cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.h6yu4x
title: Occurrence Download

description: A dataset containing 29705 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cicadella viridis (Linnaeus, 1758)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 29705 records from 499 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021432-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e9mju2
title: Occurrence Download

description: A dataset containing 3673 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 Gilia tricolor Benth."
 ]
}

 The dataset includes 3673 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021433-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jdj4vb
title: Occurrence Download

description: A dataset containing 5435 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 Gypsophila paniculata L."
 ]
}

 The dataset includes 5435 records from 267 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021434-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ehe3ms
title: Occurrence Download

description: A dataset containing 885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acacia decurrens Willd., Acacia mearnsii De Wild., Acacia pycnantha Benth., Acacia saligna (Labill.) H.L.Wendl., Mimosa distachya Cav., Acanthus mollis L., Aegilops triuncialis L., Ailanthus altissima (Mill.) Swingle, Alnus glutinosa (L.) Gaertn., Arundo donax L., Asparagus officinalis L., Asparagus setaceus (Kunth) Jessop, Bassia scoparia (L.) A.J.Scott, Brassica tournefortii Gouan, Bromus rubens L., Butomus umbellatus L., Cardamine flexuosa With., Centaurea melitensis L., Centaurea solstitialis L., Clematis vitalba L., Cotula coronopifolia L., Erodium cicutarium (L.) L'Hér., Angophora exul K.D.Hill, Eupatorium cannabinum L., Frangula alnus Mill., Genista monspessulana (L.) L.A.S.Johnson, Hedera helix L., Hypericum perforatum L., Imperata cylindrica (L.) Raeusch., Iris pseudacorus L., Lepidium latifolium L., Lotus corniculatus L., Luzula campestris (L.) DC., Lythrum salicaria L., Miconia calvescens DC., Panicum repens L., Phalaris arundinacea L., Pinus pinaster Aiton, Populus alba L., Psidium guajava L., Ranunculus ficaria Walter, 1788, Rhamnus alaternus L., Rhamnus cathartica L., Ricinus communis L., Rumex obtusifolius L., Sagina procumbens L., Salsola tragus L., Senecio vulgaris L., Tamarix aphylla (L.) H.Karst., Taxodium distichum (L.) Rich., Trapa natans L., Triadica sebifera (L.) Small, Trifolium repens L., Tussilago farfara L., Typha latifolia L., Veronica serpyllifolia L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Country is one of (Algeria)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 885 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021435-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7mh8dp
title: Occurrence Download

description: A dataset containing 4267 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lampornis sybillae (Salvin & Godman, 1892)"
 ]
}

 The dataset includes 4267 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021436-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jcpgbe
title: Occurrence Download

description: A dataset containing 18312 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lampornis viridipallens (Bourcier & Mulsant, 1846)"
 ]
}

 The dataset includes 18312 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021437-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s6mm2q
title: Occurrence Download

description: A dataset containing 312 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lophornis pavoninus Salvin & Godman, 1882"
 ]
}

 The dataset includes 312 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021438-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zv46gh
title: Occurrence Download

description: A dataset containing 2022 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 Helenium bigelovii A.Gray"
 ]
}

 The dataset includes 2022 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021439-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14787834
title: Learning the Rules of Peptide Self-assembly through Data Mining with Large Language Models

description: Peptides are biologically ubiquitous and important molecules that self-assemble into diverse structures. While extensive research has explored the effects of chemical composition and environmental conditions on self-assembly, a systematic study consolidating this data to uncover global rules is lacking. In this work, we curate a peptide assembly database through a combination of manual processing by human experts and literature mining with a large language model. As a result, we collect more than 1,000 experimental data entries with information about peptide sequence, experimental conditions and corresponding self-assembly phases. Utilizing the data, machine learning models are trained and evaluated, demonstrating excellent accuracy (> 80%) and efficiency in assembly phase classification. Moreover, we fine-tune our GPT model for peptide literature mining with the developed dataset, which exhibits markedly superior performance in extracting information from academic publications relative to the pre-trained model. This workflow can improve efficiency when exploring potential self-assembling peptide candidates, through guiding experimental work, while also deepening our understanding of the mechanisms governing peptide self-assembly.

 

--- phase_data_clean.csv stores 1000+ peptide self-assembly data under different experimental conditions.

---mined_paper_list.csv stores the corresponding papers we used to collect data.

--- trainset.jsonl and testset.jsonl are data we used for fine-tuning the LLM. 

--- fine-tuning.ipynb: code used to fine-tune ChatGPT model. 

--- pretrain.ipynb: code used to test the pretrained ChatGPT model.

--- train_and_inference.ipynb: code to use mined data to train and test a ML predictor for phase classification.
DOI: 10.5281/zenodo.14787835
title: Learning the Rules of Peptide Self-assembly through Data Mining with Large Language Models

description: Peptides are biologically ubiquitous and important molecules that self-assemble into diverse structures. While extensive research has explored the effects of chemical composition and environmental conditions on self-assembly, a systematic study consolidating this data to uncover global rules is lacking. In this work, we curate a peptide assembly database through a combination of manual processing by human experts and literature mining with a large language model. As a result, we collect more than 1,000 experimental data entries with information about peptide sequence, experimental conditions and corresponding self-assembly phases. Utilizing the data, machine learning models are trained and evaluated, demonstrating excellent accuracy (> 80%) and efficiency in assembly phase classification. Moreover, we fine-tune our GPT model for peptide literature mining with the developed dataset, which exhibits markedly superior performance in extracting information from academic publications relative to the pre-trained model. This workflow can improve efficiency when exploring potential self-assembling peptide candidates, through guiding experimental work, while also deepening our understanding of the mechanisms governing peptide self-assembly.

 

--- phase_data_clean.csv stores 1000+ peptide self-assembly data under different experimental conditions.

--- trainset.jsonl and testset.jsonl are data we used for fine-tuning the LLM.
DOI: 10.5281/zenodo.14791268
title: Learning the Rules of Peptide Self-assembly through Data Mining with Large Language Models

description: Peptides are biologically ubiquitous and important molecules that self-assemble into diverse structures. While extensive research has explored the effects of chemical composition and environmental conditions on self-assembly, a systematic study consolidating this data to uncover global rules is lacking. In this work, we curate a peptide assembly database through a combination of manual processing by human experts and literature mining with a large language model. As a result, we collect more than 1,000 experimental data entries with information about peptide sequence, experimental conditions and corresponding self-assembly phases. Utilizing the data, machine learning models are trained and evaluated, demonstrating excellent accuracy (> 80%) and efficiency in assembly phase classification. Moreover, we fine-tune our GPT model for peptide literature mining with the developed dataset, which exhibits markedly superior performance in extracting information from academic publications relative to the pre-trained model. This workflow can improve efficiency when exploring potential self-assembling peptide candidates, through guiding experimental work, while also deepening our understanding of the mechanisms governing peptide self-assembly.

 

--- phase_data_clean.csv stores 1000+ peptide self-assembly data under different experimental conditions.

--- trainset.jsonl and testset.jsonl are data we used for fine-tuning the LLM. 

--- fine-tuning.ipynb: code used to fine-tune ChatGPT model. 

--- pretrain.ipynb: code used to test the pretrained ChatGPT model.

--- train_and_inference.ipynb: code to use mined data to train and test a ML predictor for phase classification.
DOI: 10.5281/zenodo.15066962
title: Learning the Rules of Peptide Self-assembly through Data Mining with Large Language Models

description: Peptides are biologically ubiquitous and important molecules that self-assemble into diverse structures. While extensive research has explored the effects of chemical composition and environmental conditions on self-assembly, a systematic study consolidating this data to uncover global rules is lacking. In this work, we curate a peptide assembly database through a combination of manual processing by human experts and literature mining with a large language model. As a result, we collect more than 1,000 experimental data entries with information about peptide sequence, experimental conditions and corresponding self-assembly phases. Utilizing the data, machine learning models are trained and evaluated, demonstrating excellent accuracy (> 80%) and efficiency in assembly phase classification. Moreover, we fine-tune our GPT model for peptide literature mining with the developed dataset, which exhibits markedly superior performance in extracting information from academic publications relative to the pre-trained model. This workflow can improve efficiency when exploring potential self-assembling peptide candidates, through guiding experimental work, while also deepening our understanding of the mechanisms governing peptide self-assembly.

 

--- phase_data_clean.csv stores 1000+ peptide self-assembly data under different experimental conditions.

---mined_paper_list.csv stores the corresponding papers we used to collect data.

--- trainset.jsonl and testset.jsonl are data we used for fine-tuning the LLM. 

--- fine-tuning.ipynb: code used to fine-tune ChatGPT model. 

--- pretrain.ipynb: code used to test the pretrained ChatGPT model.

--- train_and_inference.ipynb: code to use mined data to train and test a ML predictor for phase classification.
DOI: 10.15468/dl.ac2nd3
title: Occurrence Download

description: A dataset containing 692 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cicadula persimilis (Edwards, 1920)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 692 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021440-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2f3xyp
title: Occurrence Download

description: A dataset containing 5266 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 Helianthus debilis Nutt."
 ]
}

 The dataset includes 5266 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021442-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rxep8c
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Month is one of (January, February)",
 "OccurrenceStatus is Present",
 "TaxonKey is Netta peposaca (Vieillot, 1816)",
 "Year 2010-2010"
 ]
}

 The dataset includes 61 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021445-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.thjmvj
title: Occurrence Download

description: A dataset containing 212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Month is one of (March, April, May, June, July, August, September, October, November, December)",
 "OccurrenceStatus is Present",
 "TaxonKey is Netta peposaca (Vieillot, 1816)",
 "Year 2010-2010"
 ]
}

 The dataset includes 212 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021443-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kcr8tx
title: Occurrence Download

description: A dataset containing 310 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aralia merrillii C.B.Shang, Ageratina adenophora (Spreng.) R.M.King & H.Rob., Ageratum conyzoides L., Bidens pilosa L., Calotropis gigantea (L.) W.T.Aiton, Cardiospermum grandiflorum Sw., Cecropia peltata L., Cenchrus ciliaris L., Chromolaena odorata (L.) R.M.King & H.Rob., Cyperus rotundus L., Eucalyptus camaldulensis Denham, Galinsoga parviflora Cav., Inga vera Willd., Ipomoea purpurea (L.) Roth, Lantana camara L., Launaea intybacea (Jacq.) Beauverd, Leucaena leucocephala (Lam.) de Wit, Lygodium microphyllum (Cav.) R.Br., Miconia calvescens DC., Montia fontana L., Opuntia stricta (Haw.) Haw., Panicum repens L., Paspalum scrobiculatum L., Microsorum scolopendria (Burm.fil.) Copel., Pittosporum viridiflorum Sims, Pontederia crassipes Mart., Rhizophora mangle L., Ricinus communis L., Rottboellia cochinchinensis (Lour.) Clayton, Senna siamea (Lam.) H.S.Irwin & Barneby, Sida rhombifolia L., Solanum mauritianum Scop., Tagetes minuta L., Tecomaria capensis (Thunb.) Spach, Tithonia diversifolia (Hemsl.) A.Gray, Trapa natans L., Tridax procumbens L., Vachellia drepanolobium (Harms ex Y.Sjöstedt) P.J.H.Hurter)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Country is one of (Angola)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 310 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021444-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.et9y4r
title: Occurrence Download

description: A dataset containing 17011 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Unknown evidence",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Machine Observation"
 ]
 },
 "TaxonKey is Proechimys J.A.Allen, 1899"
 ]
}

 The dataset includes 17011 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0143209-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sg9xq6
title: Occurrence Download

description: A dataset containing 1654 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saxifraga bulbifera L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1654 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082469-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.axo45u
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is South Australian Museum Adelaide provider for OZCAM",
 "TaxonKey is Cleidopus gloriamaris De Vis, 1882"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044749-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.txeprx
title: Occurrence Download

description: A dataset containing 1513 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Smilax spinosa Mill."
 ]
}

 The dataset includes 1513 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0143197-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tmlitr
title: Occurrence Download

description: A dataset containing 335 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cercopithecus neglectus Schlegel, 1876"
 ]
}

 The dataset includes 335 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044750-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ujwsst
title: Occurrence Download

description: A dataset containing 342595 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Odonata Central"
 ]
}

 The dataset includes 342595 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005231-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.senedc
title: Occurrence Download

description: A dataset containing 7544 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cerinthe minor L."
 ]
}

 The dataset includes 7544 records from 148 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140109-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bx2qtu
title: Occurrence Download

description: A dataset containing 4036 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rosa laevigata Michx."
 ]
}

 The dataset includes 4036 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082456-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tqkty1
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is The Pisces Collection at the Zoologische Staatssammlung München",
 "TaxonKey is Cleidopus gloriamaris De Vis, 1882"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044752-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vcauem
title: Occurrence Download

description: A dataset containing 138940 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Populus alba L."
 ]
}

 The dataset includes 138940 records from 1280 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082448-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yvat4y
title: Occurrence Download

description: A dataset containing 2311 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dromiciops gliroides Thomas, 1894"
 ]
}

 The dataset includes 2311 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047032-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ddfv94
title: Occurrence Download

description: A dataset containing 388 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phidippus apacheanus Chamberlin & Gertsch, 1929"
 ]
}

 The dataset includes 388 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0323830-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.