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172 results for “taxonomic annotation”
Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG (Sup. Material)
<p>Dataset encompassing:</p> <ul> <li>The recovered MAGs by 6 different metagenomics pipelines (ATLAS, DATMA, MetaWRAP, MUFFIN, nf-core/mag and SnakeMAGs) using a mock community as input (SRR8359173 and SRR9328980), complemented with the output from MAGFlow (v1.0.0) using these MAGs as input for their quality assessment and taxonomical annotation. </li> <li>The MAGs produced by nf-core/mag using rice/rhizosphere sequenced libraries (PRJNA663614, PRJNA448773 and PRJNA645385) in either single assembly/single binning or co-assembly/co-binning mode, complemented with the output from MAGFlow (v1.0.0) using these MAGs as input for their quality assessment and taxonomical annotation.</li> <li>Scripts, commands and configuration files to run the different pipelines (ATLAS, DATMA, MetaWRAP, MUFFIN, nf-core/mag and SnakeMAGs) and reproduce the experimental conditions.</li> <li>Outputs, commands and scripts to run Metabinner and Semibin in their default configuration using the rice soil samples co-assembly, along with the MAGFlow (v1.1.0) output to compare these binners against MetaBAT2.</li> </ul>
Planet Microbe Functional and Taxonomic annotation of Illumina WGS Prokaryotic Fraction for Semantic Web Analysis
<p>Functional and Taxonomic annotations computed from a subset of Illumina Whole-Genome Sequencing samples from the prokaryotic fraction of the <a href="https://www.planetmicrobe.org/">Planet Microbe</a> database. Data was computed using the pipeline available from https://github.com/hurwitzlab/planet-microbe-functional-annotation/, and post processing scripts from https://github.com/hurwitzlab/planet-microbe-semantic-web-analysis. Files contain total annotation counts of Interpro, GO and NCBITaxon annotations, as well as additional sample metadata. See readme.txt file for more information.</p>
Linked collectors and determiners for: An annotated taxonomic checklist of the Neotropical Gracillariidae (Lepidoptera) with links to the information on host plants and parasitoids.
Natural history specimen data linked to collectors and determiners held within, "An annotated taxonomic checklist of the Neotropical Gracillariidae (Lepidoptera) with links to the information on host plants and parasitoids". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/88192512-176a-4b60-8795-ac034f26ef66">https://bionomia.net/dataset/88192512-176a-4b60-8795-ac034f26ef66</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/88192512-176a-4b60-8795-ac034f26ef66">https://gbif.org/dataset/88192512-176a-4b60-8795-ac034f26ef66</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Annotated list of Mimallonidae (Lepidoptera, Mimallonoidea) from Trinidad and Tobago, with the description of a new species of Cicinnus Blanchard, 1852 and taxonomic notes.
Natural history specimen data linked to collectors and determiners held within, "Annotated list of Mimallonidae (Lepidoptera, Mimallonoidea) from Trinidad and Tobago, with the description of a new species of Cicinnus Blanchard, 1852 and taxonomic notes". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/73942cd9-b43b-4610-9506-5da911980691">https://bionomia.net/dataset/73942cd9-b43b-4610-9506-5da911980691</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/73942cd9-b43b-4610-9506-5da911980691">https://gbif.org/dataset/73942cd9-b43b-4610-9506-5da911980691</a>. Formatted as a Frictionless Data package.
TARA Pacific CDIV cnidarian host taxonomic annotation release version 1_1
<p>This data is the result of the primary analysis of the 18SV9 sequencing data and photos associated with the Coral Diversity dataset collected from all islands as part of the Tara Pacific expedition. A full README is contained within the data upload.</p>
Database of 16S sequences from SILVA (r114), filtered, curated and annotated to be used easily by programs of taxonomic assignments
<p>The database used for the taxonomic assignment of reads generally comes from the SILVA database (http://www.arb-silva.de/). The logic behind this database is to use the information from the best one to the worst one. This is why the curated database was splitted in two parts : the [C] sequences for Complete sequences in terms of taxonomy, and the [I] and [E] sequences, for Incomplete and Environmental sequences.</p> <p>Each sequence included into the database must have a specific format summarizing all needed information (example below):<br> >[I]AACY020336309;Archaea(superkingdom);Euryarchaeota(phylum);Thermoplasmata(class);Thermoplasmatales(order);Marine_Group_II(no_rank);;marine_metagenome</p> <p>This sequence is an incomplete one ([I]), with a specific accession number from NCBI or SILVA, or another database (AACY020336309). Then, all taxonomic data is separated using ';' characters, for each considered level (superkingdom, phylum, <br> class, order, family, and genus). The species name is the last one and separated by two ';' characters from the rest of the descriptive line. Finally, the descriptive line must not contain specific characters like spaces. If one or several levels are unknown, this is indicated by 'no_rank'.</p> <p>Another example here for [C] sequences:<br> >[C]AAAK03000010;Bacteria(superkingdom);Firmicutes(phylum);Bacilli(class);Lactobacillales(order);Enterococcaceae(family);Enterococcus(genus);;Enterococcus_faecium_DO<br> This sequence is a complete one ([C]), with a specific accession number from NCBI or SILVA, or another database (AACY020187844). Then, all taxonomic data is separated using ';' characters, for each considered level (superkingdom, phylum, <br> class, order, family, and genus). The species is the last one and separated by two ';' characters from the rest of the descriptive line. Complete sequences must have six levels of information (superkingdom, phylum, class, order, family, and genus). If it is not the case, the sequence will be considered as Incomplete ([I]) (between three and five levels), or Environmental ([E]) (with only the superkingdom and the phylum levels).</p> <p>Another example here for [E] sequences:<br> >[E]U59968;Archaea(superkingdom);Thaumarchaeota(phylum);Soil_Crenarchaeotic_Group(SCG)(no_rank);;uncultured_crenarchaeote<br> This sequence is a environmental one ([E]), with a specific accession number from NCBI or SILVA, or another database (U59968). Then, all taxonomic data is separated using ';' characters, for each considered level (superkingdom, phylum, class, order, family, and genus). The species is the last one and separated by two ';' characters from the rest of the descriptive line. Complete sequences <br> must have six levels of information (superkingdom, phylum, class, order, family, and genus). If it is not the case, the sequence will be considered as Incomplete ([I]) (between three and five levels), or Environmental ([E]) (with only the superkingdom and the phylum levels).</p> <p>More details on the steps defined to clean and define this new database can be available on demand (sebastien.terrat@inra.fr).</p>
Taxonomic and functional annotations of transcripts and proteins derived from a Metatranscriptomic study of microbial eukaryotes from Lake Pavin
<p>These data were obtain as part of a metatranscriptomic study (Monjot <em>et al.,</em> 2023, 2024). All scripts to obtain these annotations are available at https://github.com/amonjot/SSN_Monjot_2024. The sequencing data (i.e. metatranscriptomic) used to obtain this taxonomic and functional information are archived at ENA under accession number PRJEB61515.</p> <p>This repository also contains various protein sequence similarity networks (Lagoon_output.zip). As these files are very time-consuming to produce, we have provided them to complete all the steps in Monjot <em>et al,</em> 2024. All procedures to produce them are present on the following github repository : https://github.com/amonjot/SSN_Monjot_2024.</p> <p> </p>
Diamond database for taxonomic annotation of fungal metatranscriptomics
<p>This is a protein fasta dataset for use with <a href="https://github.com/bbuchfink/diamond">diamond</a>. The <strong>fasta.gz</strong> file contains protein sequences for the following:</p> <ul> <li>1,164 genomes downloaded from JGI (<strong>taxonomy_taxids.tsv</strong>)</li> <li>121 genomes that are part of the <a href="https://bitbucket.org/dbeisser/taxmapper/src/master/">taxmapper</a> database (<strong>taxmapper_taxonomy_taxids.tsv</strong>) of which 6 were fungal</li> <li>the <em>Hygrophorus russula </em>MG78<em> </em>genome downloaded from NCBI.</li> </ul> <p>For the <em>H. russula</em> genome, genes were predicted using Augustus (v. 3.2.3) with the laccaria_bicolor model.</p> <p>The final protein database consists of a total of 17,694,143 protein sequences (14,976,193 from JGI, 2,708,401 from taxmapper and 9,549 from <em>H. russula</em>).</p> <p>The fasta file and associated taxonomic information files (nodes.dmp.gz & taxonmap.gz) can be used to build a diamond database compatible with diamond version 0.9.22:</p> <pre><code class="language-bash">zcat fasta.gz | diamond makedb -d diamond --taxonmap taxonmap.gz --taxonnodes nodes.dmp</code></pre> <p> </p>
Taxonomic and functional annotations of the Integrated non-redundant Gene Catalog 9.9
<p>The Integrated non-redundant Gene Catalog (<strong>IGC</strong>) 9.9 is a database of 9.9 million genes from 1267 individual fecal samples together with the Homo sapiens database (MetaHIT project, grant agreement 201052). This repository contains the taxonomic and functional annotation of the IGC database.</p> <p><strong>full_taxonomy_MetaHIT99.tsv </strong>: Taxonomic assignment of proteins from IGC database with the sequence aligner DIAMOND against the non-redundant NCBI database, with an e-value threshold of 10<sup>-4</sup> </p> <p><strong>KEGG89_IGC_hs99.table</strong> : Functional annotation of proteins from IGC database with KEGG resource with an e-value threshold of 10<sup>-5</sup>, a bit-score threshold of 60 and using the sensitive mode of DIAMOND</p>
FIGURES 30, 31 in Annotated list of Mimallonidae (Lepidoptera, Mimallonoidea) from Trinidad and Tobago, with the description of a new species of Cicinnus Blanchard, 1852 and taxonomic notes
FIGURES 30, 31. Additional lectotypes designated in this work (for the lectotype of C. beta see Figs 1, 4), a= recto, b= verso. 30. Trogoptera guianaca male, French Guiana, Nouveau Chantier, photo courtesy of D. Herbin (USNM). 31. Cicinnus magnapuncta female, Trinidad, Tabaquite, photo courtesy of A. Giusti (NHMUK). Scale bar= 1 cm.
FIGURES 17–29 in Annotated list of Mimallonidae (Lepidoptera, Mimallonoidea) from Trinidad and Tobago, with the description of a new species of Cicinnus Blanchard, 1852 and taxonomic notes
FIGURES 17–29. Mimallonidae of Trinidad. 17. Druentica coralie male, Trinidad, Arima Valley, 800–1200 ft (AMNH). 18. D. coralie female, Trinidad, ex. Clidemia hirta, photo courtesy of M. Ramadan (HDOA). 19. D. patawa male, Trinidad, Hollis Reservoir (MJWC). 20. D. patawa female paratype, French Guiana, Kaw Rd., 286 m (CDH). 21. Lacosoma ostrinum male, Trinidad, Off Saunders Road, Inniss Field, 50 m (MJWC). 22. L. ostrinum female, Trinidad, 2.5 mi SE of Valencia, Valencia Forest (MJWC). 23. Trogoptera guianaca male, Trinidad, Morne Bleu, Textel Installation (MJWC). 24. T. belilia female, Trinidad, Off Saunders Road, Inniss Field, 50 m (MJWC). 25. L. valva male, French Guiana, Réserve des Nouragues, Inselberg DZ, photo courtesy of P. Collet (CPC). 26. L. valva female, Trinidad, 2.5 mi SE of Valencia, Valencia Forest (MJWC). 27. Mimallo amilia male, Trinidad, Curepe (MJWC). 28. M. amilia female, Trinidad, Arima Valley (MJWC). 29. Zaphanta infantilis male, Trinidad, 2.5 mi SE of Valencia, Valencia Forest (MJWC). Scale bar= 1 cm.
FIGURES 4, 5. Cicinnus male genitalia, a in Annotated list of Mimallonidae (Lepidoptera, Mimallonoidea) from Trinidad and Tobago, with the description of a new species of Cicinnus Blanchard, 1852 and taxonomic notes
FIGURES 4, 5. Cicinnus male genitalia, a= ventral, b= lateral. 4. C. beta lectotype, Costa Rica, Sixaola River, St Laurent diss.: 8-29-16:1 (USNM). 5. C. trini holotype, Trinidad, St. George, Morne Bleu Textel Installation, St Laurent diss.: 5-19-16:1 (USNM). Scale bar= 1 mm.
FIGURES 1–3. Cicinnus adults, a in Annotated list of Mimallonidae (Lepidoptera, Mimallonoidea) from Trinidad and Tobago, with the description of a new species of Cicinnus Blanchard, 1852 and taxonomic notes
FIGURES 1–3. Cicinnus adults, a= recto, b= verso. 1. C. beta male, lectotype, Costa Rica, Sixaola River (USNM). 2. C. beta male, Panama, Río Trinidad (USNM). 3. C. trini male, holotype, Trinidad, St. George, Morne Bleu Textel Installation (USNM). Scale bar= 1cm.
FIGURES 7–16 in Annotated list of Mimallonidae (Lepidoptera, Mimallonoidea) from Trinidad and Tobago, with the description of a new species of Cicinnus Blanchard, 1852 and taxonomic notes
FIGURES 7–16. Mimallonidae of Trinidad. 7. Alheita caudina male, Trinidad, 2.5 mi SE of Valencia, Valencia Forest (MJWC). 8. A. caudina female, Trinidad, La Brea Ward, Parrylands Oilfield (MJWC). 9. Cicinnus magnapuncta (putative), male, French Guiana, St. Jean du Maroni, photo courtesy of P. Collet (MNHN). 10. C. magnapuncta female, Trinidad, Cumaca Road, 4.6 mi (MJWC). 11. C. trini male, paratype, Trinidad, Hollis Reservoir (MJWC). 12. C. trini male, paratype, Trinidad, Cumaca Road, 4.6 mi (MJWC). 13. C. incerta male, Trinidad, Curepe (MJWC). 14. C. incerta female, French Guiana, Mont Itoupé, 800 m, photo courtesy of P. Collet (CPC). 15. C. joanna male, French Guiana, Saül, Point de Vue, photo courtesy of P. Collet (CPC). 16. C. joanna female, Trinidad, Brigand Hill Lighthouse (MJWC). Scale bar= 1 cm.
FIGURE 7 in Freshwater and brackish water fishes of Sakhalin Island (Russia) in inland and coastal waters: an annotated checklist with taxonomic comments
FIGURE 7. The total number of brackish-water and freshwater fish species of Sakhalin, according to various sources and our data
FIGURE 8 in Freshwater and brackish water fishes of Sakhalin Island (Russia) in inland and coastal waters: an annotated checklist with taxonomic comments
FIGURE 8. Species by habitat. Abbrevations: Fr.—freshwater species, Fr.-Br.—freshwater and brackish species, Mr.-Br.—marine and brackish species, An.—anadromous species, An-Res.—anadromous species with landlocked forms, Am—amphidromous species.
FIGURE 6 in Freshwater and brackish water fishes of Sakhalin Island (Russia) in inland and coastal waters: an annotated checklist with taxonomic comments
FIGURE 6. Map of Sakhalin Island with indication of natural entities (islands, rivers, lakes, gulfs, etc.).
Supplementary material 2 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Set of 13 Euler/X toolkit output Maximally Informative Relations: Explanation note: Set of 13 Euler/X toolkit output Maximally Informative Relations (MIR) and alignment visualizations for the input data files provided in Suppl. material 1. Each output file is saved in. csv (MIR) and. pdf (alingments) format, respectively. Dryad. doi: 10.5061/dryad.53mv1
Supplementary material 1 from: Jansen MA, Franz NM (2015) Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments. ZooKeys 528: 1-133. https://doi.org/10.3897/zookeys.528.6001
Set of 13 Euler/X toolkit input data files: Explanation note: Set of 13 Euler/X toolkit input data files for all alignments produced for Minyomerus [JF2015] use case (Figs 3, 4). Each file is saved in txt format and contains annotations and instructions for run commands to yield the alignments and visualizations shown in the corresponding figures. Dryad. doi: 10.5061/dryad.53mv1
Supplementary material 1 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The sequences renamed during the workshop. The INSDC accession number, the original INSDC name, and the new UNITE name are shown :
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.