cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30172468.v1
title: DSi_d30Si_ocim2_48L_fields.mat

description: MATLAB-readable output of a data-constrained model of the global ocean silicon cycle for analyses of DSi and d30Si along GEOTRACES section GP15 in the North Pacific. The names, sizes, and short descriptions of the fields are listed in the accompanying readme file. This model output supplements the publication:<br>Brzezinski, M.A., I. Closset, M. Holzer, J.L. Jones (2025),<br>The Silicon Isotopic Composition of the North Pacific: Insights from US GEOTRACES section GP15 and modelling, Global Biogeochem. Cycles, e2025GB008557, doi:10.1029/2025GB008557.
DOI: 10.15468/dl.nzj48f
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mirabilis nyctaginea",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000798-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vpg85z
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mirabilis nyctaginea",
 "Country is Moldova, Republic of",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000800-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ct2npy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mirabilis nyctaginea",
 "Country is Lithuania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000799-250920141307145/datasets/export for details.
DOI: 10.15468/dl.hxzuqm
title: Occurrence Download

description: A dataset containing 2755 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material citation, Material sample, Human Observation, Occurrence evidence)",
 "Country is one of (Mexico, United States of America, Jamaica, Cuba, Cayman Islands, Bahamas, Haiti, Belize)",
 "Geometry POLYGON((-97.49304 18.96873,-94.26015 18.00138,-93.19413 17.67556,-91.37936 16.8103,-90.60779 16.50472,-88.37095 15.68338,-87.83079 15.9296,-86.17992 15.96435,-85.43269 15.96435,-80.63787 15.55668,-80.15758 15.49115,-78.57511 15.72941,-75.79866 16.57525,-75.4487 17.58626,-74.87514 19.14166,-74.2141 19.7541,-73.7572 20.15267,-73.61138 20.5804,-73.99051 21.41642,-75.18622 21.91221,-76.29664 23.12572,-76.88031 23.20447,-77.61221 23.24153,-79.39561 24.70124,-79.91936 26.45954,-79.82791 27.03139,-80.9908 29.65906,-81.33929 31.4083,-86.59192 31.61695,-89.67324 30.7374,-92.25937 31.28644,-95.24917 30.86917,-96.06897 30.1855,-98.50273 28.90385,-98.16262 22.41339,-97.49304 18.96873))",
 "HasGeospatialIssue is false",
 "TaxonKey is Muricidae"
 ]
}

 The dataset includes 2755 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000801-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ahd9c
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mirabilis nyctaginea",
 "Country is Slovakia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000804-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sf94k4
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mirabilis nyctaginea",
 "Country is Romania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000803-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ywe8qd
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mirabilis nyctaginea",
 "Country is Poland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 40 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000802-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bm2ck4
title: Occurrence Download

description: A dataset containing 5817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-433.97685 4.46817,-433.99887 4.43028,-434.01603 4.38777,-433.99503 4.34833,-433.92538 4.35832,-433.8734 4.32682,-433.85931 4.33835,-433.88876 4.37548,-433.86315 4.38214,-433.88697 4.4167,-433.90028 4.45051,-433.92256 4.45614,-433.94689 4.46715,-433.97685 4.46817))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 5817 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000805-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9weg26
title: Occurrence Download

description: A dataset containing 479 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mirabilis nyctaginea",
 "Country is Ukraine",
 "HasCoordinate is true"
 ]
}

 The dataset includes 479 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000806-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17167842
title: FANTASIA V4 – LookUp Table – UniProt September 2025 – Experimental Evidence Code (Final Layer)

description: FANTASIA V4 – LookUp Table – UniProt September 2025 – Experimental Evidence Code (Layer 0 Only)

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, this dataset includes only layer 0 embeddings from each PLM, providing a compact reference table optimized for fast 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: 621,585 (last layer  for 5 models)




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)Layer: 0




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




Ankh3-Large (620M, 49 layers: 0–48)Layer: 0




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




ProstT5 (~1.2B, 25 layers: 0–24)Layer: 0





⚠️ 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.17167843
title: FANTASIA V4 – LookUp Table – UniProt September 2025 – Experimental Evidence Code (Final Layer)

description: FANTASIA V4 – LookUp Table – UniProt September 2025 – Experimental Evidence Code (Layer 0 Only)

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, this dataset includes only layer 0 embeddings from each PLM, providing a compact reference table optimized for fast 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: 621,585 (last layer  for 5 models)




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)Layer: 0




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




Ankh3-Large (620M, 49 layers: 0–48)Layer: 0




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




ProstT5 (~1.2B, 25 layers: 0–24)Layer: 0





⚠️ 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.k4e8yq
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Koenigia weyrichii",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000807-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bxyn77
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Koenigia weyrichii",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 50 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000808-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jjyzxa
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Koenigia weyrichii",
 "Country is Latvia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000809-250920141307145/datasets/export for details.
DOI: 10.15468/dl.z29cpy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Koenigia weyrichii",
 "Country is Lithuania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000810-250920141307145/datasets/export for details.
DOI: 10.15468/dl.3k39y4
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Koenigia weyrichii",
 "Country is Norway",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000811-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r2p36a
title: Occurrence Download

description: A dataset containing 528 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Koenigia weyrichii",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 528 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000812-250920141307145/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.30121735.v13
title: Logic 14 pdf NEW

description: Logic innovation
DOI: 10.15468/dl.6um4u2
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Koenigia weyrichii",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000815-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g332dz
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polygonum arenastrum",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000816-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u6cfp7
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polygonum arenastrum",
 "Country is Bulgaria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000817-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmem45
title: Occurrence Download

description: A dataset containing 411 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polygonum arenastrum",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 411 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000818-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9n9rxp
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polygonum arenastrum",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 82 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000820-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zgkfas
title: Occurrence Download

description: A dataset containing 1265 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polygonum arenastrum",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1265 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000821-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c4akx8
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polygonum arenastrum",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 65 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000819-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xttryw
title: Occurrence Download

description: A dataset containing 16492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polygonum arenastrum",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 16492 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000822-250920141307145/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.30172507
title: Supplementary data (BODIPY analysis, Histological scoring of liver, animal level data)

description: This dataset contains <b>experimental and histological data</b> from in vitro and in vivo models of metabolic dysfunction–associated fatty liver disease (MAFLD/NASH). It integrates quantitative cellular assays, morphometric image analysis, and animal histology scoring. The file is organized into <b>seven sheets</b>, each covering a distinct parameter:<b>Bodipy_TGF-AML12 model</b> – Quantitative analysis of lipid droplet accumulation in AML-12 cells exposed to TGF-β. Includes nuclei counts, droplet counts (≥0.5 µm²), droplet area, intensity (a.u.), and per-cell normalized values.<b>Bodipy_PA-AML12 model</b> – Similar Bodipy lipid droplet quantification but under palmitic acid–induced lipotoxicity. Provides droplet count, area, intensity, and per-cell normalization.<b>NAS_score + Steatosis</b> – Animal histology scoring of <b>steatosis (%) and NAS scores</b> across different treatment groups (control, MCD, MCD+THU, MCD+EW, MCD+EW+THU). Contains both raw individual data and averaged scores.<b>Lobular inflammation</b> – Quantification of inflammatory foci per field and corresponding NAS subscores for each animal across treatment groups.<b>Ballooning score</b> – Hepatocellular ballooning histology scores (0–2 scale) from control and MCD-based treatment groups.<b>Fibrosis area</b> – Percentage area of fibrosis from histological analysis, including raw individual values and averaged scores across conditions.<b>AST-ALT_Hepatic TG</b> – Biochemical markers, including hepatic triglyceride levels (mg/g liver) and liver injury enzymes (AST/ALT, depending on subsequent rows) across control and treated groups.
DOI: 10.6084/m9.figshare.30172507.v1
title: Supplementary data (BODIPY analysis, Histological scoring of liver, animal level data)

description: This dataset contains <b>experimental and histological data</b> from in vitro and in vivo models of metabolic dysfunction–associated fatty liver disease (MAFLD/NASH). It integrates quantitative cellular assays, morphometric image analysis, and animal histology scoring. The file is organized into <b>seven sheets</b>, each covering a distinct parameter:<b>Bodipy_TGF-AML12 model</b> – Quantitative analysis of lipid droplet accumulation in AML-12 cells exposed to TGF-β. Includes nuclei counts, droplet counts (≥0.5 µm²), droplet area, intensity (a.u.), and per-cell normalized values.<b>Bodipy_PA-AML12 model</b> – Similar Bodipy lipid droplet quantification but under palmitic acid–induced lipotoxicity. Provides droplet count, area, intensity, and per-cell normalization.<b>NAS_score + Steatosis</b> – Animal histology scoring of <b>steatosis (%) and NAS scores</b> across different treatment groups (control, MCD, MCD+THU, MCD+EW, MCD+EW+THU). Contains both raw individual data and averaged scores.<b>Lobular inflammation</b> – Quantification of inflammatory foci per field and corresponding NAS subscores for each animal across treatment groups.<b>Ballooning score</b> – Hepatocellular ballooning histology scores (0–2 scale) from control and MCD-based treatment groups.<b>Fibrosis area</b> – Percentage area of fibrosis from histological analysis, including raw individual values and averaged scores across conditions.<b>AST-ALT_Hepatic TG</b> – Biochemical markers, including hepatic triglyceride levels (mg/g liver) and liver injury enzymes (AST/ALT, depending on subsequent rows) across control and treated groups.
DOI: 10.15468/dl.atu5a6
title: Occurrence Download

description: A dataset containing 1107757 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Belgium, Germany, Netherlands)",
 "TaxonKey is one of (Ondatra zibethicus, Myocastor coypus)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1107757 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000813-250920141307145/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/13121277
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.st7zra
title: Occurrence Download

description: A dataset containing 394 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Reynoutria bohemica",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 394 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000824-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e5xg9t
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Reynoutria bohemica",
 "Country is Bulgaria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000825-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.