cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7103525.v1
title: Additional file 21: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: Multiple Sequence Alignments for Conserved LncRNAs. A multiple sequence alignment file generated by ClustalW is included for each of the 39 groups of lncRNAs associated with orthologous genes across all five species. (ZIP 445 kb)
DOI: 10.5281/zenodo.10031810
title: Model Counting Competition 2020: Competition Instances

description: Instances for the Model Counting Competition 2020

- Track 1 (Model Counting)- Track 2 (Weighted Model Counting)- Track 3 (Projected Model Counting)

The even instances (trackX_000.mcc2020_cnf, trackX_000.mcc2020_cnf, ...) were made public for all participants during the testing phase of the solvers, whereas the private instances (trackX_001.mcc2020_cnf, trackX_003.mcc2020_cnf, ...) were used for the final evaluation and disclosed after the submission.  For details, we refer to: https://mccompetition.org/2020/mc_description.Instances originate from various publicly available data sets and submissions made after a call for benchmarks. The full instances from which we selected is available on Zenodo under Model Counting Competition 2020: Full Instance Set.For details, see the MCC2020 report (Fichte, Hecher, Hamiti: The Model Counting Competition 2020).

2023-10-22 (v3): Updated instances to the most recent competition format (MC2021).
DOI: 10.5281/zenodo.3934426
title: Model Counting Competition 2020: Competition Instances

description: Instances for the Model Counting Competition 2020

- Track 1 (Model Counting)- Track 2 (Weighted Model Counting)- Track 3 (Projected Model Counting)

The even instances (trackX_000.mcc2020_cnf, trackX_000.mcc2020_cnf, ...) were made public for all participants during the testing phase of the solvers, whereas the private instances (trackX_001.mcc2020_cnf, trackX_003.mcc2020_cnf, ...) were used for the final evaluation and disclosed after the submission.  For details, we refer to: https://mccompetition.org/2020/mc_description.Instances originate from various publicly available data sets and submissions made after a call for benchmarks. The full instances from which we selected is available on Zenodo under Model Counting Competition 2020: Full Instance Set.For details, see the MCC2020 report (Fichte, Hecher, Hamiti: The Model Counting Competition 2020).

2023-10-22 (v3): Updated instances to the most recent competition format (MC2021).
DOI: 10.6084/m9.figshare.7103624.v1
title: Additional file 6: of Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

description: Exon Locations of Pig LncRNAs. The genomic locations of the exons of all pig lncRNAs. (GTF 9045 kb)
DOI: 10.5281/zenodo.10666962
title: Appedix I Elasmobranch identification videos
DOI: 10.5281/zenodo.10666963
title: Appedix I Elasmobranch identification videos
DOI: 10.6084/m9.figshare.14966143
title: Additional file 3 of Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency

description: Additional file 3: Table S2. Sequence of TADs and origins (TAD3 & TAD4 & TAD5).
DOI: 10.25925/20231220
title: Multi-laboratory compilation of atmospheric carbon monoxide data for the period 1989-2022; obspack_co_1_GLOBALVIEWplus_v4.0_2024-02-13

description: A full list of all creators for this product can be found at www.esrl.noaa.gov/gmd/ccgg/obspack/providerlist/obspack_co_1_GLOBALVIEWplus_v4.0_2023-02-13.html.

This product is constructed using the Observation Package (ObsPack) framework [Masarie et al., 2014; www.earth-syst-sci-data.net/6/375/2014/]. The framework is designed to bring together atmospheric greenhouse gas (GHG) observations from a variety of sampling platforms, prepare them with specific applications in mind, and package and distribute them in a self-consistent and well-documented product. ObsPack products are intended to support GHG budget studies and represent a new generation of cooperative value-added GHG data products. This product includes 312 atmospheric carbon dioxide datasets derived from observations made by 38 laboratories. Data for the period 1989-2022 (where available) are included.
DOI: 10.6084/m9.figshare.14966177.v1
title: Additional file 7 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

description: Additional file 7: Table S6. Statistics of PCH.
DOI: 10.15468/dl.bnp28e
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus lanceolatus Roth",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087754-240321170329656/datasets/export for details.
DOI: 10.15468/dl.uhxtms
title: Occurrence Download

description: A dataset containing 160 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Potentilla alsatica T.Gregor"
 ]
}

 The dataset includes 160 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087756-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.azf9sf
title: Occurrence Download

description: A dataset containing 172 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Picea crassifolia Kom.",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 172 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087757-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wavbuz
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psylliostachys suworowii (Regel) Roshkova"
 ]
}

 The dataset includes 134 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087755-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10158012
title: Hybracter v0.7.0 Benchmarking Output

description: This dataset contains:



The subsampled FASTQ files used to benchmarking Hybracter (https://github.com/gbouras13/hybracter).

Benchmarking Output for Hybracter v0.7.0 vs Unicycler v0.5.0 vs Dragonflye v1.1.2 on these files.


The full benchmarking code and explanation is available https://github.com/gbouras13/hybracter_benchmarking. 

The `hybracter_benchmarking_fastqs.tar.gz` tarball will contain subsampled FASTQs (gzipped) of the first 20 samples used to benchmarking `hybracter`. These are the JKD6159, Lerminiaux, Chitale and super-accuracy model basecelled simplex ATCC fastqs.

The `PRJNA1087001_ATCC_SUP_Duplex_FAST_Simplex_fastqs.tar.gz` tarball will contain subsampled FASTQs (gzipped) of the 10 added samples in v2 of the prepint used to benchmarking `hybracter`. These are the fast model basecelled simplex ATCC fastqs and super-accuracy model basecelled duplex ATCC fastqs.

The other 4 tarballs ( `hybracter_benchmarking_results_v0.7.0.tar.gz`, `hybracter_benchmarking_results_fast.tar.gz`, `hybracter_benchmarking_results_duplex.tar.gz` and `hybracter_depth_Lerminiaux_isolateB_benchmarking_results.tar.gz`) contain benchmarking outputs for the first 20 samples, 5 fast model basecelled simplex ATCC samples, 5 super-accuracy model basecelled duplex ATCC and the depth analysis for Lerminiaux isolate B.

The when untared, each tarball will contain:



`BENCHMARKS` - contains the time etc benchmarking for each run (sample x tool)

`DNADIFF` - contains raw chromosome Dnadiff results for each run (sample x tool)

`DNADIFF_PARSED_OUTPUT` - contains parsed chromosome Dnadiff results for each sample

`DNADIFF_PLASMIDS` - contains plasmid Dnadiff results for each run (sample x tool)

`DNADIFF_PARSED_OUTPUT_PLASMID` - contains parsed plasmid Dnadiff results for each sample

`REAL` - this contains all the actual output for each assembler. The following 5 directories will contain the all the raw output with subdirectories for each sample:



`HYBRACTER_HYBRID_OUTPUT`

`HYBRACTER_LONG_OUTPUT`

`DRAGONFLYE_HYBRID_OUTPUT`

`DRAGONFLYE_LONG_OUTPUT`

`UNICYCLER_OUTPUT`

Additionally, `hybracter_benchmarking_results_v0.7.0.tar.gz` will have `HYBRACTER_HYBRID_OUTPUT_REAL_BULK` - this contains the output for the 12 Lerminiaux et al isolates assembled using `hybracter hybrid` with modified config file `bulk_assemble_lerminiaux_config.yaml`.



It will also contain a number of other subdirectories `_SUMMARIES`, `_PLASMIDS`, `_CHROMOSOMES` with parsed summary outputs and parsed specific plasmids and chromosome assemblies for Unicycler and Dragonflye (this made the assessment a lot easier and automated).


To untar e.g.

`tar -xzf hybracter_benchmarking_results_v0.7.0.tar.gz`
DOI: 10.5281/zenodo.10158013
title: Hybracter v0.4.0 Benchmarking Output

description: This dataset contains:

The subsampled FASTQ files used to benchmarking Hybracter (https://github.com/gbouras13/hybracter).
Benchmarking Output for Hybracter v0.4.0 vs Unicycler v0.5.0 vs Dragonflye v1.1.2 on these files.
The full benchmarking code and explanation is available https://github.com/gbouras13/hybracter_benchmarking. DOI: https://zenodo.org/doi/10.5281/zenodo.10157987.
The `hybracter_benchmarking_fastqs.tar.gz` file will contain all FASTQs (gzipped) used to benchmarking `hybracter`.
The `hybracter_benchmarking_results_v0.4.0.tar.gz` file will contain:

`BENCHMARKS` - contains the time etc benchmarking for each run (sample x tool)
`DNADIFF` - contains raw chromosome Dnadiff results for each run (sample x tool)
`DNADIFF_PARSED_OUTPUT` - contains parsed chromosome Dnadiff results for each sample
`DNADIFF_PLASMIDS` - contains plasmid Dnadiff results for each run (sample x tool)
`DNADIFF_PARSED_OUTPUT_PLASMID` - contains parsed plasmid Dnadiff results for each sample
`REAL` - this contains all the actual output for each assembler. The following 5 directories will contain the all the raw output with subdirectories for each sample:

`HYBRACTER_HYBRID_OUTPUT`
`HYBRACTER_LONG_OUTPUT`

Note there will also be a `LAST` subdirectory in the `HYBRACTER_HYBRID_OUTPUT` and `HYBRACTER_LONG_OUTPUT`. The output contained in it are the sample, but where hybracter is run with `--logic last`. These were mostly done to test the functionality, not so much from a benchmarking perspective.
Additionally, it should have `HYBRACTER_HYBRID_OUTPUT_REAL_BULK` - this contains the output for the 12 Lerminiaux et al isolates assembled using `hybracter hybrid` with modified config file `bulk_assemble_lerminiaux_config.yaml`.
`DRAGONFLYE_HYBRID_OUTPUT`
`DRAGONFLYE_LONG_OUTPUT`
`UNICYCLER_OUTPUT`
It will also contain a number of other subdirectories `_SUMMARIES`, `_PLASMIDS`, `_CHROMOSOMES` with parsed summary outputs and parsed specific plasmids and chromosome assemblies for Unicycler and Dragonflye (this made the assessment a lot easier and automated).
DOI: 10.5281/zenodo.10906937
title: Hybracter v0.7.0 Benchmarking Output

description: This dataset contains:



The subsampled FASTQ files used to benchmarking Hybracter (https://github.com/gbouras13/hybracter).

Benchmarking Output for Hybracter v0.7.0 vs Unicycler v0.5.0 vs Dragonflye v1.1.2 on these files.


The full benchmarking code and explanation is available https://github.com/gbouras13/hybracter_benchmarking. 

The `hybracter_benchmarking_fastqs.tar.gz` tarball will contain subsampled FASTQs (gzipped) of the first 20 samples used to benchmarking `hybracter`. These are the JKD6159, Lerminiaux, Chitale and super-accuracy model basecelled simplex ATCC fastqs.

The `PRJNA1087001_ATCC_SUP_Duplex_FAST_Simplex_fastqs.tar.gz` tarball will contain subsampled FASTQs (gzipped) of the 10 added samples in v2 of the prepint used to benchmarking `hybracter`. These are the fast model basecelled simplex ATCC fastqs and super-accuracy model basecelled duplex ATCC fastqs.

The other 4 tarballs ( `hybracter_benchmarking_results_v0.7.0.tar.gz`, `hybracter_benchmarking_results_fast.tar.gz`, `hybracter_benchmarking_results_duplex.tar.gz` and `hybracter_depth_Lerminiaux_isolateB_benchmarking_results.tar.gz`) contain benchmarking outputs for the first 20 samples, 5 fast model basecelled simplex ATCC samples, 5 super-accuracy model basecelled duplex ATCC and the depth analysis for Lerminiaux isolate B.

The when untared, each tarball will contain:



`BENCHMARKS` - contains the time etc benchmarking for each run (sample x tool)

`DNADIFF` - contains raw chromosome Dnadiff results for each run (sample x tool)

`DNADIFF_PARSED_OUTPUT` - contains parsed chromosome Dnadiff results for each sample

`DNADIFF_PLASMIDS` - contains plasmid Dnadiff results for each run (sample x tool)

`DNADIFF_PARSED_OUTPUT_PLASMID` - contains parsed plasmid Dnadiff results for each sample

`REAL` - this contains all the actual output for each assembler. The following 5 directories will contain the all the raw output with subdirectories for each sample:



`HYBRACTER_HYBRID_OUTPUT`

`HYBRACTER_LONG_OUTPUT`

`DRAGONFLYE_HYBRID_OUTPUT`

`DRAGONFLYE_LONG_OUTPUT`

`UNICYCLER_OUTPUT`

Additionally, `hybracter_benchmarking_results_v0.7.0.tar.gz` will have `HYBRACTER_HYBRID_OUTPUT_REAL_BULK` - this contains the output for the 12 Lerminiaux et al isolates assembled using `hybracter hybrid` with modified config file `bulk_assemble_lerminiaux_config.yaml`.



It will also contain a number of other subdirectories `_SUMMARIES`, `_PLASMIDS`, `_CHROMOSOMES` with parsed summary outputs and parsed specific plasmids and chromosome assemblies for Unicycler and Dragonflye (this made the assessment a lot easier and automated).


To untar e.g.

`tar -xzf hybracter_benchmarking_results_v0.7.0.tar.gz`
DOI: 10.15468/dl.f5tvaq
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria capizensis Merr."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087758-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.55xrz9
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseuderia smithiana C.Schweinf."
 ]
}

 The dataset includes 72 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087759-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sv4axb
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pulicaria alveolosa Batt. & Trab."
 ]
}

 The dataset includes 31 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087760-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n3vvyn
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus racemosus L.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087762-240321170329656/datasets/export for details.
DOI: 10.15468/dl.fkyw9q
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer miyabei Maxim.",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 23 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087761-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hfms45
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Potentilla altaica Bunge"
 ]
}

 The dataset includes 54 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087764-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pp7cbr
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myiopardalis pardalina (Bigot, 1891)"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087763-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.txq4k8
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Larix kaempferi (Lamb.) Carrière",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 120 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087765-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98d3j8
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psylliostachys volkii Rech.fil."
 ]
}

 The dataset includes 7 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087767-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.57suvg
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria capuronii A.P.Davis & Govaerts"
 ]
}

 The dataset includes 28 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087766-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wgrb2q
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseuderia sympodialis J.J.Sm."
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087768-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5vxku
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pulicaria angustifolia DC."
 ]
}

 The dataset includes 60 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087771-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t6qn54
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus secalinus L.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087770-240321170329656/datasets/export for details.
DOI: 10.15468/dl.xk6jj5
title: Occurrence Download

description: A dataset containing 179018 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apodemus sylvaticus (Linnaeus, 1758)"
 ]
}

 The dataset includes 179018 records from 1163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087616-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b2mr4z
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer saccharum Marshall",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087773-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uzuetz
title: Occurrence Download

description: A dataset containing 352 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Potentilla anachoretica Soják"
 ]
}

 The dataset includes 352 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087772-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kjes78
title: Occurrence Download

description: A dataset containing 989 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ptaeroxylon obliquum (Thunb.) Radlk."
 ]
}

 The dataset includes 989 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087774-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.es4qqx
title: Occurrence Download

description: A dataset containing 114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudolarix amabilis (J.Nelson) Rehd.",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 114 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087775-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xnwt6t
title: Occurrence Download

description: A dataset containing 160 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria cardiochlamys (Baill.) Schltr."
 ]
}

 The dataset includes 160 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087776-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.