cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/nyp-b9y-jbt
title: Silene villosa Forssk.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/gpufuh
title: MIRRI0076290

description: Organism type: Filamentous Fungi ; Taxon name: Hypocrea pulvinata ; Collection: CBS 120643 ; Country: Germany
DOI: 10.57907/mirri/j0n7ql/hsvmwz
title: MIRRI0076264.json

description: Strain json file
DOI: 10.57907/mirri/lbadm0/18ge4l
title: MIRRI0076318.json

description: Strain json file
DOI: 10.57907/mirri/mllbln/4fnej3
title: MIRRI0076254.json

description: Strain json file
DOI: 10.57907/mirri/z7nuxp
title: MIRRI0076260

description: Organism type: Filamentous Fungi ; Taxon name: Rhizopus oryzae ; Collection: CBS 120594 ; Country: France
DOI: 10.3535/a57-4kt-1dt
title: Stipagrostis acutiflora (Trin. & Rupr.) De Winter

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/4b4ltm
title: MIRRI0077124

description: Organism type: Filamentous Fungi ; Taxon name: Striatibotrys rhabdospora ; Collection: CBS 121801 ; Country: Spain
DOI: 10.57907/mirri/7ywdwv
title: MIRRI0077005

description: Organism type: Filamentous Fungi ; Taxon name: Hypomyces odoratus ; Collection: CBS 121668 ; Country: United States of America
DOI: 10.57907/mirri/89gnbg
title: MIRRI0077192

description: Organism type: Filamentous Fungi ; Taxon name: Aspergillus aculeatinus ; Collection: CBS 121877 ; Country: Thailand
DOI: 10.57907/mirri/8vohfe
title: MIRRI0077190

description: Organism type: Filamentous Fungi ; Taxon name: Aspergillus aculeatinus ; Collection: CBS 121875 ; Country: Thailand
DOI: 10.57907/mirri/9jnm3h/266sim
title: MIRRI0077220.json

description: Strain json file
DOI: 10.57907/mirri/ad8n7h/6kl7pb
title: MIRRI0077223.json

description: Strain json file
DOI: 10.57907/mirri/dhxkh1/nberhi
title: MIRRI0076993.json

description: Strain json file
DOI: 10.57907/mirri/eowoxn/elfmwm
title: MIRRI0077169.json

description: Strain json file
DOI: 10.57907/mirri/exp1ut
title: MIRRI0076966

description: Organism type: Filamentous Fungi ; Taxon name: Aspergillus brasiliensis ; Collection: CBS 121619 ; Country: Portugal
DOI: 10.57907/mirri/gv0i1q/hsxg1y
title: MIRRI0076985.json

description: Strain json file
DOI: 10.57907/mirri/hnshb2/lj863d
title: MIRRI0077027.json

description: Strain json file
DOI: 10.57907/mirri/hoxeut/s6ihsk
title: MIRRI0076976.json

description: Strain json file
DOI: 10.57907/mirri/iyhaxm/1imjnh
title: MIRRI0076974.json

description: Strain json file
DOI: 10.57907/mirri/ksjnce
title: MIRRI0076678

description: Organism type: Filamentous Fungi ; Taxon name: Ophiognomonia setacea ; Collection: CBS 121235 ; Country: United States of America
DOI: 10.57907/mirri/m2ccc0/9tcoiz
title: MIRRI0077205.json

description: Strain json file
DOI: 10.57907/mirri/mtruf9
title: MIRRI0077230

description: Organism type: Filamentous Fungi ; Taxon name: Nannizzia polymorpha ; Collection: CBS 121947 ; Country: French Guiana
DOI: 10.57907/mirri/nhmigs
title: MIRRI0077249

description: Organism type: Filamentous Fungi ; Taxon name: Phytophthora glovera ; Collection: CBS 121970 ; Country: Brazil
DOI: 10.57907/mirri/rdknwb
title: MIRRI0077181

description: Organism type: Filamentous Fungi ; Taxon name: Didymosphaeria futilis ; Collection: CBS 121866 ; Country: South Africa
DOI: 10.57907/mirri/ssvuav/sjfxks
title: MIRRI0076975.json

description: Strain json file
DOI: 10.57907/mirri/tgqvte/cezs5s
title: MIRRI0076708.json

description: Strain json file
DOI: 10.57907/mirri/tzfusk/rziauz
title: MIRRI0077194.json

description: Strain json file
DOI: 10.57907/mirri/vm10n0
title: MIRRI0076969

description: Organism type: Filamentous Fungi ; Taxon name: Cladosporium herbarum ; Collection: CBS 121622 ; Country: United States of America
DOI: 10.57907/mirri/wly8jt/s95yjd
title: MIRRI0077165.json

description: Strain json file
DOI: 10.57907/mirri/xlk3c9/jgdytt
title: MIRRI0077178.json

description: Strain json file
DOI: 10.57907/mirri/yipqlk/rlq317
title: MIRRI0077098.json

description: Strain json file
DOI: 10.57907/mirri/ypieg4
title: MIRRI0077213

description: Organism type: Filamentous Fungi ; Taxon name: Parengyodontium album ; Collection: CBS 121919 ; Country: India
DOI: 10.57907/mirri/zt9c1m
title: MIRRI0077186

description: Organism type: Filamentous Fungi ; Taxon name: Aspergillus aculeatinus ; Collection: CBS 121871 ; Country: Thailand
DOI: 10.57907/mirri/zupfgo
title: MIRRI0077019

description: Organism type: Filamentous Fungi ; Taxon name: Fusarium sacchari ; Collection: CBS 121683 ; Country: India
DOI: 10.3535/gal-4j9-d4x
title: Vitex agnus-castus L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/vqf-fp1-9yh
title: Stipagrostis obtusa (Delile) Nees

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/0wb0mg/d8u7ly
title: MIRRI0077204.json

description: Strain json file
DOI: 10.57907/mirri/m7rjpr/jw8ure
title: MIRRI0076676.json

description: Strain json file
DOI: 10.57907/mirri/nmbo4p
title: MIRRI0077197

description: Organism type: Filamentous Fungi ; Taxon name: Stilbospora macrosperma ; Collection: CBS 121883 ; Country: Austria
DOI: 10.57907/mirri/vjpqhq/u4auyx
title: MIRRI0076982.json

description: Strain json file
DOI: 10.57907/mirri/wbtwhf/kf0lmi
title: MIRRI0077191.json

description: Strain json file
DOI: 10.57907/mirri/x4ir3o/8qkylw
title: MIRRI0076263.json

description: Strain json file
DOI: 10.57907/mirri/yqus5m
title: MIRRI0077219

description: Organism type: Filamentous Fungi ; Taxon name: Scedosporium aurantiacum ; Collection: CBS 121926 ; Country: Netherlands
DOI: 10.3535/0g7-vbk-tjh
title: Cyperus conglomeratus Rottb.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/ghp-ks7-42x
title: Helianthemum lippii (L.) Dum. Cours.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/hhcclj/d0yclk
title: MIRRI0076694.json

description: Strain json file
DOI: 10.57907/mirri/ukpsah
title: MIRRI0076306

description: Organism type: Filamentous Fungi ; Taxon name: Purpureocillium lilacinum ; Collection: CBS 120676
DOI: 10.3535/hpy-vhg-esw
title: Juncus maritimus Lam.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/qf9-d69-0m0
title: Euphorbia dracunculoides subsp. inconspicua (Ball) Maire

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/2bzxxc/fceg8y
title: MIRRI0076728.json

description: Strain json file
DOI: 10.57907/mirri/2euy9w
title: MIRRI0076360

description: Organism type: Filamentous Fungi ; Taxon name: Fusarium veterinarium ; Collection: CBS 120768 ; Country: Netherlands
DOI: 10.57907/mirri/5bx2gv
title: MIRRI0077011

description: Organism type: Filamentous Fungi ; Taxon name: Xylaria enterogena ; Collection: CBS 121674 ; Country: French Guiana
DOI: 10.57907/mirri/85vqfx/e4zojy
title: MIRRI0076271.json

description: Strain json file
DOI: 10.57907/mirri/8e5uio/hiumdn
title: MIRRI0076310.json

description: Strain json file
DOI: 10.57907/mirri/9cwjwf/rwxbsf
title: MIRRI0077007.json

description: Strain json file
DOI: 10.57907/mirri/bzhk68
title: MIRRI0076754

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria breviramosa ; Collection: CBS 121331 ; Country: Australia
DOI: 10.57907/mirri/bzhk68/pzknuz
title: MIRRI0076754.json

description: Strain json file
DOI: 10.57907/mirri/c41ebx
title: MIRRI0076327

description: Organism type: Filamentous Fungi ; Taxon name: Bisifusarium delphinoides ; Collection: CBS 120714 ; Country: South Africa
DOI: 10.57907/mirri/ckafdp/tt0cpx
title: MIRRI0076323.json

description: Strain json file
DOI: 10.57907/mirri/czi4st
title: MIRRI0076776

description: Organism type: Filamentous Fungi ; Taxon name: Pseudocercospora fijiensis ; Collection: CBS 121359 ; Country: Panama
DOI: 10.57907/mirri/dmf1yf
title: MIRRI0076345

description: Organism type: Filamentous Fungi ; Taxon name: Teratosphaeria fimbriata ; Collection: CBS 120736 ; Country: Australia
DOI: 10.25345/c5cz32h84
title: MassIVE MSV000097994 - GNPS-CCFA_Complex_food_Spiking
title: Complex foods Kale pasta spiking with cheese and Trail mix spiked with walnuts at different proportions!!
DOI: 10.15468/dl.rtjsm6
title: Occurrence Download

description: A dataset containing 562 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cabassous centralis (Miller, 1899)"
 ]
}

 The dataset includes 562 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002019-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s9rwb5
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Mammal Collection (MHNG-MAMO) of Muséum d'histoire naturelle de la Ville de Genève",
 "Country is Croatia"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002020-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jjxsbm
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is ZMAA Insect collections of Åbo Akademi",
 "Country is Croatia"
 ]
}

 The dataset includes 30 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002018-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jxexyc
title: Occurrence Download

description: A dataset containing 399 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.40343 5.92082,-74.43178 5.92082,-74.43178 7.10527,-76.40343 7.10527,-76.40343 5.92082))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Argiope argentata (Fabricius, 1775)"
 ]
}

 The dataset includes 399 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002022-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15482231
title: MD Data set for the paper "UMD H2ase" - Part 2

description: This is the Part 2 of the UMD simulation Data of (un)binding pathways of H2 in complex with Df and Mdg H2ase. This part, Part 2, contains Trajectory files of Replica38 to Replica75 of Df H2ase.Also you can find the samples files (initial files) used to run the simulations for Df H2ase.
DOI: 10.5281/zenodo.15482230
title: MD Data set for the paper "UMD H2ase" - Part 2

description: This is the Part 2 of the UMD simulation Data of (un)binding pathways of H2 in complex with Df and Mdg H2ase. This part, Part 2, contains Trajectory files of Replica38 to Replica75 of Df H2ase.Also you can find the samples files (initial files) used to run the simulations for Df H2ase.
DOI: 10.5281/zenodo.15520947
title: MD Data set for the paper "UMD H2ase" - Part 2

description: This is the Part 2 of the UMD simulation Data of (un)binding pathways of H2 in complex with Df and Mdg H2ase. This part, Part 2, contains Trajectory files of Replica38 to Replica75 of Df H2ase.Also you can find the samples files (initial files) used to run the simulations for Df H2ase.
DOI: 10.17909/g701-t514
title: Solar EUV Evolution with COS N V Spectroscopy
DOI: 10.5524/100396
title: Supporting data for "eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database"

description: The structural information on proteins in their ligand-bound conformational state is invaluable for protein function studies and rational drug design. Compared to the number of available sequences, the repertoire of the experimentally determined structures of holo-proteins is not only limited, but also these structures do not always include pharmacologically relevant compounds at their binding sites. In addition, binding affinity databases provide vast quantities of information on interactions between drug-like molecules and their targets, however, often lacking structural data. On that account, there is a need for computational methods to complement existing repositories by constructing the atomic-level models of drug-protein assemblies that will not be determined experimentally in the near future. We created eModel-BDB, a database of 200,005 comparative models of drug-bound proteins based on 1,391,403 interaction data obtained from the Binding Database and the PDB library of January 31, 2017. Complex models in eModel-BDB were generated with a collection of the state-of-the-art techniques, including protein meta-threading, template-based structure modeling, refinement and binding site detection, and ligand similarity-based docking. In addition to a rigorous quality control maintained during dataset generation, a subset of weakly homologous models were selected for the retrospective validation against experimental structural data recently deposited to the Protein Data Bank. Validation results indicate that eModel-BDB contains models that are accurate not only at the global protein structure level, but also with respect to the atomic details of bound ligands. Freely available eModel-BDB can be used to support structure-based drug discovery and repositioning, drug target identification, and protein structure determination.
DOI: 10.5281/zenodo.1054086
title: Single Molecule, Full-Length Transcript Sequencing Provides Insight Into The Extreme Metabolism Of Ruby-Throated Hummingbird Archilochus Colubris

description: Hummingbirds can support their high metabolic rates exclusively by oxidizing ingested sugars, which is unsurprising given their sugar-rich nectar diet and use of energetically expensive hovering flight. However, they cannot rely on dietary sugars as a fuel during fasting periods, such as during the night, at first light, or when undertaking long-distance migratory flights, and must instead rely exclusively on onboard lipids. This metabolic flexibility is remarkable both in that the birds can switch between exclusive use of each fuel type within minutes and in that de novo lipogenesis from dietary sugar precursors is the principle way in which fat stores are built, sometimes at exceptionally high rates, such as during the few days prior to a migratory flight. The hummingbird hepatopancreas is the principle location of de novo lipogenesis and likely plays a key role in fuel selection, fuel switching, and glucose homeostasis. Yet understanding how this tissue, and the whole organism, achieves and moderates high rates of energy turnover is hampered by a fundamental lack of information regarding how genes coding for relevant enzymes differ in their sequence, expression, and regulation in these unique animals. To address this knowledge gap, we generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding a total of 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, including classification of reads and clustering of isoforms (ICE) followed by error-correction (Arrow). We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. We also aligned our transcriptome against the Calypte anna genome where possible. Finally, we closely examined homology of critical lipid metabolic genes between our transcriptome data and avian and human genomes. We confirmed high levels of sequence divergence within hummingbird lipogenic enzymes, suggesting a high probability of adaptive divergent function in the lipogenic liver pathways. Our results have leveraged cutting-edge technology and a novel bioinformatics pipeline to provide a compelling first direct look at the transcriptome of this incredible organism.
description: This dataset contains high quality Arrow-polished Pacbio Iso-seq data (HQD), Cogent dataset for gene family prediction and redundancy reduction, and ANGEL predictions for coding sequence (.cds), protein sequence (.pep), and untranslated region (.utr) from both HQD and Cogent. Additionally, Cogent annotations predicted using BLAST best match are included.

Pacific Biosciences for reagents and SMRTcells as well as technical support. M. Schatz, E. Jarvis, J. Korlach, Y. Guo for discussion. HFSP grant #RGP0062/2016. Natural Sciences and Engineering Research Council of Canada Discovery Grant (#386466) to KCW.
DOI: 10.5524/100378
title: Supporting data for "circlncRNAnet: An integrated web-based resource for mapping functional networks of long or circular forms of non-coding RNAs"

description: Despite their lack of protein-coding potential, lncRNAs and circRNAs have emerged as key determinant in gene regulation, acting to fine-tune transcriptional and signaling output. At the mechanistic level, regardless of the forms, these non-coding RNA transcripts have been known to impact expression of messenger RNAs (mRNAs) via epigenetic and post-transcriptional regulation. Given their widespread target spectrum as well as extensive modes of action, a complete understanding of their biological relevance will depend on integrative analyses of systems data at various levels. While a handful of publicly available databases have been reported, existing tools do not fully capture from a network perspective the functional implications of lncRNAs or circRNAs of interest. Through an integrated and streamlined design, circlncRNAnet is aimed to broaden the understanding of ncRNA candidates by testing in silico several hypotheses of ncRNA-based functions on the basis of large-scale RNA-seq data. It is implemented with several features representing advances in the bioinformatics of ncRNAs: 1) a flexible framework that accepts and processes user-defined NGS-based expression data; 2) multiple analytic modules that assigns and productively assesses the regulatory networks of user-selected ncRNAs by cross-referencing extensively curated databases; 3) an all-purpose, information-rich workflow design that is tailored to all types of ncRNAs. Outputs on expression profiles, co-expression networks &amp pathways, and molecular interactomes, are dynamically and interactively displayed according to user-defined criteria. In short, users may apply circlncRNAnet to obtain, in real time, multiple lines of functionally relevant information on the circRNAs/lncRNAs of their interest. In summary, circlncRNAnet is the first of its kind in the regulatory RNA research field, providing a "one-stop" resource for in-depth analyses of ncRNA biology.
DOI: 10.5524/100393
title: Supporting data for "The developmental transcriptome atlas of the spoon worm Urechis unicinctus (Echiurida: Annelida)"

description: Echiurida is one of the most intriguing major subgroups of the phylum Annelida, because unlike most other annelids, echiurids lack metameric body segmentation as adults. For this reason, transcriptome analyses from various developmental stages of Echiurid can be of substantial value for understanding precise expression levels and the complex regulatory networks during early and larval development.
A total of 914 million raw RNA-Seq reads were produced from 14 developmental stages of Urechis unicinctus, and were de novo assembled into contigs spanning 63,928,225 bp with an N50 length of 2,700 bp. The resulting comprehensive transcriptome database of the early developmental stages of U. unicinctus consists of 20,305 representative functional protein-coding transcripts. Approximately 66 % of unigenes were assigned to superphylum-level taxa, including Lophotrochozoa (40%). The completeness of the transcriptome assembly was assessed using BUSCO, and 75.7 % of the metazoan single-copy orthologs were presented in our transcriptome database. We observed three distinct patterns of global transcriptome profiles from 14 developmental stages, and identified a total of 12,705 genes that showed dynamic regulation patterns during the differentiation and maturation of U. unicinctus cells.
We present the first large-scale developmental transcriptome dataset of U. unicinctus and provide a general overview of the dynamics of global gene expression changes during its early developmental stages. The analysis of time-course gene expression data is a first step toward understanding the complex developmental gene regulatory networks in U. unicinctus, and will furnish a valuable resource for analyzing the functions of gene repertoires in various developmental phases.
DOI: 10.5524/100394
title: Supporting data for "Improving draft genome contiguity with reference-derived in silico mate-pair libraries"

description: Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. In order to improve genome contiguity, we have developed Cross-Species Scaffolding - a new pipeline which imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ~30x coverage of shotgun sequencing data.
DOI: 10.5524/100395
title: Supporting data for "Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing"

description: More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of two Illumina platforms.
<br>
Using fecal samples from 20 healthy individuals we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency, was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform versus the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the two Illumina platforms against each other.
<br>
By a newly developed overall accuracy quality control method, an average of 82.45 million high quality reads (96.06% of raw reads) per sample with 90.56% of bases scoring Q30 and above was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02% -3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias towards genes with higher GC content being enriched on the HiSeq platforms.
<br>
Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.