cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.sql5my
title: Occurrence Download

description: A dataset containing 108576 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Arabidopsis thaliana (L.) Heynh.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 108576 records from 397 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009046-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2thmhg
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vanda javierae D.Tiu ex Fessel & Lückel"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0131793-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmdfdr
title: Occurrence Download

description: A dataset containing 9407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nisaetus nipalensis Hodgson, 1836",
 "HasCoordinate is True",
 "Year is greater than or equal to 1900",
 "Year is less than or equal to 2021",
 "Month is greater than or equal to January",
 "Month is less than or equal to December",
 "HasGeospatialIssue is False"
 ]
}

 The dataset includes 9407 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002116-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z72nv5
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Brazil",
 "Country is Bolivia (Plurinational State of)",
 "Country is Argentina",
 "Country is Paraguay"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ficus carica L.",
 "Year 1970-2020"
 ]
}

 The dataset includes 34 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082855-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.huv9kp
title: Occurrence Download

description: A dataset containing 165 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ebenus sibthorpii DC."
 ]
}

 The dataset includes 165 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031151-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7mqvc5
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-110.69824 26.01563,-104.28223 26.01563,-104.28223 31.11328,-110.69824 31.11328,-110.69824 26.01563))",
 "HasCoordinate is true",
 "TaxonKey is Parmotrema stuppeum (Taylor) Hale"
 ]
}

 The dataset includes 17 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063120-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sz3s8p
title: Occurrence Download

description: A dataset containing 44814 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-86.3360741399999938 43.1893334499999995, -86.3360741399999938 43.2017499399999991, -86.3360741399999938 43.2180465699999985, -86.3360741399999938 43.2258068800000004, -86.3360741399999938 43.2389993899999965, -86.3360741399999938 43.2552960299999967, -86.3360741399999938 43.2669364799999983, -86.3189709699999952 43.2669364799999983, -86.3057537600000018 43.2669364799999983, -86.2832067599999988 43.2669364799999983, -86.2715445200000062 43.2669364799999983, -86.2544398900000004 43.2669364799999983, -86.2373352700000027 43.2669364799999983, -86.2155657499999961 43.2669364799999983, -86.2031274699999983 43.2669364799999983, -86.2031274699999983 43.2529679399999978, -86.2031274699999983 43.2405514499999981, -86.2031274699999983 43.2289109999999965, -86.2031274699999983 43.2118383299999991, -86.2031274699999983 43.2025259700000035, -86.2031274699999983 43.1893334499999995, -86.2163432300000068 43.1893334499999995, -86.2295604400000002 43.1893334499999995, -86.2482200299999988 43.1893334499999995, -86.2606597599999958 43.1893334499999995, -86.2785418600000042 43.1893334499999995, -86.2972014500000029 43.1893334499999995, -86.3205259399999960 43.1893334499999995, -86.3360741399999938 43.1893334499999995))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 44814 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0118531-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3tbnd9
title: Occurrence Download

description: A dataset containing 117 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Lophozosterops javanicus (Horsfield, 1821)"
 ]
}

 The dataset includes 117 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030640-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yhy8t3
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stilbia philopalis Graslin, 1852"
 ]
}

 The dataset includes 46 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091542-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rn9l4j
title: Occurrence Download

description: A dataset containing 418 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "TaxonKey is Dasyprocta Illiger, 1811",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 418 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009047-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5q9fqa
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Eos histrio (Statius Muller, 1776)"
 ]
}

 The dataset includes 18 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030654-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yx9t3f
title: Occurrence Download

description: A dataset containing 199 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cinara cupressi (Buckton, 1881)"
 ]
}

 The dataset includes 199 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0118514-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.447r3a
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kinosternon dunni Schmidt, 1947"
 ]
}

 The dataset includes 75 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082408-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4j28ce
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eugenia cowanii McVaugh"
 ]
}

 The dataset includes 33 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0131795-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c8q43v
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dysoxylum medogense C.Y.Wu & H.Li"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030680-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n9pvwk
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tricliceras xylorhizum Verdc."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0131794-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p87csq
title: Occurrence Download

description: A dataset containing 2026 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyla gratiosa LeConte, 1856"
 ]
}

 The dataset includes 2026 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127671-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.27umd5
title: Occurrence Download

description: A dataset containing 1744 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Camellia sinensis (L.) Kuntze",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 1744 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009047-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6rhmvb
title: Occurrence Download

description: A dataset containing 492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is eDNA from Gulf of Mexico Ecosystems and Carbon Cruise 2021 (GOMECC-4)",
 "EventId is gomecc4_cancun_sta118_dcm_c_18s"
 ]
}

 The dataset includes 492 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030667-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xnp6gh
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-102.36004 10.28864,-74.21784 10.28864,-74.21784 21.53864,-102.36004 21.53864,-102.36004 10.28864))",
 "HasCoordinate is true",
 "TaxonKey is Hemileia vastatrix Berk. & Broome",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 25 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009047-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ydddcf
title: Occurrence Download

description: A dataset containing 6455990 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 6455990 records from 1607 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0347566-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15110229
title: gnomAD V4.1 Annotation Resource for Talos

description: This file is an echtvar-encoded extract of the gnomAD V4.1 joint dataset, limited to genic regions +/-2kb

---

Talos is a Variant Prioritisation tool, designed to be used in clinical analysis of rare disease cases. This tool aims to sift through entire datasets (which can be whole genome, exome, or panels), and identify variants which are likely to be causative of disease based on a range of heuristics. The selection and filtering of variants is done on the basis of annotations - population frequencies, per-transcript consequences, in silico predictions of consequence, and presence of variants in the ClinVar clinical database.

To be as portable as possible, and present a consistent collection of annotations regardless of site, Talos takes responsibility for all annotation steps. As described in the Talos project README, an annotation pipeline written in NextFlow can take individual VCFs and a handful of annotation sources, and generate a fully formatted MatrixTable object, ready to be used in Talos. The majority of the annotation inputs (an Ensembl GFF3 file, a summary file from MANE, AlphaMissense data) are small enough to be collected and processed as part of this workflow, but the gnomAD population frequencies are too large to easily distribute.

The Talos pipeline makes use of Echtvar to rapidly apply gnomAD annotations to an input VCF. Echtvar contains an encoding process, where select attributes from an annotation source are extracted and densified into a compressed representation. This file contains the compressed representation of:



gnomAD v4.1 Joint (exomes and genomes)

Reduced to genic regions (a union of all gene/ncRNA/snRNA, +/-2kb) in the Ensembl 113 GFF3 file

Echtvar encoding extracted and renamed the fields defined in this config file


This file can be dropped into the Talos annotation workflow per instructions in the README. It is not a general purpose annotation source usable for applying gnomAD frequencies to whole-genome data, users should be aware that this is a subset of annotations and a subset of sites.

 

This file is identical to the original version, with the exception of the filename - ".zip" has been removed as a file extension, as it leads to the false assumption the file needs to be opened/unpacked to be used. This data should be used as-is.
DOI: 10.5281/zenodo.15110230
title: gnomAD V4.1 Annotation Resource for Talos

description: This file is an echtvar-encoded extract of the gnomAD V4.1 joint dataset, limited to genic regions +/-2kb

---

Talos is a Variant Prioritisation tool, designed to be used in clinical analysis of rare disease cases. This tool aims to sift through entire datasets (which can be whole genome, exome, or panels), and identify variants which are likely to be causative of disease based on a range of heuristics. The selection and filtering of variants is done on the basis of annotations - population frequencies, per-transcript consequences, in silico predictions of consequence, and presence of variants in the ClinVar clinical database.

To be as portable as possible, and present a consistent collection of annotations regardless of site, Talos takes responsibility for all annotation steps. As described in the Talos project README, an annotation pipeline written in NextFlow can take individual VCFs and a handful of annotation sources, and generate a fully formatted MatrixTable object, ready to be used in Talos. The majority of the annotation inputs (an Ensembl GFF3 file, a summary file from MANE, AlphaMissense data) are small enough to be collected and processed as part of this workflow, but the gnomAD population frequencies are too large to easily distribute.

The Talos pipeline makes use of Echtvar to rapidly apply gnomAD annotations to an input VCF. Echtvar contains an encoding process, where select attributes from an annotation source are extracted and densified into a compressed representation. This file contains the compressed representation of:



gnomAD v4.1 Joint (exomes and genomes)

Reduced to genic regions (a union of all gene/ncRNA/snRNA, +/-2kb) in the Ensembl 113 GFF3 file

Echtvar encoding extracted and renamed the fields defined in this config file


This file can be dropped into the Talos annotation workflow per instructions in the README. It is not a general purpose annotation source usable for applying gnomAD frequencies to whole-genome data, users should be aware that this is a subset of annotations and a subset of sites.
DOI: 10.5281/zenodo.15222100
title: gnomAD V4.1 Annotation Resource for Talos

description: This file is an echtvar-encoded extract of the gnomAD V4.1 joint dataset, limited to genic regions +/-2kb

---

Talos is a Variant Prioritisation tool, designed to be used in clinical analysis of rare disease cases. This tool aims to sift through entire datasets (which can be whole genome, exome, or panels), and identify variants which are likely to be causative of disease based on a range of heuristics. The selection and filtering of variants is done on the basis of annotations - population frequencies, per-transcript consequences, in silico predictions of consequence, and presence of variants in the ClinVar clinical database.

To be as portable as possible, and present a consistent collection of annotations regardless of site, Talos takes responsibility for all annotation steps. As described in the Talos project README, an annotation pipeline written in NextFlow can take individual VCFs and a handful of annotation sources, and generate a fully formatted MatrixTable object, ready to be used in Talos. The majority of the annotation inputs (an Ensembl GFF3 file, a summary file from MANE, AlphaMissense data) are small enough to be collected and processed as part of this workflow, but the gnomAD population frequencies are too large to easily distribute.

The Talos pipeline makes use of Echtvar to rapidly apply gnomAD annotations to an input VCF. Echtvar contains an encoding process, where select attributes from an annotation source are extracted and densified into a compressed representation. This file contains the compressed representation of:



gnomAD v4.1 Joint (exomes and genomes)

Reduced to genic regions (a union of all gene/ncRNA/snRNA, +/-2kb) in the Ensembl 113 GFF3 file

Echtvar encoding extracted and renamed the fields defined in this config file


This file can be dropped into the Talos annotation workflow per instructions in the README. It is not a general purpose annotation source usable for applying gnomAD frequencies to whole-genome data, users should be aware that this is a subset of annotations and a subset of sites.

 

This file is identical to the original version, with the exception of the filename - ".zip" has been removed as a file extension, as it leads to the false assumption the file needs to be opened/unpacked to be used. This data should be used as-is.
DOI: 10.15468/dl.egvjn8
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Inversodicraea torrei (C.Cusset) Cheek"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000095-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.arg3u9
title: Occurrence Download

description: A dataset containing 738945 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is Benin",
 "GadmGid is BEN",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 738945 records from 214 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000086-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g5xhxd
title: Occurrence Download

description: A dataset containing 9763736 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is China"
 ]
}

 The dataset includes 9763736 records from 4780 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0131680-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/8t1-lwc-70t
title: Eupithecia nanata (Hübner, [1813])

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/spt-q7a-bv4
title: Diarsia mendica Fabricius, 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/y3l-njl-stp
title: Agrochola (Leptologia) Prout, 1901

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/cnt-0cn-k1b
title: Pyralis Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/mjv-ppf-yq9
title: Pediasia aridella Thunberg, 1788

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/czc-7w5-t90
title: Arctia plantaginis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/t7j-f6s-s7h
title: Diarsia mendica Fabricius, 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/xcq-eep-n98
title: Agonopterix ocellana Fabricius, 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/9vs-aex-dv1
title: Naenia typica Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/he5-tcx-399
title: Spaelotis suecica Aurivillius, 1889

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15468/dl.9f9cbr
title: Occurrence Download

description: A dataset containing 700460 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "DecimalLatitude is greater than or equal to 44.085278",
 "DecimalLatitude is less than or equal to 49.085278",
 "DecimalLongitude is greater than or equal to -80.0",
 "DecimalLongitude is less than or equal to -75.0",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 700460 records from 214 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028857-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/vem-vve-l5t
title: Phycitodes binaevella Hübner

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.