GloBI configuration to help index Kau et al. 2025. Umbrella, keystone…

…, or flagship? An integrated framework for identifying effective surrogate species. Biological Conservation. https://doi.org/10.1016/j.biocon.2025.111025

.github/workflows/review.yml

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+# 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

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+.elton/
+add_travis_artifact_upload_keys.sh
+datasets/

README.md

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+[![GloBI Review by Elton](../../actions/workflows/review.yml/badge.svg)](../../actions/workflows/review.yml) [![GloBI](https://api.globalbioticinteractions.org/interaction.svg?accordingTo=globi:globalbioticinteractions/kau2025&refutes=true&refutes=false)](https://globalbioticinteractions.org/?accordingTo=globi:globalbioticinteractions/kau2025)
+
+Configuration to help Global Biotic Interactions (GloBI, https://globalbioticinteractions.org) index: 
+
+@article{KAU2025111025,title = {Umbrella, keystone, or flagship? An integrated framework for identifying effective surrogate species},journal = {Biological Conservation},volume = {303},pages = {111025},year = {2025},issn = {0006-3207},doi = {https://doi.org/10.1016/j.biocon.2025.111025},author = {Minyi Kau and Byron V. Weckworth and Sheng Li and Mathias M. Pires and Daiying Jin and Michela Pacifici and Carlo Rondinini and Luigi Boitani and Thomas M. McCarthy and Zhi Lu and George B. Schaller and Steven R. Beissinger and Juan Li}}

data/2a/5d/2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a

@@ -0,0 +1 @@
+hash://sha256/561546b2ae1e5ba6828c22727470322e8f52ae047c801be5ad1705e5e2cbe217

data/56/15/561546b2ae1e5ba6828c22727470322e8f52ae047c801be5ad1705e5e2cbe217

@@ -0,0 +1,19 @@
+<https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#SoftwareAgent> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<https://preston.guoda.bio> <http://purl.org/dc/terms/description> "Preston is a software program that finds, archives and provides access to biodiversity datasets."@en <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> <http://purl.org/dc/terms/description> "A crawl event that discovers biodiversity archives."@en <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> <http://www.w3.org/ns/prov#startedAtTime> "2025-02-14T13:38:41.202Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> <http://www.w3.org/ns/prov#wasStartedBy> <https://preston.guoda.bio> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<https://doi.org/10.5281/zenodo.1410543> <http://www.w3.org/ns/prov#usedBy> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<https://doi.org/10.5281/zenodo.1410543> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/dc/dcmitype/Software> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<https://doi.org/10.5281/zenodo.1410543> <http://purl.org/dc/terms/bibliographicCitation> "Jorrit Poelen, Icaro Alzuru, & Michael Elliott. 2018-2024. Preston: a biodiversity dataset tracker (Version 0.10.6-SNAPSHOT@ae30d66f4c9349439fed95106ab0c7ffd736b9fc) [Software]. Zenodo. https://doi.org/10.5281/zenodo.1410543"@en <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/dc/terms/description> "A biodiversity dataset graph archive."@en <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> .
+<hash://sha256/462844e9e541437f7ef19ca7d70ac1778529cdca8ecb9830c16f35deadae635d> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> <urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> .
+<hash://sha256/462844e9e541437f7ef19ca7d70ac1778529cdca8ecb9830c16f35deadae635d> <http://www.w3.org/ns/prov#qualifiedGeneration> <urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> <urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> .
+<urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> <http://www.w3.org/ns/prov#generatedAtTime> "2025-02-14T13:38:41.940Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> .
+<urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Generation> <urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> .
+<urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> <http://www.w3.org/ns/prov#wasInformedBy> <urn:uuid:439c4d24-835e-44d3-8627-f665069eee9e> <urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> .
+<urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> <http://www.w3.org/ns/prov#used> <https://ars.els-cdn.com/content/image/1-s2.0-S000632072500062X-mmc1.xlsx> <urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> .
+<https://ars.els-cdn.com/content/image/1-s2.0-S000632072500062X-mmc1.xlsx> <http://purl.org/pav/hasVersion> <hash://sha256/462844e9e541437f7ef19ca7d70ac1778529cdca8ecb9830c16f35deadae635d> <urn:uuid:0db14758-f743-4635-b810-262c1d1d725f> .

globi.json

@@ -0,0 +1,54 @@
+{
+  "@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" : "tableS5.tsv",
+    "dcterms:bibliographicCitation" : "@article{KAU2025111025,title = {Umbrella, keystone, or flagship? An integrated framework for identifying effective surrogate species},journal = {Biological Conservation},volume = {303},pages = {111025},year = {2025},issn = {0006-3207},doi = {https://doi.org/10.1016/j.biocon.2025.111025},author = {Minyi Kau and Byron V. Weckworth and Sheng Li and Mathias M. Pires and Daiying Jin and Michela Pacifici and Carlo Rondinini and Luigi Boitani and Thomas M. McCarthy and Zhi Lu and George B. Schaller and Steven R. Beissinger and Juan Li}}",
+    "delimiter" : "\t",
+    "headerRowCount" : 1,
+    "interactionTypeName": "preyedUponBy",
+    "interactionTypeId": "http://purl.obolibrary.org/obo/RO_0002458",
+    "null" : [ "" ],
+    "tableSchema" : {
+      "columns" : [ {
+        "name" : "http://www.w3.org/ns/prov#wasDerivedFrom",
+        "titles" : "http://www.w3.org/ns/prov#wasDerivedFrom",
+        "datatype" : "string"
+      }, {
+        "name" : "http://purl.org/dc/elements/1.1/format",
+        "titles" : "http://purl.org/dc/elements/1.1/format",
+        "datatype" : "string"
+      }, {
+        "name" : "sourceTaxonName",
+        "titles" : "Prey",
+        "datatype" : "string"
+      }, {
+        "name" : "targetTaxonName",
+        "titles" : "Predator",
+        "datatype" : "string"
+      }, {
+        "name" : "Source Study",
+        "titles" : "Source Study",
+        "datatype" : "string"
+      }, {
+        "name" : "basisOfRecord",
+        "titles" : "Method",
+        "datatype" : "string"
+      }, {
+        "name" : "Data Recorded Location",
+        "titles" : "Data Recorded Location",
+        "datatype" : "string"
+      }, {
+        "name" : "referenceCitation",
+        "titles" : "Full Reference",
+        "datatype" : "string"
+      } ]
+    }
+  } ]
+}

tableS5.sh

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+#!/bin/bash 
+#
+# Tracks data supplement and extract table S5
+#
+# Prequisites are preston[1] and miller[2].
+# 
+# References
+#
+# [1] Elliott M.J., Poelen J.H., Fortes J.A.B. (2020). Toward Reliable Biodiversity Dataset References. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2020.101132 hash://sha256/136c3c1808bcf463bb04b11622bb2e7b5fba28f5be1fc258c5ea55b3b84f482c
+# [2] Elliott M.J., Poelen, J.H. & Fortes, J.A.B. (2023) Signing data citations enables data verification and citation persistence. Sci Data. https://doi.org/10.1038/s41597-023-02230-y hash://sha256/f849c870565f608899f183ca261365dce9c9f1c5441b1c779e0db49df9c2a19d
+# [3] Miller is a command-line tool for querying, shaping, and reformatting data files in various formats including CSV, TSV, JSON, and JSON Lines. https://miller.readthedocs.io/ accessed on 2025-02-14.
+#
+
+preston track https://ars.els-cdn.com/content/image/1-s2.0-S000632072500062X-mmc1.xlsx\
+ | preston xlsx-stream\
+ | grep Table%20S5\
+ | mlr --ijsonl --otsvlite cat\
+ > tableS5.tsv