├── LICENSE.md ├── Topic 1 Finding the lost parents └── readme.md ├── Topic 10 An IPFS-Blockchain Interface └── readme.md ├── Topic 2 How good are Triple IDs in ENA └── readme.md ├── Topic 3 Enhance the GBIF clustering algorithms ├── .gitignore ├── export-gbif.md ├── pom.xml ├── readme.md ├── results │ ├── bicikl_hack.sql │ ├── pieters_cluster_explore.html │ ├── pieters_cluster_explore.ipynb │ ├── plazi.html │ ├── plazi.ipynb │ ├── recordedby_first_team_member.ipynb │ └── results_ENA_iBOLD_Plazi.ipynb ├── run-clustering.md └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── gbif │ │ │ └── pipelines │ │ │ ├── clustering │ │ │ └── RowOccurrenceFeatures.java │ │ │ └── core │ │ │ └── parsers │ │ │ └── clustering │ │ │ ├── Haversine.java │ │ │ ├── OccurrenceFeatures.java │ │ │ ├── OccurrenceRelationships.java │ │ │ └── RelationshipAssertion.java │ └── scala │ │ └── org │ │ └── gbif │ │ └── pipelines │ │ └── clustering │ │ ├── Cluster.scala │ │ └── package.scala │ └── test │ ├── java │ └── org │ │ └── gbif │ │ └── pipelines │ │ ├── clustering │ │ ├── BaseSparkTest.java │ │ ├── OccurrenceFeaturesSparkTest.java │ │ └── OccurrenceRelationshipsSparkTest.java │ │ └── core │ │ └── parsers │ │ └── clustering │ │ ├── HaversineTest.java │ │ ├── OccurrenceFeaturesPojo.java │ │ └── OccurrenceRelationshipsTest.java │ └── resources │ └── sample.parquet ├── Topic 4 Assigning latin scientific names to OTUs based on sequence clusters └── readme.md ├── Topic 5 Registering biodiversity-related vocabulary as Wikidata lexemes and link their senses to Wikidata items └── readme.md ├── Topic 6 FAIR Digital Object design from multiple sources └── readme.md ├── Topic 7 Enriching Wikidata with information from OpenBiodiv about taxonomic name usages in context from different literature sources ├── readme.md ├── taxa_catalogs_collections_holotypes.openrefine.tar.gz └── wikidata_schema.json ├── Topic 8 Linking specimen with material citation and vice versa └── readme.md ├── Topic 9 Hidden women in science └── readme.md └── readme.md /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/LICENSE.md -------------------------------------------------------------------------------- /Topic 1 Finding the lost parents/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 1 Finding the lost parents/readme.md -------------------------------------------------------------------------------- /Topic 10 An IPFS-Blockchain Interface/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 10 An IPFS-Blockchain Interface/readme.md -------------------------------------------------------------------------------- /Topic 2 How good are Triple IDs in ENA/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 2 How good are Triple IDs in ENA/readme.md -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/.gitignore: -------------------------------------------------------------------------------- 1 | .idea 2 | target 3 | clustering-gbif-hackathon.iml 4 | -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/export-gbif.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/export-gbif.md -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/pom.xml -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/readme.md -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/results/bicikl_hack.sql: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/results/bicikl_hack.sql -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/results/pieters_cluster_explore.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/results/pieters_cluster_explore.html -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/results/pieters_cluster_explore.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/results/pieters_cluster_explore.ipynb -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/results/plazi.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/results/plazi.html -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/results/plazi.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/results/plazi.ipynb -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/results/recordedby_first_team_member.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/results/recordedby_first_team_member.ipynb -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/results/results_ENA_iBOLD_Plazi.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/results/results_ENA_iBOLD_Plazi.ipynb -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/run-clustering.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/run-clustering.md -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/clustering/RowOccurrenceFeatures.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/clustering/RowOccurrenceFeatures.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/core/parsers/clustering/Haversine.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/core/parsers/clustering/Haversine.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/core/parsers/clustering/OccurrenceFeatures.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/core/parsers/clustering/OccurrenceFeatures.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/core/parsers/clustering/OccurrenceRelationships.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/core/parsers/clustering/OccurrenceRelationships.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/core/parsers/clustering/RelationshipAssertion.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/main/java/org/gbif/pipelines/core/parsers/clustering/RelationshipAssertion.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/main/scala/org/gbif/pipelines/clustering/Cluster.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/main/scala/org/gbif/pipelines/clustering/Cluster.scala -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/main/scala/org/gbif/pipelines/clustering/package.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/main/scala/org/gbif/pipelines/clustering/package.scala -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/clustering/BaseSparkTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/clustering/BaseSparkTest.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/clustering/OccurrenceFeaturesSparkTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/clustering/OccurrenceFeaturesSparkTest.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/clustering/OccurrenceRelationshipsSparkTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/clustering/OccurrenceRelationshipsSparkTest.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/core/parsers/clustering/HaversineTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/core/parsers/clustering/HaversineTest.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/core/parsers/clustering/OccurrenceFeaturesPojo.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/core/parsers/clustering/OccurrenceFeaturesPojo.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/core/parsers/clustering/OccurrenceRelationshipsTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/test/java/org/gbif/pipelines/core/parsers/clustering/OccurrenceRelationshipsTest.java -------------------------------------------------------------------------------- /Topic 3 Enhance the GBIF clustering algorithms/src/test/resources/sample.parquet: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 3 Enhance the GBIF clustering algorithms/src/test/resources/sample.parquet -------------------------------------------------------------------------------- /Topic 4 Assigning latin scientific names to OTUs based on sequence clusters/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 4 Assigning latin scientific names to OTUs based on sequence clusters/readme.md -------------------------------------------------------------------------------- /Topic 5 Registering biodiversity-related vocabulary as Wikidata lexemes and link their senses to Wikidata items/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 5 Registering biodiversity-related vocabulary as Wikidata lexemes and link their senses to Wikidata items/readme.md -------------------------------------------------------------------------------- /Topic 6 FAIR Digital Object design from multiple sources/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 6 FAIR Digital Object design from multiple sources/readme.md -------------------------------------------------------------------------------- /Topic 7 Enriching Wikidata with information from OpenBiodiv about taxonomic name usages in context from different literature sources/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 7 Enriching Wikidata with information from OpenBiodiv about taxonomic name usages in context from different literature sources/readme.md -------------------------------------------------------------------------------- /Topic 7 Enriching Wikidata with information from OpenBiodiv about taxonomic name usages in context from different literature sources/taxa_catalogs_collections_holotypes.openrefine.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 7 Enriching Wikidata with information from OpenBiodiv about taxonomic name usages in context from different literature sources/taxa_catalogs_collections_holotypes.openrefine.tar.gz -------------------------------------------------------------------------------- /Topic 7 Enriching Wikidata with information from OpenBiodiv about taxonomic name usages in context from different literature sources/wikidata_schema.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 7 Enriching Wikidata with information from OpenBiodiv about taxonomic name usages in context from different literature sources/wikidata_schema.json -------------------------------------------------------------------------------- /Topic 8 Linking specimen with material citation and vice versa/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 8 Linking specimen with material citation and vice versa/readme.md -------------------------------------------------------------------------------- /Topic 9 Hidden women in science/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/Topic 9 Hidden women in science/readme.md -------------------------------------------------------------------------------- /readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pensoft/BiCIKL/HEAD/readme.md --------------------------------------------------------------------------------