cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.tuf5mf
title: Occurrence Download

description: A dataset containing 196 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sisymbrium volgense",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 196 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011348-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2l85rt
title: CCDC 2391146: Experimental Crystal Structure Determination

description: Related Article: Yu-Qian Tang, Chu-Xing Liang, Hui Cui, Xiao Liang, Shu-Hua Qi|2026|Phytochemistry|241|114655|doi:10.1016/j.phytochem.2025.114655
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.hwbygz
title: Occurrence Download

description: A dataset containing 383568 species occurrences available in GBIF matching the query:
{
 "and" : [
 "MediaType is Image",
 "TaxonKey is one of (Lagopus lagopus, Ibidorhyncha struthersii, Larus hyperboreus, Larus delawarensis, Larus glaucoides, Larus schistisagus, Larus armenicus, Larus marinus, Larus fuscus, Larus glaucescens, Larus crassirostris, Irania gutturalis, Lanius bucephalus, Lanius nubicus, Lanius sphenocercus, Lanius isabellinus, Lanius senator, Lanius tigrinus, Lanius phoenicuroides, Larus smithsonianus, Lagopus muta, Lagopus muta nadezdae, Lagopus lagopus brevirostris, Lagopus lagopus maior, Ketupa blakistoni, Iduna rama, Iduna caligata, Iduna pallida, Larus vegae, Lanius excubitor homeyeri, Larus cachinnans cachinnans, Larus canus heinei, Larvivora sibilans, Lanius schach erythronotus, Junco hyemalis oreganus, Jynx torquilla torquilla, Larvivora cyane, Larvivora akahige, Lanius isabellinus isabellinus, Iduna pallida elaeica, Ichthyaetus melanocephalus, Ichthyaetus relictus, Lanius excubitor excubitor, Lanius borealis sibiricus, Lanius schach, Lanius borealis mollis, Larus glaucoides thayeri, Lanius borealis funereus)"
 ]
}

 The dataset includes 383568 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011225-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b2gh8d
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Schistura pridii)",
 "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/0011349-250914085247600/datasets/export for details.
DOI: 10.15468/dl.n9df46
title: Occurrence Download

description: A dataset containing 2761939 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-70.09784 -4.52932,-68.98453 -1.62952,-69.46858 -0.3228,-68.83931 -0.12918,-68.7425 0.98409,-67.8228 1.03249,-67.29035 0.16125,-66.22543 0.79049,-66.90311 3.20909,-67.87121 3.20909,-72.27608 3.54734,-76.19689 2.77404,-78.1331 0.64529,-76.10008 -0.12918,-73.4378 -2.5486,-70.6303 -2.69366,-71.21116 -4.19147,-70.09784 -4.52932))",
 "HasGeospatialIssue is false",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 2761939 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011300-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17101275
title: Biological Query and Pes2o Corpus Embedding Dataset

description: This dataset contains the query and pes2o embeddings associated with the paper "Exploring Distributed Vector Databases Performance on HPC Platforms: A Study with Qdrant", which was published in the SC'25 workshop Frontiers in Generative AI for HPC Science and Engineering: Foundations, Challenges, and Opportunities. All embeddings are generated using Qwen3-Embedding-4B.

Workload Description

Edited Excerpt from our TPC paper

 



We consider an end-to-end workflow that leverages vector databases to contextualize raw data records with information from papers, which is intended to be used in biological RAGs ... The target workload uses ... terms related to genomes available through BV-BRC ... Each term is used to generate a query that searches the papers contained within the pes2o dataset ... for data related to the term. The intuition is that searching across a collection of research papers allows us to find data directly related to the target term, thereby providing better context for the information that would be supplied to a RAG system.


The workload is exemplar and a prototype. Future work will further improve upon it.  

Queries

The queries are generated from a 22,723 term subset of the full BV-BRC dataset. 

 

The "queries.npz" file has two keys:



"data" - contains the raw embeddings.

"meta" - contains integers that refer to a line of text in "query_text.csv". Note that the integers are zero-indexed, meaning the corresponding line +1's text was used to generate that embedding.


"queries_v1.npz" contains the query embeddings used in the paper’s evaluation. "queries_v2.npz" contains the same queries, re-generated using the keyword argument prompt_name="query".

Text Corpus

We generate corpus embeddings from the full papers in the pes2o dataset, comprising 8,293,485 embeddings. A single embedding is produced for each paper.

 

The "corpus.npz" file has two keys:



"data" - contains the raw embeddings.

"meta" - contains the ID corresponding to an extracted version of a paper's text stored in a JSON file internally at Argonne. If possible, we will release a way to associate it with the source text in the future.


 

Prefered Citation

@misc{ockerman2025exploringdistributedvectordatabases,      title={Exploring Distributed Vector Databases Performance on HPC Platforms: A Study with Qdrant},       author={Seth Ockerman and Amal Gueroudji and Song Young Oh and Robert Underwood and Nicholas Chia and Kyle Chard and Robert Ross and Shivaram Venkataraman},      year={2025},      eprint={2509.12384},      archivePrefix={arXiv},      primaryClass={cs.DC},      url={https://arxiv.org/abs/2509.12384}, }
DOI: 10.5281/zenodo.17101276
title: Biological Query and Pes2o Corpus Embedding Dataset

description: This dataset contains the query and pes2o embeddings associated with the paper "Exploring Distributed Vector Databases Performance on HPC Platforms: A Study with Qdrant", which was published in the SC'25 workshop Frontiers in Generative AI for HPC Science and Engineering: Foundations, Challenges, and Opportunities. All embeddings are generated using Qwen3-Embedding-4B.

Workload Description

Edited Excerpt from our TPC paper

 



We consider an end-to-end workflow that leverages vector databases to contextualize raw data records with information from papers, which is intended to be used in biological RAGs ... The target workload uses ... terms related to genomes available through BV-BRC ... Each term is used to generate a query that searches the papers contained within the pes2o dataset ... for data related to the term. The intuition is that searching across a collection of research papers allows us to find data directly related to the target term, thereby providing better context for the information that would be supplied to a RAG system.


The workload is exemplar and a prototype. Future work will further improve upon it.  

Queries

The queries are generated from a 22,723 term subset of the full BV-BRC dataset. 

 

The "queries.npz" file has two keys:



"data" - contains the raw embeddings.

"meta" - contains integers that refer to a line of text in "query_text.csv". Note that the integers are zero-indexed, meaning the corresponding line +1's text was used to generate that embedding.


"queries_v1.npz" contains the query embeddings used in the paper’s evaluation. "queries_v2.npz" contains the same queries, re-generated using the keyword argument prompt_name="query".

Text Corpus

We generate corpus embeddings from the full papers in the pes2o dataset, comprising 8,293,485 embeddings. A single embedding is produced for each paper.

 

The "corpus.npz" file has two keys:



"data" - contains the raw embeddings.

"meta" - contains the ID corresponding to an extracted version of a paper's text stored in a JSON file internally at Argonne. If possible, we will release a way to associate it with the source text in the future.


 

Prefered Citation

@misc{ockerman2025exploringdistributedvectordatabases,      title={Exploring Distributed Vector Databases Performance on HPC Platforms: A Study with Qdrant},       author={Seth Ockerman and Amal Gueroudji and Song Young Oh and Robert Underwood and Nicholas Chia and Kyle Chard and Robert Ross and Shivaram Venkataraman},      year={2025},      eprint={2509.12384},      archivePrefix={arXiv},      primaryClass={cs.DC},      url={https://arxiv.org/abs/2509.12384}, }
DOI: 10.15468/dl.ufy78c
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lamelliconcha unicolor",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 17 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011350-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nuvqxh
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011351-250914085247600/datasets/export for details.
DOI: 10.6084/m9.figshare.30149191
title: Results from the PICs

description: These are the results from the PICs we ran on diversification rates and environmental variables for each species.
DOI: 10.6084/m9.figshare.30149191.v1
title: Results from the PICs

description: These are the results from the PICs we ran on diversification rates and environmental variables for each species.
DOI: 10.15468/dl.4q9rmg
title: Occurrence Download

description: A dataset containing 1492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chlorogomphus papilio, Heliogomphus retroflexus, Libellula angelina, Ophiogomphus spinicornis, Teinopalpus aureus, Luehdorfia chinensis, Bhutanitis mansfieldi, Sasakia funebris, Papilio elwesi, Troides aeacus)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((73.67 3.85,135.08 3.85,135.08 53.55,73.67 53.55,73.67 3.85))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1492 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011352-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/27221
title: Chandra X-ray Observatory ObsId 27221

description: Recurring AGN feedback in the galaxy group NEST 200047
DOI: 10.15468/dl.v7ja9z
title: Occurrence Download

description: A dataset containing 26135 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Acer saccharum"
 ]
 },
 "HasCoordinate is TRUE",
 "Year is greater than or equal to 2010",
 "Year is less than or equal to 2024",
 "DecimalLatitude is greater than or equal to 27.72628235976724",
 "DecimalLatitude is less than or equal to 56.95264697098938",
 "DecimalLongitude is greater than or equal to -90.41184314974709",
 "DecimalLongitude is less than or equal to -59.60830582776985",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 26135 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011353-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n2expr
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011354-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.57tw2z
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sisymbrium volgense",
 "Country is Lithuania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011355-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8kzmf4
title: Occurrence Download

description: A dataset containing 269 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Hyalinobatrachium tatayoi"
 ]
}

 The dataset includes 269 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011356-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qq6rz2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepidocardia floridella",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011357-250914085247600/datasets/export for details.
DOI: 10.15468/dl.da6bfd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sicyopterus lengguru)",
 "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/0011359-250914085247600/datasets/export for details.
DOI: 10.6084/m9.figshare.30149251
title: Melissodes spp. Trees

description: The 100 trees we used in our analyses.
DOI: 10.6084/m9.figshare.30149251.v1
title: Melissodes spp. Trees

description: The 100 trees we used in our analyses.
DOI: 10.15468/dl.wga3vv
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sisymbrium volgense",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 125 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011360-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5286/isis.e.rb2510645-1
title: Evolution of Water Dynamics in MOF-303 for Efficient Atmospheric Water Harvesting

description: Water scarcity poses a significant global challenge, and atmospheric water represents an abundant, untapped resource. Recent advancements in sorbent-assisted water harvesting systems have enabled the efficient extraction of potable water from arid environments. Metal–organic frameworks (MOFs), particularly MOF-303 (Al(OH)(PZDC)), exhibit remarkable potential as sorbents due to their high-water uptake capacity, rapid kinetics at low relative humidity, and exceptional stability. The aim of proposed study to investigate the dynamics of confined water within MOF-303 under various loadings using quasielastic neutron scattering.
DOI: 10.5286/isis.e.rb2510645
title: Evolution of Water Dynamics in MOF-303 for Efficient Atmospheric Water Harvesting

description: Water scarcity poses a significant global challenge, and atmospheric water represents an abundant, untapped resource. Recent advancements in sorbent-assisted water harvesting systems have enabled the efficient extraction of potable water from arid environments. Metal–organic frameworks (MOFs), particularly MOF-303 (Al(OH)(PZDC)), exhibit remarkable potential as sorbents due to their high-water uptake capacity, rapid kinetics at low relative humidity, and exceptional stability. The aim of proposed study to investigate the dynamics of confined water within MOF-303 under various loadings using quasielastic neutron scattering.
DOI: 10.5281/zenodo.17144249
title: Spontaneous spread of woody plant species in the urban parks of Ljubljana, Maribor and Zagreb

description: This Excel file contains all original datasets collected for the master’s thesis on spontaneous spread of woody plant species in the urban parks of Ljubljana, Maribor and Zagreb. The data include measurements and observations for individual species and locations, organized across multiple sheets, providing a comprehensive record of the research
DOI: 10.5281/zenodo.17144250
title: Spontaneous spread of woody plant species in the urban parks of Ljubljana, Maribor and Zagreb

description: This Excel file contains all original datasets collected for the master’s thesis on spontaneous spread of woody plant species in the urban parks of Ljubljana, Maribor and Zagreb. The data include measurements and observations for individual species and locations, organized across multiple sheets, providing a comprehensive record of the research
DOI: 10.15468/dl.gv72hj
title: Occurrence Download

description: A dataset containing 281 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantago rigida"
 ]
}

 The dataset includes 281 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011361-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aw9px2
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sisymbrium volgense",
 "Country is Poland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 64 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011362-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2qnvmk
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sisymbrium volgense",
 "Country is Ukraine",
 "HasCoordinate is true"
 ]
}

 The dataset includes 80 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011363-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nan8fm
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leukoma asperrima",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011364-250914085247600/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.30149242
title: Sup.Table 2A

description: Transcription factors were found in significant co-exprressed genes
DOI: 10.6084/m9.figshare.30149242.v1
title: Sup.Table 2A

description: Transcription factors were found in significant co-exprressed genes
DOI: 10.15468/dl.v3jrv2
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sisymbrium volgense",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 22 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011366-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.awbman
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hemiancistrus guahiborum)",
 "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 73 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011365-250914085247600/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.30149257
title: Melissodes coordinates and ranges.

description: These are the coordinates from gbif and the ranges calculated from them.
DOI: 10.6084/m9.figshare.30149257.v1
title: Melissodes coordinates and ranges.

description: These are the coordinates from gbif and the ranges calculated from them.
DOI: 10.15468/dl.3aumq5
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leukoma columbiensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 17 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011367-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.