cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14030663
title: Reanalysis of PXD024291

description: This repository contains a dataset analyzed in "De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution".

Specifically, this repository contains the reanalysis of the protein-SIP data obtained from PXD024291 ("Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities using protein-based stable isotope probing proteomics (Protein-SIP)") that was published in Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolić N, Sachsenberg T, McCalder J, Lipton MS, Strous M. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome. 2023 11(1):24 based on data from Starke R, Oliphant K, Jehmlich N, Schäpe SS, Sachsenberg T, Kohlbacher O, et al. Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. J Proteomics. 2020;222:103791.

mztab files originate from Casanovo

tsv files originate from PepNet

xlsx files originate from merging Unipept and MetaProSIP output and BLASTp of peptides not referenced in the reference database nor UniProt.
DOI: 10.5281/zenodo.16318031
title: Reanalysis of PXD024291

description: This repository contains a dataset analyzed in "De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution".

Specifically, this repository contains the reanalysis of the protein-SIP data obtained from PXD024291 ("Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities using protein-based stable isotope probing proteomics (Protein-SIP)") that was published in Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolić N, Sachsenberg T, McCalder J, Lipton MS, Strous M. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome. 2023 11(1):24 based on data from Starke R, Oliphant K, Jehmlich N, Schäpe SS, Sachsenberg T, Kohlbacher O, et al. Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. J Proteomics. 2020;222:103791.

mztab files originate from Casanovo

tsv files originate from PepNet

xlsx files originate from merging Unipept and MetaProSIP output and BLASTp of peptides not referenced in the reference database nor UniProt.
DOI: 10.15468/dl.kyg69q
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Neolamprologus schreyeni)",
 "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 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011443-250802193616735/datasets/export for details.
DOI: 10.15468/dl.cj7g89
title: Occurrence Download

description: A dataset containing 1106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lophoceros pallidirostris)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 1106 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011442-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14030686
title: Analysis of PXD057215

description: This repository contains a dataset analyzed in "De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution".

Specifically, this repository contains the analysis of the protein-SIP data deposited to PXD057215 ("De novo assembled databases allow species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition").

xlsx file originates from merging Unipept and MetaProSIP output and BLASTp of peptides not referenced in the reference database nor UniProt.
DOI: 10.5281/zenodo.16318298
title: Analysis of PXD057215

description: This repository contains a dataset analyzed in "De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution".

Specifically, this repository contains the analysis of the protein-SIP data deposited to PXD057215 ("De novo assembled databases allow species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition").

xlsx file originates from merging Unipept and MetaProSIP output and BLASTp of peptides not referenced in the reference database nor UniProt.
DOI: 10.5281/zenodo.14030388
title: Reanalysis of PXD024174

description: This repository contains a dataset analyzed in "De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution".

Specifically, this repository contains the reanalysis of the protein-SIP data obtained from PXD024174 ("Mock microbial community with spike-ins of 13C-labeled Escherichia coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)") that was published in Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolić N, Sachsenberg T, McCalder J, Lipton MS, Strous M. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome. 2023 11(1):24.

mztab files originate from Casanovo

tsv files originate from PepNet

xlsx files originate from merging Unipept and MetaProSIP output and BLASTp of peptides not referenced in the reference database nor UniProt.
DOI: 10.5281/zenodo.16317854
title: Reanalysis of PXD024174

description: This repository contains a dataset analyzed in "De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution".

Specifically, this repository contains the reanalysis of the protein-SIP data obtained from PXD024174 ("Mock microbial community with spike-ins of 13C-labeled Escherichia coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)") that was published in Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolić N, Sachsenberg T, McCalder J, Lipton MS, Strous M. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome. 2023 11(1):24.

mztab files originate from Casanovo

tsv files originate from PepNet

xlsx files originate from merging Unipept and MetaProSIP output and BLASTp of peptides not referenced in the reference database nor UniProt.
DOI: 10.15468/dl.cdutvk
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Smilogobius obliquus"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011444-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14030620
title: Reanalysis of PXD041414

description: This repository contains a dataset analyzed in "De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution".

Specifically, this repository contains the reanalysis of the protein-SIP data obtained from PXD041414 ("1% 2% 5% 25% 50% 100% 13C-labeled E. coli protein") that was published in Xiong Y, Mueller RS, Feng S, Guo X, Pan C. Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins. Microbiome. 2024;12:148

mztab files originate from Casanovo

tsv files originate from PepNet

xlsx file originates from merging Unipept and MetaProSIP output
DOI: 10.5281/zenodo.15537146
title: Reanalysis of PXD041414

description: This repository contains a dataset analyzed in "De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution".

Specifically, this repository contains the reanalysis of the protein-SIP data obtained from PXD041414 ("1% 2% 5% 25% 50% 100% 13C-labeled E. coli protein") that was published in Xiong Y, Mueller RS, Feng S, Guo X, Pan C. Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins. Microbiome. 2024;12:148

mztab files originate from Casanovo

tsv files originate from PepNet

xlsx file originates from merging Unipept and MetaProSIP output
DOI: 10.15468/dl.qyq29q
title: Occurrence Download

description: A dataset containing 620 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((153.70307 -27.43853,151.79023 -27.70952,149.38327 -30.61064,150.05276 -35.28112,154.05375 -34.65945,155.40867 -28.52247,153.70307 -27.43853))",
 "TaxonKey is Petermannia"
 ]
}

 The dataset includes 620 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011445-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ryttwn
title: Occurrence Download

description: A dataset containing 4347 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-115.1647 37.65684,-115.378 37.67373,-115.4271 37.50599,-115.4504 37.61634,-115.6779 37.54731,-115.5296 37.24377,-115.7473 37.02409,-116.0185 37.27166,-115.928 36.99763,-115.9906 36.93546,-116.6995 36.9972,-116.8065 37.28315,-116.9092 37.19524,-117.0246 37.43963,-117.1808 37.52838,-117.879 37.40723,-117.9617 37.28309,-117.8731 37.28723,-117.7944 37.07732,-117.9544 37.00084,-117.9515 36.88746,-117.8227 36.66252,-117.5905 36.53221,-117.702 36.54888,-117.7001 36.33985,-117.8002 36.52408,-117.9937 36.60588,-118.0845 36.84138,-118.2462 36.70385,-118.0401 36.46577,-117.8747 35.6612,-118.1077 35.52994,-118.0064 35.30001,-118.067 35.21965,-118.7917 34.78093,-118.4387 34.71956,-117.4643 34.26589,-117.1769 34.41801,-116.4889 34.32896,-116.5167 34.16457,-116.3997 34.13626,-116.4803 34.10575,-116.3148 34.09686,-115.9023 33.67817,-115.4918 33.71225,-115.3721 33.95609,-115.2841 33.87187,-115.5649 34.39096,-115.3579 34.50802,-115.2336 34.50913,-115.1734 34.281,-115.0287 34.49015,-114.9045 34.48742,-114.8483 34.31828,-114.0637 34.52534,-113.7549 34.46349,-113.6928 34.6298,-113.9285 34.76649,-114.0439 35.11463,-113.8177 35.22367,-113.8187 35.40141,-113.7145 35.4153,-113.8815 35.71407,-114.0844 35.81357,-113.816 36.22755,-113.7161 36.52703,-113.7669 36.72443,-113.3502 36.84576,-113.2794 37.29557,-113.8386 37.20913,-113.9632 37.38364,-114.3332 37.26329,-114.575 37.38097,-114.8029 37.22457,-114.8184 37.32927,-114.9423 37.28012,-115.1626 37.47778,-115.1647 37.65684))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Oreoscoptes montanus"
 ]
}

 The dataset includes 4347 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011446-250802193616735/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.29825066
title: DEG values and WGCNA enrichment

description: DEGs estimated by DESeq2 and the WGCNA modules
DOI: 10.6084/m9.figshare.29825066.v1
title: DEG values and WGCNA enrichment

description: DEGs estimated by DESeq2 and the WGCNA modules
DOI: 10.15468/4q3usa
title: Selezione di fossili ‘Life evolution’ della collezione geopaleontologica Domenico Dal Lago | 'Life evolution' fossils selection of the Domenico Dal Lago's geo-paleontological collection

description: Life evolution is a selection of fossils arranged to tell the evolution of life and landscape in the Agno valley (north-eastern Italy) along almost 3,000,000 years. They are part of the historical collection “Domenico Dal Lago”, consisting of more than 12,000 (mainly) fossil specimens, donated in 1929 by Domenico Dal Lago himself to the Valdagno Municipality. Unfortunately the original Dal Lago's catolgue was lost, but some specimens have data regarding collection locality.
DOI: 10.15468/dl.c5qvn4
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011447-250802193616735/datasets/export for details.
DOI: 10.15468/dl.hg7frp
title: Occurrence Download

description: A dataset containing 6638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.64626 7.87133,-76.27222 7.87133,-76.27222 8.104,-76.64626 8.104,-76.64626 7.87133))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 6638 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011448-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gs7b3h
title: Occurrence Download

description: A dataset containing 10502 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lophoceros semifasciatus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 10502 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011449-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9abaf5
title: Occurrence Download

description: A dataset containing 0 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 (Empidonax wrightii)",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011451-250802193616735/datasets/export for details.
DOI: 10.25934/pr00011263
title: Identifying Factors That Predict Treatment Success in Patients with Chronic Pouchitis Using Vedolizumab

description: Pouchitis is a condition that can occur in people who have had surgery to remove their colon due to a disease called ulcerative colitis (a condition that causes long-term inflammation in the colon and the rectum.) In this surgery, a small part of the small intestine is used to create an internal “pouch” that stores stool. When this pouch becomes swollen and inflamed for a long time, it’s called chronic pouchitis. This ongoing inflammation causes problems like pain, frequent bowel movements, and other uncomfortable symptoms.

A recent study (called the EARNEST trial) tested a medication known as vedolizumab in people with chronic pouchitis that was not controlled by antibiotics (a type of medicine used to treat infections caused by bacteria). Vedolizumab turns off the gut-directed immune traffic, allowing the pouch lining to heal without suppressing the whole immune system. While antibiotics are useful for short, acute episodes, for people who keep flaring (especially after many antibiotic courses) vedolizumab may offer better and longer-lasting control, fewer side-effects and avoids the growing problem of antibiotic resistance (where bacteria change so that antibiotic medicines can't kill them or stop their growth).

In the study people felt better with the medication, but not everyone responded to the medication in the same way. 

Our research will look closely at the information from this study to find out what patient characteristics, such as their medical history, how serious their disease is, or results from lab tests, might help in understanding who will benefit most from vedolizumab.

By studying why some people respond better to the medication, this study aims to help doctors make more personalized decisions among these patients. This could lead to better treatment outcomes for patients suffering from chronic pouchitis and an improved quality of life.
DOI: 10.15468/dl.78txpv
title: Occurrence Download

description: A dataset containing 9632 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 (Empidonax wrightii)",
 "Country is one of (Anguilla, Antigua and Barbuda, Argentina, Aruba, Bahamas, Barbados, Belize, Bolivia (Plurinational State of), Bonaire, Sint Eustatius and Saba, Bouvet Island, Brazil, Cayman Islands, Chile, Colombia, Costa Rica, Cuba, Curaçao, Dominica, Dominican Republic, Ecuador, El Salvador, Falkland Islands (Malvinas), French Guiana, Grenada, Guadeloupe, Guatemala, Guyana, Haiti, Honduras, Jamaica, Martinique, Mexico, Montserrat, Nicaragua, Panama, Paraguay, Peru, Puerto Rico, Saint Barthélemy, Saint Kitts and Nevis, Saint Lucia, Saint Martin (French part), Saint Vincent and the Grenadines, Sint Maarten (Dutch part), South Georgia and the South Sandwich Islands, Suriname, Trinidad and Tobago, Turks and Caicos Islands, Uruguay, Venezuela (Bolivarian Republic of), Virgin Islands (British), Virgin Islands (U.S.))"
 ]
}

 The dataset includes 9632 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011452-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.642z8h
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvia glutinosa",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 35 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011456-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6vde8h
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ipomoea alba",
 "Country is Nepal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011453-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8uz3uc
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Iris barnumiae",
 "Geometry POLYGON ((26.04335 1.226334, 135.0263 1.226334, 135.0263 55.38525, 26.04335 55.38525, 26.04335 1.226334))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011454-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jn5quy
title: Occurrence Download

description: A dataset containing 40709 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lopholaimus antarcticus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 40709 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011457-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yku2m9
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Anableps microlepis)",
 "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 55 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011458-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5065/w096-4v91
title: ICARUS Chamber Experiment: UCR-CECERT-APL-Cocker Group_20110416_M-XYLENE/H2O2_Hydroxyl radical_No Seed_EPA1412B - Shun

description: Goals: Photooxidation of 2,4-DMP with OH under black lightsSummary: Targets: 2,4-DMP 200 ppb (A), m-xylene 200ppb (B), H2O2 1ppm (both) INSTRUMENTS: PILS-ToF, GC1,2, SMPS, vTDMA, APM, AMS, filtersOrganization: UCR-CECERT-APL-Cocker Group Lab Affiliation: University of California, Riverside, CE-CERT Chamber: EPA chamberExperiment Category: Photolysis, any phase, Aerosol formation, Aerosol aging, Blank/Control Oxidant: Hydroxyl radical Reactants: m-xylene, H2O2 Reaction Type: Photooxidation Relative Humidity: 0.01 Temperature: 28 Pressure: 0.015'' H2O
DOI: 10.3886/e230941
title: National Neighborhood Data Archive (NaNDA): PRISM Climate of Census Tracts, United States, 1981-2024

description: The PRISM NaNDA dataset provides daily weather data—minimum temperature (tmin), maximum temperature (tmax), and precipitation (ppt)—for all census tracts in the contiguous United States (CONUS) from 1981 to 2024. These data are derived from Oregon State University’s PRISM Climate Group (Northwest Alliance for Computational Science & Engineering & Oregon State University, 2025), which produces high-resolution (4 km x 4 km) gridded climate estimates.In addition to daily values, the dataset includes two types of annual tract-level summary measures:Percentiles (0.5th, 1st, 5th, 95th, 99th, and 99.5th), calculated using a rolling 10-year window of historical data, available for tmin, tmax, and ppt. Percents, representing the proportion of days per year that fall above or below these percentile thresholds, available for tmin and tmax only.These features enable robust analyses of long-term environmental trends, extreme weather events, and their potential impacts on population health.<br>
description: United States Census Tracts. Smallest Geographic Unit: United States Census Tracts