cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13315968
title: Water Body Checklists: Laccadive Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Laccadive Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315969
title: Water Body Checklists: Laccadive Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Laccadive Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315966
title: Water Body Checklists: Arabian Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Arabian Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315967
title: Water Body Checklists: Arabian Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Arabian Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316018
title: Water Body Checklists: Bering Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Bering Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316019
title: Water Body Checklists: Bering Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Bering Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315948
title: Water Body Checklists: Mozambique Channel Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Mozambique Channel using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315949
title: Water Body Checklists: Mozambique Channel Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Mozambique Channel using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316064
title: Water Body Checklists: Bismarck Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Bismarck Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316065
title: Water Body Checklists: Bismarck Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Bismarck Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316072
title: Water Body Checklists: Tasman Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Tasman Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316073
title: Water Body Checklists: Tasman Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Tasman Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316052
title: Water Body Checklists: Ceram Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Ceram Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316053
title: Water Body Checklists: Ceram Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Ceram Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315881
title: Water Body Checklists: Norwegian Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Norwegian Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315880
title: Water Body Checklists: Norwegian Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Norwegian Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315884
title: Water Body Checklists: Irish Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Irish Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315885
title: Water Body Checklists: Irish Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Irish Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13151017
title: Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts".

description: Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts". The data set consists of five folders: “Codon_usage_amoebae_and_viruses”, "Genome_annotations_amoebae", "Phylogenetic_trees_18S_amoebae", “Phylogenomic_trees_amoebae”, and "Viral_integration_detection_amoebae". The “Codon_usage_amoebae_and_viruses” folder contains for each amoeba host the calculated codon usage tables in the subfolder "codon_usage_table_host", the calculated codon usage preferences using different scores in the subfolder "codon_usage_scores_host", and the calculated codon usage preferences of giant viruses versus each host in the subfolder "codon_usage_scores_viruses_vs_host". The giant viruses in the subfolder "codon_usage_scores_viruses_vs_host" are organised by viral family and genus in separate sub-subfolders. The "Genome_annotations_amoebae" folder contains the generated genome annotations in different formats and the manually curated mitochondrial genome annotations for each amoeba host.  The "Phylogenetic_trees_18S_amoebae" contains for the eukaryotic phyla Discosea, Heterolobosea, and Tubulinea, the 18S rRNA nucleotide alignments, distance matrices, and computed phylogenetic trees. The folder "Phylogenomic_trees_amoebae" contains for the eukaryotic clades Amoebozoa and Discoba, the protein alignment matrices and computed phylogenomic trees. The folder "Viral_integration_detection_amoebae" contains the fasta file, alignment file, HMM profile and DIAMOND BLASTX database of MCP sequences collected in this study combined with sequences collected by Bellas & Sommaruga, 2021.
DOI: 10.5281/zenodo.13151016
title: Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts".

description: Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts". The data set consists of five folders: “Codon_usage_amoebae_and_viruses”, "Genome_annotations_amoebae", "Phylogenetic_trees_18S_amoebae", “Phylogenomic_trees_amoebae”, and "Viral_integration_detection_amoebae". The “Codon_usage_amoebae_and_viruses” folder contains for each amoeba host the calculated codon usage tables in the subfolder "codon_usage_table_host", the calculated codon usage preferences using different scores in the subfolder "codon_usage_scores_host", and the calculated codon usage preferences of giant viruses versus each host in the subfolder "codon_usage_scores_viruses_vs_host". The giant viruses in the subfolder "codon_usage_scores_viruses_vs_host" are organised by viral family and genus in separate sub-subfolders. The "Genome_annotations_amoebae" folder contains the generated genome annotations in different formats and the manually curated mitochondrial genome annotations for each amoeba host.  The "Phylogenetic_trees_18S_amoebae" contains for the eukaryotic phyla Discosea, Heterolobosea, and Tubulinea, the 18S rRNA nucleotide alignments, distance matrices, and computed phylogenetic trees. The folder "Phylogenomic_trees_amoebae" contains for the eukaryotic clades Amoebozoa and Discoba, the protein alignment matrices and computed phylogenomic trees. The folder "Viral_integration_detection_amoebae" contains the MCP databases used (fasta file, alignment file, HMM profile and DIAMOND BLASTX database) and the MCP sequences detected in this study and the blast results of these.
DOI: 10.5281/zenodo.14210530
title: Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts".

description: Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts". The data set consists of five folders: “Codon_usage_amoebae_and_viruses”, "Genome_annotations_amoebae", "Phylogenetic_trees_18S_amoebae", “Phylogenomic_trees_amoebae”, and "Viral_integration_detection_amoebae". The “Codon_usage_amoebae_and_viruses” folder contains for each amoeba host the calculated codon usage tables in the subfolder "codon_usage_table_host", the calculated codon usage preferences using different scores in the subfolder "codon_usage_scores_host", and the calculated codon usage preferences of giant viruses versus each host in the subfolder "codon_usage_scores_viruses_vs_host". The giant viruses in the subfolder "codon_usage_scores_viruses_vs_host" are organised by viral family and genus in separate sub-subfolders. The "Genome_annotations_amoebae" folder contains the generated genome annotations in different formats and the manually curated mitochondrial genome annotations for each amoeba host.  The "Phylogenetic_trees_18S_amoebae" contains for the eukaryotic phyla Discosea, Heterolobosea, and Tubulinea, the 18S rRNA nucleotide alignments, distance matrices, and computed phylogenetic trees. The folder "Phylogenomic_trees_amoebae" contains for the eukaryotic clades Amoebozoa and Discoba, the protein alignment matrices and computed phylogenomic trees. The folder "Viral_integration_detection_amoebae" contains the MCP databases used (fasta file, alignment file, HMM profile and DIAMOND BLASTX database) and the MCP sequences detected in this study and the blast results of these.
DOI: 10.5281/zenodo.13315876
title: Water Body Checklists: North Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the North Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315877
title: Water Body Checklists: North Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the North Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316048
title: Water Body Checklists: Banda Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Banda Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316049
title: Water Body Checklists: Banda Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Banda Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315916
title: Water Body Checklists: Ligurian Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Ligurian Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315917
title: Water Body Checklists: Ligurian Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Ligurian Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315868
title: Water Body Checklists: North Pacific Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the North Pacific Ocean region using effechecka and a modified polygon from the International Hydrographic Association.
DOI: 10.5281/zenodo.13315869
title: Water Body Checklists: North Pacific Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the North Pacific Ocean region using effechecka and a modified polygon from the International Hydrographic Association.
DOI: 10.5281/zenodo.13315938
title: Water Body Checklists: Hudson Bay Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Hudson Bay using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315939
title: Water Body Checklists: Hudson Bay Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Hudson Bay using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315864
title: Water Body Checklists: Arctic Ocean Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Arctic Ocean region using effechecka and modified polygons from the International Hydrographic Organization.
DOI: 10.5281/zenodo.13315865
title: Water Body Checklists: Arctic Ocean Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Arctic Ocean region using effechecka and modified polygons from the International Hydrographic Organization.
DOI: 10.5281/zenodo.13315940
title: Water Body Checklists: Baffin Bay Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Baffin Bay using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315941
title: Water Body Checklists: Baffin Bay Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Baffin Bay using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316042
title: Water Body Checklists: Savu Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Savu Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316043
title: Water Body Checklists: Savu Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Savu Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316036
title: Water Body Checklists: Makassar Strait Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Makassar Strait using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316037
title: Water Body Checklists: Makassar Strait Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Makassar Strait using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316077
title: Water Body Checklists: Northwestern Passages Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Northwestern Passages using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13316076
title: Water Body Checklists: Northwestern Passages Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Northwestern Passages using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315874
title: Water Body Checklists: South Atlantic Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the South Atlantic Ocean region using effechecka and a modified polygon from the International Hydrographic Association.
DOI: 10.5281/zenodo.13315875
title: Water Body Checklists: South Atlantic Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the South Atlantic Ocean region using effechecka and a modified polygon from the International Hydrographic Association.
DOI: 10.5281/zenodo.13315975
title: Water Body Checklists: Andaman Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Andaman Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315974
title: Water Body Checklists: Andaman Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Andaman Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315903
title: Water Body Checklists: Black Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Black Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
DOI: 10.5281/zenodo.13315902
title: Water Body Checklists: Black Sea Species List

description: Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.List of species collected from the Black Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.