0002-2818-5890"
+ },
+ {
+ "@type": "Person",
+ "givenName": "Volker",
+ "familyName": "Hofmann",
+ "email": "v.hofmann@fz-juelich.de",
+ "@id": "https://orcid.org/0000-0002-5149-603X"
+ },
+ {
+ "@type": "Person",
+ "givenName": "Stefan",
+ "familyName": "Sandfeld",
+ "email": "s.sandfeld@fz-juelich.de",
+ "@id": "https://orcid.org/0000-0001-9560-4728"
+ }
+ ],
+ "url": "https://github.com/Materials-Data-Science-and-Informatics/rdf-graph-visualization"
+}
\ No newline at end of file
diff --git a/eslint.config.js b/eslint.config.js
index 092408a..360139f 100644
--- a/eslint.config.js
+++ b/eslint.config.js
@@ -8,7 +8,7 @@ export default tseslint.config(
{ ignores: ['dist'] },
{
extends: [js.configs.recommended, ...tseslint.configs.recommended],
- files: ['**/*.{ts,tsx}'],
+ files: ['{**/*,*}.{js,ts,jsx,tsx,html,vue},{!node_modules/*}'],
languageOptions: {
ecmaVersion: 2020,
globals: globals.browser,
diff --git a/examples/config.yml b/examples/config.yml
new file mode 100644
index 0000000..717e17f
--- /dev/null
+++ b/examples/config.yml
@@ -0,0 +1,59 @@
+# links will be created from these properties
+relationProperties:
+ - "http://schema.org/affiliation"
+ - "http://schema.org/dataPublished"
+ - "http://schema.org/dateModified"
+ - "http://schema.org/provider"
+ - "http://schema.org/license"
+ - "http://schema.org/publisher"
+ - "http://schema.org/author"
+ - "http://schema.org/creator"
+ - "http://schema.org/keywords"
+
+# labels will be created from these properties
+labelProperties:
+ - "http://schema.org/name"
+ - "http://schema.org/text"
+ - "http://schema.org/comment"
+
+# groups will be created from these properties
+groups:
+ - name: 'Organization'
+ types: # below types will be in the organization group
+ - 'http://schema.org/Organization'
+ properties: # object of below properties will be in the organization group
+ - 'http://schema.org/affiliation'
+ - 'http://schema.org/provider'
+ - 'http://schema.org/publisher'
+ color: '#008000' # color of the nodes in this group on 3D view
+ - name: 'Person'
+ types:
+ - 'http://schema.org/Person'
+ properties:
+ - 'http://schema.org/author'
+ - 'http://schema.org/creator'
+ color: '#FF0000'
+ - name: 'Dataset'
+ types:
+ - 'http://schema.org/Dataset'
+ color: '#0000FF'
+ - name: 'Software'
+ types:
+ - 'http://schema.org/SoftwareSourceCode'
+ color: '#FFFF00'
+ - name: 'Document'
+ types:
+ - 'http://schema.org/Document'
+ color: '#FFA500'
+ - name: 'Article'
+ types:
+ - 'http://schema.org/Article'
+ color: '#4B0082'
+ - name: 'CreativeWork'
+ types:
+ - 'http://schema.org/CreativeWork'
+ color: '#8A2BE2'
+ - name: 'Service'
+ types:
+ - 'http://schema.org/Service'
+ color: '#00FFFF'
\ No newline at end of file
diff --git a/examples/large-graph.ttl b/examples/large-graph.ttl
new file mode 100644
index 0000000..8c63ba7
--- /dev/null
+++ b/examples/large-graph.ttl
@@ -0,0 +1,10027 @@
+@prefix owl: .
+@prefix rdf: .
+@prefix xml: .
+@prefix xsd: .
+@prefix rdfs: .
+@prefix schema: .
+@prefix rdf: .
+@prefix ns1: .
+@prefix schema: .
+ns1:Publ-31165 rdf:type schema:CreativeWork .
+ rdf:type schema:CreativeWork ;
+ schema:datePublished "1994"^^schema:Date ;
+ schema:identifier "ftp://ftp.bsrn.awi.de/bou/bou1194.dat.gz" ,
+ ;
+ schema:name "BSRN Station-to-archive file for station Boulder (1994-11)" ;
+ schema:url ;
+ schema:creator _:b12680894 ,
+ _:b5516088 ,
+ _:b9086543 ,
+ _:b7603557 .
+ rdf:type schema:CreativeWork ,
+ schema:PublicationIssue ;
+ schema:isPartOf _:b5516114 ;
+ schema:issueNumber "49(8)" ;
+ schema:pagination "1825-1835" ;
+ schema:datePublished "1985"^^schema:Date ;
+ schema:identifier ;
+ schema:name "Alkaline permanganate oxidation of kerogens from Cretaceous black shales thermally altered by diabase intrusions and laboratory simulations" ;
+ schema:url ;
+ schema:creator _:b5516158 ,
+ _:b5516138 ,
+ _:b5516123 .
+ rdf:type schema:CreativeWork ,
+ schema:PublicationIssue ;
+ schema:isBasedOn ;
+ schema:isPartOf _:b9168175 ,
+ _:b7647084 ,
+ _:b6160758 ,
+ _:b5516275 ;
+ schema:issueNumber "177" ;
+ schema:pagination "186-200" ;
+ schema:datePublished "2019"^^schema:Date ;
+ schema:identifier "https://doi.org/10.1016/j.gloplacha.2019.04.005" ,
+ ;
+ schema:name "Sediment residence time reveals Holocene shift from climatic to vegetation control on catchment erosion in the Balkans" ;
+ schema:url ;
+ schema:creator ,
+ _:b5516255 ,
+ _:b5516271 ,
+ ,
+ ,
+ _:b9168157 ,
+ _:b9168147 ,
+ ,
+ ,
+ _:b7647040 ,
+ _:b7647044 ,
+ ,
+ ,
+ _:b6160756 ,
+ _:b6160748 ,
+ .
+ rdf:type schema:CreativeWork ,
+ schema:PublicationIssue ;
+ schema:isBasedOn ;
+ schema:isPartOf _:b5516542 ;
+ schema:issueNumber "172" ;
+ schema:pagination "1-12" ;
+ schema:datePublished "2001"^^schema:Date ;
+ schema:identifier ;
+ schema:name "High-resolution carbonate content estimated from diffuse spectral reflectance for Leg 172 sites" ;
+ schema:url ;
+ schema:creator ,
+ _:b5516551 ,
+ _:b5516532 ,
+ _:b5516533 ,
+ ,
+ .
+ rdf:type schema:CreativeWork ,
+ schema:WebPage ;
+ schema:identifier ;
+ schema:name "Parameter comments for Helgoland Roads Mesozooplankton, 2009" ;
+ schema:url .
+ rdf:type schema:CreativeWork ,
+ schema:Dataset ;
+ schema:comment "Carbon per cell of prey and grazer calculated using the following equation of Menden-Deuer and Lessard (2000): picogram carbon per cell = 0.216*biovolume**0.939." ;
+ schema:conditionsOfAccess "unrestricted" ;
+ schema:inLanguage "en" .
+@prefix xsd: .
+ schema:isAccessibleForFree "true"^^xsd:boolean ;
+ schema:size _:b5516977 ;
+ schema:variableMeasured _:b5516962 ,
+ _:b5516964 ,
+ _:b5516965 ,
+ _:b5516971 ,
+ _:b5516968 ,
+ _:b5516974 ,
+ _:b5516972 ,
+ _:b5516973 ,
+ _:b5516978 ,
+ _:b5516982 ,
+ _:b5516983 ,
+ _:b5516986 ,
+ _:b5516985 ,
+ _:b5516991 ,
+ _:b5516989 ,
+ _:b5516998 ,
+ _:b5516996 ;
+ schema:datePublished "2014"^^schema:Date ,
+ "2014-01-22"^^schema:Date ;
+ schema:description "Carbon per cell of prey and grazer calculated using the following equation of Menden-Deuer and Lessard (2000): picogram carbon per cell = 0.216*biovolume**0.939." ;
+ schema:distribution _:b5516975 ,
+ _:b5516967 ;
+ schema:identifier ,
+ "https://doi.org/10.1594/PANGAEA.825554" ;
+ schema:includedInDataCatalog _:b5516990 ;
+ schema:license ;
+ schema:name "Feeding, growth and grazing rates of the oligotrich ciliate Strombidium sulcatum determined experimentally" ;
+ schema:publisher _:b5516988 ;
+ schema:url ;
+ schema:citation ,
+ ;
+ schema:creator ,
+ .
+ rdf:type schema:CreativeWork ;
+ schema:datePublished "2005"^^schema:Date ;
+ schema:identifier ;
+ schema:name "BSRN Station-to-archive file for station Chesapeake Light (2005-04)" ;
+ schema:url ;
+ schema:creator _:b5517045 .
+ rdf:type schema:Dataset ,
+ schema:CreativeWork ;
+ schema:conditionsOfAccess "unrestricted" ;
+ schema:inLanguage "en" ;
+ schema:isAccessibleForFree "true"^^xsd:boolean ;
+ schema:size _:b12456253 ;
+ schema:sourceOrganization ;
+ schema:spatialCoverage _:b12456247 ;
+ schema:temporalCoverage "2015-08-01T00:10:00/2015-08-22T23:50:15" ;
+ schema:variableMeasured _:b12456244 ,
+ _:b12456245 ,
+ _:b12456254 ,
+ _:b12456251 ,
+ _:b12456249 ;
+ schema:workExample ;
+ schema:datePublished "2015"^^schema:Date ,
+ "2015-12-03"^^schema:Date ;
+ schema:description "This dataset is about: Station list and links to master tracks in different resolutions of HEINCKE cruise HE449, Trondheim - Troms\u00F8, 2015-08-01 - 2015-08-22." ;
+ schema:distribution _:b12456255 ,
+ _:b12456246 ;
+ schema:identifier ,
+ "https://doi.org/10.1594/PANGAEA.855526" ;
+ schema:includedInDataCatalog _:b12456250 ;
+ schema:license ;
+ schema:name "Station list and links to master tracks in different resolutions of HEINCKE cruise HE449, Trondheim - Troms\u00F8, 2015-08-01 - 2015-08-22" ;
+ schema:publisher _:b12456248 ;
+ schema:url ;
+ schema:citation ,
+ ,
+ ,
+ ;
+ schema:creator .
+ rdf:type schema:Dataset ,
+ schema:CreativeWork ;
+ schema:conditionsOfAccess "unrestricted" ;
+ schema:inLanguage "en" ;
+ schema:isAccessibleForFree "true"^^xsd:boolean ;
+ schema:size _:b14727408 ;
+ schema:sourceOrganization ;
+ schema:spatialCoverage _:b14727401 ;
+ schema:temporalCoverage "2015-08-04T16:27:00/2015-08-18T08:39:00" ;
+ schema:variableMeasured _:b14727379 ,
+ _:b14727380 ,
+ _:b14727381 ,
+ _:b14727387 ,
+ _:b14727384 ,
+ _:b14727388 ,
+ _:b14727371 ,
+ _:b14727374 ,
+ _:b14727375 ,
+ _:b14727373 ,
+ _:b14727411 ,
+ _:b14727395 ,
+ _:b14727393 ,
+ _:b14727399 ,
+ _:b14727402 ,
+ _:b14727403 ,
+ _:b14727404 ;
+ schema:datePublished "2016-04-15"^^schema:Date ,
+ "2016"^^schema:Date ;
+ schema:description "This dataset is about: Physical oceanography during HEINCKE cruise HE449." ;
+ schema:distribution _:b14727382 ,
+ _:b14727398 ;
+ schema:identifier "https://doi.org/10.1594/PANGAEA.859616" ,
+ ;
+ schema:includedInDataCatalog _:b14727370 ;
+ schema:license ;
+ schema:name "Physical oceanography during HEINCKE cruise HE449" ;
+ schema:publisher _:b14727385 ;
+ schema:url ;
+ schema:citation ;
+ schema:creator _:b14727396 ,
+ _:b5517068 ,
+ .
+@prefix ns4: .
+ns4:srep42997 rdf:type schema:CreativeWork ,
+ schema:PublicationIssue ;
+ schema:isBasedOn ;
+ schema:isPartOf _:b14175771 ,
+ _:b15039982 ,
+ _:b6587400 ,
+ _:b5517075 ,
+ _:b14342417 ;
+ schema:issueNumber "7" ;
+ schema:pagination "42997" ;
+ schema:datePublished "2017"^^schema:Date ;
+ schema:identifier "https://doi.org/10.1038/srep42997" ,
+ ns4:srep42997 ;
+ schema:name "Widespread methane seepage along the continental margin off Svalbard - from Bj\u00F8rn\u00F8ya to Kongsfjorden" ;
+ schema:url ns4:srep42997 ;
+ schema:creator _:b14175775 ,
+ ,
+ _:b14342405 ,
+ ,
+ _:b6587391 ,
+ ,
+ ,
+ ,
+ ,
+ _:b5517067 ,
+ ,
+ ,
+ ,
+ _:b15039973 ,
+ .
+ rdf:type schema:Dataset ,
+ schema:CreativeWork ;
+ schema:conditionsOfAccess "unrestricted" ;
+ schema:inLanguage "en" ;
+ schema:isAccessibleForFree "true"^^xsd:boolean ;
+ schema:size _:b5568195 ;
+ schema:sourceOrganization ;
+ schema:spatialCoverage _:b5568194 ;
+ schema:temporalCoverage "2015-08-25T08:40:00/2015-09-07T15:20:00" ;
+ schema:variableMeasured _:b5568185 ,
+ _:b5568191 ,
+ _:b5568189 ,
+ _:b5568182 ,
+ _:b5568183 ,
+ _:b5568180 ;
+ schema:datePublished "2016"^^schema:Date ,
+ "2016-07-28"^^schema:Date ;
+ schema:description "This dataset is about: Continuous thermosalinograph oceanography along HEINCKE cruise track HE450." ;
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+ schema:description "The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides raw validated data of continuous measurements made with a Biospherical Instrument Inc. QCR-2150 surface PAR sensor mounted on a sensor mast at the stern of the ship (ca. 8m above deck) and time synchronized with the CTD recording unit. The sensor consists of a cosine collector and was also utilized to correct the CTD PAR sensor data. The dark was computed as the lowest 0.01% voltage of the signal that was found to be very stable (0.00965V) for all the legs except for the 2nd leg of the polar circle where there was no complete night (the manufacturer dark was 0.0097V). [\u2026]" ;
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+ schema:abstract "The Tara Oceans Expedition (2009-2013) was a global survey of ocean ecosystems aboard the Sailing Vessel Tara. It carried out extensive measurements of environmental conditions and collected plankton (viruses, bacteria, protists and metazoans) for later analysis using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data publication provides permanent links to original and updated versions of validated data files containing navigation and meteorological data collected during the entire Tara Oceans Expedition (2009-2013)." ;
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+ schema:description "The Tara Oceans Expedition (2009-2013) was a global survey of ocean ecosystems aboard the Sailing Vessel Tara. It carried out extensive measurements of environmental conditions and collected plankton (viruses, bacteria, protists and metazoans) for later analysis using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data publication provides permanent links to original and updated versions of validated data files containing navigation and meteorological data collected during the entire Tara Oceans Expedition (2009-2013)." ;
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+ schema:name "[RAW VALIDATED DATA] Navigation and meteorological data during the Tara Oceans expedition 2009-2013" ;
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+ schema:abstract "The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides raw validated data of continuous measurements made with a WETLabs Eco-FL sensor mounted on the flowthrough system between June 4th, 2011 and March 30th, 2012. Data was recorded approximately every 10s. Two issues affected the data: 1. Periods when the water 0.2\u00B5m filtered water were used as blanks and 2. Periods where fluorescence was affected by non-photochemical quenching (NPQ, chlorophyll fluorescence is reduced when cells are exposed to light, e.g. Falkowski and Raven, 1997). Median data and their standard deviation were binned to 5min bins with period of light/dark indicated by an added variable (so that NPQ affected data could be neglected if the user so chooses). Data was first calibrated using HPLC data collected on the Tara (there were 36 data within 30min of each other). Fewer were available when there was no evident NPQ and the resulting scale factor was 0.0106 mg Chl m-3/count. To increase the calibration match-ups we used the AC-S data which provided a robust estimate of Chlorophyll (e.g. Boss et al., 2013). Scale factor computed over a much larger range of values than HPLC was 0.0088 mg Chl m-3/count (compared to 0.0079 mg Chl m-3/count based on manufacturer). In the archived data the fluorometer data is merged with the TSG, raw data is provided as well as manufacturer calibration constants, blank computed from filtered measurements and chlorophyll calibrated using the AC-S. For a full description of the processing of the Eco-FL please see Taillandier (2015)." ;
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+ schema:description "The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides raw validated data of continuous measurements made with a WETLabs Eco-FL sensor mounted on the flowthrough system between June 4th, 2011 and March 30th, 2012. Data was recorded approximately every 10s. Two issues affected the data: 1. Periods when the water 0.2\u00B5m filtered water were used as blanks and 2. Periods where fluorescence was affected by non-photochemical quenching (NPQ, chlorophyll fluorescence is reduced when cells are exposed to light, e.g. Falkowski and Raven, 1997). [\u2026]" ;
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+ schema:abstract "The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides raw validated data of continuous measurements made with an Aquatic Laser Fluorescence Analyzer (ALFA) (Chekalyuk et al., 2014), connected in-line to the TARA flow through system during 2013. The ALFA instrument provides dual-wavelength excitation (405 and 514 nm) of laser-stimulated emission (LSE) for spectral and temporal analysis. It offers in vivo fluorescence assessments of phytoplankton pigments, biomass, photosynthetic yield (Fv/Fm), phycobiliprotein (PBP)-containing phytoplankton groups, and chromophoric dissolved organic matter (CDOM) (Chekalyuk and Hafez, 2008; 2013A). Spectral deconvolution (SDC) is used to assess the overlapped spectral bands of aquatic fluorescence constituents and water Raman scattering (R). The Fv/Fm measurements are spectrally corrected for non-chlorophyll fluorescence background produced by CDOM and other constituents (Chekalyuk and Hafez, 2008). The sensor was cleaned weakly following the manufacturer recommended protocol." ;
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+ schema:description "The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides raw validated data of continuous measurements made with an Aquatic Laser Fluorescence Analyzer (ALFA) (Chekalyuk et al., 2014), connected in-line to the TARA flow through system during 2013. The ALFA instrument provides dual-wavelength excitation (405 and 514 nm) of laser-stimulated emission (LSE) for spectral and temporal analysis. It offers in vivo fluorescence assessments of phytoplankton pigments, biomass, photosynthetic yield (Fv/Fm), phycobiliprotein (PBP)-containing phytoplankton groups, and chromophoric dissolved organic matter (CDOM) (Chekalyuk and Hafez, 2008; 2013A). [\u2026]" ;
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+ schema:name "[RAW VALIDATED DATA] Properties of seawater and particulate matter from a WETLabs ALFA hyperspectral laser spectrofluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013" ;
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