From 56b09e4d9f33bf2d149f3cfbd2c622a65ecc7c05 Mon Sep 17 00:00:00 2001
From: Jorrit Poelen <jhpoelen+git@jhpoelen.nl>
Date: Wed, 27 Sep 2023 09:40:32 -0500
Subject: [PATCH] add first attempt to index @tkuhn nanopubs; see related
 https://github.com/globalbioticinteractions/globalbioticinteractions/issues/923

---
 .github/workflows/review.yml | 27 ++++++++++++++++++++
 .gitignore                   |  3 +++
 README.md                    |  5 ++++
 get-taxontaxon-nanopubs.csv  |  3 +++
 globi.json                   | 49 ++++++++++++++++++++++++++++++++++++
 5 files changed, 87 insertions(+)
 create mode 100644 .github/workflows/review.yml
 create mode 100644 .gitignore
 create mode 100644 README.md
 create mode 100644 get-taxontaxon-nanopubs.csv
 create mode 100644 globi.json

diff --git a/.github/workflows/review.yml b/.github/workflows/review.yml
new file mode 100644
index 0000000..22ed8d3
--- /dev/null
+++ b/.github/workflows/review.yml
@@ -0,0 +1,27 @@
+# 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:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v1
+        with:
+          java-version: 1.8
+      - name: download review script
+        run: curl --silent -L "https://raw.githubusercontent.com/globalbioticinteractions/globinizer/master/check-dataset.sh" > check-dataset.sh
+      - name: review dataset
+        run: bash check-dataset.sh "${GITHUB_REPOSITORY}"
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..9172584
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,3 @@
+.elton/
+add_travis_artifact_upload_keys.sh
+datasets/
\ No newline at end of file
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..da2f801
--- /dev/null
+++ b/README.md
@@ -0,0 +1,5 @@
+[![GloBI Review by Elton](../../actions/workflows/review.yml/badge.svg)](../../actions/workflows/review.yml) [![GloBI](https://api.globalbioticinteractions.org/interaction.svg?accordingTo=globi:globalbioticinteractions/knowledgepixels&refutes=true&refutes=false)](https://globalbioticinteractions.org/?accordingTo=globi:globalbioticinteractions/knowledgepixels)
+
+Configuration to help Global Biotic Interactions (GloBI, https://globalbioticinteractions.org) index: 
+
+Species Interactions as published in nanopublications available through Biodiversity Data Journal and Knowledge Pixels.
diff --git a/get-taxontaxon-nanopubs.csv b/get-taxontaxon-nanopubs.csv
new file mode 100644
index 0000000..10d0bf3
--- /dev/null
+++ b/get-taxontaxon-nanopubs.csv
@@ -0,0 +1,3 @@
+"np","label","subjtaxonname","rel","objtaxonname","source","date"
+"http://purl.org/np/RAOgLBuvJRusIKPJyhXbx7sMI1aKj_AI0l1oG6XXsO4pU","Canis lupus Linnaeus, 1758 (species) - preys on - Bison bison (species)","https://www.checklistbank.org/dataset/9880/taxon/QLXL","http://purl.obolibrary.org/obo/RO_0002439","https://www.checklistbank.org/dataset/2169/taxon/9901","https://doi.org/10.1007/s10344-023-01676-0",2023-09-15T08:54:31.806Z
+"http://purl.org/np/RALX2suiPKea3pm65RjS97EL6k9iY1Jew_mb30hO5Zjv0","Canis lupus Linnaeus, 1758 (species) - eats - Odocoileus virginianus (Zimmermann, 1780) (species)","https://www.checklistbank.org/dataset/9880/taxon/QLXL","http://purl.obolibrary.org/obo/RO_0002470","https://www.checklistbank.org/dataset/9880/taxon/48NBQ","https://doi.org/10.2307/3800561",2023-09-10T07:15:55.875Z
diff --git a/globi.json b/globi.json
new file mode 100644
index 0000000..9017e24
--- /dev/null
+++ b/globi.json
@@ -0,0 +1,49 @@
+{
+  "@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" : "file:///home/jorrit/proj/globi/data-new/knowledgepixels/get-taxontaxon-nanopubs.csv",
+    "url" : "https://grlc.knowledgepixels.com/api-git/knowledgepixels/bdj-nanopub-api/get-taxontaxon-nanopubs.csv",
+    "dcterms:bibliographicCitation" : "Species Interactions as published in nanopublications available through Biodiversity Data Journal and Knowledge Pixels.",
+    "delimiter" : ",",
+    "headerRowCount" : 1,
+    "null" : [ "" ],
+    "tableSchema" : {
+      "columns" : [ {
+        "name" : "referenceUrl",
+        "titles" : "np",
+        "datatype" : "string"
+      }, {
+        "name" : "referenceCitation",
+        "titles" : "label",
+        "datatype" : "string"
+      }, {
+        "name" : "sourceTaxonId",
+        "titles" : "subjtaxonname",
+        "datatype" : "string"
+      }, {
+        "name" : "interactionTypeId",
+        "titles" : "rel",
+        "datatype" : "string"
+      }, {
+        "name" : "targetTaxonId",
+        "titles" : "objtaxonname",
+        "datatype" : "string"
+      }, {
+        "name" : "referenceDoi",
+        "titles" : "source",
+        "datatype" : "string"
+      }, {
+        "name" : "date",
+        "titles" : "date",
+        "datatype" : "string"
+      } ]
+    }
+  } ]
+}