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Annotation and Post-Assembly Files associated with Talaromyces sp. UPCC 4333
<p>This is a companion dataset to the MRA-submitted article on the draft genome of <em>Talaromyces </em>sp. UPCC 4333. The dataset contains Bracker3 annotations, BUSCO results, and fungiSMASH files. </p>
Complete Medline abstracts corpus between 2015-2019 annotated Whatizit text annotation tool
<p><strong>Background: </strong></p> <p>Whatizit is a text processing system that allows you to do text-mining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Identified terms are wrapped with XML tags that carry additional information, such as the primary keys to the databases where all the relevant information is kept. The wrapping XML is translated into HTML hypertext links. This service is highly appreciated by people who are reading literature and need to quickly find more information about a particular term, e.g. its Gene Ontology term.</p> <p>Whatizit is used in identifying formalized language patterns, specialized, syntactically formalized, technical notation. The annotation speed of a given pipeline is almost independent of the size of the vocabulary behind it and is currently based on pattern matching. In addition, several vocabularies can be integrated in a single pipeline.</p> <p><strong>Methodology:</strong></p> <p>The pipeline used is comprised of 175k Gene Ontology terms (preferred labels + synonyms).<br> The annotation on Medline 2015-2019 corpus is done with <em>Gene Ontology (GO)</em> integrated dictionary.</p> <p>The .zip file contains 10 XML files - each file is for half an year of MEDLINE annotated abstracts.<br> In addition to the abstract, the title is also annotated for further information enrichment.</p> <p>Respective DOIs, PMIDs are also included in the XML, when applicable.</p> <p><strong>Further development:</strong></p> <p>The XML files can be converted into JSON, JSON-LD format.</p> <p> </p> <p> </p>
Figure 4 in The lycaenid butterfly fauna (Lepidoptera) of Cosñipata, Peru: annotated checklist, elevational patterns, and rarity
Figure 4. El Mirador (red marking), a site occupied by territorial males at 1,720m (image courtesy S. Kinyon).
Accurate annotation of protein coding sequences with IDTAXA - Training Data
<p>Training data used to test IDTAXA, HMMER, and BLAST performance of classification of amino acid and nucleotide sequences.</p>
Accurate annotation of protein coding sequences with IDTAXA - classification results
<p>Raw classification results generated by IDTAXA, BLAST, and HMMER on a training set scraped from KEGG of > 1.5M sequences. HMMER and BLAST results are also converted into IDTAXA like objects for ease of comparison.</p>
A New Comprehensive Annotation of Leucine-Rich Repeat-Containing Receptors in Rice
<p>Datasets for preprint (https://doi.org/10.1101/2021.01.29.428842) entitled "<strong>A new comprehensive Annotation of Leucine-Rich Repeat-Containing Receptors in Rice</strong>".</p> <p>This paper describes an in-depth manual curation of LRR-CR annotations including genes containing nonsense mutations, tagged as 'non-canonical', by opposition to 'canonical', that have expected gene models.</p> <p> </p> <p>Contains 7 files for each rice cultivar:</p> <p>- domain annotation for each LRR-CR protein (xxx_LRR_domains_filtered.csv)</p> <p>- gff file containing LRR-CR gene model annotations</p> <p>- fasta file (1): the complete genes 'gene' (nucleotide sequence, exons and introns)</p> <p>- fasta file (2): the coding sequences 'CDS' (nucleotide sequence, exons, translatable). Note that for genes experiencing frameshift, the one or two bases that cause the frameshift are avoided in order to have nucleotide sequence that can be translated. Terminal and in frame stop codons are encoded by a '*'.</p> <p>- fasta file (3): protein sequences 'PEP' (amino acid sequence, exons, corresponding to translation of CDS (2) )</p> <p>- fasta file (4): 'cDNA' (nucleotide sequence, exons). Note that for genes experiencing frameshift, the translated protein sequence will not correspond to the one present in the file (3). For all other genes, the files "CDS" and "cDNA" retrieve the same nucleotide sequences.</p> <p>- fasta file (5): 'cDNA_wFrameshit' (nucleotide sequence, exons) : same sequences than in (4) except for genes experiencing frameshift whose sequences are completed with one or two "!" characters at the position of the frameshift in order to conserve the right reading frame (also used by V. Ranwez et al. for the MACSE programs <a href="https://dx.doi.org/10.1093/molbev/msy159">https://dx.doi.org/10.1093/molbev/msy159</a> ).</p> <p> </p>
FIG. 5 in Annotated catalogue of types of Hawaiian land and freshwater snails (Mollusca: Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 5. — Amastridae: A, Helix textilis Férussac, 1825, possible syntype MNHN IM-2000-30770, 15.0 mm; B, Helix tristis Férussac, 1825, lectotype MNHN IM- 2000-30843, 19.3 mm, fig. 6 of Férussac in Quoy & Gaimard (1825); C, Helicteres turgidula Pease, 1870, lectotype MNHN IM-2000-30845, 13.7 mm; D, Helix turritella Férussac, 1821, possible syntype MNHN IM-2000-30846, 18.5 mm; E, Helix ventulus Férussac, 1825, lectotype MNHN IM-2000-30848, 12.9 mm. Ellobiidae: F, Auricula sandwichiensis Souleyet, 1852, lectotype MNHN IM-2000-30849, 11.5 mm, figs 31 & 32 of Souleyet (1852). Endodontidae: G, Endodonta henshawi Ancey, 1904, syntype MNHN IM-2000-9654, 2.1 mm (shell width), fig. 15 of Ancey (1904b). Lymnaeidae: H, Lymnaea oahouensis Souleyet, 1852, lectotype MNHN IM-2000-30850, 11.7 mm, figs 39 & 41 of Souleyet (1852). Punctidae: I, Endodonta horneri Ancey, 1904, syntype MNHN IM-2000-9655, 1.0 mm (shell width), fig. 11 of Ancey (1904b). Scale bars: A-F, H, 5 mm; G, I, 1 mm. Dimensions given are shell height unless otherwise stated; reproductions of original illustrations not to scale.
FIG. 4 in Annotated catalogue of types of Hawaiian land and freshwater snails (Mollusca: Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 4. — Amastridae: A, Helicteres laevis Pease, 1870, lectotype MNHN IM-2000-30828, 9.2 mm; B, Helix luteola Férussac, 1825, holotype MNHN IM-2000-30829, 17.0 mm; C, Helicter pachystoma Pease, 1869, lectotype MNHN IM-2000-30830, 13.0 mm; D, Helicteres rugulosa Pease, 1870, lectotype MNHN IM-2000-30831, 12.8 mm; E, Helicter simplex Pease, 1869, lectotype MNHN IM-2000-30834, 7.3 mm; F, Helicter solida Pease, 1869, syntype MNHN IM-2000-30836, 14.0 mm; G, Helicteres sphaerica Pease, 1870, lectotype MNHN IM-2000-30837, 10.1 mm; H, Helix spirizona Férussac, 1825, lectotype MNHN IM-2000-30839, 22.3 mm; I, Helicteres tenebrosa Pease, 1870, lectotype MNHN IM-2000-30841, 12.7 mm. Scale bars: 5 mm. Dimensions given are shell height.
FIG. 3 in Annotated catalogue of types of Hawaiian land and freshwater snails (Mollusca: Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 3. — Amastridae Pilsbry, 1910: A, Helicteres antiqua Pease, 1870, lectotype MNHN IM-2000-30817, not measured; B, Helicteres balteata Pease, 1870, lectotype MNHN IM-2000-30818, 11.8 mm; C, Helicter brevicula Pease, 1869, lectotype MNHN IM-2000-30819, 7.7 mm; D, Helicteres costulosa Pease, 1870, lectotype MNHN IM-2000-30821, 14.0 mm; E, Helicter cylindrata Pease, 1869, lectotype MNHN IM-2000-30822, 8.2 mm; F, Helicter erecta Pease, 1869, lectotype MNHN IM-2000-30824, 14.6 mm; G, Helix gravida Férussac, 1825, lectotype MNHN IM-2000-30825, 22.5 mm, fig. 4 of Férussac in Quoy & Gaimard (1825); H, Achatinella helvina Baldwin, 1895, possible syntype MNHN IM-2000-30133, 15.8 mm, fig. 30 of Baldwin (1895). Scale bars: A-F, 1 mm; G, 10 mm; H, 5 mm. Dimensions given are shell height; reproductions of original illustrations not to scale.
FIG. 2 in Annotated catalogue of types of Hawaiian land and freshwater snails (Mollusca: Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 2. — Achatinellidae Gulick, 1873: A, Tornatellina macromphala Ancey, 1904, syntype MNHN IM-2000-20013, 2.6 mm, fig. 3 of Ancey (1904a); B, Auriculella pulchra Pease, 1868, lectotype MNHN IM-2000-30813, 9.5 mm; C, Auriculella uniplicata Pease, 1868, lectotype MNHN IM-2000-30814, 7.3 mm, fig. 7 of Pease (1868); D, Helix vulpina Férussac, 1825, possible syntype MNHN IM-2000-30816, 18.0 mm, fig. 13 of Férussac in Quoy & Gaimard (1825). Scale bars: A-C, 1 mm; D, 10 mm. Dimensions given are shell height; reproductions of original illustrations not to scale.
FIG. 1 in Annotated catalogue of types of Hawaiian land and freshwater snails (Mollusca: Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 1. — Achatinellidae Gulick, 1873: A, Tornatellina cincta Ancey, 1904, syntype MNHN IM-2000-20012, 3.8 mm, fig. 5 of Ancey (1904a); B, Helicter compta Pease, 1869, lectotype MNHN IM-2000-30805, 24.7 mm; C, Helix decora Férussac, 1821, possible syntype MNHN IM-2000-30806,18.0 mm, fig. 3015 of Chemnitz (1795); D, Auriculella expansa Pease, 1868, lectotype MNHN IM-2000-30807, 6.4 mm, fig. 8 of Pease (1868); E, Helix lorata Férussac, 1825, lectotype MNHN IM-2000-30808, 14.2 mm, fig. 8 of Férussac in Quoy & Gaimard (1825); F, Helix lugubris Férussac, 1821, possible syntype MNHN IM-2000-30810, 17.2 mm, fig. 2062 of Chemnitz (1795). Scale bars: A, D, 1 mm; B, C, E, F, 10 mm. Dimensions given are shell height; reproductions of original illustrations not to scale.
Figure 3. Acanthoscelides camerinoi. A in The Bruchidae (Insecta: Coleoptera) of La Reserva de la Biósfera Sierra de Huautla, Morelos, Mexico, with descriptions of two new species and an annotated checklist
Figure 3. Acanthoscelides camerinoi. A) Male dorsal view. B) Male lateral view. C) Female dorsal view. D) Female lateral view.
Figure 1. Amblycerus montalvoi. A in The Bruchidae (Insecta: Coleoptera) of La Reserva de la Biósfera Sierra de Huautla, Morelos, Mexico, with descriptions of two new species and an annotated checklist
Figure 1. Amblycerus montalvoi. A) Male dorsal view. B) Male lateral view. C) Female dorsal view. D) Female lateral view.
FIG. 1. — A in Annotated catalogue of the types of Ampullariidae (Mollusca, Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 1. — A, Ampullaria aulanieri Deville & Huppé, 1850,lectotype MNHN 23072, 48.2 mm; B, Ampullaria baeri Dautzenberg,1902, lectotype MNHN 4493, 27.0 mm; C, Ampullaria begini Morlet, 1889, syntype MNHN 4499, 21.4 mm; D, Ampullaria belizensis Crosse & Fischer in Fischer & Crosse, 1888, holotype MNHN 5139, 61.8 mm; E, Meladomus bloyeti Bourguignat, 1889, lectotype MNHN 4501, 63.3 mm; F, Ampullaria bruguieri Deshayes, 1830, lectotype MNHN 23074, 72.1 mm; G, Ampullaria carinata Olivier, 1804, lectotype MNHN 23075, 28.5 mm; H, Ampullaria castanea Deshayes, 1830, lectotype MNHN 4710, 42.2 mm.
FIG. 5. — A in Annotated catalogue of the types of Ampullariidae (Mollusca, Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 5. — A, Lanistes neritoides Brown & Berthold, 1990, holotype MNHN 4515, 12.9 mm; B, Ampullaria neritoides d'Orbigny, 1835, probable syntype MNHN 4519, 97.2 mm; C, Afropomus balanoideus nimbae Binder, 1963, lectotype MNHN 4497, 18.8 mm; D, Ampullaria occlusa Crosse & Fischer in Fischer & Crosse, 1888, holotype MNHN 4514, 49.6 mm; E, Ampullaria ovata Olivier, 1804, syntype MNHN 4513, 64.3 mm; F, Ampullaria oviformis Deshayes, 1830, syntype MNHN 4512, 43.4 mm; G, Ampullaria perakensis Morgan, 1885, lectotype MNHN 4511, 33.6 mm; H, Ampullaria peristomata d'Orbigny, 1835,syntype MNHN 4509, 38.7 mm; I, Ampullaria pesmei Morlet, 1889, lectotype MNHN 4508, 30.2 mm.
FIG. 7. — A in Annotated catalogue of the types of Ampullariidae (Mollusca, Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 7. — A, Ampullaria simplicula Mabille,1889, lectotype MNHN 4520, 29.1 mm; B, Lanistes ellipticus var. β trapeziformis Furtado, 1886, lectotype MNHN 23089, 52.8 mm; C, Ampullaria violacea Valenciennes, 1833, holotype MNHN 4530, 43.1 mm; D, Ampullaria virescens Deshayes in Bory de Saint-Vincent,1824,holotype MNHN 24513,54.7 mm (also lectotype of Ampullaria polita Deshayes,1830);E, Ampullaria wellesleyensis Morgan, 1885, lectotype MNHN 24514, 34.1 mm; F, Lanistes zambesianus Furtado, 1886,holotype MNHN 4525, 55.6 mm; G, Ampullaria zonata d'Orbigny, 1835, syntype MNHN 4523, 38.2 mm (also lectotype of Ampullaria spixii d'Orbigny, 1838).
FIG. 3. — A, Ampullaria elegans d in Annotated catalogue of the types of Ampullariidae (Mollusca, Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 3. — A, Ampullaria elegans d'Orbigny, 1835, syntype MNHN 23081, 31.5 mm; B, Ampullaria turbinis var. erythrochila Dautzenberg & Fischer, 1905, lectotype MNHN 4738, 49.0 mm; C, Ampullaria eumicra Crosse & Fischer, 1890, lectotype MNHN 23082, 29.8 mm; D, Ampullaria gevesensis Deshayes, 1838,syntype MNHN 4473, 31.9 mm; E, Ampullaria (Lanistes) grasseti Morelet, 1863,probable syntype MNHN 4457, 29.5 mm; F, Ampullaria guyanensis Lamarck,1822, paralectotype MNHN 4459, 86.8 mm; G, Ampullaria insularum d'Orbigny, 1835, syntype MNHN 4463, 76.0 mm; H, Ampullaria intermedia Férussac in Quoy & Gaimard, 1825, lectotype MNHN 23083, 36.0 mm.
FIG. 2. — A in Annotated catalogue of the types of Ampullariidae (Mollusca, Gastropoda) in the Muséum national d'Histoire naturelle, Paris, with lectotype designations
FIG. 2. — A, Ampullaria castelnaudi Hupé, 1857, lectotype MNHN 23076, 103.9 mm; B, Ampullaria celebensis Quoy & Gaimard, 1834, lectotype MNHN 23077, 70.5 mm; C, Ampullaria chariensis Germain, 1905, lectotype MNHN 4478, 38.7 mm; D, Ampullaria columbiensis Reeve, 1856, syntype MNHN 4480, 36.8 mm; E, Ampullaria cousini Jousseaume, 1887, lectotype MNHN 4483, 43.0 mm; F, Ampullaria decocta Mabille, 1887, lectotype MNHN 23078, 29.7 mm; G, Ampullaria decussata Moricand, 1836, possible syntype MNHN 23079, 28.0 mm.
BiblIA - an Open Annotated Dataset
<p>Version 1.0, 6.8.2021, Daniel Stökl Ben Ezra (daniel.stoekl@ephe.psl.eu)</p> <p>This dataset for Handwritten Text Recognition includes layout segmentation (regions, toplines and linepolygons) and unicode-transcriptions in alto 4.2 XML for 202 images of Medieval Hebrew manuscripts from the Bibliothèque nationale de France (BnF, National Library of France) and the Biblioteca Apostolica Vaticana (BAV, Vatican Library) corresponding to the article "BiblIA - a General Model for Medieval Hebrew Manuscripts and an Open Annotated Dataset" by Daniel Stökl Ben Ezra, Bronson Brown-DeVost, Pawel Jablonski, Benjamin Kiessling, Elena Lolli, and Hayim Lapin, published in HIP@ICDAR 2021 held in Lausanne, September 2021.<br> The catalogue.txt file contains the information about the images, the shelfmarks of the manuscripts, their script-style (Ashkenazy, Italian, Sephardi), genre (Biblical, Rabbinic), date (where known), image-type (color or grayscale), iiif-manifest and links to download the images where it was impossible to include them directly here for copyright issues. The 132 corresponding images from the BnF are included here. For the 70 images from the BAV, the iiif-links are given in the catalogue.txt.<br> The schema for the alto files is http://www.loc.gov/standards/alto/v4/alto-4-2.xsd.<br> To create these files, we used the open source kraken OCR/HTR engine kraken (now at version 3.05) and the eScriptorium virtual research environment (https://escripta.hypotheses.org) created by the digital and computational task force of the research laboratory Archéologie & Philologie d'Orient et d'Occident (UMR 8546, CNRS - PSL (EPHE, ENS)).<br> This work was funded by the projects Scripta-PSL, Biblissima+ (Équipex ANR-11-EQPX-0007), Resilience (Horizon 2020 Grant Agreement 871127), and in particular Sofer Mahir.</p> <p>Licence CC-BY-NC-SA 4.0: https://creativecommons.org/licenses/by-nc-sa/4.0/</p> <p> </p>
Figures 16-19. Cayman Islands beetles. 16 in An annotated checklist of the Coleoptera (Insecta) of the Cayman Islands, West Indies
Figures 16-19. Cayman Islands beetles. 16) Melyrodes floridana (Melyridae). 17) Pelonium sp. A (Cleridae). 18) Charaphloeus bituberculatus (Laemophloeidae). 19) Hemipeplus marginipennis (Mycteridae).
ScienceDex guides
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.