cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14046824
title: gapseq reference sequence databases for Bacteria and Archaea

description: The repository contains the protein sequences used by gapseq to predict the presence of metabolic reactions and to construct metabolic models.

The workflow using gapseq to generate this set of reference protein sequences:

 

```sh

# delete all "old" datarm dat/seq/Bacteria/rev/*.fastarm dat/seq/Bacteria/unrev/*.fastarm dat/seq/Bacteria/rxn/*.fastarm dat/seq/Archaea/rev/*.fastarm dat/seq/Archaea/unrev/*.fastarm dat/seq/Archaea/rxn/*.fasta

# run gapseq find to re-download everything## the genome is irrelevant as no blasting is performed ('-x')gapseq find -p all -t Bacteria -n -x -U toy/ecoli.faa.gz > bac_update.log 2>&1gapseq find -p all -t Archaea -n -x -U toy/ecoli.faa.gz > ar_update.log 2>&1

# create all sequence .tar.gz archives (rev/unrev/rxn)cd dat/seq/Bacteria/rev/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Bacteria/unrev/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Bacteria/rxn/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Archaea/rev/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Archaea/unrev/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Archaea/rxn/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../

# create md5sum table for all tar.gz archivescd dat/seq/find -mindepth 2 -type f -name "*.tar.gz" -exec md5sum {} \; > md5sums.txt

# create taxon-specific final archive for Zenodo uploadtar -czvf Bacteria.tar.gz Bacteria/*/*.tar.gztar -czvf Archaea.tar.gz Archaea/*/*.tar.gz

# Upload Bacteria.tar.gz, Archaea.tar.gz, and md5sums.txt  to Zenodo via the web-interface

```
DOI: 10.15468/dl.9w3mtf
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Digitaria angolensis Rendle",
 "Continent is Africa"
 ]
}

 The dataset includes 113 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000667-241106120511685/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vepm2a
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Naturalis Biodiversity Center (NL) - Pisces",
 "Country is Croatia"
 ]
}

 The dataset includes 22 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000664-241106120511685/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7294/26331772
title: Dangerous Harbor Project - Old Rappahannock County - Reel 22 - 1692-1695 - TIFFs 251-276

description: This dataset includes 26 TIFF files showing court orders from Old Rappahannock County in Virginia. They were created to settle disputes between residents within Old Rappahannock County and ultimately issue punishments, judgments, and fines. These documents were used to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape.<br>To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.7294/26331772.v1
title: Dangerous Harbor Project - Old Rappahannock County - Reel 22 - 1692-1695 - TIFFs 251-276

description: This dataset includes 26 TIFF files showing court orders from Old Rappahannock County in Virginia. They were created to settle disputes between residents within Old Rappahannock County and ultimately issue punishments, judgments, and fines. These documents were used to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape.<br>To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.15468/dl.jrzx9s
title: Occurrence Download

description: A dataset containing 398 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dendroctonus adjunctus Blandford, 1897"
 ]
}

 The dataset includes 398 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000666-241106120511685/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.78ge7n
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Occurrence of mammalia relicts at site Velika Pecina",
 "Country is Croatia"
 ]
}

 The dataset includes 20 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000668-241106120511685/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n4hqfy
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Occurrence records of southern African aquatic biodiversity",
 "Country is Croatia"
 ]
}

 The dataset includes 23 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000669-241106120511685/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6r7w4r
title: Occurrence Download

description: A dataset containing 329 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Digitaria brazzae (Franch.) Stapf",
 "Continent is Africa"
 ]
}

 The dataset includes 329 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000670-241106120511685/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wt2hqd
title: Occurrence Download

description: A dataset containing 2930113 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Philippines"
 ]
}

 The dataset includes 2930113 records from 1581 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000581-241106120511685/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/e5uerh
title: Study on the intraspecific variation of Capila lineata lineata Chou & Gu, 1994, with some taxonomic notes on the related taxa (Hesperiidae, Pyrginae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Xue, Guoxi, Xie, Yunxiao, Shen, Guangcai, Li, Xiaojuan, Li, Meng, Guo, Yingcheng (2024): Study on the intraspecific variation of Capila lineata lineata Chou & Gu, 1994, with some taxonomic notes on the related taxa (Hesperiidae, Pyrginae). Zootaxa 5446 (4): 573-580, DOI: 10.11646/zootaxa.5446.4.9, URL: http://dx.doi.org/10.11646/zootaxa.5446.4.9AbstractThe history with regard to questions on Capila lineata lineata Chou & Gu, 1994, C. lineata magna Devyatkin & Monastyrskii, 1999, C. lineata irregularis Devyatkin & Monastyrskii, 2002 and C. neolineata Fan, Wang & Huang, 2003 was reviewed. The intraspecific variation of C. lineata lineata was explored by DNA barcoding and morphological comparison. The results revealed a remarkable variability in wing patterns and a slight variability in female genitalia, whereas characters of the male genitalia were uniform. C. lineata irregularis syn. n. and C. neolineata syn. n. are treated as junior subjective synonyms of C. lineata lineata because morphological characters of the two taxa fall into the range of individual variation of the latter.
DOI: 10.15468/jrqb3x
title: The late Givetian (Middle Devonian) ammonoid Epitornoceras Frech, 1902 from Argentina (southwestern Gondwana)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Allaire, Ninon, Rustán, Juan J., Korn, Dieter, Vaccari, Emilio, Ezpeleta, Miguel, Balseiro, Diego (2024): The late Givetian (Middle Devonian) ammonoid Epitornoceras Frech, 1902 from Argentina (southwestern Gondwana). Geodiversitas 46 (7): 327-341, DOI: 10.5252/geodiversitas2024v46a7, URL: https://sciencepress.mnhn.fr/sites/default/files/articles/pdf/g2024v46a7.pdfABSTRACTDuring the Early to Middle Devonian, southwestern Gondwana was characterized by circumpolar marine environments with striking phases of increased endemism and near absence of typical Paleozoic groups (mainly conodonts, graptolites and stromatoporoids), which defined the Malvinoxhosan (Malvinokaffric) Realm. One of these clades is the Ammonoida. They are extremely rare: only a few occurrences were reported in Bolivia and Argentina in deposits ranging from early Eifelian to early Frasnian. The taxonomy of the only Devonian ammonoid species known from Argentina, Tornoceras baldisi Leanza, 1968, was revised based on type material and new specimens from the type area (Chigua Formation, Precordillera, western Argentina). The stratigraphic polarity of the sedimentary succession was reinterpreted, and ammonoid fossils occur in the uppermost interval of the Chigua Formation. Tornoceras baldisi is herein assigned to the genus Epitornoceras Frech, 1902, and consequently a late Givetian age is proposed for those levels. These occurrences better constrain the age of the upper part of the Chigua Formation (Chavela Member), which is now considered younger than the Belén and Huamampampa formations from Bolivia and possibly coeval to the upper part of the Iquiri Formation. Although the ammonoids indicate a biogeographic dilution of the Malvinoxhosan signature during the late Middle Devonian, the realm is still recognizable on the basis of endemic trilobites as typical indicators.
DOI: 10.15468/dl.64wsye
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cousinia litvinovii Kult. ex Juz., 1940"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149810-230224095556074/datasets/export for details.
DOI: 10.15468/dl.humzdr
title: Occurrence Download

description: A dataset containing 1798 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 1798 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003876-150316153013904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.brmsxb
title: Occurrence Download

description: A dataset containing 7665 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phascolarctos cinereus (Goldfuss, 1817)",
 "Year 2020-2020"
 ]
}

 The dataset includes 7665 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149838-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hzoopp
title: Occurrence Download

description: A dataset containing 299902 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lotus corniculatus L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 299902 records from 630 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003875-150811131857512/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bgag4d
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lupinus tarapacensis C.P.Sm."
 ]
}

 The dataset includes 47 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149815-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.34jfcc
title: Occurrence Download

description: A dataset containing 4100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cinnamomum camphora (L.) J.Presl",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4100 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003875-150922153815467/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pnffxy
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cousinia lyrata Bunge"
 ]
}

 The dataset includes 9 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149818-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.klecpz
title: Occurrence Download

description: A dataset containing 5706 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Picea glauca (Moench) Voss"
 ]
}

 The dataset includes 5706 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003875-160509122628363/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h45krn
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cousinia mindshelkensis B.Fedtsch."
 ]
}

 The dataset includes 13 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149848-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yikitx
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucheria oligocephala J.Rémy"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003875-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.94b4u4
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cousinia malacophylla Rech.fil."
 ]
}

 The dataset includes 12 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149826-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cmt4yz
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Olea europaea subsp. cerasiformis G.Kunkel & Sunding"
 ]
}

 The dataset includes 24 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003875-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ey66sb
title: Occurrence Download

description: A dataset containing 9948 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phascolarctos cinereus (Goldfuss, 1817)",
 "Year 2017-2017"
 ]
}

 The dataset includes 9948 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149822-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmark0
title: Occurrence Download

description: A dataset containing 74345 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "DecimalLatitude is greater than 33.493212747744",
 "DecimalLatitude is less than 34.3085099561726",
 "DecimalLongitude is greater than -116.671398014941",
 "DecimalLongitude is less than -115.04659228296"
 ]
}

 The dataset includes 74345 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003875-171025204727650/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.degcg3
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cousinia macrolepis Boiss. & Hausskn."
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149823-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qer5ru
title: Occurrence Download

description: A dataset containing 230 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Pipilo albicollis P.L.Sclater, 1858"
 ]
}

 The dataset includes 230 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003875-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hc98e6
title: Occurrence Download

description: A dataset containing 7503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phascolarctos cinereus (Goldfuss, 1817)",
 "Year 2018-2018"
 ]
}

 The dataset includes 7503 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149827-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3jpxd3
title: Occurrence Download

description: A dataset containing 1963525 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1963525 records from 1097 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149829-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8s88bm
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Knema lampongensis W.J.de Wilde"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035595-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r4rgp6
title: Occurrence Download

description: A dataset containing 657395 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Year 1310-2017",
 "Geometry POLYGON((-100.098 37.195,-100.098 49.466,-70.591 49.466,-70.591 37.195,-100.098 37.195))",
 "HasCoordinate is true",
 "TaxonKey is Tracheophyta",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 657395 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008025-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6e44rw
title: Occurrence Download

description: A dataset containing 160 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 Craugastor saltator (Taylor, 1941)"
 ]
}

 The dataset includes 160 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042246-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uzf4yn
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Knema lunduensis (Sinclair) W.J.de Wilde"
 ]
}

 The dataset includes 70 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035624-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aigipd
title: Occurrence Download

description: A dataset containing 2098 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "DecimalLatitude is greater than 59.1844535388506",
 "DecimalLatitude is less than 59.9752534001862",
 "DecimalLongitude is greater than -135.894639389728",
 "DecimalLongitude is less than -134.56318547787"
 ]
}

 The dataset includes 2098 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008025-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9azrfr
title: Occurrence Download

description: A dataset containing 98 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Knema lenta Pierre ex Warb."
 ]
}

 The dataset includes 98 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035609-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9kwjd4
title: Occurrence Download

description: A dataset containing 343 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alchemilla tenuis Buser"
 ]
}

 The dataset includes 343 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043624-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s2kdbl
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Stenotritidae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is not null"
 ]
}

 The dataset includes 94 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008026-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e43t4t
title: Occurrence Download

description: A dataset containing 26524 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adonis vernalis L."
 ]
}

 The dataset includes 26524 records from 288 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016832-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.