add GloBI index config related to globalbioticinteractions/globalbiot…

…icinteractions#1012 fyi @Ritten11

.github/workflows/review.yml

@@ -0,0 +1,41 @@
+# This workflow will review a GloBI indexed dataset.
+# For more information see: https://globalbioticinteractions.org
+
+name: GloBI review by Elton
+
+on:
+  push:
+    branches: [ '*' ]
+  pull_request:
+    branches: [ '*' ]
+  schedule:
+    - cron: "0 0 * * 1"
+
+jobs:
+  review:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '8'
+      - name: download review script
+        run: curl --silent -L "https://raw.githubusercontent.com/globalbioticinteractions/globinizer/master/check-dataset.sh" > check-dataset.sh
+      - name: download network compiler script
+        run: |
+          curl --silent -L "https://raw.githubusercontent.com/globalbioticinteractions/globinizer/master/compile-network.sh" > compile-network.sh
+          chmod +x compile-network.sh
+      - name: review dataset
+        run: bash check-dataset.sh "${GITHUB_REPOSITORY}"
+      - name: Share review report
+        uses: actions/upload-artifact@v4
+        with:
+          name: review-report
+          path: |
+            README.txt
+            datasets/
+            index.*
+            indexed-*
+            review*

.gitignore

@@ -2,3 +2,4 @@ sources/
 **/target/**
 **/.idea/**
 .vscode/**
+datasets/

README.md

@@ -27,3 +27,9 @@ To run the front- and back-end you simply run the docker compose in this directo
 - Install java and mvn for the backend
 - Compile the back-end (from the Companion-Queries folder) using the command "./mvnw clean package". This produces the necessary jar file for the next command to work.
 - execute "docker compose build" and then "docker compose up" from this folder.
+
+## Indexing
+
+Host-pests claims included in this repository are configured to be indexed by Global Biotic Interactions (GloBI, https://globalbioticinteractions.org).
+
+[![GloBI Review by Elton](../../actions/workflows/review.yml/badge.svg)](../../actions/workflows/review.yml) [![GloBI](https://api.globalbioticinteractions.org/interaction.svg?accordingTo=globi:kai-vu/companion-planting-decision-support&refutes=true&refutes=false)](https://globalbioticinteractions.org/?accordingTo=globi:kai-vu/companion-planting-decision-support)

globi.json

@@ -0,0 +1,91 @@
+{
+  "@context" : [ "http://www.w3.org/ns/csvw", {
+    "@language" : "en"
+  } ],
+  "rdfs:comment" : [ "inspired by https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/" ],
+  "tables" : [ {
+    "@context" : [ "http://www.w3.org/ns/csvw", {
+      "@language" : "en"
+    } ],
+    "rdfs:comment" : [ "inspired by https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/" ],
+    "url" : "datasets/eppo-practicalplants-hosts.csv",
+    "dcterms:bibliographicCitation" : "Configuration to help GloBI index Companion Planting Ontology, a resource developed by the Knowledge in AI group of Vrije Universiteit Amsterdam.",
+    "delimiter" : ",",
+    "headerRowCount" : 1,
+    "null" : [ "" ],
+    "tableSchema" : {
+       "foreignKeys": [
+          {
+            "columnReference": "targetTaxonId",
+            "reference": {
+              "columnReference": "targetTaxonId"
+            }
+          }
+       ],
+      "columns" : [ {
+        "name" : "",
+        "titles" : "",
+        "datatype" : "string"
+      }, {
+        "name" : "codeid",
+        "titles" : "codeid",
+        "datatype" : "string"
+      }, {
+        "name" : "targetTaxonName",
+        "titles" : "fullname",
+        "datatype" : "string"
+      }, {
+        "name" : "targetTaxonId",
+        "titles" : "eppocode",
+        "datatype": {
+           "base" : "string",
+           "valueUrl" : "https://gd.eppo.int/taxon/{targetTaxonId}"
+         }
+      } ]
+    }
+  }, {
+    "@context" : [ "http://www.w3.org/ns/csvw", {
+      "@language" : "en"
+    } ],
+    "rdfs:comment" : [ "inspired by https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/" ],
+    "url" : "datasets/eppo-practicalplants-pests.csv",
+    "dcterms:bibliographicCitation" : "Configuration to help GloBI index Companion Planting Ontology, a resource developed by the Knowledge in AI group of Vrije Universiteit Amsterdam.",
+    "delimiter" : ",",
+    "headerRowCount" : 1,
+    "null" : [ "" ],
+    "tableSchema" : {
+      "primaryKey": "targetTaxonId",
+      "columns" : [ {
+        "name" : "",
+        "titles" : "",
+        "datatype" : "string"
+      }, {
+        "name" : "targetTaxonId",
+        "titles" : "eppocode",
+        "datatype": {
+           "base" : "string",
+           "valueUrl" : "https://gd.eppo.int/taxon/{targetTaxonId}"
+         }
+      }, {
+        "name" : "sourceTaxonId",
+        "titles" : "pests_eppocode",
+        "datatype": {
+           "base" : "string",
+           "valueUrl" : "https://gd.eppo.int/taxon/{sourceTaxonId}"
+         }
+      }, {
+        "name" : "idclass",
+        "titles" : "idclass",
+        "datatype" : "string"
+      }, {
+        "name" : "interactionTypeName",
+        "titles" : "labelclass",
+        "datatype" : "string"
+      }, {
+        "name" : "sourceTaxonName",
+        "titles" : "fullname",
+        "datatype" : "string"
+      }  ]
+    }
+  } ]
+}

interaction_types_mapping.csv

@@ -0,0 +1,7 @@
+provided_interaction_type_label,provided_interaction_type_id,mapped_to_interaction_type_label,mapped_to_interaction_type_id
+Alternate,,interactsWith,http://purl.obolibrary.org/obo/RO_0002437
+Doubtful host,,interactsWith,http://purl.obolibrary.org/obo/RO_0002437
+Experimental,,interactsWith,http://purl.obolibrary.org/obo/RO_0002437
+Host,,hasHost,http://purl.obolibrary.org/obo/RO_0002454
+Major host,,hasHost,http://purl.obolibrary.org/obo/RO_0002454
+Wild/Weed,,interactsWith,http://purl.obolibrary.org/obo/RO_0002437