cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4257039
title: Nov2025 reference datasets for Mitohelper

description: Reference datasets (Nov 2025 update) for Mitohelper (https://github.com/aomlomics/mitohelper)



The MitoFish database underwent a major update since September 30th (UTC + 9) where duplicated records were combined into one entry. The Nov2025 version of Mitohelper's reference datasets was de-deduplicated based on updated records in the September 30th version of the MitoFish database.


Mitohelper is a repository built to facilitate experimental design, alignment visualization, and reference sequence analysis in fish eDNA studies. Refer to our paper and Mitohelper's wiki for database construction pipeline.

I. Reference database files in tab-separated format, containing gene, taxonomy, and sequence information:



mitofish.all.Nov.2025.tsv (558,313 de-duplicated records)

mitofish.12S.Mar2025.tsv (64,059 records of 12S rRNA gene >50 bp long)

mitofish.12S.Mar2025_NR.fasta (FASTA file of 12S rRNA gene records)

mitofish.COI.Mar2025.tsv (200,911 de-duplicated records)


II. De-replicated QIIME 2-compatible 12S/12S+16S+18S rRNA reference datasets:



12S-seqs-derep-uniq.qza

12S-tax-derep-uniq.qza

12S-16S-18S-seqs.qza

12S-16S-18S-tax.qza


If you use Mitohelper, please cite:Jean Lim, S, Thompson, LR. Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies. Environmental DNA. 2021; 00: 1– 10.  https://doi.org/10.1002/edn3.187
DOI: 10.5281/zenodo.17538550
title: Code and Datasets for MassNet: Database Search Workflows, Retention Time Prediction, and PSM Rescoring

description: This repository compiles the core resources used to construct the MassNet dataset, including:

1) FASTA sequence files for each species, used for database searching;

2) Standardized database search workflows based on FragPipe and Sage engines for unified processing of raw DDA-MS data and high-confidence peptide identification.

Additionally, the repository provides the following data resources and supporting tools for downstream AI tasks:

1) Retention time (RT) prediction task: training and validation datasets constructed from FragPipe and Sage results, along with corresponding RT prediction model outputs;

2) Peptide-spectrum match (PSM) rescoring task: PSM datasets for training and evaluation results;

Dataset construction tools: complete code and documentation for generating the above task-specific datasets.

For detailed model training procedures and usage instructions, please refer to the following official repositories:DeepLC: https://github.com/CompOmics/DeepLCDDA-BERT: https://github.com/guomics-lab/DDA-BERT

All resources provided in this repository enable full reproduction of the core experimental and analytical results reported in the manuscript "MassNet: billion-scale AI-ready mass spectrometry corpus enabling scalable deep Learning in proteomics".
DOI: 10.5281/zenodo.17538551
title: Code and Datasets for MassNet: Database Search Workflows, Retention Time Prediction, and PSM Rescoring

description: This repository compiles the core resources used to construct the MassNet dataset, including:

1) FASTA sequence files for each species, used for database searching;

2) Standardized database search workflows based on FragPipe and Sage engines for unified processing of raw DDA-MS data and high-confidence peptide identification.

Additionally, the repository provides the following data resources and supporting tools for downstream AI tasks:

1) Retention time (RT) prediction task: training and validation datasets constructed from FragPipe and Sage results, along with corresponding RT prediction model outputs;

2) Peptide-spectrum match (PSM) rescoring task: PSM datasets for training and evaluation results;

Dataset construction tools: complete code and documentation for generating the above task-specific datasets.

For detailed model training procedures and usage instructions, please refer to the following official repositories:DeepLC: https://github.com/CompOmics/DeepLCDDA-BERT: https://github.com/guomics-lab/DDA-BERT

All resources provided in this repository enable full reproduction of the core experimental and analytical results reported in the manuscript "MassNet: billion-scale AI-ready mass spectrometry corpus enabling scalable deep Learning in proteomics".
DOI: 10.15468/dl.rytpt9
title: Occurrence Download

description: A dataset containing 1002 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sceloporus melanorhinus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1002 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032344-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ch57x4
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Equus kiang",
 "Year 1990-2025"
 ]
}

 The dataset includes 132 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032347-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tk6jnu
title: Occurrence Download

description: A dataset containing 7043 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sceloporus merriami",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 7043 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032348-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rr6y59
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((135.15402 19.23919,117.07322 51.16312,103.2301 43.81778,92.21203 14.15397,121.31087 3.70107,135.15402 19.23919))",
 "TaxonKey is Zelkova schneideriana"
 ]
}

 The dataset includes 144 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032346-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xcqm7c
title: Occurrence Download

description: A dataset containing 1405 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sceloporus minor",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1405 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032349-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57783/d7vf-ch09
title: LibreChat-TEST
DOI: 10.15468/dl.bqx2rx
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-108.2688 21.59913, -108.1188 21.59913, -108.1188 21.74913, -108.2688 21.74913, -108.2688 21.59913))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032350-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7n6bxm
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Equus kiang",
 "Year 1990-2025"
 ]
}

 The dataset includes 132 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032352-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pf72ck
title: Occurrence Download

description: A dataset containing 2061 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sceloporus mucronatus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2061 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032351-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h4d69g
title: Occurrence Download

description: A dataset listing the 392 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Flora of Sumatra: Vascular plant collection of selected families deposited at Herbarium of Andalas University (ANDA)"
 ]
}

 The dataset's 392 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032342-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tdg5qx
title: Occurrence Download

description: A dataset containing 2437 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sceloporus nelsoni",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2437 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032353-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rjjn3k
title: Occurrence Download

description: A dataset containing 570 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Fossil)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tupaia belangeri"
 ]
}

 The dataset includes 570 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032354-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xxbswm
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-108.1188 21.59913, -107.9688 21.59913, -107.9688 21.74913, -108.1188 21.74913, -108.1188 21.59913))"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032355-251025141854904/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.30615905
title: Aggregated Data

description: This is the full data set used in my geography extended essay. It is the standardized version of the original data set and defines hospop as hospitals per person.
DOI: 10.6084/m9.figshare.30615905.v1
title: Aggregated Data

description: This is the full data set used in my geography extended essay. It is the standardized version of the original data set and defines hospop as hospitals per person.
DOI: 10.15468/dl.ak2nk8
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((140.80429 18.67409,101.53503 40.9926,78.65151 11.8938,96.44981 -28.22298,136.21621 -12.68473,140.80429 18.67409))",
 "TaxonKey is Oreocnide sylvatica"
 ]
}

 The dataset includes 17 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032356-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnr4n5
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Passiflora salpoensis"
 ]
}

 The dataset includes 17 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032357-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pnf356
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-107.9688 21.59913, -107.8188 21.59913, -107.8188 21.74913, -107.9688 21.74913, -107.9688 21.59913))"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032358-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pukmag
title: Occurrence Download

description: A dataset containing 1886 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((151.25725 34.49481,136.56655 41.27511,115.66066 44.66527,71.87122 31.38716,105.49021 -24.55034,144.75946 -8.16461,151.25725 34.49481))",
 "TaxonKey is Nekemias cantoniensis"
 ]
}

 The dataset includes 1886 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032359-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gtbpkd
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Megaphasma denticrus"
 ]
}

 The dataset's 2 records were derived from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032345-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.56gh4w
title: Occurrence Download

description: A dataset containing 5937 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Rhodopentas parvifolia, Scolopia theifolia, Scorodophloeus fischeri, Seddera hirsuta, Senecio moorei, Senna baccarinii, Senna longiracemosa, Sesamothamnus busseanus, Sesamothamnus rivae, Sesamum latifolium, Solanecio tuberosus, Solanum mauense, Solanum setaceum, Spathionema kilimandscharicum, Sphaeranthus bullatus, Spirostachys venenifera, Sterculia rhynchocarpa, Strophanthus mirabilis, Synaptolepis kirkii, Synaptolepis kirkii, Syzygium micklethwaitii, Tennantia sennii, Terminalia brevipes, Terminalia kilimandscharica, Terminalia orbicularis, Terminalia polycarpa, Terminalia spinosa, Thespesia danis, Thilachium thomasii, Tragia insuavis, Urochloa lachnantha, Urochloa rudis, Uvaria denhardtiana, Uvaria leptocladon, Uvaria scheffleri, Vachellia ancistroclada, Vachellia bussei, Vachellia elatior, Vachellia lahai, Vachellia paolii, Vahlia somalensis, Vepris uguenensis, Vernonia wakefieldii, Vitex strickeri, Volkensinia prostrata, Warburgia stuhlmannii, Wrightia demartiniana, Zanthoxylum usambarense, Ziziphus hamur)"
 ]
}

 The dataset includes 5937 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032361-251025141854904/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.28498139
title: Foliar fungal pathogens inhibit decomposition by increasing recalcitrant substances and secondary metabolites and reducing saprophytic fungi

description: The data and code for "Foliar fungal pathogens inhibit decomposition by increasing recalcitrant substances and secondary metabolites and reducing saprophytic fungi"
DOI: 10.6084/m9.figshare.28498139.v1
title: Foliar fungal pathogens inhibit decomposition by increasing recalcitrant substances and secondary metabolites and reducing saprophytic fungi

description: The data and code for "Foliar fungal pathogens inhibit decomposition by increasing recalcitrant substances and secondary metabolites and reducing saprophytic fungi"
DOI: 10.15468/dl.49n8nm
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-107.8188 21.59913, -107.6688 21.59913, -107.6688 21.74913, -107.8188 21.74913, -107.8188 21.59913))"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032362-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7pvkzs
title: Occurrence Download

description: A dataset containing 3559 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((154.08237 44.94777,122.44095 53.14063,67.63351 30.53964,87.12681 -11.27217,126.3961 -20.31257,145.60692 -0.81921,154.08237 44.94777))",
 "TaxonKey is Vitis flexuosa"
 ]
}

 The dataset includes 3559 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032363-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/2jfldy
title: Asiloid Flies: new taxa of Diptera: Apioceridae, Asilidae, and Mydidae

description: Taxon names of newly described species and genera of Apioceridae, Asilidae, and Mydidae
DOI: 10.5281/zenodo.17605416
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS251114d Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS251114d Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.5281/zenodo.17605417
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS251114d Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS251114d Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.15468/dl.3smc3j
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nasa weigendii"
 ]
}

 The dataset includes 13 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032364-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8a6xe7
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-107.6688 21.59913, -107.5188 21.59913, -107.5188 21.74913, -107.6688 21.74913, -107.6688 21.59913))"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032365-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v4ckvk
title: Occurrence Download

description: A dataset containing 8520 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Hyla eximia"
 ]
}

 The dataset includes 8520 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032366-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25919/7k27-9e97
title: NBDL Data Download
DOI: 10.15468/dl.vgr3f5
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-107.5188 21.59913, -107.3688 21.59913, -107.3688 21.74913, -107.5188 21.74913, -107.5188 21.59913))"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032367-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6pvddj
title: Occurrence Download

description: A dataset containing 83431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Allobates femoralis, Ambystoma mexicanum, Ameerega trivittata, Anomaloglossus beebei, Atelopus chiriquiensis, Atelopus limosus, Bolitoglossa pesrubra, Boophis occidentalis, Boophis tsilomaro, Cophixalus ornatus, Duttaphrynus melanostictus, Dyscophus antongilii, Dyscophus guineti, Eleutherodactylus coqui, Euphlyctis cyanophlyctis, Euphlyctis hexadactylus, Fejervarya cancrivora, Fejervarya limnocharis, Geotrypetes seraphini, Hemisus marmoratus, Hoplobatrachus tigerinus, Hylarana nigrovittata, Hyperolius castaneus, Hyperolius cinnamomeoventris, Hyperolius kivuensis, Hyperolius lateralis, Hyperolius nitidulus, Hyperolius viridiflavus, Limnonectes macrodon, Mantella baroni, Mantella betsileo, Mantella cowanii, Mantella crocea, Mantella laevigata, Melanophryniscus moreirae, Microhyla ornata, Nimbaphrynoides occidentalis, Odorrana swinhoana, Osteopilus septentrionalis, Phrynobatrachus guineensis, Polypedates maculatus, Pseudis platensis, Ranitomeya ventrimaculata, Rhinella diptycha, Rhinella diptycha, Rhinella ornata, Scaphiophryne gottlebei, Sclerophrys pentoni, Thoropa miliaris, Trachycephalus nigromaculatus, Tylototriton ziegleri, Agama gracilimembris, Anolis apletophallus, Anolis cupreus, Anolis gemmosus, Anolis gundlachi, Anolis limifrons, Anolis mariarum, Anolis nebulosus, Anolis polylepis, Anolis stratulus, Anolis tropidolepis, Trioceros hoehnelii, Lygodactylus capensis, Lygodactylus chobiensis, Loxopholis guianense, Micrablepharus atticolus, Conolophus subcristatus, Ichnotropis capensis, Meroles anchietae, Sceloporus bicanthalis, Sceloporus macdougalli, Sceloporus variabilis, Panaspis wahlbergii, Trachylepis varia, Gonatodes vittatus, Sphaerodactylus vincenti, Aspidoscelis rodecki, Cnemidophorus murinus, Holcosus quadrilineatus, Microlophus delanonis, Tropidurus torquatus, Opisthocomus hoazin, Centropus toulou, Laterallus ruber, Eudocimus ruber, Balaeniceps rex, Tyto glaucops, Strix fulvescens, Psitteuteles versicolor, Trichoglossus euteles, Neopelma aurifrons, Contopus pertinax, Cormobates placens, Xanthotis flaviventer, Ptilorrhoa caerulescens, Pachycephala lanioides, Corvus splendens, Fraseria cinerascens, Ploceus baglafecht, Neochmia phaeton)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Material sample, Material citation)"
 ]
}

 The dataset includes 83431 records from 307 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032360-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.