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

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glyptothorax gracilis (Günther, 1864)",
 "Country is India"
 ]
}

 The dataset includes 72 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011941-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pvw6s2
title: Occurrence Download

description: A dataset containing 3087 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bipes biporus (Cope, 1894)"
 ]
}

 The dataset includes 3087 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010196-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bur98a
title: Occurrence Download

description: A dataset containing 5 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 Eremias aria Anderson & Leviton, 1967"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093370-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b5a6u9
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Ecuador",
 "Country is Peru"
 ]
 },
 "TaxonKey is Vasconcellea stipulata (V.M.Badillo) V.M.Badillo"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011941-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmwy2e
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Polioptila clementsi B.M.Whitney & J.A.Alonso, 2005"
 ]
}

 The dataset includes 48 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010207-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.www5gv
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carex heudesii H.Lév. & Vaniot"
 ]
}

 The dataset includes 59 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093292-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vlerky
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cheilanthes hirta var. nemorosa W.Jacobsen & N.Jacobsen"
 ]
}

 The dataset includes 78 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011941-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/3rms-jj73
title: microwave detection

description: Near-field microwave detection plays a crucial role in various applications such as medical diagnosis, non-destructive and electromagnetic compatibility (EMC) tests. This dataset presents the original data of the microwave sensor exploiting the magnon-photon coupling properties. This scheme offers a novel approach to microwave metrology with promising applications in microwave imaging, EMC tests, and integrated circuit design.
DOI: 10.15468/dl.a4xd3u
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cissus arguta Hook.fil."
 ]
}

 The dataset includes 121 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093291-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxgcfr
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Genista sylvestris Scop.",
 "HasCoordinate is true",
 "Continent is Europe",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 35 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020227-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5atrha
title: Occurrence Download

description: A dataset containing 365 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myotis thysanodes Miller, 1897",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 365 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011942-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ahuwt
title: Occurrence Download

description: A dataset listing the 4004022 species recorded in GBIF matching the query:
{ }

 The dataset's 4004022 records were derived from 73788 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038931-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ejy6f
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bothriechis supraciliaris (Taylor, 1954)"
 ]
}

 The dataset includes 50 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010216-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nnwws9
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clerodendrum excavatum De Wild."
 ]
}

 The dataset includes 130 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093296-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zyalvx
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vasconcellea weberbaueri (Harms) V.M.Badillo"
 ]
}

 The dataset includes 37 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011942-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekxpmy
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alnus henryi C.K.Schneid."
 ]
}

 The dataset includes 14 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001773-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9k2xeg
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvia officinalis",
 "Country is Bulgaria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 36 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014538-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z4mbuu
title: Occurrence Download

description: A dataset containing 22880646 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Branta canadensis, Ommatotriton ophryticus, Trachemys ornata)",
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Specimen, Unknown evidence, Machine Observation, Occurrence evidence)",
 "Year is greater than or equal to 1971",
 "Year is less than or equal to 2024",
 "HasCoordinate is true"
 ]
}

 The dataset includes 22880646 records from 1482 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014434-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gt52p5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Oryzias timorensis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014539-250914085247600/datasets/export for details.
DOI: 10.5281/zenodo.17141481
title: Data from simulated flooding experiments on soil under blackcurrant cultivation and meadows.

description: The aim of this study was to determine how cultivation affects the quality of the soil environment under flood conditions.
DOI: 10.5281/zenodo.17141482
title: Data from simulated flooding experiments on soil under blackcurrant cultivation and meadows.

description: The aim of this study was to determine how cultivation affects the quality of the soil environment under flood conditions.
DOI: 10.15468/dl.dxhm74
title: Occurrence Download

description: A dataset containing 231 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvia officinalis",
 "Country is Canada",
 "HasCoordinate is true"
 ]
}

 The dataset includes 231 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014541-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.grrkuv
title: Occurrence Download

description: A dataset listing the 438 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-13.41922 29.20465,-13.44853 29.22327,-13.46918 29.18106,-13.46973 29.16889,-13.45517 29.15819,-13.42807 29.15303,-13.4194 29.17479,-13.41461 29.20465,-13.41922 29.20465))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 438 records were derived from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014525-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sexqvc
title: Occurrence Download

description: A dataset containing 160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025",
 "Geometry POLYGON ((157.5586 23.63081, 157.6376 24.28179, 157.5785 24.93409, 157.3827 25.56123, 157.0581 26.13588, 156.6104 26.64579, 156.0662 27.06108, 155.4327 27.37609, 154.7463 27.57165, 154.0335 27.64301, 153.313 27.58795, 152.6182 27.40701, 151.9845 27.11104, 151.4263 26.70809, 150.9626 26.21127, 150.6149 25.64024, 150.3982 25.01687, 150.3201 24.36335, 150.3832 23.70629, 150.5887 23.06189, 150.9212 22.47497, 151.3701 21.95784, 151.9132 21.53379, 152.5425 21.21128, 153.2231 21.00901, 153.9378 20.9339, 154.6506 20.99123, 155.3388 21.17824, 155.9651 21.48122, 156.5279 21.89973, 156.9886 22.40641, 157.3379 22.99043, 157.5586 23.63081), (153.9853 24.28086, 153.9836 24.29771, 153.9844 24.29771, 153.9853 24.28086))",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 160 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014543-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cmf39d
title: Occurrence Download

description: A dataset containing 4352 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025",
 "Geometry POLYGON ((157.5586 23.63081, 157.6376 24.28179, 157.5785 24.93409, 157.3827 25.56123, 157.0581 26.13588, 156.6104 26.64579, 156.0662 27.06108, 155.4327 27.37609, 154.7463 27.57165, 154.0335 27.64301, 153.313 27.58795, 152.6182 27.40701, 151.9845 27.11104, 151.4263 26.70809, 150.9626 26.21127, 150.6149 25.64024, 150.3982 25.01687, 150.3201 24.36335, 150.3832 23.70629, 150.5887 23.06189, 150.9212 22.47497, 151.3701 21.95784, 151.9132 21.53379, 152.5425 21.21128, 153.2231 21.00901, 153.9378 20.9339, 154.6506 20.99123, 155.3388 21.17824, 155.9651 21.48122, 156.5279 21.89973, 156.9886 22.40641, 157.3379 22.99043, 157.5586 23.63081), (153.9853 24.28086, 153.9836 24.29771, 153.9844 24.29771, 153.9853 24.28086))",
 "TaxonKey is Bacteria"
 ]
}

 The dataset includes 4352 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014544-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13076835
title: Palestine Dataset 2025
DOI: 10.5281/zenodo.17151846
title: FANTASIA V4 – LookUp Table – UniProt September 2025 – Experimental Evidence Code (Final & Intermediate Layers)

description: Release: UniProt September 2025System: Protein Information System (PIS v3.0.0)Compatibility: FANTASIA V4



📖 Overview

This PostgreSQL database backup uses the pgvector extension to store high-dimensional protein embeddings.It contains precomputed embeddings and functional annotations from the UniProt September 2025 release, restricted to entries with experimental evidence only.

The lookup table was generated with PIS v3.0.0 (Protein Information System), an integrated platform for automated extraction, processing, and management of protein-related data.PIS consolidates information from UniProt, PDB, and GOA, enabling efficient retrieval of sequences, structures, and annotations.

This release is designed for direct use with FANTASIA V4, an advanced pipeline for large-scale functional annotation using Protein Language Models (PLMs).Unlike previous releases, it includes both final and selected intermediate layers of embeddings, improving similarity searches and annotation transfer.

At runtime, FANTASIA:





Loads relevant embeddings into memory




Performs high-speed nearest-neighbor searches in embedding space




Transfers GO terms from experimentally annotated proteins to query sequences





📊 Dataset Details





Total proteins: 127,546




Total sequences: 124,397




Total embeddings: 3,729,510




Total GO annotations: 627,932




Proteins with experimental annotations: 127,546





🔬 Evidence Codes (GO – Experimental Only)





EXP – Inferred from Experiment




IDA – Inferred from Direct Assay




IPI – Inferred from Physical Interaction




IMP – Inferred from Mutant Phenotype




IGI – Inferred from Genetic Interaction




IEP – Inferred from Expression Pattern




TAS – Traceable Author Statement




IC – Inferred by Curator





🧩 Included Embedding Models

ESM-2 (650M, 34 layers: 0–33)

Layers: 0, 1, 2, 16, 17, 18

ESM3c (Cambrian 600M, 36 layers: 0–35)

Layers: 0, 1, 2, 17, 18, 19

Ankh3-Large (620M, 49 layers: 0–48)

Layers: 0, 1, 2, 23, 24, 25

ProtT5-XL-UniRef50 (~1.2B, 25 layers: 0–24)

Layers: 0, 1, 2, 11, 12, 13

ProstT5 (~1.2B, 25 layers: 0–24)

Layers: 0, 1, 2, 11, 12, 13



⚠️ Missing Proteins

A small subset of proteins could not be processed on Finisterrae III (CESGA) due to memory limitations with 40 GB A100 GPUs.





Affected UniProt IDs are listed in: missing_embeddings.csv




These entries are excluded from the final lookup table
DOI: 10.5281/zenodo.17151847
title: FANTASIA V4 – LookUp Table – UniProt September 2025 – Experimental Evidence Code (Final & Intermediate Layers)

description: Release: UniProt September 2025System: Protein Information System (PIS v3.0.0)Compatibility: FANTASIA V4



📖 Overview

This PostgreSQL database backup uses the pgvector extension to store high-dimensional protein embeddings.It contains precomputed embeddings and functional annotations from the UniProt September 2025 release, restricted to entries with experimental evidence only.

The lookup table was generated with PIS v3.0.0 (Protein Information System), an integrated platform for automated extraction, processing, and management of protein-related data.PIS consolidates information from UniProt, PDB, and GOA, enabling efficient retrieval of sequences, structures, and annotations.

This release is designed for direct use with FANTASIA V4, an advanced pipeline for large-scale functional annotation using Protein Language Models (PLMs).Unlike previous releases, it includes both final and selected intermediate layers of embeddings, improving similarity searches and annotation transfer.

At runtime, FANTASIA:





Loads relevant embeddings into memory




Performs high-speed nearest-neighbor searches in embedding space




Transfers GO terms from experimentally annotated proteins to query sequences





📊 Dataset Details





Total proteins: 127,546




Total sequences: 124,397




Total embeddings: 3,729,510




Total GO annotations: 627,932




Proteins with experimental annotations: 127,546





🔬 Evidence Codes (GO – Experimental Only)





EXP – Inferred from Experiment




IDA – Inferred from Direct Assay




IPI – Inferred from Physical Interaction




IMP – Inferred from Mutant Phenotype




IGI – Inferred from Genetic Interaction




IEP – Inferred from Expression Pattern




TAS – Traceable Author Statement




IC – Inferred by Curator





🧩 Included Embedding Models

ESM-2 (650M, 34 layers: 0–33)

Layers: 0, 1, 2, 16, 17, 18

ESM3c (Cambrian 600M, 36 layers: 0–35)

Layers: 0, 1, 2, 17, 18, 19

Ankh3-Large (620M, 49 layers: 0–48)

Layers: 0, 1, 2, 23, 24, 25

ProtT5-XL-UniRef50 (~1.2B, 25 layers: 0–24)

Layers: 0, 1, 2, 11, 12, 13

ProstT5 (~1.2B, 25 layers: 0–24)

Layers: 0, 1, 2, 11, 12, 13



⚠️ Missing Proteins

A small subset of proteins could not be processed on Finisterrae III (CESGA) due to memory limitations with 40 GB A100 GPUs.





Affected UniProt IDs are listed in: missing_embeddings.csv




These entries are excluded from the final lookup table
DOI: 10.15468/dl.dh32mb
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvia officinalis",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 27 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014546-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tzd9t5
title: Occurrence Download

description: A dataset containing 1096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvia officinalis",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1096 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014545-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m3e4ww
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "StateProvince is one of (青海, 西藏自治区, 甘肃省, 云南省, 四川省, 新疆维吾尔自治区)",
 "TaxonKey is Kobresia capillifolia"
 ]
}

 The dataset includes 94 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014547-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8x9bxn
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "IucnRedListCategory is LC",
 "OccurrenceStatus is Present",
 "TaxonKey is Elasmobranchii"
 ]
}

 The dataset includes 78 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014548-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9c86f3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Mormyrops oudoti)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014549-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eqd7qd
title: Occurrence Download

description: A dataset containing 868 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025",
 "Geometry POLYGON ((157.5586 23.63081, 157.6376 24.28179, 157.5785 24.93409, 157.3827 25.56123, 157.0581 26.13588, 156.6104 26.64579, 156.0662 27.06108, 155.4327 27.37609, 154.7463 27.57165, 154.0335 27.64301, 153.313 27.58795, 152.6182 27.40701, 151.9845 27.11104, 151.4263 26.70809, 150.9626 26.21127, 150.6149 25.64024, 150.3982 25.01687, 150.3201 24.36335, 150.3832 23.70629, 150.5887 23.06189, 150.9212 22.47497, 151.3701 21.95784, 151.9132 21.53379, 152.5425 21.21128, 153.2231 21.00901, 153.9378 20.9339, 154.6506 20.99123, 155.3388 21.17824, 155.9651 21.48122, 156.5279 21.89973, 156.9886 22.40641, 157.3379 22.99043, 157.5586 23.63081), (153.9853 24.28086, 153.9836 24.29771, 153.9844 24.29771, 153.9853 24.28086))",
 "TaxonKey is Chromista"
 ]
}

 The dataset includes 868 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014551-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.