cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15236857
title: Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq - parameter optimization output data

description: Description: 

This repository is in supplementary to the main respository (https://doi.org/10.5281/zenodo.15223778) of the following study: 

Hefei Zhang#, Xuhang Li#, Dongyuan Song, Onur Yukselen, Shivani Nanda, Alper Kucukural, Jingyi Jessica Li, Manuel Garber, Albertha J.M. Walhout. Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq. (2025) Nature Communications, in press (# equal contribution, *: correspondng author)

This repository contains only a single file. This file contains the output directory of the EmpirDE parameter optimization and experimental benchmarking. To use it, please unzip the file and move the resulting 'output' folder to the following folder from the main repository 

output/ ==> "MetabolicLibrary/2_DE/output/" 

Please refer to the main repository for more details. 

Contact:

For any questions, please contact Xuhang (Hang) Li at Xuhang.Li@umassmed.edu.
DOI: 10.5281/zenodo.15236858
title: Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq - parameter optimization output data

description: Description: 

This repository is in supplementary to the main respository (https://doi.org/10.5281/zenodo.15223778) of the following study: 

Hefei Zhang#, Xuhang Li#, Dongyuan Song, Onur Yukselen, Shivani Nanda, Alper Kucukural, Jingyi Jessica Li, Manuel Garber, Albertha J.M. Walhout. Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq. (2025) Nature Communications, in press (# equal contribution, *: correspondng author)

This repository contains only a single file. This file contains the output directory of the EmpirDE parameter optimization and experimental benchmarking. To use it, please unzip the file and move the resulting 'output' folder to the following folder from the main repository 

output/ ==> "MetabolicLibrary/2_DE/output/" 

Please refer to the main repository for more details. 

Contact:

For any questions, please contact Xuhang (Hang) Li at Xuhang.Li@umassmed.edu.
DOI: 10.5281/zenodo.15238386
title: Lemmatized Beowulf Data

description: Three versions of Beowulf (Klaeber with diacritics, Klaeber without diacritics, and Complete corpus of Anglo-Saxon Poetry) all lemmatized by Stanza's Old English model.
DOI: 10.6084/m9.figshare.28821629.v1
title: data_simulation.xlsx

description: The data is for the simulation part of paper 'Coordinated Risk-Averse Bidding Strategy for a System of MultipleVirtual Power Plants with Demand Response' by Junan Wang and Zhengtao Ding
DOI: 10.15468/dl.nh6xb8
title: Occurrence Download

description: A dataset containing 349 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is ITA.17.1.17_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset includes 349 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0210205-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fuddny
title: Occurrence Download

description: A dataset containing 21252 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Helictotrichon pratense (L.) Besser"
 ]
}

 The dataset includes 21252 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036806-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pgctub
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caecum rapanuiense Raines & Pizzini, 2005"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080269-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fvrmny
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kitagawia macilenta (Franch.) Pimenov"
 ]
}

 The dataset includes 29 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071688-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kguw87
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calcarovula longirostrata (G.B.Sowerby I, 1828)"
 ]
}

 The dataset includes 139 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080351-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ze4ev
title: Occurrence Download

description: A dataset containing 2429 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Milium vernale M.Bieb.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2429 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080356-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gj4n79
title: Occurrence Download

description: A dataset containing 742 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Nonea micrantha Boiss. & Reut."
 ]
}

 The dataset includes 742 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014396-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.82an6e
title: Occurrence Download

description: A dataset containing 17529 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-74.0079448999999983 40.6230661999999967, -74.0079448999999983 40.6276302699999974, -74.0079448999999983 40.6310037200000025, -74.0079448999999983 40.6335834100000000, -74.0079448999999983 40.6357662300000015, -74.0079448999999983 40.6395365500000025, -74.0079448999999983 40.6429100000000005, -74.0027987800000062 40.6429100000000005, -73.9992364499999979 40.6429100000000005, -73.9950803899999983 40.6429100000000005, -73.9921117800000019 40.6429100000000005, -73.9885494499999936 40.6429100000000005, -73.9859766499999978 40.6429100000000005, -73.9806331599999965 40.6429100000000005, -73.9772681999999975 40.6429100000000005, -73.9772681999999975 40.6387428000000028, -73.9772681999999975 40.6341787300000021, -73.9772681999999975 40.6314005999999992, -73.9772681999999975 40.6276302699999974, -73.9772681999999975 40.6230661999999967, -73.9828101399999980 40.6230661999999967, -73.9881536299999993 40.6230661999999967, -73.9929034099999967 40.6230661999999967, -73.9960699300000044 40.6230661999999967, -73.9994343500000014 40.6230661999999967, -74.0022050599999943 40.6230661999999967, -74.0079448999999983 40.6230661999999967))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 17529 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088673-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pbn6fq
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Foudia eminentissima",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 35 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071682-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wsse9z
title: Occurrence Download

description: A dataset containing 353 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Schizothorax richardsonii (Gray, 1832)"
 ]
}

 The dataset includes 353 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0126871-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pvjkyw
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eurytemora raboti Richard, 1897"
 ]
}

 The dataset includes 75 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0119257-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ztpchg
title: Occurrence Download

description: A dataset containing 241 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melilotus polonicus (L.) Pall."
 ]
}

 The dataset includes 241 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0126358-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5zvc46
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pendanthura picardi Kensley & Schotte, 2000"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0128732-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tythwn
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Annesorhiza lateriflora (Eckl. & Zeyh.) B.-E.van Wyk"
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071662-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6cpne
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-74.0963182999999930 40.8418672999999970, -74.0963182999999930 40.8440180300000009, -74.0963182999999930 40.8461687599999976, -74.0963182999999930 40.8494665500000025, -74.0963182999999930 40.8526209500000022, -74.0963182999999930 40.8562055000000015, -74.0921629599999960 40.8562055000000015, -74.0898703999999952 40.8562055000000015, -74.0868614299999990 40.8562055000000015, -74.0847121700000031 40.8562055000000015, -74.0825628999999992 40.8562055000000015, -74.0798403999999948 40.8562055000000015, -74.0798403999999948 40.8527643299999994, -74.0798403999999948 40.8496099299999997, -74.0798403999999948 40.8467422900000017, -74.0798403999999948 40.8440180300000009, -74.0798403999999948 40.8418672999999970, -74.0818464799999958 40.8418672999999970, -74.0847121700000031 40.8418672999999970, -74.0864315799999957 40.8418672999999970, -74.0898703999999952 40.8418672999999970, -74.0920196699999991 40.8418672999999970, -74.0963182999999930 40.8418672999999970))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 159 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080307-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b9nxg9
title: Occurrence Download

description: A dataset containing 333 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Senna stipulacea (Aiton) H.S.Irwin & Barneby"
 ]
}

 The dataset includes 333 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0125321-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v2kz5q
title: Occurrence Download

description: A dataset containing 1299 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Peucedanum japonicum Thunb."
 ]
}

 The dataset includes 1299 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071645-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wtm4zc
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oithona minuta Scott T., 1894"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0126868-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t6kehd
title: Occurrence Download

description: A dataset containing 408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "TaxonKey is Cyperus eragrostis Lam."
 ]
}

 The dataset includes 408 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0102052-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vn3jzh
title: Occurrence Download

description: A dataset containing 3000 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Formicarius nigricapillus",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 3000 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071635-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vqk9ez
title: Occurrence Download

description: A dataset containing 484572 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 one of (Pardalotus striatus (Gmelin, 1789))",
 "Year is greater than or equal to 1980"
 ]
}

 The dataset includes 484572 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0125310-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sfabp4
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caelatura tigrina Absalão, 2002"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080342-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hukuwj
title: Occurrence Download

description: A dataset containing 18290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Pelophylax perezi (López-Seoane, 1885)"
 ]
}

 The dataset includes 18290 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036814-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6pxx4b
title: Occurrence Download

description: A dataset containing 3662 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Juncus minutulus (Albert & Jahand.) Prain"
 ]
}

 The dataset includes 3662 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109305-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nswafn
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anthoxanthum tongo (Trin.) Stapf"
 ]
}

 The dataset includes 150 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036851-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ztbkkc
title: Occurrence Download

description: A dataset containing 97030 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Streptopelia decaocto (Frivaldszky, 1838)"
 ]
}

 The dataset includes 97030 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109323-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.86kb95
title: Occurrence Download

description: A dataset containing 1500 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for prokaryotes or protist."
 ]
}

 The dataset includes 1500 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036831-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q74kek
title: Occurrence Download

description: A dataset containing 2657 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-117.2671928000000037 32.8431488000000016, -117.2671928000000037 32.8449333399999972, -117.2671928000000037 32.8462374200000014, -117.2671928000000037 32.8471983199999968, -117.2671928000000037 32.8487769500000013, -117.2671928000000037 32.8500123999999971, -117.2655461199999962 32.8500123999999971, -117.2647913999999929 32.8500123999999971, -117.2634877999999929 32.8500123999999971, -117.2614980900000035 32.8500123999999971, -117.2604003200000022 32.8500123999999971, -117.2593711600000006 32.8500123999999971, -117.2583419999999990 32.8500123999999971, -117.2569697800000057 32.8500123999999971, -117.2553230999999982 32.8500123999999971, -117.2553230999999982 32.8481592300000003, -117.2553230999999982 32.8467865100000012, -117.2553230999999982 32.8458255999999977, -117.2553230999999982 32.8441783399999991, -117.2553230999999982 32.8431488000000016, -117.2571070000000049 32.8431488000000016, -117.2588908799999956 32.8431488000000016, -117.2601258699999960 32.8431488000000016, -117.2610178099999985 32.8431488000000016, -117.2623900300000059 32.8431488000000016, -117.2633505799999938 32.8431488000000016, -117.2651344500000050 32.8431488000000016, -117.2663008399999995 32.8431488000000016, -117.2671928000000037 32.8431488000000016))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 2657 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080247-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tc6p52
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-73.9601145999999972 40.8632711999999998, -73.9601145999999972 40.8640066099999970, -73.9601145999999972 40.8647420300000022, -73.9601145999999972 40.8655935600000007, -73.9601145999999972 40.8663676800000033, -73.9601145999999972 40.8671417999999989, -73.9590665099999995 40.8671417999999989, -73.9583677100000045 40.8671417999999989, -73.9577465600000039 40.8671417999999989, -73.9566983499999964 40.8671417999999989, -73.9555337999999978 40.8671417999999989, -73.9555337999999978 40.8667160299999992, -73.9555337999999978 40.8660580299999978, -73.9555337999999978 40.8654000300000035, -73.9555337999999978 40.8648581500000034, -73.9555337999999978 40.8642388499999996, -73.9555337999999978 40.8632711999999998, -73.9564266000000003 40.8632711999999998, -73.9573971500000056 40.8632711999999998, -73.9580183099999999 40.8632711999999998, -73.9586394699999943 40.8632711999999998, -73.9593382700000035 40.8632711999999998, -73.9601145999999972 40.8632711999999998))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080272-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y978es
title: Occurrence Download

description: A dataset containing 16096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Phaseolus vulgaris L."
 ]
}

 The dataset includes 16096 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036862-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q9zz5y
title: Occurrence Download

description: A dataset containing 43391 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Moneses uniflora (L.) A.Gray"
 ]
}

 The dataset includes 43391 records from 441 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036863-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.