cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14983178
title: Phenotype Driven Data Augmentation Methods for Transcriptomic Data

description: This repository contains the data and associated results of all experiments conducted in our work "Phenotype Driven Data Augmentation Methods for Transcriptomic Data". In this work, we introduce two classes of phenotype driven data augmentation approaches – signature-dependent and signature-independent. The signature-dependent methods assume the existence of distinct gene signatures describing some phenotype and are simple, non-parametric, and novel data augmentation methods. The signature-independent methods are a modification of the established Gamma-Poisson and Poisson sampling methods for gene expression data. We benchmark our proposed methods against random oversampling, SMOTE, unmodified versions of Gamma-Poisson and Poisson sampling, and unaugmented data.  

This repository contains data used for all our experiments. This includes the original data based off which augmentation was performed, the cross validation split indices as a json file, the training and validation data augmented by the various augmentation methods mentioned in our study, a test set (containing only real samples) and an external test set standardised accordingly with respect to each augmentation method and training data per CV split. 

The compressed files 5x5stratified_{x}percent.zip contains data that were augmented on x% of the available real data. brca_public.zip contains data used for the breast cancer experiments. distribution_size_effect.zip contains data used for hyperparameter tuning the reference set size for the modified Poisson and Gamma-Poisson methods. 

The compressed file results.zip contains all the results from all the experiments. This includes the parameter files used to train the various models, the metrics (balanced accuracy and auc-roc) computed including p-values, as well as the latent space of train, validation and test (for the (N)VAE) for all 25 (5x5) CV splits.

PLEASE NOTE: If any part of this repository is used in any form for your work, please attribute the following, in addition to attributing the original data source  - TCGA, CPTAC, GSE20713 and METABRIC, accordingly:

@article{janakarajan2025phenotype,  title={Phenotype driven data augmentation methods for transcriptomic data},  author={Janakarajan, Nikita and Graziani, Mara and Rodr{\'\i}guez Mart{\'\i}nez, Mar{\'\i}a},  journal={Bioinformatics Advances},  volume={5},  number={1},  pages={vbaf124},  year={2025},  publisher={Oxford University Press}}
DOI: 10.5281/zenodo.8383202
title: Phenotype Driven Data Augmentation Methods for Transcriptomic Data

description: This repository contains the data and associated results of all experiments conducted in our work "Phenotype Driven Data Augmentation Methods for Transcriptomic Data". In this work, we introduce two classes of phenotype driven data augmentation approaches – signature-dependent and signature-independent. The signature-dependent methods assume the existence of distinct gene signatures describing some phenotype and are simple, non-parametric, and novel data augmentation methods. The signature-independent methods are a modification of the established Gamma-Poisson and Poisson sampling methods for gene expression data. We benchmark our proposed methods against random oversampling, SMOTE, unmodified versions of Gamma-Poisson and Poisson sampling, and unaugmented data.  

This repository contains data used for all our experiments. This includes the original data based off which augmentation was performed, the cross validation split indices as a json file, the training and validation data augmented by the various augmentation methods mentioned in our study, a test set (containing only real samples) and an external test set standardised accordingly with respect to each augmentation method and training data per CV split. 

The compressed files 5x5stratified_{x}percent.zip contains data that were augmented on x% of the available real data. brca_public.zip contains data used for the breast cancer experiments. distribution_size_effect.zip contains data used for hyperparameter tuning the reference set size for the modified Poisson and Gamma-Poisson methods. 

The compressed file results.zip contains all the results from all the experiments. This includes the parameter files used to train the various models, the metrics (balanced accuracy and auc-roc) computed including p-values, as well as the latent space of train, validation and test (for the (N)VAE) for all 25 (5x5) CV splits.

PLEASE NOTE: If any part of this repository is used in any form for your work, please attribute the following, in addition to attributing the original data source  - TCGA, CPTAC, GSE20713 and METABRIC, accordingly:

@article{janakarajan2025phenotype,  title={Phenotype driven data augmentation methods for transcriptomic data},  author={Janakarajan, Nikita and Graziani, Mara and Rodr{\'\i}guez Mart{\'\i}nez, Mar{\'\i}a},  journal={Bioinformatics Advances},  volume={5},  number={1},  pages={vbaf124},  year={2025},  publisher={Oxford University Press}}
DOI: 10.15468/dl.75aprd
title: Occurrence Download

description: A dataset containing 4413 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'NE'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence."year" &gt;= 2000 AND occurrence."year" &lt;= 2025)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 4413 records were derived from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036075-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tz4c4n
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sclerophrys pusilla (Mertens, 1937)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((32.064 -28.9416,32.4847 -28.5786,30.5701 -28.5786,30.5701 -30.7329,30.6252 -30.6659,31.4179 -29.4257,31.8178 -29.0299,32.064 -28.9416))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036091-250525065834625/datasets/export for details.
DOI: 10.15468/dl.hhrr85
title: Occurrence Download

description: A dataset containing 2246 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "Geometry POLYGON((6.48919 51.17337,7.20578 51.1792,7.20783 51.18056,7.19951 51.52649,7.19776 51.55505,6.48478 51.55568,6.48919 51.17337))",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Vulpes vulpes (Linnaeus, 1758), Capreolus capreolus (Linnaeus, 1758), Pipistrellus pipistrellus (Schreber, 1774))"
 ]
}

 The dataset includes 2246 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036092-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nc9t8m
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((9.43631 46.92653,9.28074 46.71129,9.43465 46.52664,9.80754 46.45366,10.02777 46.55778,10.049 46.78415,9.8578 46.96318,9.43631 46.92653))",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Passer domesticus (Linnaeus, 1758), Capra ibex Linnaeus, 1758, Podarcis muralis (Laurenti, 1768))"
 ]
}

 The dataset includes 163 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036093-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/j3qk-s378
title: "Exploited Security Vulnerabilities (2014 to 2022)"

description: "The dataset is sourced from the CISA Known Exploited Vulnerabilities (KEV) catalog, documents security vulnerabilities that were actively exploited in during the period 2014 and 2022. The dataset comprises of 629 records, capturing detailed information on software supply chain vulnerabilities. Each entry includes a unique CVE identifier (cve_id), the vendor or project affected, the product name, and a description of the vulnerability. Our vulnerability dataset is rich with 16 columns of information. For each vulnerability, we capture critical timelines (date added, publication date, action due date) and detailed severity insights through CVSS scores, attack vectors, complexity, and overall severity ratings. Complementary data includes CWE codes, recommended remediation steps, the impacted cloud component (e.g., IaaS), and the specific vulnerability type (e.g., \"Network,\" \"Data\"). Fifteen columns are categorical or textual, with the sole exception of the numerical CVSS score."
DOI: 10.26188/29276009
title: Datasets of zebrafish larvae poses - annotated frames and videos

description: These are three datasets of videos and annotated frames of zebrafish larvae poses. The datasets are named "Main", "Benchmarking" and "Additional". The main dataset contains 1641 annotated frames, from 28 videos and their metadata. The benchmarking datasets are two sets of data. Finally, the additional dataset has 512 frames selected from 12 different videos. The annotations were done using DeepLabCut/napari annotator and are in the DLC project format.
DOI: 10.26188/29276009.v1
title: Datasets of zebrafish larvae poses - annotated frames and videos

description: These are three datasets of videos and annotated frames of zebrafish larvae poses. The datasets are named "Main", "Benchmarking" and "Additional". The main dataset contains 1641 annotated frames, from 28 videos and their metadata. The benchmarking datasets are two sets of data. Finally, the additional dataset has 512 frames selected from 12 different videos. The annotations were done using DeepLabCut/napari annotator and are in the DLC project format.
DOI: 10.15468/dl.p9ssdu
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sclerophrys pusilla (Mertens, 1937)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.5808 -24.13,35.5909 -24.0715,30.5701 -24.0715,30.5701 -28.5786,32.4847 -28.5786,32.55 -28.5222,33.0346 -26.8668,32.9741 -26.7838,33.0415 -26.059,32.9304 -26.0011,32.7994 -26.1281,32.6834 -26.0015,32.813 -25.8728,32.8513 -25.7166,33.3048 -25.3731,35.1489 -24.6699,35.5808 -24.13))"
 ]
}

 The dataset includes 24 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036095-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9dphnp
title: Occurrence Download

description: A dataset containing 3588030 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Occurrence evidence",
 "OccurrenceStatus is Present",
 "Year 2015-2025"
 ]
}

 The dataset includes 3588030 records from 372 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036083-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6basyj
title: Occurrence Download

description: A dataset containing 38354 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Linaria alpina (L.) Mill."
 ]
}

 The dataset includes 38354 records from 366 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036094-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3mnwnt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Asparagus crassicladus",
 "Geometry POLYGON((29.76451 -26.09643, 32.1599 -26.09643, 32.1599 -22.51877, 29.76451 -22.51877, 29.76451 -26.09643))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036097-250525065834625/datasets/export for details.
DOI: 10.15468/dl.jz83k3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Aristida diffusa",
 "Geometry POLYGON((29.76451 -26.09643, 32.1599 -26.09643, 32.1599 -22.51877, 29.76451 -22.51877, 29.76451 -26.09643))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036096-250525065834625/datasets/export for details.
DOI: 10.15468/dl.fgaqe5
title: Occurrence Download

description: A dataset containing 3500 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hyalomma C.L.Koch, 1844"
 ]
}

 The dataset includes 3500 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036099-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3mvv3t
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Asparagus sp.",
 "Geometry POLYGON((29.76451 -26.09643, 32.1599 -26.09643, 32.1599 -22.51877, 29.76451 -22.51877, 29.76451 -26.09643))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036098-250525065834625/datasets/export for details.
DOI: 10.25824/redu/533z2h
title: Formulação cosmética com atividade de inibição de tirosinase

description: Composição percentual da formulação de gel cosmético contendo o extrato botânico que apresentou o maior potencial de inibição da enzima tirosinase. Resultados do teste de estabilidade acelerada, onde por 70 dias coletou-se os dados físico-químicos (pH e viscosidade) e aspectos organolépticos (coloração e odor).
DOI: 10.25824/redu/grcrfe
title: Cálculo de porcentagem de extrato em cosméticos com atividade de inibição de tirosinase

description: Dados referentes ao estudo da cinética enzimática da enzima tirosinase. Os coeficientes foram obtidos através de modelagem computacional, a qual se baseia nas equações descritas pela literatura (Michalis-Menten). Utilizando a modelagem computacional, calculou-se o coeficiente de inibição enzimático (Ki) de 13 extratos botânicos, feitos a partir de diferentes líquidos extratores e o ativo padrão 3-O-Ethyl Ascorbic Acid. Após a comparação dos coeficientes de inibição obtidos e seleção do extrato com maior potencial inibitório, prosseguiu-se para mensurar a porcentagem de extrato botânico em uma formulação cosmética, a fim de teoricamente inibir em 99% a atividade enzimática da tirosinase, utilizando dados derivados de modelagem computacional e as características inerentes da histologia cutânea.
DOI: 10.15468/dl.e6jcme
title: Occurrence Download

description: A dataset containing 1654 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "GbifRegion is Europe and Central Asia",
 "MediaType is Image",
 "TaxonKey is Centaurea jacea L.",
 "Year is one of (2020, 2024)"
 ]
}

 The dataset includes 1654 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036100-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ustevf
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sclerophrys pusilla (Mertens, 1937)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((31.8862 -21.3285,30.5701 -20.3186,30.5701 -24.0715,35.5909 -24.0715,35.6007 -24.0157,35.6007 -23.8125,35.4969 -23.7035,35.6007 -23.165,35.6007 -22.9702,35.227 -22.2482,34.6862 -21.6944,34.013 -21.3095,33.5 -21.1593,32.9675 -21.1092,32.4352 -21.1612,31.8862 -21.3285))"
 ]
}

 The dataset includes 34 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036101-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15640447
title: S1: List of specimens used for DNA barcoding (with sampling sites and date, sequence length (bp), Sample/Process ID, Genbank accession, Institution).

description: List of specimens used for DNA barcoding of genus Crinipus (with sampling sites and date, sequence length, Sample/Process ID, Genbank accession, Institution)
DOI: 10.5281/zenodo.15640448
title: S1: List of specimens used for DNA barcoding (with sampling sites and date, sequence length (bp), Sample/Process ID, Genbank accession, Institution).

description: List of specimens used for DNA barcoding of genus Crinipus (with sampling sites and date, sequence length, Sample/Process ID, Genbank accession, Institution)
DOI: 10.21227/91br-ej98
title: "AN INTERNSHIP REPORT ON E-HELPING HOUSING SOCIETY PROJECT REPORT"

description: "The basic concept of this society system, we create global web based application in asp.net with C# language to manage Society with House and Owner of house detail. We provide platform to register society to our system, and there are many houses according to each society. Each house allocated to owner of house, all the owner are members of our project. After becoming a member they can login to give his house on rent or sell for all users. The people can easily find search the rent house or sell house in which society and get contact detail of owner of house by visiting our website. All members can make online complain related home to society management."
DOI: 10.17632/hctf2rgcnk
title: Transition from exhumation to orogen-parallel extension in the Adula unit (Central Alps)

description: The Adula unit (Central Alps) exposes high- and ultra-high-pressure (HP-UHP) metamorphic rocks, providing key insights into the subduction and exhumation dynamics of the former distal European margin. In the San Bernardino pass area (Switzerland) it is possible to reconstruct the tectonometamorphic evolution or the Adula unit from HP conditions to exhumation and subsequent shearing during orogen-parallel extension. The P-T-d-t evolution of eclogites and host rocks fhas been determined by thermodynamic modelling and Ar-Ar dating of syntectonic minerals. This dataset contains location and description of studied samples, mineral chemistry data obtaine by electron microprobe analyses and Ar-Ar data on white micas in eclogites and hosting orthogneisses.
DOI: 10.15468/dl.jfs4yj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sclerophrys pusilla (Mertens, 1937)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((27.1586 -33.5889,28.2048 -32.9007,25.5395 -32.9007,25.5395 -34.1098,25.6468 -34.1222,25.7787 -34.0734,25.7098 -33.9109,25.8639 -33.797,26.4806 -33.8473,27.1586 -33.5889))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036103-250525065834625/datasets/export for details.
DOI: 10.17632/hctf2rgcnk.1
title: Transition from exhumation to orogen-parallel extension in the Adula unit (Central Alps)

description: The Adula unit (Central Alps) exposes high- and ultra-high-pressure (HP-UHP) metamorphic rocks, providing key insights into the subduction and exhumation dynamics of the former distal European margin. In the San Bernardino pass area (Switzerland) it is possible to reconstruct the tectonometamorphic evolution or the Adula unit from HP conditions to exhumation and subsequent shearing during orogen-parallel extension. The P-T-d-t evolution of eclogites and host rocks fhas been determined by thermodynamic modelling and Ar-Ar dating of syntectonic minerals. This dataset contains location and description of studied samples, mineral chemistry data obtaine by electron microprobe analyses and Ar-Ar data on white micas in eclogites and hosting orthogneisses.