add index configuration for Ollerton J, et al. The diversity and evol…

…ution of pollination systems in large plant clades: Apocynaceae as a case study. Ann Bot. 2019 Jan 23;123(2):311-325. doi: 10.1093/aob/mcy127. PMID: 30099492; PMCID: PMC6344220 see also globalbioticinteractions/globalbioticinteractions#1019
globalbioticinteractions · Oct 7, 2024 · 875be1e · 875be1e
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diff --git a/.github/workflows/review.yml b/.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*
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,3 @@
+.elton/
+add_travis_artifact_upload_keys.sh
+datasets/
diff --git a/README.md b/README.md
@@ -0,0 +1,53 @@
+[![GloBI Review by Elton](../../actions/workflows/review.yml/badge.svg)](../../actions/workflows/review.yml) [![GloBI](https://api.globalbioticinteractions.org/interaction.svg?accordingTo=globi:globalbioticinteractions/pollinators-of-apocynaceae-database&refutes=true&refutes=false)](https://globalbioticinteractions.org/?accordingTo=globi:globalbioticinteractions/pollinators-of-apocynaceae-database)
+
+Configuration to help Global Biotic Interactions (GloBI, https://globalbioticinteractions.org) index: 
+
+Ollerton J, Liede-Schumann S, Endress ME, Meve U, Rech AR, Shuttleworth A, Keller HA, Fishbein M, Alvarado-Cárdenas LO, Amorim FW, Bernhardt P, Celep F, Chirango Y, Chiriboga-Arroyo F, Civeyrel L, Cocucci A, Cranmer L, da Silva-Batista IC, de Jager L, Deprá MS, Domingos-Melo A, Dvorsky C, Agostini K, Freitas L, Gaglianone MC, Galetto L, Gilbert M, González-Ramírez I, Gorostiague P, Goyder D, Hachuy-Filho L, Heiduk A, Howard A, Ionta G, Islas-Hernández SC, Johnson SD, Joubert L, Kaiser-Bunbury CN, Kephart S, Kidyoo A, Koptur S, Koschnitzke C, Lamborn E, Livshultz T, Machado IC, Marino S, Mema L, Mochizuki K, Morellato LPC, Mrisha CK, Muiruri EW, Nakahama N, Nascimento VT, Nuttman C, Oliveira PE, Peter CI, Punekar S, Rafferty N, Rapini A, Ren ZX, Rodríguez-Flores CI, Rosero L, Sakai S, Sazima M, Steenhuisen SL, Tan CW, Torres C, Trøjelsgaard K, Ushimaru A, Vieira MF, Wiemer AP, Yamashiro T, Nadia T, Queiroz J, Quirino Z. The diversity and evolution of pollination systems in large plant clades: Apocynaceae as a case study. Ann Bot. 2019 Jan 23;123(2):311-325. doi: 10.1093/aob/mcy127. PMID: 30099492; PMCID: PMC6344220.
+
+More specifically, the first sheet from 
+
+```
+https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344220/bin/mcy127_suppl_supplementary_material-s02.xlsx
+```
+
+ with content id 
+
+```
+hash://sha256/b97e46916d6df97d60cb43f25db86aef7ac6beb8eceb5b78c347248b43210f17
+```
+
+ was translated into
+
+```
+mcy127_suppl_supplementary_material-s02.csv
+```
+
+by extracting the first "sheet" from the suppl_supplementary_material-s02.xlsx in comma-separated values format.
+
+
+
+## Technical Metatadata
+
+This section is meant for machines, not for humans.
+
+```
+<https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#SoftwareAgent> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<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:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <http://purl.org/dc/terms/description> "A crawl event that discovers biodiversity archives."@en <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <http://www.w3.org/ns/prov#startedAtTime> "2024-10-07T23:07:18.909Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <http://www.w3.org/ns/prov#wasStartedBy> <https://preston.guoda.bio> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<https://doi.org/10.5281/zenodo.1410543> <http://www.w3.org/ns/prov#usedBy> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<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:faf9232c-0630-41c7-8511-32c916578205> .
+<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 0.9.9-SNAPSHOT) [Software]. Zenodo. https://doi.org/10.5281/zenodo.1410543"@en <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<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:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/dc/terms/description> "A biodiversity dataset graph archive."@en <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<hash://sha256/b97e46916d6df97d60cb43f25db86aef7ac6beb8eceb5b78c347248b43210f17> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<hash://sha256/b97e46916d6df97d60cb43f25db86aef7ac6beb8eceb5b78c347248b43210f17> <http://www.w3.org/ns/prov#qualifiedGeneration> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <http://www.w3.org/ns/prov#generatedAtTime> "2024-10-07T23:07:21.254Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Generation> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <http://www.w3.org/ns/prov#wasInformedBy> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <http://www.w3.org/ns/prov#used> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344220/bin/mcy127_suppl_supplementary_material-s02.xlsx> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344220/bin/mcy127_suppl_supplementary_material-s02.xlsx> <http://purl.org/pav/hasVersion> <hash://sha256/b97e46916d6df97d60cb43f25db86aef7ac6beb8eceb5b78c347248b43210f17> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+```
diff --git a/data/2a/5d/2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a b/data/2a/5d/2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a
@@ -0,0 +1 @@
+hash://sha256/f63b73e8262469c1d301149ecda14107fe652c49be3c1c026d9c5812e860f2b6
diff --git a/data/b9/7e/b97e46916d6df97d60cb43f25db86aef7ac6beb8eceb5b78c347248b43210f17 b/data/b9/7e/b97e46916d6df97d60cb43f25db86aef7ac6beb8eceb5b78c347248b43210f17
diff --git a/data/f6/3b/f63b73e8262469c1d301149ecda14107fe652c49be3c1c026d9c5812e860f2b6 b/data/f6/3b/f63b73e8262469c1d301149ecda14107fe652c49be3c1c026d9c5812e860f2b6
@@ -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:faf9232c-0630-41c7-8511-32c916578205> .
+<https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<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:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <http://purl.org/dc/terms/description> "A crawl event that discovers biodiversity archives."@en <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <http://www.w3.org/ns/prov#startedAtTime> "2024-10-07T23:07:18.909Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <http://www.w3.org/ns/prov#wasStartedBy> <https://preston.guoda.bio> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<https://doi.org/10.5281/zenodo.1410543> <http://www.w3.org/ns/prov#usedBy> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<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:faf9232c-0630-41c7-8511-32c916578205> .
+<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 0.9.9-SNAPSHOT) [Software]. Zenodo. https://doi.org/10.5281/zenodo.1410543"@en <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<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:faf9232c-0630-41c7-8511-32c916578205> .
+<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/dc/terms/description> "A biodiversity dataset graph archive."@en <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> .
+<hash://sha256/b97e46916d6df97d60cb43f25db86aef7ac6beb8eceb5b78c347248b43210f17> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<hash://sha256/b97e46916d6df97d60cb43f25db86aef7ac6beb8eceb5b78c347248b43210f17> <http://www.w3.org/ns/prov#qualifiedGeneration> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <http://www.w3.org/ns/prov#generatedAtTime> "2024-10-07T23:07:21.254Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Generation> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <http://www.w3.org/ns/prov#wasInformedBy> <urn:uuid:faf9232c-0630-41c7-8511-32c916578205> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> <http://www.w3.org/ns/prov#used> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344220/bin/mcy127_suppl_supplementary_material-s02.xlsx> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
+<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344220/bin/mcy127_suppl_supplementary_material-s02.xlsx> <http://purl.org/pav/hasVersion> <hash://sha256/b97e46916d6df97d60cb43f25db86aef7ac6beb8eceb5b78c347248b43210f17> <urn:uuid:6873ee73-2c59-42b0-9c68-66c7ff69cc79> .
diff --git a/globi.json b/globi.json
@@ -0,0 +1,65 @@
+{
+  "@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" : "mcy127_suppl_supplementary_material-s02.csv",
+    "dcterms:bibliographicCitation" : "Ollerton J, Liede-Schumann S, Endress ME, Meve U, Rech AR, Shuttleworth A, Keller HA, Fishbein M, Alvarado-Cárdenas LO, Amorim FW, Bernhardt P, Celep F, Chirango Y, Chiriboga-Arroyo F, Civeyrel L, Cocucci A, Cranmer L, da Silva-Batista IC, de Jager L, Deprá MS, Domingos-Melo A, Dvorsky C, Agostini K, Freitas L, Gaglianone MC, Galetto L, Gilbert M, González-Ramírez I, Gorostiague P, Goyder D, Hachuy-Filho L, Heiduk A, Howard A, Ionta G, Islas-Hernández SC, Johnson SD, Joubert L, Kaiser-Bunbury CN, Kephart S, Kidyoo A, Koptur S, Koschnitzke C, Lamborn E, Livshultz T, Machado IC, Marino S, Mema L, Mochizuki K, Morellato LPC, Mrisha CK, Muiruri EW, Nakahama N, Nascimento VT, Nuttman C, Oliveira PE, Peter CI, Punekar S, Rafferty N, Rapini A, Ren ZX, Rodríguez-Flores CI, Rosero L, Sakai S, Sazima M, Steenhuisen SL, Tan CW, Torres C, Trøjelsgaard K, Ushimaru A, Vieira MF, Wiemer AP, Yamashiro T, Nadia T, Queiroz J, Quirino Z. The diversity and evolution of pollination systems in large plant clades: Apocynaceae as a case study. Ann Bot. 2019 Jan 23;123(2):311-325. doi: 10.1093/aob/mcy127. PMID: 30099492; PMCID: PMC6344220.",
+    "doi": "10.1093/aob/mcy127",
+    "delimiter" : ",",
+    "headerRowCount" : 7,
+    "null" : [ "", "?" ],
+    "tableSchema" : {
+      "columns" : [ {
+        "name" : "Clade number",
+        "titles" : "Clade number",
+        "datatype" : "string"
+      }, {
+        "name" : "sourceTaxonSubfamilyName",
+        "titles" : "Subfamily",
+        "datatype" : "string"
+      }, {
+        "name" : "sourceTaxonTribeName",
+        "titles" : "Tribe",
+        "datatype" : "string"
+      }, {
+        "name" : "sourceTaxonSubtribeName",
+        "titles" : "Subtribe",
+        "datatype" : "string"
+      }, {
+        "name" : "sourceTaxonSpeciesName",
+        "titles" : "Species",
+        "datatype" : "string"
+      }, {
+        "name" : "countryName",
+        "titles" : "Country",
+        "datatype" : "string"
+      }, {
+        "name" : "targetTaxonName",
+        "titles" : "Pollinators/Flower visitors",
+        "datatype" : "string"
+      }, {
+        "name" : "Higher taxon",
+        "titles" : "Higher taxon",
+        "datatype" : "string"
+      }, {
+        "name" : "interactionTypeName",
+        "titles" : "Code",
+        "datatype" : "string"
+      }, {
+        "name" : "referenceCitation",
+        "titles" : "Reference",
+        "datatype" : "string"
+      }, {
+        "name" : "Name used in original publication",
+        "titles" : "Name used in original publication",
+        "datatype" : "string"
+      } ]
+    }
+  } ]
+}
diff --git a/interaction_types_mapping.csv b/interaction_types_mapping.csv
@@ -0,0 +1,27 @@
+provided_interaction_type_label,provided_interaction_type_id,mapped_to_interaction_type_label,mapped_to_interaction_type_id
+?,,hasFlowersVisitedBy,http://purl.obolibrary.org/obo/RO_0002623
+0,,hasFlowersVisitedBy,http://purl.obolibrary.org/obo/RO_0002623
+1,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+1?,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+1A,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+1B,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+2,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+2A,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+2AB,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+2B,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+3,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+3?,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+3(2),,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+3(2)A,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+3(4),,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+3(4)A,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+3A,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+3B,,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+3 (herbivore),,pollinatedBy,http://purl.obolibrary.org/obo/RO_0002456
+4,,eats,http://purl.obolibrary.org/obo/RO_0002470
+4?,,eats,http://purl.obolibrary.org/obo/RO_0002470
+4(3),,eats,http://purl.obolibrary.org/obo/RO_0002470
+4(3)A,,eats,http://purl.obolibrary.org/obo/RO_0002470
+4(A),,eats,http://purl.obolibrary.org/obo/RO_0002470
+4A,,eats,http://purl.obolibrary.org/obo/RO_0002470
+4B,,eats,http://purl.obolibrary.org/obo/RO_0002470