cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14205427
title: EvoWeaver Supplemental Datafiles

description: This dataset contains additional files related to EvoWeaver. The following are included:



ProteinComplexTrees.RData: All phylogenetic trees for Complexes benchmark. These are stored in a list object with one tree per gene group.

ModulesEvoWeaver.RData: EvoWeaver object for Modules benchmark, containing phylogenetic trees for the Modules and Multiclass benchmark. `ModulePredAllPairs.RData` was made using this object.

CORUM_Blast_Results.RData: All results from pairwise BLAST of proteomes against human reference genes.

CORUM_proteomes.zip: all proteomes for all organisms used. Some of these are length 0, if an assembly could not be programatically found or retrieval failed to work.

CORUMOrthogroupsWithIndices.RData: Orthogroups for the CORUM benchmark with gene index data included

KOsWithPositions.RData: Gene index data for KO groups used in this study

ModsWithPositions.RData: Gene index data for modules used in this study

AllKEGGModules.RData: KEGG module taxonomy, names, and pathways for all modules used at time of download

KEGGModuleComplexes.RData: All complexes in a KEGG module at time of download

KEGGModuleDefinitions.RData: All KEGG module definitions at time of download

ModulesPositionData.RData: Gene index information for Modules benchmark

COG.links.detailed.v12.0.txt.tar.gz: STRING evidence streams between COGs (compressed, 1.44GB uncompressed)

COG.mappings.v12.0.txt.tar.gz: STRING COG definitions (compressed, 5.80GB uncompressed)

AllHumanGenes.fa: Human gene sequences used for BLASTing against in the CORUM benchmark

AllKEGGCDSs.RData: all sets of available genes from all genomes used in KEGG.

corum_bitscores.tsv: corum bitscores used as inputs to CladeOScope

corum_npp.tsv: corum normalized phylogenetic profiles used as inputs to CladeOScope

EukaryoteEWData.RData: Same as ModulesEvoWeaver.RData, but restricted to only eukaryotic sequences


Note that internal algorithm names may not exactly match those in published material due to computational requirements (e.g., difficulty naming functions/variables with special characters). See the GitHub page for a description of which internal names correspond to algorithms in the text.
DOI: 10.5281/zenodo.8423024
title: EvoWeaver Supplemental Datafiles

description: This dataset contains additional files related to EvoWeaver. The following are included:



ProteinComplexTrees.RData: All phylogenetic trees for Complexes benchmark. These are stored in a list object with one tree per gene group.

ModulesEvoWeaver.RData: EvoWeaver object for Modules benchmark, containing phylogenetic trees for the Modules and Multiclass benchmark. `ModulePredAllPairs.RData` was made using this object.

CORUM_Blast_Results.RData: All results from pairwise BLAST of proteomes against human reference genes.

CORUM_proteomes.zip: all proteomes for all organisms used. Some of these are length 0, if an assembly could not be programatically found or retrieval failed to work.

CORUMOrthogroupsWithIndices.RData: Orthogroups for the CORUM benchmark with gene index data included

KOsWithPositions.RData: Gene index data for KO groups used in this study

ModsWithPositions.RData: Gene index data for modules used in this study

AllKEGGModules.RData: KEGG module taxonomy, names, and pathways for all modules used at time of download

KEGGModuleComplexes.RData: All complexes in a KEGG module at time of download

KEGGModuleDefinitions.RData: All KEGG module definitions at time of download

ModulesPositionData.RData: Gene index information for Modules benchmark

COG.links.detailed.v12.0.txt.tar.gz: STRING evidence streams between COGs (compressed, 1.44GB uncompressed)

COG.mappings.v12.0.txt.tar.gz: STRING COG definitions (compressed, 5.80GB uncompressed)

AllHumanGenes.fa: Human gene sequences used for BLASTing against in the CORUM benchmark

AllKEGGCDSs.RData: all sets of available genes from all genomes used in KEGG.

corum_bitscores.tsv: corum bitscores used as inputs to CladeOScope

corum_npp.tsv: corum normalized phylogenetic profiles used as inputs to CladeOScope

EukaryoteEWData.RData: Same as ModulesEvoWeaver.RData, but restricted to only eukaryotic sequences


Note that internal algorithm names may not exactly match those in published material due to computational requirements (e.g., difficulty naming functions/variables with special characters). See the GitHub page for a description of which internal names correspond to algorithms in the text.
DOI: 10.5281/zenodo.8423025
title: EvoWeaver Supplemental Datafiles

description: This dataset contains additional files related to EvoWeaver. The following are included: ComplexSpeciesTree.RData: Species tree for Complexes benchmark ModulesSpeciesTree.RData: Species tree for Modules benchmark ProteinComplexTrees.RData: All phylogenetic trees for Complexes benchmark ModulesEvoWeaver.RData: EvoWeaver object for Modules benchmark ModulesPositionData.RData: Gene index information for Modules benchmark ModulePredsAllPairs.RData: predictions for all pairs of modules ModuelsMulticlassData.RData: multiclass classification data for Modules benchmark
DOI: 10.15468/dl.spy4ct
title: Occurrence Download

description: A dataset containing 31586 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "OccurrenceStatus is Present",
 "TaxonKey is Molinia caerulea (L.) Moench",
 "Year 1960-1990"
 ]
}

 The dataset includes 31586 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028691-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/bxh354
title: Unveiling Azorean Pollinators: A Critical Step for Biodiversity and Conservation

description: Azorean biodiversity has become relatively well understood thanks to significant scientific contributions over the past three decades. This research has produced a comprehensive arthropod species checklist for the archipelago, greatly advancing knowledge of species abundance, ecology, and distribution. It has also informed conservation management and research priorities. However, a key functional group—pollinators—remains poorly studied in the Azores. Little is known about their presence across various habitats and islands in the archipelago. Insect pollinators are essential for maintaining ecological balance and provide invaluable ecosystem services, making it crucial to gather basic data on their abundance, distribution, and ecology, as well as insights into the status of their populations. Such information is essential for ensuring the long-term sustainability of terrestrial ecosystems. Additionally, island ecosystems are increasingly impacted by land use changes, climate change, and the introduction of alien species, highlighting an urgent need to assess how these pressures affect pollinators and the process of pollination across the Azores.

Here, we present an inventory of pollinator species found across various habitat types on Terceira, covering a gradient of disturbance across 30 sites distributed throughout the island. We identified 2,549 pollinators representing 40 species, primarily from the Diptera and Hymenoptera orders, and recorded new information on species distribution and ecological associations. Many of the taxa are native, including three Azorean endemics, although 14 species are alien to the archipelago. Notably, our use of standardized sampling techniques enabled a comparative analysis of their effectiveness, and, more importantly, the data collected will aid in assessing the impacts of human activities on pollinator abundance and diversity, supporting informed habitat management decisions for pollinator conservation in the Azores.
DOI: 10.15468/dl.xmffws
title: Occurrence Download

description: A dataset containing 828613 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prunus spinosa L."
 ]
}

 The dataset includes 828613 records from 3428 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028683-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nt4xak
title: Occurrence Download

description: A dataset containing 212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Malephora lutea (Haw.) Schwantes)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 212 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009633-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cukjkw
title: Occurrence Download

description: A dataset containing 2881 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cupressus arizonica Greene)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 2881 records from 248 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009632-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28747574
title: New York Squirrel Census 2020-2021: training sample dataset

description: Two sample datasets created for training purposes from The Squirrel Census https://www.thesquirrelcensus.com/ hosted by NYC OpenData 2018 Central Park Squirrel Census - Squirrel Data | NYC Open Data, no reuse license specified.
DOI: 10.15468/dl.kzw6wm
title: Occurrence Download

description: A dataset containing 9610 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (Africa, Antarctica, Asia, Oceania, Europe, North America, South America)",
 "TaxonKey is Larix sibirica Ledeb."
 ]
}

 The dataset includes 9610 records from 138 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009637-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4xjaqm
title: Occurrence Download

description: A dataset containing 12615 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cupressus lusitanica Mill.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 12615 records from 252 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009638-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xqguv7
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Malephora purpureocrocea (Haw.) Schwantes)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 210 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009639-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gadcqf
title: Occurrence Download

description: A dataset containing 34757 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (Africa, Antarctica, Asia, Oceania, Europe, North America, South America)",
 "TaxonKey is Cocos nucifera L."
 ]
}

 The dataset includes 34757 records from 421 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009640-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bhwjk2
title: Occurrence Download

description: A dataset containing 165 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Egypt",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pterois volitans (Linnaeus, 1758)",
 "Year 2005-2015"
 ]
}

 The dataset includes 165 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009642-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mpvxjx
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Geometry POLYGON((-103 -26,106 -26,106 28,-103 28,-103 -26))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Abelia dielsii (Graebn.) Rehder"
 ]
}

 The dataset includes 77 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009643-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ymwvbm
title: Occurrence Download

description: A dataset containing 7083 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cupressus macrocarpa Hartw. ex Gordon)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 7083 records from 219 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009644-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e462xj
title: Occurrence Download

description: A dataset containing 6191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Malus baccata (L.) Borkh.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 6191 records from 159 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009645-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w85xyz
title: Occurrence Download

description: A dataset containing 774232 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is Madagascar",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (NE, DD, LC, NT, VU, EN, CR, EW, EX)",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 774232 records from 263 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009634-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/m4xjee
title: Schlupfwespenfunde aus der Gattungsgruppe der Amblytelina (Hymenoptera, Ichneumonidae, Ichneumoninae, Ichneumonini) in der Schweiz

description: This dataset contains the digitized treatments in Plazi based on the original journal article Artmann-Graf, Georg (2017): Schlupfwespenfunde aus der Gattungsgruppe der Amblytelina (Hymenoptera, Ichneumonidae, Ichneumoninae, Ichneumonini) in der Schweiz. Entomo Helvetica 10: 55-61, DOI: 10.5169/seals-986070Abstract: Observations on Ichneumonidae of the subtribe Amblytelina (Hymenoptera, Ichneumoninae, Ichneumonini) in Switzerland. – Thirty-three species collected in Switzerland by the author and Peter Müller are presented.Zusammenfassung: Aus der Gattungsgruppe Amblytelina (Hymenoptera, Ichneumonidae, Ichneumoninae, Ichneumonini) werden 33 in der Schweiz vom Autor und Peter Müller gesammelte Arten vorgestellt.
DOI: 10.15468/bsnken
title: Description of eight new species of the genus Acanthocephala Laporte, 1833 from South America (Hemiptera, Coreidae, Acanthocephalinae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Olivera, Leonela, Dellapé, Pablo M., Melo, María Cecilia (2024): Description of eight new species of the genus Acanthocephala Laporte, 1833 from South America (Hemiptera, Coreidae, Acanthocephalinae). Zoosystema 46 (12): 285-318, DOI: 10.5252/zoosystema2024v46a12, URL: https://sciencepress.mnhn.fr/sites/default/files/articles/pdf/zoosystema2024v46a12.pdfABSTRACTEight new species of the leaf-footed bug genus Acanthocephala Laporte, 1833 (Coreidae, Acanthocephalini) from Colombia and Brazil are described, and Acanthocephala pleuritica (Costa, 1863) is redescribed giving the first known locality record of the species. The descriptions include novel characters from male and female genitalia, and from external morphology such as armature of legs. For each species, we provide a habitus photograph of the adult, as well as photographs of male and female genitalia and a distributional map. Affinities with the other species of the genus are also discussed.
DOI: 10.15468/75rsm7
title: The mantis shrimp genus Clorida Eydoux & Souleyet, 1842 (Crustacea: Stomatopoda: Squillidae) in Japan, with the first Japanese record of Cloridina ichneumon (Fabricius, 1798)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Nakajima, Hiroki, Ueda, Tetsuya, Itani, Gyo, Osawa, Masayuki (2024): The mantis shrimp genus Clorida Eydoux & Souleyet, 1842 (Crustacea: Stomatopoda: Squillidae) in Japan, with the first Japanese record of Cloridina ichneumon (Fabricius, 1798). Zootaxa 5463 (4): 501-523, DOI: 10.11646/zootaxa.5463.4.3, URL: http://dx.doi.org/10.11646/zootaxa.5463.4.3AbstractWe revised the previous records of Clorida japonica Manning, 1978 and conducted extensive field and museum material surveys in Japan. The material examined included five species of the genus Clorida Eydoux & Souleyet, 1842 as follows: C. japonica; C. albolitura Ahyong & Naiyanetr, 2000; C. denticauda (Chhapgar & Sane, 1967); C. rotundicauda (Miers, 1880); and C. seversi Moosa, 1973. Among them, C. albolitura, C. denticauda, C. rotundicauda, and C. seversi are new to the Japanese stomatopod fauna. Re-examination of the Japanese specimens previously reported as C. japonica has shown that they partially belong to Cloridina ichneumon (Fabricius, 1798), a new record from Japan as well. A key to the Japanese species of Clorida and Cloridina reported in this study is also provided.
DOI: 10.15468/unb83p
title: The potter wasp genus Allorhynchium from Vietnam, with descriptions of three new species and a new country record (Hymenoptera, Vespidae, Eumeninae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Nguyen, Lien Thi Phuong, Nguyen, Anh D., Tran, Ngat Thi, Nguyen, Manh Thanh, Engel, Michael S. (2023): The potter wasp genus Allorhynchium from Vietnam, with descriptions of three new species and a new country record (Hymenoptera, Vespidae, Eumeninae). ZooKeys 1166: 1-32, DOI: http://dx.doi.org/10.3897/zookeys.1166.102674, URL: http://dx.doi.org/10.3897/zookeys.1166.102674
DOI: 10.15468/sdxsra
title: Integrative taxonomy reveals the Caridina clinata Cai, Nguyen & Ng, 1999 species complex (Crustacea, Decapoda, Atyidae), with descriptions of eight new species from Hainan Island, China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Hou, Junjie, Zhang, Jiping, Chen, Bing, Zhang, Yixuan, Chen, Wenjian, Guo, Zhaoliang (2025): Integrative taxonomy reveals the Caridina clinata Cai, Nguyen & Ng, 1999 species complex (Crustacea, Decapoda, Atyidae), with descriptions of eight new species from Hainan Island, China. Zoosystematics and Evolution 101 (4): 2295-2336, DOI: 10.3897/zse.101.172207AbstractIntegrative analyses revealed that Caridina clinata Cai, Nguyen & Ng, 1999 represents a species complex comprising nine sibling species distributed across Hainan Island (China) and Vietnam. Among these, C. clinata sensu stricto (the nominal species itself) occurs in both regions, C. haivanensis is endemic to Vietnam, and the seven newly described species are endemic to Hainan Island. Evidence showed that the C. clinata population reported by Cai (2014) from Wuzhishan was actually a new species, herein described as C. caii sp. nov. This study documents nine Caridina species from Hainan Island, including eight new species and one newly recorded species. The new species are: C. wenchangensis sp. nov., C. qiongzhongensis sp. nov., C. huangi sp. nov., C. hepingensis sp. nov., C. fontinalis sp. nov., C. tunchengensis sp. nov., C. brevilineata sp. nov., and C. caii sp. nov. Additionally, Caridina clinata is recorded for the first time from Ledong, Hainan, and is redescribed herein. For each species, we provide comprehensive morphological descriptions, illustrations, taxonomic notes, habitat parameters, and IUCN threat assessments. Furthermore, we clarify the phylogenetic relationships between the newly discovered species and their congeners.
DOI: 10.15468/dl.b9yxgk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Phengaris arion",
 "HasCoordinate is true",
 "CoordinateUncertaintyInMeters is less than or equal to 1000",
 "Year is greater than or equal to 1970",
 "Country is one of (Italy, Switzerland, Germany, Austria, Slovenia, France)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066194-251120083545085/datasets/export for details.
DOI: 10.15468/dl.77hn6u
title: Occurrence Download

description: A dataset containing 259556 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "DecimalLatitude is greater than or equal to -3.414722",
 "DecimalLatitude is less than or equal to -0.914722",
 "DecimalLongitude is greater than or equal to -80.0",
 "DecimalLongitude is less than or equal to -77.5",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 259556 records from 237 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066180-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.