cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.6qqqjr
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Hippeastrum angustifolium Pax"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090608-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nyy8hy
title: Occurrence Download

description: A dataset containing 120976 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Canis lupus Linnaeus, 1758"
 ]
}

 The dataset includes 120976 records from 297 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016949-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y58ypy
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Edwardsiana nigriloba (Edwards, 1924))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 25 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041817-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q7sauk
title: Occurrence Download

description: A dataset containing 8312 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anacardium occidentale L."
 ]
}

 The dataset includes 8312 records from 312 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0117873-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sgkmuz
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hilliella rivulorum (Dunn) Y.H.Zhang & H.W.Li"
 ]
}

 The dataset includes 66 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0062936-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.1bmpgp
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Canis simensis Rüppell, 1840"
 ]
}

 The dataset includes 59 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016955-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kuka5c
title: Occurrence Download

description: A dataset containing 278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Zephyranthes Herb."
 ]
}

 The dataset includes 278 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090605-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gqxm3p
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hormathophylla lapeyrouseana (Jord.) P.Küpfer"
 ]
}

 The dataset includes 159 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0062948-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vgujrm
title: Occurrence Download

description: A dataset containing 173200 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Achillea ptarmica Richardson, 1823"
 ]
}

 The dataset includes 173200 records from 451 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000528-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gkzmtc
title: Occurrence Download

description: A dataset containing 42454 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "Month is January",
 "Month is February",
 "Month is March",
 "Month is October",
 "Month is November",
 "Month is December"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Circaetus gallicus (Gmelin, 1788)",
 "Year 1992-2020"
 ]
}

 The dataset includes 42454 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127171-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g895nd
title: Occurrence Download

description: A dataset containing 141383 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is New Zealand Freshwater Fish Database"
 ]
}

 The dataset includes 141383 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0062938-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9c0u8o
title: Occurrence Download

description: A dataset containing 743 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Bisons Collection"
 ]
}

 The dataset includes 743 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008855-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bf5rhu
title: Occurrence Download

description: A dataset containing 9356 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hydnellum peckii Banker"
 ]
}

 The dataset includes 9356 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127181-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uz3gcs
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Material citation",
 "OccurrenceStatus is Present",
 "TaxonKey is Halimeda tuna (J.Ellis & Sol.) J.V.Lamour."
 ]
}

 The dataset includes 37 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0062945-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b9tael
title: Occurrence Download

description: A dataset containing 5856 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Specimen"
 ]
 },
 "TaxonKey is Afrosoricida"
 ]
}

 The dataset includes 5856 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016954-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uf94a7
title: Occurrence Download

description: A dataset containing 16053 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Ulmus minor Mill."
 ]
}

 The dataset includes 16053 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0130142-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ztw2bz
title: Occurrence Download

description: A dataset containing 2439 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hieracium bifidum subsp. bifidum, Hieracium bifidum subsp. domugledense Zahn, Hieracium bifidum subsp. mesopsis, Hieracium bifidum subsp. cuhanum, Hieracium bifidum subsp. caloldenense, Hieracium bifidum subsp. pseudodollineriforme, Hieracium bifidum subsp. leucopoliozum, Hieracium bifidum subsp. melanochloreaelema, Hieracium bifidum subsp. lonchopodoides, Hieracium bifidum subsp. lobulatum, Hieracium bifidum subsp. pseudosinuosifrons, Hieracium bifidum subsp. stenoxydon, Hieracium bifidum subsp. pseudocanitiosum, Hieracium bifidum subsp. pseudocanitiosiforme, Hieracium bifidum subsp. biformatifrons, Hieracium bifidum subsp. cryptadenanthelum, Hieracium bifidum subsp. cympphorum, Hieracium bifidum subsp. psilacrum, Hieracium eriopodoides var. molliceps Murr & Zahn, Hieracium bifidum subsp. stenolepioides, Hieracium bifidum subsp. lissobifidum, Hieracium bifidum subsp. sokolensiforme, Hieracium bifidum subsp. chlorostenolepis, Hieracium bifidum subsp. pseudocardiobasiforme, Hieracium bifidum subsp. steriptothricum, Hieracium bifidum subsp. laceridentifrons, Hieracium bifidum subsp. subextraticeps, Hieracium bifidum subsp. melanochloreilema, Hieracium bifidum subsp. flocciceps, Hieracium bifidum Kit. ex Hornem., Hieracium bifidum subsp. finkhii, Hieracium bifidum subsp. oszadanum, Hieracium bifidum subsp. solarueliense, Hieracium bifidum subsp. cordatoovalifrons, Hieracium bifidum subsp. hemilonchodes Zahn, Hieracium bifidum subsp. pseudodontophyton, Hieracium bifidum subsp. scapiforme, Hieracium bifidum subsp. duplicatodentatum, Hieracium bifidum subsp. floccinervosum, Hieracium bifidum var. bifidum, Hieracium bifidum subsp. inflaticeps, Hieracium vulgatum subsp. bifidum (Kit. ex Hornem.) H.Lindb., Hieracium plumbeum var. bifidum (Kit. ex Hornem.) Norrl.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 2439 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002913-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h6tmwz
title: Occurrence Download

description: A dataset listing the 91 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Occurrence evidence, Human Observation, Material sample, Specimen, Material citation)",
 "Continent is Africa",
 "Country is Angola",
 "Geometry POLYGON((12.17101 -5.33208,12.20341 -5.40594,12.23674 -5.39986,12.25365 -5.39378,12.24989 -5.35639,12.23909 -5.31665,12.22078 -5.30356,12.18932 -5.32086,12.17101 -5.33208))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (LC, NT, VU, EN, CR, NE)"
 ]
}

 The dataset's 91 records were derived from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002904-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14231261
title: Thread-Modular Abstract Interpretation: The Local Perspective

description: Thread-Modular Abstract Interpretation: The Local Perspective


This artifact contains the software and data necessary to reproduce the results described in the chapter entitled Experimental Evaluation of the manuscript Thread-Modular Abstract Interpretation: The Local Perspective by Michael Schwarz.


It is structured as follows:


- The folder analyzer contains the Goblint analyzer in the version used for the experiments (Branch michael-schwarz-dissertation).

- The folder bench contains the Goblint benchmark repository in the version used for the experiments which also contains scripts to run the experiments (Branch michael-schwarz-dissertation).

- The archive bench_raw.tar.xz contains the raw benchmark results.

- The folder data contains spreadsheets, CSV files, and scripts necessary to extract relevant information from the raw benchmark results.


This artifact is unfortunately documented relatively poorly at the moment. A good starting point for understanding the various scripts etc. are our previous artifacts on which this evaluation builds and their rather comprehensive READMEs.


- ESOP '23: https://zenodo.org/records/7767778

- SAS '21: https://zenodo.org/records/5148608


If you want to reproduce these results but have trouble getting started, you are very much encouraged to bother me, e.g., by emailing me at `m DOT schwarz AT tum DOT de`


The contents of `analyzer` and `bench` all are published under the respective licenses mentioned in folders or individual files.
DOI: 10.5281/zenodo.14231262
title: Thread-Modular Abstract Interpretation: The Local Perspective

description: Thread-Modular Abstract Interpretation: The Local Perspective


This artifact contains the software and data necessary to reproduce the results described in the chapter entitled Experimental Evaluation of the manuscript Thread-Modular Abstract Interpretation: The Local Perspective by Michael Schwarz.


It is structured as follows:


- The folder analyzer contains the Goblint analyzer in the version used for the experiments (Branch michael-schwarz-dissertation).

- The folder bench contains the Goblint benchmark repository in the version used for the experiments which also contains scripts to run the experiments (Branch michael-schwarz-dissertation).

- The archive bench_raw.tar.xz contains the raw benchmark results.

- The folder data contains spreadsheets, CSV files, and scripts necessary to extract relevant information from the raw benchmark results.


This artifact is unfortunately documented relatively poorly at the moment. A good starting point for understanding the various scripts etc. are our previous artifacts on which this evaluation builds and their rather comprehensive READMEs.


- ESOP '23: https://zenodo.org/records/7767778

- SAS '21: https://zenodo.org/records/5148608


If you want to reproduce these results but have trouble getting started, you are very much encouraged to bother me, e.g., by emailing me at `m DOT schwarz AT tum DOT de`


The contents of `analyzer` and `bench` all are published under the respective licenses mentioned in folders or individual files.
DOI: 10.15468/dl.vz6du6
title: Occurrence Download

description: A dataset containing 986 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hieracium bupleuroides C.C.Gmel., Hieracium bupleuroides var. bupleuroides, Hieracium glaucum subsp. bupleuroides (C.C.Gmel.) Bonnier)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 986 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002914-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3uczmh
title: Occurrence Download

description: A dataset containing 1007 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Gopherus morafkai Murphy, Berry, Edwards, Leviton, Lathrop & Riedle, 2011"
 ]
}

 The dataset includes 1007 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002915-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xx3d86
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hieracium chlorophyton Preissm. & Zahn)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 14 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002916-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14231365
title: OFA evaluation datasets
DOI: 10.5281/zenodo.14231366
title: OFA evaluation datasets
DOI: 10.5281/zenodo.14033162
title: Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery

description: Understanding transcriptional responses to chemical perturbations is central to drug discovery, but exhaustive experimental screening of diseasecompound combinations is unfeasible. To overcome this limitation, here we introduce PRnet, a perturbation-conditioned deep generative model that predicts transcriptional responses to novel chemical perturbations that have never experimentally perturbed at bulk and single-cell levels. Evaluations indicate that PRnet outperforms alternative methods in predicting responses across novel compounds, pathways, and cell lines. PRnet enables gene-level response interpretation and in-silico drug screening for diseases based on gene signatures. PRnet further identifies and experimentally validates novel compound candidates against small cell lung cancer and colorectal cancer. Lastly, PRnet generates a large-scale integration atlas of perturbation profiles, covering 88 cell lines, 52 tissues, and various compound libraries. PRnet provides a robust and scalable candidate recommendation workflow and successfully recommends drug candidates for 233 diseases. Overall, PRnet is an effective and valuable tool for gene-based therapeutics screening.
DOI: 10.5281/zenodo.14033163
title: Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery

description: Understanding transcriptional responses to chemical perturbations is central to drug discovery, but exhaustive experimental screening of diseasecompound combinations is unfeasible. To overcome this limitation, here we introduce PRnet, a perturbation-conditioned deep generative model that predicts transcriptional responses to novel chemical perturbations that have never experimentally perturbed at bulk and single-cell levels. Evaluations indicate that PRnet outperforms alternative methods in predicting responses across novel compounds, pathways, and cell lines. PRnet enables gene-level response interpretation and in-silico drug screening for diseases based on gene signatures. PRnet further identifies and experimentally validates novel compound candidates against small cell lung cancer and colorectal cancer. Lastly, PRnet generates a large-scale integration atlas of perturbation profiles, covering 88 cell lines, 52 tissues, and various compound libraries. PRnet provides a robust and scalable candidate recommendation workflow and successfully recommends drug candidates for 233 diseases. Overall, PRnet is an effective and valuable tool for gene-based therapeutics screening.
DOI: 10.5281/zenodo.14230870
title: Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery

description: Understanding transcriptional responses to chemical perturbations is central to drug discovery, but exhaustive experimental screening of diseasecompound combinations is unfeasible. To overcome this limitation, here we introduce PRnet, a perturbation-conditioned deep generative model that predicts transcriptional responses to novel chemical perturbations that have never experimentally perturbed at bulk and single-cell levels. Evaluations indicate that PRnet outperforms alternative methods in predicting responses across novel compounds, pathways, and cell lines. PRnet enables gene-level response interpretation and in-silico drug screening for diseases based on gene signatures. PRnet further identifies and experimentally validates novel compound candidates against small cell lung cancer and colorectal cancer. Lastly, PRnet generates a large-scale integration atlas of perturbation profiles, covering 88 cell lines, 52 tissues, and various compound libraries. PRnet provides a robust and scalable candidate recommendation workflow and successfully recommends drug candidates for 233 diseases. Overall, PRnet is an effective and valuable tool for gene-based therapeutics screening.
DOI: 10.15468/dl.dpzy5k
title: Occurrence Download

description: A dataset containing 14928586 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Argentina"
 ]
}

 The dataset includes 14928586 records from 2089 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002877-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e2q3af
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-78.36182 -47.63916,-76.0669 -53.93799,-67.66113 -57.48535,-56.48682 -53.10791,-47.75208 -26.48499,-49.37653 -24.21051,-49.5221 -22.99378,-51.0846 -22.70081,-53.39173 -22.40784,-54.27063 -23.86047,-55.11963 -23.66455,-55.44068 -22.03735,-57.78443 -21.9397,-57.61353 -20.81665,-58.04932 -19.51416,-60.1001 -18.78174,-61.90003 -19.50256,-62.81372 -21.30493,-64.49829 -22.18384,-66.52466 -21.67114,-67.35474 -22.55005,-67.88147 -21.67542,-67.96692 -19.99085,-69.11255 -17.52075,-69.91455 -17.41455,-70.45166 -18.39111,-78.36182 -47.63916))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Microlepia C.Presl"
 ]
}

 The dataset includes 11 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0350203-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wgqfgt
title: Occurrence Download

description: A dataset containing 694 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhododendron caucasicum Pall."
 ]
}

 The dataset includes 694 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263162-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xapaaf
title: Occurrence Download

description: A dataset listing the 2568 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "StateProvince is one of (choco)"
 ]
}

 The dataset's 2568 records were derived from 150 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013345-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ysmdnf
title: Occurrence Download

description: A dataset listing the 106 species recorded in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Especies silvestres de nopales mexicanos",
 "TaxonKey is Opuntia Mill."
 ]
}

 The dataset's 106 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013440-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.