cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14558683
title: Process Data from Red Hat Public Jira Dataset 2001-2024

description: The Red Hat Public Process dataset is a extract of Standard Issue types from each of the publically accessible Red Hat Jira Projects available on https://issues.redhat.com/issues/. 

It contains data on 490,000 Product Backlog Items (PBIs) in 238 software development systems created over a 23 year period. The dataset contains only the following fields:



Issue key    

Issue Type    

Status    

Project key    

Project name    

Project type    

Resolution    

Created    

Resolved


The data was extracted between 15 Nov 2024 and 21 Nov 2024 (with minor corrections / additions until 27 Nov 2024).  

Steps to recreate:



Each Jira Project was opened and for those with more than 30 PBIs the data was extracted to a CSV file with the naming convention [SystemName].csv. 

For Jira Projects with more than 1000 PBIs the data was sliced using Jira query language using the creation date in a string like "AND createdDate >= 2001-1-1 and createdDate < 2025-1-1". The data was sliced into downloadable chunks of fewer than 1000 PBIs reversing from the 1 Jan 2025 and proceeding to the date of the first PBI created or 1 Jan 2001 - whichever was earlier.

 The extracted data was recombined and then filtered to remove all but the required fields, listed above. 


The data in teh INPUT zip file can be used for comparing processes between different systems.

We have included some outputs of programmatic analysis of these files in the Outputs zip file. For further information on the Outputs please contact us.
DOI: 10.5281/zenodo.14558684
title: Process Data from Red Hat Public Jira Dataset 2001-2024

description: The Red Hat Public Process dataset is a extract of Standard Issue types from each of the publically accessible Red Hat Jira Projects available on https://issues.redhat.com/issues/. 

It contains data on 490,000 Product Backlog Items (PBIs) in 238 software development systems created over a 23 year period. The dataset contains only the following fields:



Issue key    

Issue Type    

Status    

Project key    

Project name    

Project type    

Resolution    

Created    

Resolved


The data was extracted between 15 Nov 2024 and 21 Nov 2024 (with minor corrections / additions until 27 Nov 2024).  

Steps to recreate:



Each Jira Project was opened and for those with more than 30 PBIs the data was extracted to a CSV file with the naming convention [SystemName].csv. 

For Jira Projects with more than 1000 PBIs the data was sliced using Jira query language using the creation date in a string like "AND createdDate >= 2001-1-1 and createdDate < 2025-1-1". The data was sliced into downloadable chunks of fewer than 1000 PBIs reversing from the 1 Jan 2025 and proceeding to the date of the first PBI created or 1 Jan 2001 - whichever was earlier.

 The extracted data was recombined and then filtered to remove all but the required fields, listed above. 


The data in teh INPUT zip file can be used for comparing processes between different systems.

We have included some outputs of programmatic analysis of these files in the Outputs zip file. For further information on the Outputs please contact us.
DOI: 10.15468/dl.ghftcd
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Month is one of (January, February)",
 "OccurrenceStatus is Present",
 "TaxonKey is Sterna paradisaea Pontoppidan, 1763",
 "Year 2011-2011"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049851-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25623779
title: A prognostic risk model based on lactate metabolism and transport-related lncRNAs for gastric adenocarcinoma

description: Increased lactate levels and metastasis in tumours are strongly associated with dismal outcomes. But prognostic value of lactate metabolism and transport-related lncRNAs in gastric adenocarcinoma (GA) patients remains unaddressed. Gene expression data of GA were provided by The Cancer Genome Atlas. Lactate metabolism and transport-related gene data were accessed from GSEA. LncRNAs related to lactate metabolism and transport were identified by correlation analysis. A prognostic model was built by regression analysis. Validity of prognostic model was confirmed through survival analysis and receiver operating characteristic (ROC) curve. Immunity of each risk group was evaluated by immune correlation analysis .LncRNA-mRNA network was built by correlation analysis using Cytoscape software. A 12-gene prognostic model based on lactate metabolism and transport-related lncRNAs was built in GA. Median riskscore was utilized to classify GA samples into high- and low-risk groups. Survival analysis and ROC curves demonstrated validity of prognostic model. Most immune checkpoint molecules and TIDE scores were lower in the low-risk group. LINC01303 and LINC01545 may be the key prognostic factors in patients with GA. This study successfully built a prognostic model of lactate metabolism and transport-related lncRNAs in GA. The findings guide prognostic management of GA patients.
DOI: 10.6084/m9.figshare.25623779.v1
title: A prognostic risk model based on lactate metabolism and transport-related lncRNAs for gastric adenocarcinoma

description: Increased lactate levels and metastasis in tumours are strongly associated with dismal outcomes. But prognostic value of lactate metabolism and transport-related lncRNAs in gastric adenocarcinoma (GA) patients remains unaddressed. Gene expression data of GA were provided by The Cancer Genome Atlas. Lactate metabolism and transport-related gene data were accessed from GSEA. LncRNAs related to lactate metabolism and transport were identified by correlation analysis. A prognostic model was built by regression analysis. Validity of prognostic model was confirmed through survival analysis and receiver operating characteristic (ROC) curve. Immunity of each risk group was evaluated by immune correlation analysis .LncRNA-mRNA network was built by correlation analysis using Cytoscape software. A 12-gene prognostic model based on lactate metabolism and transport-related lncRNAs was built in GA. Median riskscore was utilized to classify GA samples into high- and low-risk groups. Survival analysis and ROC curves demonstrated validity of prognostic model. Most immune checkpoint molecules and TIDE scores were lower in the low-risk group. LINC01303 and LINC01545 may be the key prognostic factors in patients with GA. This study successfully built a prognostic model of lactate metabolism and transport-related lncRNAs in GA. The findings guide prognostic management of GA patients.
DOI: 10.15468/dl.sjenns
title: Occurrence Download

description: A dataset listing the 16147 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation)",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2024-2024"
 ]
}

 The dataset's 16147 records were derived from 198 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049852-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14558840
title: A proposed workflow to robustly analyze bacterial transcripts in RNAseq data from Extracellular Vesicles

description: The microbiota has been unequivocally linked to various diseases, yet the mechanisms underlying these associations remain incompletely understood. One potential contributor to this relationship is the extracellular vesicles produced by bacteria (bEVs). However, the detection of these bEVs is challenging. Therefore, we propose a novel workflow to identify bacterial RNA present in circulating extracellular vesicles using Total EV RNA-seq data. As a proof of concept, we applied this workflow to a dataset from individuals with multiple sclerosis (MS).

We analyzed Total EV RNA-seq data from blood samples of healthy controls and individuals with MS, encompassing both the Relapsing-Remitting (RR) and Secondary Progressive (SP) phases of the disease. Our workflow incorporates multiple reference mapping steps against the host genome, followed by a consensus selection of bacterial genera based on various taxonomic profiling tools. This consensus approach utilizes a flagging system to exclude species with low abundance or high variability across profilers.  Additionally, including biological samples from known cultured species and generating artificial reads constitute two key aspects of this workflow to validate the high specificity of the approach.

Our findings demonstrate that bacterial RNA can indeed be detected in Total EV RNA-seq from blood samples, suggesting that this workflow can be a powerful tool for reanalyzing RNA-seq data from EV studies. Additionally, we identified promising bacterial candidates with differential expression between the RR and SP phases of MS. This approach provides valuable insights into the potential role of bEVs in the microbiota-host communication. Finally, this approach is translatable to other experiments using total RNA, where the lack of a robust pipeline can lead to an increased false positive detection of microbial species. 

The workflow is available at the following repository: https://github.com/NanoNeuro/EV_taxprofiling
DOI: 10.5281/zenodo.14558841
title: A proposed workflow to robustly analyze bacterial transcripts in RNAseq data from Extracellular Vesicles

description: The microbiota has been unequivocally linked to various diseases, yet the mechanisms underlying these associations remain incompletely understood. One potential contributor to this relationship is the extracellular vesicles produced by bacteria (bEVs). However, the detection of these bEVs is challenging. Therefore, we propose a novel workflow to identify bacterial RNA present in circulating extracellular vesicles using Total EV RNA-seq data. As a proof of concept, we applied this workflow to a dataset from individuals with multiple sclerosis (MS).

We analyzed Total EV RNA-seq data from blood samples of healthy controls and individuals with MS, encompassing both the Relapsing-Remitting (RR) and Secondary Progressive (SP) phases of the disease. Our workflow incorporates multiple reference mapping steps against the host genome, followed by a consensus selection of bacterial genera based on various taxonomic profiling tools. This consensus approach utilizes a flagging system to exclude species with low abundance or high variability across profilers.  Additionally, including biological samples from known cultured species and generating artificial reads constitute two key aspects of this workflow to validate the high specificity of the approach.

Our findings demonstrate that bacterial RNA can indeed be detected in Total EV RNA-seq from blood samples, suggesting that this workflow can be a powerful tool for reanalyzing RNA-seq data from EV studies. Additionally, we identified promising bacterial candidates with differential expression between the RR and SP phases of MS. This approach provides valuable insights into the potential role of bEVs in the microbiota-host communication. Finally, this approach is translatable to other experiments using total RNA, where the lack of a robust pipeline can lead to an increased false positive detection of microbial species. 

The workflow is available at the following repository: https://github.com/NanoNeuro/EV_taxprofiling
DOI: 10.60525/04teye511/gvvx0m
title: Conjunto de datos: The macroecology of fish migration

description: We still lack a consensus on the main variables driving changes in migratory strategies. Different hypotheses have been proposed: productivity, energy, environmental heterogeneity, and genetic predisposition. This work takes an integrative view and analyzes migrations from a macroecological perspective estimating the extent to which different environmental variables and historic factors influence migratory life histories
DOI: 10.60525/04teye511/gvvx0m/ppbaxa
title: KineticEnergyData.csv

description: :unav
DOI: 10.60525/04teye511/gvvx0m/czzwqh
title: GBIF_OBIS_db.zip

description: :unav
DOI: 10.60525/04teye511/gvvx0m/zcaf4v
title: EnvironmentalData&PhylogeneticFilters.zip

description: :unav
DOI: 10.60525/04teye511/gvvx0m/sjbbvn
title: SpeciesCommunityData.zip

description: :unav
DOI: 10.60525/04teye511/gvvx0m/8qv1bk
title: file.DS_Store

description: :unav
DOI: 10.60525/04teye511/gvvx0m/bh1dwg
title: readme.txt

description: :unav
DOI: 10.15468/dl.uuvfp9
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is da86174a-a605-43a4-a5e8-53d484152cd3",
 "TaxonKey is Syngonium angustatum Schott"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049856-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qe4np4
title: Occurrence Download

description: A dataset containing 15259692 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cathartes aura (Linnaeus, 1758)"
 ]
}

 The dataset includes 15259692 records from 668 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049853-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.akgtbg
title: Occurrence Download

description: A dataset containing 1401 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Juncus wallichianus J.Gay ex Laharpe",
 "TaxonKey is Juniperus bermudiana L.",
 "TaxonKey is Juniperus chinensis L."
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1401 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013839-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hzgsmj
title: Occurrence Download

description: A dataset containing 13745 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Helianthus annuus L.",
 "Country is one of (United States of America, Canada)",
 "Year is greater than or equal to 1979"
 ]
}

 The dataset includes 13745 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0269059-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.82bduf
title: Occurrence Download

description: A dataset containing 91135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Naturalis Biodiversity Center (NL) - Chelicerata and Myriapoda"
 ]
}

 The dataset includes 91135 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0226427-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qu6ebw
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Fossil",
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Observation"
 ]
 },
 {
 "or" : [
 "Continent is North America",
 "Continent is South America"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "VerbatimScientificName is Chione californiensis"
 ]
}

 The dataset includes 41 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016464-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tzrtko
title: Occurrence Download

description: A dataset containing 106 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Berardius arnuxii Duvernoy, 1851"
 ]
}

 The dataset includes 106 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013839-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98awwu
title: Occurrence Download

description: A dataset containing 14462 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "OccurrenceStatus is Present",
 "TaxonKey is Pharomachrus mocinno La Llave, 1832"
 ]
}

 The dataset includes 14462 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0271982-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5vwt8
title: Occurrence Download

description: A dataset containing 7126462 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Fossil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7126462 records from 4610 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0226421-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wt7v5g
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Punctelia caseana Lendemer & B.P.Hodk."
 ]
}

 The dataset includes 24 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0158345-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gsh4rx
title: Occurrence Download

description: A dataset containing 1441 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Corythucha marmorata (Uhler, 1878)"
 ]
}

 The dataset includes 1441 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180036-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xm937a
title: Occurrence Download

description: A dataset containing 6369 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 Formicivora rufa (Wied-Neuwied, 1831)"
 ]
}

 The dataset includes 6369 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003838-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rnaf4r
title: Occurrence Download

description: A dataset containing 220985 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herbarium GB, University of Gothenburg"
 ]
}

 The dataset includes 220985 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004206-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g6w3lt
title: Occurrence Download

description: A dataset containing 6818 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Year 1000-1901",
 "TaxonKey is Caudata"
 ]
}

 The dataset includes 6818 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034225-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rw59bg
title: Occurrence Download

description: A dataset containing 3979 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Festuca pulchella Schrad."
 ]
}

 The dataset includes 3979 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003833-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mfamws
title: Occurrence Download

description: A dataset containing 539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((172.45765 -43.72812,172.45864 -43.72361,172.45516 -43.71945,172.45336 -43.71567,172.45186 -43.71353,172.45027 -43.70945,172.44233 -43.71198,172.44254 -43.71439,172.44138 -43.72258,172.44855 -43.73078,172.45765 -43.72812))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 539 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0171979-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.iknzd8
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paratecoma peroba (Record) Kuhlm."
 ]
}

 The dataset includes 96 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034223-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9xzkp3
title: Occurrence Download

description: A dataset containing 1099 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pasteurella multocida_A"
 ]
}

 The dataset includes 1099 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045759-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.epnwsf
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Genista pseudoretamoides (Maire) Rivas Mart., Molero Mesa, Marfíl & G.Benítez"
 ]
}

 The dataset includes 17 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003819-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.