cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.4nsjey
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Odontochilus nakaianus (F.Maek.) T.Yukawa",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 26 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198024-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e2644b
title: Occurrence Download

description: A dataset containing 1983 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "RecordedById is https://orcid.org/0000-0002-0735-9812"
 ]
}

 The dataset includes 1983 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0229012-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qehsm9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Papilionanthe teres (Roxb.) Schltr.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198028-220831081235567/datasets/export for details.
DOI: 10.15468/dl.6hqnqd
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Asarum wulingense C.F.Liang"
 ]
}

 The dataset includes 69 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0241936-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2yg9ze
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ceropria induta (Wiedemann, 1819)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 130 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198029-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3nkmsu
title: Occurrence Download

description: A dataset containing 1747 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Epomophorus gambianus (Ogilby, 1835)",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1990",
 "Year is less than or equal to 2022",
 "Continent is Africa"
 ]
}

 The dataset includes 1747 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0229000-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ca3hvf
title: Occurrence Download

description: A dataset containing 239 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gamochaeta purpurea (L.) Cabrera",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 239 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192058-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ckguz
title: Occurrence Download

description: A dataset containing 99573 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-6.32292 37.71655,-6.66176 36.45196,-5.74206 35.89516,-4.73765 36.00292,-3.98737 36.60755,-3.84216 37.25564,-4.56823 37.75484,-6.32292 37.71655))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 99573 records from 128 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036383-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pb3xy5
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Byctiscus fausti Sharp, 1889",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 49 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198035-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qexfyj
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Protaetia pryeri (Janson, 1888)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 23 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192074-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnycgv
title: Occurrence Download

description: A dataset containing 1759928 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "StateProvince is one of (valle del cauca)"
 ]
}

 The dataset includes 1759928 records from 648 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0229014-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ejernx
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Cygnus olor)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 124 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045167-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gjb2yb
title: Occurrence Download

description: A dataset containing 4405 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Cygnus olor)",
 "Country is one of (American Samoa, Australia, Christmas Island, Cocos (Keeling) Islands, Cook Islands, Fiji, French Polynesia, Guam, Heard Island and McDonald Islands, Kiribati, Marshall Islands, Micronesia (Federated States of), Nauru, New Caledonia, New Zealand, Niue, Norfolk Island, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn, Samoa, Solomon Islands, Tokelau, Tonga, Tuvalu, United States Minor Outlying Islands, Vanuatu, Wallis and Futuna)"
 ]
}

 The dataset includes 4405 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045165-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60893/figshare.apl.29538095
title: Revise supp

description: revision supplementary file
DOI: 10.60893/figshare.apl.29538095.v1
title: Revise supp

description: revision supplementary file
DOI: 10.15468/dl.2vgk99
title: Occurrence Download

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

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045168-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8pbeb8
title: Occurrence Download

description: A dataset containing 866953 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 866953 records from 129 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045136-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3wmxn2
title: Occurrence Download

description: A dataset containing 181885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Belgium",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (CR, EN, VU, EX, EW)",
 "OccurrenceStatus is Present",
 "PublishingCountry is Belgium",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 181885 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045134-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jgpw2c
title: Occurrence Download

description: A dataset containing 287 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Psathyrostachys juncea",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 287 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045173-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/79pcck
title: Replication Data for: "Undeserving Heirs: How the Origins of Wealth Shape Attitudes Towards Redistribution"

description: This package contains produces all code and data to reproduce the results contained in ‘Undeserving Heirs: How the Origins of Wealth Shape Attitudes Towards Redistribution’. Tables and figures are also saved to the folder ‘output’.
DOI: 10.15468/dl.83wf56
title: Occurrence Download

description: A dataset containing 1092 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bassia scoparia",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1092 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045177-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g7mk2f
title: Occurrence Download

description: A dataset containing 292 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myotis blythii",
 "MediaType is Image"
 ]
}

 The dataset includes 292 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045175-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7jgqdk
title: Occurrence Download

description: A dataset containing 183 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bassia scoparia",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 183 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045176-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w285nw
title: Occurrence Download

description: A dataset containing 1992 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fallopia japonica",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1992 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045174-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gpr5aw
title: Occurrence Download

description: A dataset containing 70282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Belgium",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 70282 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045142-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jpu7d5
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myotis brandtii",
 "MediaType is Image"
 ]
}

 The dataset includes 135 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045179-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h7cugn
title: Occurrence Download

description: A dataset containing 638 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Evermannella balbo"
 ]
}

 The dataset includes 638 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045178-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c5d9fj
title: Occurrence Download

description: A dataset containing 179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudosasa japonica",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 179 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045182-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c5qx6q
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Callinectes sapidus",
 "Country is Bahamas",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045183-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dqnhb7
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Priocharax ariel)",
 "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 46 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045180-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rntftq
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bassia scoparia",
 "Country is Greece",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045181-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16419266
title: Dataset from:An Evaluation of Large Language Models in Bioinformatics Research

description: This repository contains the data and code to reproduce the results of our paper: An Evaluation of Large Language Models in Bioinformatics Research

 Authors: Hengchuang Yin; Lun Hu

 

Abstract: Large language models, such as the GPT series, have revolutionized natural language processing by demonstrating strong capabilities in text generation and reasoning. However, their potential in the field of bioinformatics, characterized by complex biological data and specialized knowledge, has not been fully evaluated. In this study, we systematically assess the performance of multiple advanced and widely used LLMs on six diverse bioinformatics tasks: drug-drug interaction prediction, antimicrobial and anticancer peptide identification, molecular optimization, gene and protein named entity recognition, single-cell type annotation, and bioinformatics problem solving.Our experimental results demonstrate that, with appropriate prompt design and limited task-specific fine-tuning, general-purpose LLMs can achieve competitive or even superior performance compared to traditional models that require extensive computational resources and technical design across various tasks. Our analysis further uncovers the current limitations of LLMs in handling structurally complex and knowledge-intensive bioinformatics problems. Overall, this study demonstrates the broad prospects of LLMs in bioinformatics while emphasizing their limitations, providing valuable insights for future research at the intersection of LLMs and bioinformatics.

 

 

 

 

 

 

Section_A_ddi:

ddinter_positive_samples.csv: Positive drug–drug interaction (DDI) pairs curated from the DDInter database.

ddinter_negative_samples.csv: Negative drug–drug interaction (DDI) pairs (no known interactions), used for supervised classification.

drug_description_embeddings_all-mpnet-base-v2.npy: Drug description embeddings generated using the all-mpnet-base-v2 model.

drug_description_embeddings_bge-large-en-v1.5.npy: Drug description embeddings generated using the bge-large-en-v1.5 model.

drug_description_embeddings_e5-small-v2.npy: Drug description embeddings generated using the e5-small-v2 model.

drug_description_embeddings_gtr-t5-large.npy: Drug description embeddings generated using the gtr-t5-large model.

drug_description_embeddings_text_embedding_3_large.npy: Drug description embeddings generated using OpenAI's text-embedding-3-large model.

drug_description_embeddings_text_embedding_3_small.npy: Drug description embeddings generated using OpenAI's text-embedding-3-small model.

drug_description_embeddings_text_embedding_ada_002.npy: Drug description embeddings generated using OpenAI's text-embedding-ada-002 model.

 

 

 

 

 

 

We hereby confirm that the dataset associated with the research described in this work is made available to the public under the Creative Commons Zero (CC0) license.

 

 

Contact 

If you have any questions, please don't hesitate to ask me: yinhengchuang@ms.xjb.ac.cn or hulun@ms.xjb.ac.cn
DOI: 10.15468/dl.mjf8b8
title: Occurrence Download

description: A dataset containing 80233 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Motacilla flava",
 "MediaType is Image"
 ]
}

 The dataset includes 80233 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045145-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.82261/anpg-qk88
title: World Historical Gazetteer
title: WHG
DOI: 10.15468/dl.b9kd3e
title: Occurrence Download

description: A dataset containing 11002 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Dataset of Phenology of flora of mediterranean high-mountains meadows (Sierra Nevada)"
 ]
}

 The dataset includes 11002 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045184-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b4gaqf
title: Occurrence Download

description: A dataset containing 1108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myotis myotis",
 "MediaType is Image"
 ]
}

 The dataset includes 1108 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045185-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wyqgag
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045187-250717081556266/datasets/export for details.
DOI: 10.15468/dl.8anhrb
title: Occurrence Download

description: A dataset containing 223 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Impatiens glandulifera",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 223 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045189-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.crj3ss
title: Occurrence Download

description: A dataset containing 12708 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Impatiens glandulifera",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12708 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045188-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.