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5,247 results for “cataloguing”
Crosswalk between CESSDA Data Catalogue (CDC) Metadata Profile and ECRIN Metadata Schema.
<p>This dataset contains two files: (1) a crosswalk between CESSDA Data Catalogue (CDC) DDI2.5 Metadata Profile (<a href="https://cmv.cessda.eu/profiles/cdc/ddi-2.5/1.0.4/profile.html">https://cmv.cessda.eu/profiles/cdc/ddi-2.5/1.0.4/profile.html</a>) and ECRIN Metadata Schema for Clinical Research Data Objects Version 6.0 (August 2021) (<a href="https://zenodo.org/record/5554961">https://zenodo.org/record/5554961</a>) with an extension to “geographical data” and (2) vice versa.</p>
New Soil Metagenome-Assembled Genomes Catalogue Boosts Genetic Resources
<p><strong>Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conducted the first large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalog) from 3,304 soil metagenomes. We identified 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which greatly expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8,545 CRISPR-Cas genes. Additionally, we determined that uSGBs contributed 84.6% of novel viral-host associations identified from the SMAG catalog. Our results propose the SMAG catalog, a novel and expansive genomic resource that brings the soil microbial biodiversity and novel genetic resources to light.</strong></p>
CLUSTER Data Catalogue
<p>This data catalogue describes the key metadata for all the CLUSTER datasets. For all datasets, the number of patients, treatment and timepoints available are described, In addition, for GWAS and omics datasets, tissue type, cell population, analysis platform and number of samples are provided.</p> <p>We are open to collaborating and sharing data with researchers who have research questions that may be answered by our data. Access to CLUSTER data is regulated according to the conditions of patient consent, study ethics and the CLUSTER Consortium’s policies. Access is available to researchers via an application to the CLUSTER data access committee - more details are available on <a href="http://www.clusterconsortium.org.uk">CLUSTER's website</a></p>
Catalogue of tools for digital scholarly editing
<p>This dataset is <strong>a catalogue of software products and computer tools that can be used to create digital scholarly editions (DSE)</strong>. The catalogue includes both tools specifically designed for use in the field of digital philology, mostly created by scholars and researchers in the field, and general-purpose tools that have been widely adopted in this field.</p> <p>For each tool, the following information is presented:</p> <ul> <li> <p>“<strong>Name</strong>”: the name of the tool.</p> </li> <li> <p>“<strong>Website</strong>”: the address of the official website, repository, or wiki that the creators of the tool offer as a showcase to learn about the tool.</p> </li> <li> <p>“<strong>Category</strong>”: one of the three macro-categories identified during the creation of the catalogue: “Visualization”, tools intended exclusively for the visualization (or publication) of a DSE; “Mixed”, tools that can be used for both processing and publishing a DSE; and finally, “Production”, tools that can replace or complement the philologist in a particular phase of the editorial process. The distinction between the proposed categories is not always clear-cut; tools have generally been categorized based on their main functionalities and the type of output or result they allow to obtain. A tool is categorized as either for visualization or mixed when it allows the production of a result that can be defined as a digital scholarly edition.</p> </li> <li> <p>“<strong>TaDiRAH activity</strong>”: one or more of the activities listed in the <a href="https://vocabs.dariah.eu/tadirah/en/">TaDiRAH taxonomy</a> that best describe the main functionalities of the tools.</p> </li> <li> <p>“<strong>Begin date</strong>”: the date in which the first public version of the tool was released. In cases where the tool was produced experimentally without reaching an official first version, the date of creation of the respective source code repository or the date indicated by the creator as the creation date on the website or in a publication is considered. When only the year is available the date is set on January first of that year. Respectively, when only the year and month are available, the date is set on the first day of the month.</p> </li> <li> <p>“<strong>End date</strong>”: the date in which the development of the tool was discontinued. When only the year is available the date is set on January first of that year. Respectively, when only the year and month are available, the date is set on the first day of the month.</p> </li> <li> <p>“<strong>Description</strong>”: a more or less brief text used on the website, repository, or wiki of the tool to present it to potential users. It is a more “commercial” than technical text, as its purpose is to encourage the use of the tool, and it briefly describes the main features and characteristics of the tool, with references to partner organizations. The description is included because it is interesting to analyze the words with which the creator presents their tool.</p> </li> <li> <p>“<strong>Institutional Partner(s)</strong>”: organizations that financially contributed to the development of the tool. These can be universities, research centers, cultural institutions, public projects, and funds. Since many of these funds are time-limited, I chose to include this information as it helps understand how stable a tool is in terms of development, maintenance, and user support.</p> </li> <li> <p>“<strong>Creator</strong>”: the name of the creator or creators of the tool. In the case of commercial software, the name of the company that produced it is provided. Similarly, if the tool was produced by a research center, a collective, or another type of group with an official name, the group’s name is provided. If the tool was created by one or more scholars, their respective names and affiliations are indicated.</p> </li> <li> <p>“<strong>Input Format(s)</strong>”: the various formats accepted by the tool as input. In some cases, it is not possible to obtain exact formats, as official sources indicate “text” or “image” generically. In these cases, the most commonly used formats, which are likely supported, are listed: TXT for text and JPEG for images.</p> </li> <li> <p>“<strong>Output Format(s)</strong>”: the output formats in which the tool allows exporting the DSE or other types of data. It should be noted that some tools, especially among mixed or visualization-only ones, do not provide data export.</p> </li> <li> <p>“<strong>Technologies</strong>”: programming languages, tools, libraries, and frameworks used to develop the tool. Some of the listed tools have been integrated into other tools (for example, OpenSeadragon and VisColl have been integrated into EVT).</p> </li> <li> <p>“<strong>System requirements</strong>”: indicates the nature of the tool, such as desktop software, a web-based service, a library, a web-based application, etc., and system requirements (e.g. compatible operating systems).</p> </li> <li> <p>“<strong>Collaborative working</strong>": indicates whether the tool is designed for collaborative work, allowing multiple users to work simultaneously on the same materials.</p> </li> <li> <p>“<strong>Open Source</strong>”: indicates whether the source code of the tool is freely accessible.</p> </li> <li> <p>“<strong>Repository</strong>”: the address of the repository where the source code of the tool is stored.</p> </li> <li> <p>“<strong>License</strong>”: the license under which the tool is available. If the tool is available for a fee, it is indicated as “for a fee”. If the tool is free but the exact open-source license is not specified, the license is simply marked as “Free”.</p> </li> <li> <p>“<strong>Current Version</strong>”: the number of the latest publicly released version of the tool.</p> </li> <li> <p>“<strong>Editions</strong>”: the titles of DSEs that have been created using the tool. This field is very useful for potential user-editors as it allows them to see concretely how a DSE is presented thanks to the tool and/or what scientific results the tool enables. The names are hyperlinks to the respective official websites of the DSEs.</p> </li> <li> <p>“<strong>Publications</strong>”: bibliographic references to publications in which the creators present their tool or other scholars review or report their experience using the software with a concrete use case.</p> </li> </ul> <p>For many tools, it was not possible to provide all the above-listed information, either because it was not available in official sources (primarily websites and repositories) or because it was not possible to identify updated and reliable bibliographic sources. The omission of information does not imply that it cannot be obtained through further in-depth study or by contacting the creators themselves. Furthermore, the information may no longer be up-to-date or valid; for example, hyperlinks to websites may no longer be active.</p> <p>The catalogue is not exhaustive, as it mainly includes tools produced in Italy, Europe, and the United States. The main objective of the work is to provide an initial overview of tools for digital philology, albeit partial and incomplete, and to propose useful categories for analyzing and classifying these tools from the perspective of user-editors who wish to create an DSE. This review constitutes the starting point for a larger research project that I would like to undertake in the future, namely, creating a catalog of computer tools for digital philology.</p> <p>I would like to thank Professors Roberto Rosselli Del Turco and Lino Leonardi for providing references to several of the analyzed tools.</p> <p>The list is also <a href="https://airtable.com/appmd2Z1LsaYMaYEF/shrb1dVa8QsJ4P8Ga">available for consultation online</a>.</p>
Figure 1 in Notes on the Amydetinae (Coleoptera: Lampyridae) in McDermott's 1966 catalogue of Lampyridae
Figure 1. McDermott's original handwritten literature notecards. a) Notecard showing the citation for the original description of Dryptelytra fulvipennis. b) Notecard showing McDermott's incorrect citation for Magnoculus marginatus.
Figs 19–27 in Annotated catalogue of the flower bugs from India (Heteroptera: Anthocoridae, Lasiochilidae)
Figs 19–27. Life stages of Indian anthocorids (egg, nymph, adult). 19–21 – Cardiastethus exiguus Poppius, 1913; 22–24 – Blaptostethus pallescens Poppius, 1909; 25–27 – Xylocoris flavipes (Reuter, 1875). Photo credits: C. Ballal.
Figs 1–12 in Annotated catalogue of the flower bugs from India (Heteroptera: Anthocoridae, Lasiochilidae)
Figs 1–12. Habitus photographs of selected Indian Anthocoridae. 1 – Amphiareus constrictus (Stål, 1860); 2 – Anthocoris muraleedharani Yamada, 2010; 3 – Physopleurella armata Poppius, 1909, from Thailand; 4 – Xylocoris (Arrostelus) flavipes (Reuter, 1875); 5 – Xylocoris (Proxylocoris) afer (Reuter, 1884); 6 – Blaptostethoides sp.; 7 – Montandoniola indica Yamada, 2011 (source: www.nbair.res.in); 8 – Xylocoris (Arrostelus) ampoli Yamada & Yasunaga, 2013; 9 – Carayonocoris indicus Muraleedharan, 1977; 10 – Xylocoris (Proxylocoris) confusus Carayon, 1972; 11 – Bilia sp. (this specimen is not examined); 12 – Buchananiella indica Muraleedharan, 1977. Photo credits: C. Ballal (1–2, 4–7, 9–12), K. Yamada (3, 8).
Figure 3 in Miscellaneous notes on the fireflies (Coleoptera: Lampyridae) in McDermott's 1966 catalogue of Lampyridae
Figure 3. McDermott's original handwritten literature notecards. a) Notecard showing the incorrect citation for the for Pyrocoelia tappana. b) Notecard showing the correct citation for Lamprocera latreillei. c) Notecard showing McDermott's incorrect citation for Tenaspis semifusca.
FIG. 3. — A, Pelocarcinus marchei A in Annotated type-catalogue of Brachyura (Crustacea, Decapoda) of the Muséum national d'Histoire naturelle, Paris. Part II. Gecarcinidae and Grapsidae (Thoracotremata, Grapsoidea), with an Appendix of pre-1900 collectors
FIG. 3. — A, Pelocarcinus marchei A. Milne-Edwards, 1890, MNHN-IU-2000-3752 (= MNHN-B3752), lectotype, ♂; B, Thelphusa rotunda Quoy & Gaimard, 1824, MNHN-IU-2000-3745 (= MNHN-B3745), lectotype, ♂; C, Grapsus brevipes H. Milne Edwards, 1853, MNHN-IU-2000-10978 (= MNHN-B10978), lectotype, ♂; D, Grapsus cruentatus Latreille, 1803, MNHN-IU-2000-3407 (= MNHN-B3407), neotype, ♂; E, Grapsus fourmanoiri Crosnier, 1965, MNHN-IU-2008-10635 (= MNHN-B11803), lectotype, ♂; F, Grapsus gracilipes H. Milne Edwards, 1853, MNHN-IU-2000-3411 (= MNHN-B3411), lectotype, ♂; G, Grapsus granulosus H. Milne Edwards, 1853, MNHN-IU-2000-3417 (= MNHN-B3417), lectotype, ♂; H, Grapsus grayi H. Milne Edwards, 1853, MNHN-IU-2000-3421 (= MNHN-B3421), lectotype, ♀. Scale bars: A-D, F, H, 2 cm; E, 10 mm; G, 5 cm.
FIG. 2. — A, Cardisoma urvillei H. Milne Edwards, 1853 in Annotated type-catalogue of Brachyura (Crustacea, Decapoda) of the Muséum national d'Histoire naturelle, Paris. Part II. Gecarcinidae and Grapsidae (Thoracotremata, Grapsoidea), with an Appendix of pre-1900 collectors
FIG. 2. — A, Cardisoma urvillei H. Milne Edwards, 1853, MNHN-IU-2000-3735 (= MNHN-B3735), lectotype, ♂; B, Discoplax gracilipes Ng & Guinot, 2001, MNHN-IU-2014-11214 (= MNHN-B26950), paratype, ♀; C, Discoplax longipes A. Milne-Edwards, 1867, MNHN-IU-2000-3763 (= MNHN-B3763), lectotype, ♂; D, Gecarcinus digueti Bouvier, 1895, MNHN-IU-2000-10951 (= MNHN-B10951), holotype, ♂; E, Gecarcinus lagostoma H. Milne Edwards, 1837, MNHN-IU-2000-3750 (= MNHN-B3750), lectotype, ♂; F, Gecarcinus lateralis Fréminville in Guérin-Méneville, 1832, MNHN-IU-2000-3758 (= MNHN-B3758), neotype, ♂; G, Gecarcinus nobilii Perger & Wall, 2014, MNHN-IU-2014-11211 (= MNHN-B12314), paratype, ♀; H, Pelocarcinus cailloti A. Milne-Edwards, 1890, MNHN-IU-2000-3751 (= MNHN-B3751), holotype, ♂. Scale bars: A, E, 5 cm; B-D, F-H, 2 cm.
FIG. 6. — A, Leptograpsus ansoni H. Milne Edwards, 1853 in Annotated type-catalogue of Brachyura (Crustacea, Decapoda) of the Muséum national d'Histoire naturelle, Paris. Part II. Gecarcinidae and Grapsidae (Thoracotremata, Grapsoidea), with an Appendix of pre-1900 collectors
FIG. 6. — A, Leptograpsus ansoni H. Milne Edwards, 1853, MNHN-IU-2000-4023 (= MNHN-B4023), lectotype, ♂; B, Leptograpsus bertheloti H. Milne Edwards, 1853, MNHN-IU-2000-10944 (= MNHN-B10944), lectotype, ♀; C, Leptograpsus gayi H. Milne Edwards, 1853, MNHN-IU-2000-3531 (= MNHN-B3531), lectotype, ♂; D, Leptograpsus rugulosus H. Milne Edwards, 1853, MNHN-IU-2000-3534 (= MNHN-B3534), lectotype, ♂; E, Leptograpsus verreauxi H. Milne Edwards, 1853, MNHN-IU-2000-4024 (= MNHN-B4024), lectotype, ♂; F, Metopograpsus eydouxi H. Milne Edwards, 1853, MNHN-IU-2000-3547 (= MNHN-B3547), lectotype, ♂. Scale bars: A, D, F, 10 mm; B, C, E, 2 cm.
Fig. 1 in A preliminary catalogue of the Hymenoptera (Insecta) of the Republic of Djibouti
Fig. 1: Hemiscorpius sp. (Scorpionides: Hemiscorpiidae) and its prey Anochetus sp. (Formicidae) at Dimbiya near Karta (Photo: M.A. Jäch, 27.01.2016).
Fig. 11 in The Earwig Collection (Dermaptera) of the Manchester Museum, UK, with a complete type catalogue
Fig. 11. The only specimen at MMUE mounted with wings unfurled, Purex remotus (Burr, 1899) from Panama, the Manchester Museum. Scale bar = 1 cm.
Figs 59–63 in The Earwig Collection (Dermaptera) of the Manchester Museum, UK, with a complete type catalogue
Figs 59–63. Other material, presumed manuscript names, in the collection of the Manchester Museum. 59. Nesogaster spatulus Brindle (det. 1983). 60. Metalabis subcarinata Brindle (det. 1987). 61. Carcinophora rossi Hincks (no date). 62. Tagalina flavolineata Brindle (det. 1980). 63. Brindle's handwritten label for the Tagalina flavolineata specimen (Fig. 62). Scale bars = 1 cm.
Fig. 6 in The Earwig Collection (Dermaptera) of the Manchester Museum, UK, with a complete type catalogue
Fig. 6. Walter Douglas Hincks (1906–1961), Keeper of Entomology at the Manchester Museum (1947– 1961), photographed in the late 1950s.
Fig. 5 in The Earwig Collection (Dermaptera) of the Manchester Museum, UK, with a complete type catalogue
Fig. 5. The collection's earliest dated specimen, Apachyus chartaceus (Haan, 1842), dated 1878, the Manchester Museum. Scale bar = 1 cm.
Figs 34–39 in The Earwig Collection (Dermaptera) of the Manchester Museum, UK, with a complete type catalogue
Figs 34–39. Holotypes (♂) of Pygidicranidae and Labiduridae in the collection of the Manchester Museum. 34. Esphalmenus mucronatus Hincks, 1959. 35. E. kuscheli Hincks, 1959. 36. E. argentinus Hincks, 1959. 37. E. dentatus Hincks, 1959. 38. Tagalina curta Brindle, 1975. 39. Gonolabidura nathani Brindle, 1965. Scale bars = 1 cm.
Fig. 10 in The Earwig Collection (Dermaptera) of the Manchester Museum, UK, with a complete type catalogue
Fig. 10. Alan Brindle (1915–2001), Keeper of Entomology at the Manchester Museum (1961–1982), photographed in the mid 1980s.
Figs 7–8 in The Earwig Collection (Dermaptera) of the Manchester Museum, UK, with a complete type catalogue
Figs 7–8. Two items from Hincks' archive retained at the Manchester Museum. 7. An illustration of Pyragra paraguayensis Borelli, 1904 (♂) by Hincks for his Dermaptera monograph (Hincks 1959: 195) (item 597). 8. A page from Hincks' 'Typomap of Africa' (item 15).
Fig. 1 in The Earwig Collection (Dermaptera) of the Manchester Museum, UK, with a complete type catalogue
Fig. 1. The author and two of the three cabinets (drawers 21–60) housing the dry, mounted specimens in the worldwide Dermaptera collection, the Manchester Museum.
ScienceDex guides
Understand access before you commit
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.