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The e-NDP project : collaborative digital edition of the Chapter registers of Notre-Dame of Paris (1326-1504). Ground-truth for handwriting text recognition (HTR) on late medieval manuscripts.
<p>The <a href="https://endp.hypotheses.org/">e-NDP project</a>, funded by the ANR, is led by the <a href="https://lamop.hypotheses.org/6870">LaMOP</a> (Julie Claustre and Darwin Smith).</p> <p>The project's partners are the Archives nationales, the Bibliothèque nationale de France (Department of Manuscripts, Bibliothèque de l'Arsenal), the École nationale des chartes and the Bibliothèque Mazarine.</p> <p>The e-NDP project aims at renewing our knowledge on <strong>Notre-Dame de Paris cathedral</strong> through the creation of a collaborative digital edition of the registers of its Chapter (1326-1504, <em>AN LL 105-128</em>), the community of 51 canons meeting three times a week on set days to take all administrative, financial and practical decisions pertaining to the cathedral, its estate and the society living in its cloister. This corpus has never been the object of a comprehensive study to understand the workings and history of this urban enclave and powerful community. The collaborative digital edition is based on a process of<strong> handwriting text recognition (HTR)</strong>, tested and supervised by scholars, researchers and engineers combining expertise in Medieval history, paleography, philology and digital humanities. The edition shall allow a better insight into the Chapter’s administration, into its economical and political power within Paris, and the relationships it maintained with other institutions in the city.</p> <p> </p> <p><strong>Section 1 : The e-NDP ground-truth dataset for Handwriting text recognition.</strong></p> <p>The full e-NDP corpus kept today in the French National Archives and was entirely digitized and described in its <a href="https://www.siv.archives-nationales.culture.gouv.fr/siv/rechercheconsultation/consultation/ir/consultationIR.action?formCaller=GENERALISTE&irId=FRAN_IR_059635">catalog</a> in 2022.</p> <p>The first major goal of the e-NDP projet is to propose a first automatic transcription of the 14k pages composing the 26 chapter registers. To achieve this goal representative samples from each one of the volumes were selected and transcribed in order to train a specialized HTR model able to propose a high quality automatic transcription. The collected ground-truth released on this repository currently has <strong>512 pages from the 26 registers</strong> of the cathedral chapter preserved in the National Archives (LL105 - LL128, <strong>1326-1504</strong>). The transcriptions were manually completed in <strong>two rounds</strong> by a group of 12 contributors, historians and paleographers, over the course of 2021-2022 using <a href="https://escriptorium.paris.inria.fr/">eScriptorium </a>as annotation environment. </p> <p> </p> <p><strong>Ground-truth features :</strong></p> <p><br> <em>Number of hands </em>: according to our estimates no fewer than 18 main hands were involved in the writing of the registers during the medieval period. </p> <p><em>Language</em> : More than 98% of the content of the registers was written in Latin, the rest in French. The exact percentage is hard to estimate because the vernacular language is often used in formulae, notes and comments. It is rare to find entire pages or blocks written in French. </p> <p><em>Script family</em> : The registers were written using a Cursive script (ca. late XIIIe - XVIe).</p> <p><em>Documental typology</em> : The volumes containing the chapter conclusions were conceived to serve as memorial records, but above all as documents for regular use and consultation in the daily practice of administration and management. In diplomatics the notion of "documentary manuscripts" is used to describe this kind of sources also by opposition to books and litterary or normative manuscripts.</p> <table align="center"> <caption><strong>Ground truth statistics</strong></caption> <tbody> <tr> <th>Text units</th> <th>Count</th> </tr> <tr> <td>Pages</td> <td>512</td> </tr> <tr> <td>Annotated regions (see section 2)</td> <td>2448</td> </tr> <tr> <td>Lines of text</td> <td>34231</td> </tr> <tr> <td>Tokens</td> <td>205083</td> </tr> <tr> <td>Characters</td> <td>3320407</td> </tr> </tbody> </table> <p> </p> <p><strong>Rules of transcription :</strong></p> <ul> <li>The abbreviations have been resolved, both those by suspension (<code>facimꝰ</code> ---> <code>facimus</code>) and by contraction (<code>dñi</code> --> <code>domini</code>). Likewise, those using conventional signs (<code>⁊</code> --> <code>et</code> ; <code>ꝓ</code> --> <code>pro</code>) have been resolved. </li> <li>The named entities (names of persons, places and institutions) have been <code>capitalized</code>. The beginning of a block of text as well as the original capitals used by the notary are also capitalized.</li> <li>The consonantal <code>i</code> and <code>u</code> characters have been transcribed as <code>j</code> and <code>v</code> in both French and Latin.</li> <li>The punctuation marks used in the text: <code>.</code> and <code>/</code> have been transcribed, but the transcription has not been standardized with modern punctuation.</li> <li>Corrections and words that appear cancelled in the manuscript have been transcribed surrounded by the sign <code>$</code> at the beginning and at the end.</li> <li>More specific transcription rules can be found into the file <code>transcription_guidelines.pdf</code></li> </ul> <p> </p> <p><strong>Section 2. e-NDP Layout Segmentation.</strong></p> <p>Layout segmentation is a compulsory step before HTR recognition in order to distinguish sections and regions inside a document. This process intend to separate interdependant page zones to produce a recognition in a section-sequence order and not in a line-sequence order which mix textual and peri-textual content.</p> <p>The regions of 364 pages (see <code>GT-layout_list</code>) of the e-NDP corpus were annotated using a 5 sections vocabulary (see <code>endp_layout_regions</code>) in order to describe the page distribution in all the 26 volumes :</p> <ol> <li><em>Block</em> : All the central text blocks, that normally corresponds to the main content called "conclusions" in registers.</li> <li><em>Liste</em> : List of names of the canons who were present during the meeting. Normally located before the <em>conclusions</em>.</li> <li><em>Entrée</em> : Marginal notes or entries to inform about the content of <em>conclusions</em>.</li> <li><em>Date</em> : Paragraph contending the date. Normally at the head of a <em>conclusion</em>, but separate of the main body.</li> <li><em>Numérotation</em> : Page numbers in roman or arabic. Usually appear in the top corners of the pages.</li> </ol> <table align="center"> <caption><strong>Layout GT statistics</strong></caption> <tbody> <tr> <th>Region</th> <th>Count</th> </tr> <tr> <td>block</td> <td>833</td> </tr> <tr> <td>liste</td> <td>431</td> </tr> <tr> <td>date</td> <td>448</td> </tr> <tr> <td>entrée</td> <td>205</td> </tr> <tr> <td>numérotation</td> <td>531</td> </tr> </tbody> </table> <p> </p> <p><strong>Section 3. The e-NDP HTR modeling.</strong></p> <p>The e-NDP project has progressively trained several HTR models adapted to work on late medieval cursive in order to accelerate the production of ground truth. Currently the best model delivers an average <strong>CER (Character error ratio) of 9.7%</strong> in handwriting recognition on the 26 registers (see <code>endp_learning_curve</code>) and can serve as generalist model for other manuscripts of the same period and similar script family. These models and their training implementation details can be found in the project's github <a href="https://github.com/chartes/e-NDP_HTR">repository</a>. </p> <p>Additionally, the automatic HTR transcriptions of the 26 registers (14k pages, 4.5M tokens) enriched with lexical and semantical information has been the subject of a first <a href="https://nosketch-engine.lamop.fr/#dashboard?corpname=endp">online publication</a> using the NoSketch engine that allows advanced data mining based on the combination of data, metadata and NLP features. </p> <p> </p> <p><strong>Section 4. Dataset content.</strong></p> <p>This zip dataset contains :</p> <p>- <code>HTR_ground_truth</code> : Two folders containing the jpg / jpeg images and their curated transcriptions in PAGE XML format.</p> <p>- <code>images_docs</code> : 4 files illustrating the different phases of the project (list of GT for layout segmentation, layout ontologie, transcription guideline and HTR evaluation curves)</p>
Riparian remnant species registered at headwater streams in San Juan Zitácuaro, Mich.
Studying riparian vegetation allows understanding the floristic diversity patterns along the fluvial network, and because of the level of transformation they show, it is essential to generate knowledge to guide further recovery. This paper analyzed the remaining riparian tree vegetation in 30 sites in streams located in the Monarch Butterfly Biosphere Reserve, by describing the structure, species richness, and geographic setting (elevation, precipitation, hydrological order, and land cover), and by identifying possible invasive species. Elevation of the sites was associated with precipitation, hydrologic order, and land cover being crossed by the streams. Fifty-six mostly tree species were recorded, which increased in density and height with elevation. Some of the species with the highest importance value include Roldana angulifolia, Cestrum fulvescens, Ilex tolucana, Alnus acuminata, Buddleja cordata, and Fraxinus udhei. Four physiognomic groups emerged based on the number of species, genera and families, the number of branches, and the number, height, and diameter of individuals. High species turnover was found between sites, mainly with those located at higher elevations. The occurrence of potentially invasive species was shown to be associated with the density of individuals, with Shannon's diversity index (H'), and with geographic attributes such as elevation and hydrological order. The analyzed riverbanks show human intervention, being necessary to discriminate those impacts associated with flow alteration from those associated with land cover change.
Publication rate and consistency of registered trials of motor-based stroke rehabilitation
<p><strong>Table e1 - Eligible records</strong></p> <p>A list of registered randomized controlled trials (RCTs) meeting the following criteria:</p> <ol> <li>RCTs of motor-based interventions in individuals with stroke (including transient ischemic attack);</li> <li>Started on or after 1 July 2005;</li> <li>Completed before 1 April 2017 (actual or expected end date);</li> <li>Included human adult participants (≥18 years old);</li> <li>Included at least one outcome (primary or secondary) related to motor control, mobility, or physical functioning and performance of upper and/or lower extremities or the body as a whole; and</li> <li>Registered in English.</li> </ol> <p>This list was obtained by searching the following registries between 23 November 2017 and 22 February 2018: the International Clinical Trials Registry Platform, Clinicaltrials.gov (USA), Australian New Zealand Clinical Trial Registry, Chinese Clinical Trial Registry, Clinical Research Information Service (Republic of Korea), Clinical Trial Registry of India, Cuban Public Registry of Clinical Trials, European Union Clinical Trials Register, German Clinical Trials Register, Iranian Registry of Clinical Trials, International Standard Randomised Controlled Trials Number registry (UK), Center for Clinical Trials-Japan Medical Association, University Hospital Medical Information Network-Clinical Trial Registry (Japan), Thai Clinical Trials Registry, Netherlands Trials Registry, Pan African Clinical Trials Registry, Peruvian Clinical Trials Registry, and Sri Lanka Clinical Trials Registry. </p> <p><em>Variable definitions</em></p> <p>UIN: Unified identification number (obtained from the trial registry)</p> <p>Status: whether or not a peer-reviewed publication reporting the trial findings for the primary outcome/outcome was found</p> <ul> <li>Paper available: a publication reporting the trial findings for the primary outcome/objective was found</li> <li>Paper available (not English): a publication, published in a language other than English, reporting the trial findings for the primary outcome/objective was found</li> <li>Secondary paper available: a publication reporting study findings is available, but not for the primary objectives/outcome</li> <li>Results available: trial findings for the primary objective/outcome are available in a non-peer reviewed format (e.g., conference publication, non-peer reviewed journal, or uploaded to the trial registry)</li> <li>Discontinued: the trial registry record indicates that the trial was discontinued, so no publication is expected</li> <li>No paper/results: none of the above apply</li> </ul> <p>Source: database or method we used to find the publication reporting the trial findings for the primary objective/outcome</p> <ul> <li>Pubmed: the publication was found by searching for the UIN in Pubmed</li> <li>EMBASE/OVID: the publication was found by searching for the UIN in Embase or OVID Medline</li> <li>Google Scholar: the publication was found by searching for the UIN in Google Scholar</li> <li>Registry: the publication was listed in the trial registry</li> <li>Internet: the publication was found by a superficial internet search for the UIN</li> <li>Protocol: the publication was found through a cited reference search for the published protocol</li> <li>Author: the publication was found by contacting the trial investigators</li> <li>Other: the publication was found by some other means</li> <li>None: no publication reporting the trial findings for the primary objective/outcome was found</li> </ul> <p><strong>Table e2 - Published papers consistency</strong></p> <p>The subset of trials from Table e1 where an English-language publication reporting the trial findings for the primary objective/outcome was found.</p> <p><em>Variable definitions</em></p> <p>UIN: Unified identification number (obtained from the trial registry)</p> <p>DOI: digital objective identifier of the publication</p> <p>First_author: last name of the first author of the publication</p> <p>Year: year of the publication</p> <p>Journal: journal of the publication (abbreviated journal names are used, where available)</p> <p>Reg_Trial_End_Date: end date of the trial, as stated in the trial registry (format DD-MMM-YY)</p> <p>Date_Submitted: date when the paper was submitted to the journal for publication (where available; format: DD-MMM-YY)</p> <p>Time_To_Submit: difference, in days, between Reg_Trial_End_Date and Date_Submitted</p> <p>Date_Published: date when the paper was published, either online or in print, whichever is earlier (format: DD-MMM-YY)</p> <p>Time_To_Publish: difference, in days, between Reg_Trial_End_Date and Time_To_Publish</p> <p>UIN_Paper_Location: location of the UIN in the publication</p> <p>Reg_Pilot: whether the trial was defined as a pilot or feasibility study in the registry record (0=no, 1=yes)</p> <p>Paper_Pilot: whether the trial was defined as a pilot or feasibility study in the publication (0=no, 1=yes)</p> <p>Consistency_pilot: whether Reg_Pilot = Paper_Pilot (0=no, 1=yes)</p> <p>Consistency_Primary_Objective: whether the trial registry record and publication were consistent in terms of the primary objective (0=no, 1=yes)</p> <p>Consistency_Primary_Outcome: whether the trial registry record and publication were consistent in terms of the primary outcome (0=no, 1=yes)</p> <p>Target_N: target sample size, as indicated in the trial registry record</p> <p>Paper_N: number of participants recruited to the study, as indicated in the publication</p> <p>Consistency_N: whether the trial registry record and publication were consistent in terms of the sample size (i.e., Paper_N is within +/-10% of Target_N; 0=no, 1=yes)</p> <p>N_direction: for those trials that were inconsistent in terms of the sample size, whether Paper_N was less than (Under) or more then (Over) Target_N</p> <p>Eligibility_Consistency: whether the trial registry record and publication were consistent in terms of the eligibility criteria</p> <p>UIN_in_paper: the UIN that was included in the paper, exactly as it was published</p> <p>UIN_consistency: whether UIN = UIN_in_paper (0=no, 1=yes)</p> <p>Reg_Type: whether the trial was registered before recruiting the first participant (Prospective), after recruiting the first participant but before the trial was completed (Retro - pre-completion), or after the trial was completed (Retro - post-completion)</p> <p><strong>Table e3 - Inconsistency details</strong></p> <p>The subset of trials from Table e2 where the trial registry record and publication were inconsistent on only one of the criteria examined. This table provides further details of these inconsistencies, and details of any explanations for changes to the protocol since registration, if available.</p>
TEI-XML-Datenset der Tagebücher, Briefe, Dokumente, Forschungsbeiträge, Chronologieeinträge und Register der edition humboldt digital
<p>Das Datenset enthält alle edierten Texte (Tagebücher, Briefe und weitere Dokumente) sowie Paratexte (Forschungsbeiträge, Einträge der Chronologie zu Alexander von Humboldts Leben, Register und Glossar) der Version 11 der <a href="https://edition-humboldt.de">edition humboldt digital</a>, die am 4. Juni 2025 erschienen ist. Das Datenset enthält gegenüber der HTML-Version technische Fehlerkorrekturen, daher wird es als Version 11.0.1 veröffentlicht.</p> <p>Die Editionsrichtlinien stehen auf <a href="https://edition-humboldt.de/richtlinien/index.html">edition-humboldt.de</a> zur Vefügung. Das Datenmodell ist in drei verschiedene ODDs aufgeteilt (für edierte Texte, Registereinträge und Forschungsbeiträge). Dem Datenset liegen die drei RNG-Schemata bei, die ODD-Ursprungsdateien sind im GitHub-Repository <a href="https://github.com/telota/ediarum.AVHR.data-model/">ediarum.AVHR.data-model</a> zu finden. Beachten Sie bitte, dass es für das Pflanzenregister derzeit noch kein Schema gibt, da dieses aus dem Tagging automatisch erstellt wird.</p> <p>Weitere Hinweise zur digitalen Methodik finden sich in <a href="https://edition-humboldt.de/H0016212">Dumont 2024</a> und zum Editionsvorhaben im Allgemeinen in <a href="https://doi.org/10.25365/wdr-01-03-02">Kraft/Dumont 2020</a>.</p> <p>Dieses Datenset ist auch auf <a href="https://github.com/telota/edition-humboldt-digital">GitHub</a> zugänglich.</p>
GRETIL - Göttingen Register of Electronic Texts in Indian Languages. TEI
<p>GRETIL - Göttingen Register of Electronic Texts in Indian Languages. TEI</p>
GRETIL - Göttingen Register of Electronic Texts in Indian Languages. PLAIN TEXT
<p>GRETIL - Göttingen Register of Electronic Texts in Indian Languages. PLAIN TEXT</p>
Historical Mine Register & Place Gazetteer: Schwaz / Rottenburg / Rattenberg, Tyrol; 17th Century
<p>The data of the historical registers is based on the historical document “Bergbeschau Schwaz/Rottenburg/Rattenberg” of the 17<sup>th</sup> century (approx. 1666). The document is currently stored by the Salinenarchiv Bad Ischl) using the Identifier XXD6.The document contains 6 coloured maps of the mining areas in the mining district of Schwaz (Falkenstein, Ringenwechsel, Mehren/Merach, Reichental, Palleiten) as well as the mining district of Rattenberg (Groß-, Kleinkogel, Geyer). Furthermore, it contains detailed mine descriptions and localisations of the mines in the maps.</p> <p>Historical Mine Register: Sorting is done by mining area, main pit / mine and associated mine sections. The historical writings of the mines and mine sections are summarized in separate columns (alternate writing). Mines written in capital letters symbolize latin characters within the historical document. All mines received an Identifier and URIs which lead to a Knowledge Graph (graph_Link). In a separate column the mines also received a standard spelling (mine_name_standard). The mentioned mines were compared to two geological maps created by Herwig Pirkl (1961). Mines that could be also be georeferenced by comparison also received a geo_link to OpenStreetMap as well as HIK (‘Historische Kartenwerke Tirol’). Finally, the historical mines of the “Bergbeschau” are also linked to the Knowledge Graph TMMMT (DOI: 10.5281/zenodo.6276586) of the UIBK Project „Text Mining Medieval Mining Texts“, whenever possible.</p> <p>The historical place gazetteer is in alphabetical order by place_standard. The historical writings of the place names are summarized in a separate column (alternate writing). Places written in capital letters symbolize latin characters within the historical document. All places received an Identifier and URIs which lead to a Knowledge Graph (graph_Link). In a separate column the places received their current standard spelling (place_standard). Places that could be also be georeferenced also received coordinates as well as a geo_link to OpenStreetMap. Finally, the historical places of the “Bergbeschau” are also linked to the Knowledge Graph TMMMT (DOI: 10.5281/zenodo.6276586) of the UIBK Project „Text Mining Medieval Mining Texts“, whenever possible.</p>
SURCOM pH and temperature data collection registered at Cortegada Platform (Ria de Arousa - Spain) from 2020 to 2021
<p>This dataset comprises the data recorded by the SURCOM production prototype deployed from 2020 to 2021 at Cortegada Platform (42º 37' 40" N, 8º 46' 57" W), located in the National Park of Atlantic Islands at Ria de Arousa, in the NW of Spain.</p> <p>The measurements were taken continuously with pH and temperature collected at a frecuency of 10.3 minutes<sup>-1</sup>.</p> <p>Real-time adquired data is displayed and can be also downloaded from the following web panel:</p> <ul> <li><a href="https://co2.iim.csic.es/monitoring/d/surcom_cortegada/surcom-cortegada">https://co2.iim.csic.es/monitoring/d/surcom_cortegada/surcom-cortegada</a></li> </ul> <p>These results have been obtained thanks to the support of <a href="http://pti-waterios.csic.es/">CSIC PTI WATER:iOS</a> and are, therefore, a contribution to its efforts.</p>
Survey for online registered users of HistoricGraves platform
<div>This survey is being conducted by Eachtra Archaeological Projects as part of INCULTUM (2021-2024), a tourism-oriented HORIZON2020 funded project. The main goal of this survey was to better understand users and usage of the Historic Graves website and how to improve the visitor experience.</div>
BIFROST: A method for registering diverse imaging datasets
<p>The heterogeneity of brain imaging methods in neuroscience provides rich data that cannot be captured by a single technique, and our interpretations benefit from approaches that enable easy comparison both within and across different data types. For example, comparing brain-wide neural dynamics across experiments and aligning such data to anatomical resources, such as gene expression patterns or connectomes, requires precise alignment to a common set of anatomical coordinates. However, this is challenging because registering in vivo functional imaging data to ex vivo reference atlases requires accommodating differences in imaging modality, microscope specification, and sample preparation. We overcome these challenges in Drosophila by building an in vivo reference atlas from multiphoton-imaged brains, called the Functional Drosophila Atlas (FDA). We then develop a two-step pipeline, BrIdge For Registering Over Statistical Templates (BIFROST), for transforming neural imaging data into this common space and for importing ex vivo resources such as connectomes. Using genetically labeled cell types as ground truth, we demonstrate registration with a precision of less than 10 microns. Overall, BIFROST provides a pipeline for registering functional imaging datasets in the fly, both within and across experiments.</p>
Рис. 2. ЗΑание ТЦ «Москва», гΑе быΛо найΑено наибоΛьшее чисΛо погибших от стоΛкновения птиц. Фото Δ. А. БеΛяева Fig. 2. The building of the "Moskva" shopping center, where the highest number of bird window collision deaths was registered. Photo by D. A. Belyaev in Deaths Resulting From Bird Window Collisions In Ussuriysk (Primorsky Krai)
Рис. 2. ЗΑание ТЦ «Москва», гΑе быΛо найΑено наибоΛьшее чисΛо погибших от стоΛкновения птиц. Фото Δ. А. БеΛяева Fig. 2. The building of the "Moskva" shopping center, where the highest number of bird window collision deaths was registered. Photo by D. A. Belyaev
World Register of Marine Species (WoRMS) Repackaged hash://sha256/4e969a1c8243b523b093d3a05fd5f7683479c2919e7d83e8b1383c5e5ef1d4e5 hash://md5/fb7559ce707d11f96a878d8a8a79a661
<h1>Introduction</h1> <p>The World Register of Marine Species (WoRMS) (Ahyong et al. 2024) aims to “[…] provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. While the highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature. […]”</p> <p>This data publication contains a verifiable copy of the World Register of Marine Species as well as a streamable version in json-line format. The aims of this publication are to:</p> <ol> <li> <p>provide a signed citation (Elliott, Poelen, and Fortes 2023) for a copy of WoRMS</p> </li> <li> <p>prepare WoRMS to be included in the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2023).</p> </li> <li> <p>pre-process the World Register of Marine Species to facilitate optimized indexing and offline taxonomic name alignments using tools like Nomer (J. Poelen and Salim 2023).</p> </li> </ol> <p>Overall, the publications aims to facilitate taxonomic name alignment using the wealth of information provided by the World Register of Marine Species (WoRMS) to help enable fast, reproduceable, offline-enabled alignment of namelists with taxonomic resources of known provenance (or origin).</p> <p>An example of an application facilitated by this publication is the Taxonomic Name Alignment tool as provided through https://github.com/globalbioticinteractions/name-alignment-template. This template repository implements an automated workflow using GitHub Action to align scientific names in csv/tsv files and darwin core archive with common taxonomic name lists like WoRMS, NCBI Taxonomy, Integrated Taxonomic Information System (ITIS), and GBIF Backbone taxonomy.</p> <h2><a name="methods"></a>Methods</h2> <p>To capture and process WoRMS, the following steps were taken:</p> <ol> <li> <p>re-use a tracked and archived copy of WoRMS</p> </li> <li> <p>make WoRMS archive streamable by translating the WoRMS DwC-A into a line-json</p> </li> <li> <p>assign an alias to the processed resources</p> </li> </ol> <p>Steps 1-3 are captured and documented using Preston, a biodiversity data tracker. Preston not only helps to documents the steps, but also includes the digital resources that were used and produced.</p> <h3><a name="reuse-versioned-worms-archive"></a>Reuse Versioned WoRMS Archive</h3> <p>To reuse a versioned copy of June 2024 WoRMS as provided through Checklist Bank, the following command was issued:</p> <pre># define dependency on a June 2024 version of Checklist Bank. preston use hash://sha256/763edde4043c32ff53b9d8fc945a67b6409adccc0757a3bff1e52cccd4802476 # resolve WoRMS by their Checklist Bank Alias preston cat hash://sha256/763edde4043c32ff53b9d8fc945a67b6409adccc0757a3bff1e52cccd4802476\ --remote https://linker.bio\ | grep hasVersion\ | grep "https://api.checklistbank.org/dataset/2011/archive.zip"\ | head -1\ | preston dwc-stream --remote https://linker.bio\ | gzip\ | preston track # define an alias short cut to the generated json.gz archive preston head\ | preston cat\ | grep hasVersion\ | grep -oE "hash://[a-z0-9]+/[a-f0-9]+"\ | xargs -L1 preston alias worms:worms.json.gz</pre> <p>With this, a previously archived copy of https://api.checklistbank.org/dataset/2011/archive.zip is downloaded and their sha256 checksum (or hash) is calculated. Also, the download process was previously captured machine-readable rdf/nquads statement of hash://sha256/763edde4043c32ff53b9d8fc945a67b6409adccc0757a3bff1e52cccd4802476.</p> <p>An example record from the derived dataset worms:worms.json.gz included in this publication can be found using:</p> <pre>preston alias\ --anchor hash://sha256/4e969a1c8243b523b093d3a05fd5f7683479c2919e7d83e8b1383c5e5ef1d4e5\ --remote https://zenodo.org/deposit/8327611/files\ worms:worms.json.gz\ | preston cat\ | gunzip\ | head -n1\ | jq .</pre> <p>and is</p> <pre>{ "http://www.w3.org/ns/prov#wasDerivedFrom": "line:zip:hash://sha256/ca4baa1a90f4ce80d27ec7d1525f54a75fa679d76a66ed6143b17031287dea09!/taxon.txt!/L2", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "http://rs.tdwg.org/dwc/terms/Taxon", "http://rs.tdwg.org/dwc/text/id": "urn:lsid:marinespecies.org:taxname:1", "http://rs.tdwg.org/dwc/terms/scientificNameAuthorship": null, "http://rs.tdwg.org/dwc/terms/nomenclaturalStatus": null, "http://rs.tdwg.org/dwc/terms/acceptedNameUsage": "Biota", "http://rs.tdwg.org/dwc/terms/infraspecificEpithet": null, "http://rs.tdwg.org/dwc/terms/taxonRank": null, "http://rs.tdwg.org/dwc/terms/phylum": null, "http://rs.tdwg.org/dwc/terms/scientificNameID": "urn:lsid:marinespecies.org:taxname:1", "http://rs.tdwg.org/dwc/terms/scientificName": "Biota", "http://rs.tdwg.org/dwc/terms/parentNameUsage": "Biota", "http://rs.tdwg.org/dwc/terms/datasetName": "World Register of Marine Species (WoRMS)", "http://purl.org/dc/terms/references": "https://www.marinespecies.org/aphia.php?p=taxdetails&id=1", "http://rs.tdwg.org/dwc/terms/subgenus": null, "http://purl.org/dc/terms/rightsHolder": "WoRMS Editorial Board", "http://rs.tdwg.org/dwc/terms/family": null, "http://rs.tdwg.org/dwc/terms/order": null, "http://rs.tdwg.org/dwc/terms/class": null, "http://purl.org/dc/terms/bibliographicCitation": "WoRMS (2024). Biota. Accessed at: https://www.marinespecies.org/aphia.php?p=taxdetails&id=1", "http://rs.tdwg.org/dwc/terms/genus": null, "http://purl.org/dc/terms/license": "http://creativecommons.org/licenses/by/4.0/", "http://rs.tdwg.org/dwc/terms/namePublishedInYear": null, "http://rs.tdwg.org/dwc/terms/institutionCode": "VLIZ", "http://rs.tdwg.org/dwc/terms/acceptedNameUsageID": "urn:lsid:marinespecies.org:taxname:1", "http://rs.tdwg.org/dwc/terms/kingdom": null, "http://rs.tdwg.org/dwc/terms/taxonID": "urn:lsid:marinespecies.org:taxname:1", "http://rs.tdwg.org/dwc/terms/parentNameUsageID": null, "http://rs.tdwg.org/dwc/terms/datasetID": "https://doi.org/10.14284/170", "http://rs.tdwg.org/dwc/terms/nomenclaturalCode": null, "http://rs.tdwg.org/dwc/terms/namePublishedInID": null, "http://purl.org/dc/terms/modified": "2004-12-21", "http://rs.tdwg.org/dwc/terms/taxonomicStatus": "accepted", "http://rs.tdwg.org/dwc/terms/namePublishedIn": null, "http://rs.tdwg.org/dwc/terms/specificEpithet": null }</pre> <p>which shows the first json-line object retrieved from the WoRMS DwC-A.</p> <h1><a name="results"></a>Results</h1> <p>As described in our methods, this publication derived the resource with alias worms:worms.json.gz and content id hash://sha256/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7 . This resource contains a streamable line-json archive derived from a versioned copy package retrieved from https://api.checklistbank.org/dataset/2011/archive.zip with content identifier hash://sha256/ca4baa1a90f4ce80d27ec7d1525f54a75fa679d76a66ed6143b17031287dea09.</p> <p>The following tools were used to process the WoRMS resource:</p> <p>Tools used in this data publication</p> <table> <tbody> <tr> <th> <p>tool name</p> </th> </tr> </tbody> <tbody> <tr> <td> <p><a href="https://github.com/bio-guoda/preston">preston</a></p> </td> </tr> <tr> <td> <p><a href="https://en.wikipedia.org/wiki/Bash_(Unix_shell)">bash</a></p> </td> </tr> <tr> <td> <p><a href="https://en.wikipedia.org/wiki/Gzip">gzip</a></p> </td> </tr> <tr> <td> <p><a href="https://en.wikipedia.org/wiki/Sed">sed</a></p> </td> </tr> <tr> <td> <p><a href="https://en.wikipedia.org/wiki/Head_(Unix)">head</a></p> </td> </tr> </tbody> </table> <h1><a name="discussion"></a>Discussion</h1> <p>This publication is intended to facilitate re-use of the WoRMS data package in taxonomic name alignment workflows. While the primary goal was to generate a resource for use in Nomer v0.4.9 (J. Poelen and Salim 2023), other usage can be imagined such as:</p> <ol> <li> <p>Lots of Copies Keeps Stuff Safe (LOCKSS (Maniatis et al. 2005)): keep an identical copy of WoRMS data package outside of the Checklist Bank/ WoRMS infrastructure.</p> </li> <li> <p>making a json-line streamable copy of WoRMS available via https://zenodo.org/record/12112610/files/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7 for use in workflows like looking up the first record that contain <em>Enhydra lutris</em> (Sea otter):</p> </li> </ol> <pre> curl -L 'https://zenodo.org/record/12112610/files/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7'\ | gunzip\ | grep "Enhydra lutris"\ | head -n1\ | jq .</pre> <p>producing</p> <pre>{ "http://www.w3.org/ns/prov#wasDerivedFrom": "line:zip:hash://sha256/ca4baa1a90f4ce80d27ec7d1525f54a75fa679d76a66ed6143b17031287dea09!/taxon.txt!/L111764", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "http://rs.tdwg.org/dwc/terms/Taxon", "http://rs.tdwg.org/dwc/text/id": "urn:lsid:marinespecies.org:taxname:242598", "http://rs.tdwg.org/dwc/terms/scientificNameAuthorship": "(Linnaeus, 1758)", "http://rs.tdwg.org/dwc/terms/nomenclaturalStatus": null, "http://rs.tdwg.org/dwc/terms/acceptedNameUsage": "Enhydra lutris", "http://rs.tdwg.org/dwc/terms/infraspecificEpithet": null, "http://rs.tdwg.org/dwc/terms/taxonRank": "Species", "http://rs.tdwg.org/dwc/terms/phylum": "Chordata", "http://rs.tdwg.org/dwc/terms/scientificNameID": "urn:lsid:marinespecies.org:taxname:242598", "http://rs.tdwg.org/dwc/terms/scientificName": "Enhydra lutris", "http://rs.tdwg.org/dwc/terms/parentNameUsage": "Enhydra", "http://rs.tdwg.org/dwc/terms/datasetName": "World Register of Marine Species (WoRMS)", "http://purl.org/dc/terms/references": "https://www.marinespecies.org/aphia.php?p=taxdetails&id=242598", "http://rs.tdwg.org/dwc/terms/subgenus": null, "http://purl.org/dc/terms/rightsHolder": "WoRMS Editorial Board", "http://rs.tdwg.org/dwc/terms/family": "Mustelidae", "http://rs.tdwg.org/dwc/terms/order": "Carnivora", "http://rs.tdwg.org/dwc/terms/class": "Mammalia", "http://purl.org/dc/terms/bibliographicCitation": "WoRMS (2024). Enhydra lutris (Linnaeus, 1758). Accessed at: https://www.marinespecies.org/aphia.php?p=taxdetails&id=242598", "http://rs.tdwg.org/dwc/terms/genus": "Enhydra", "http://purl.org/dc/terms/license": "http://creativecommons.org/licenses/by/4.0/", "http://rs.tdwg.org/dwc/terms/namePublishedInYear": null, "http://rs.tdwg.org/dwc/terms/institutionCode": "VLIZ", "http://rs.tdwg.org/dwc/terms/acceptedNameUsageID": "urn:lsid:marinespecies.org:taxname:242598", "http://rs.tdwg.org/dwc/terms/kingdom": "Animalia", "http://rs.tdwg.org/dwc/terms/taxonID": "urn:lsid:marinespecies.org:taxname:242598", "http://rs.tdwg.org/dwc/terms/parentNameUsageID": "urn:lsid:marinespecies.org:taxname:242597", "http://rs.tdwg.org/dwc/terms/datasetID": "https://doi.org/10.14284/170", "http://rs.tdwg.org/dwc/terms/nomenclaturalCode": "ICZN", "http://rs.tdwg.org/dwc/terms/namePublishedInID": null, "http://purl.org/dc/terms/modified": "2010-05-20", "http://rs.tdwg.org/dwc/terms/taxonomicStatus": "accepted", "http://rs.tdwg.org/dwc/terms/namePublishedIn": null, "http://rs.tdwg.org/dwc/terms/specificEpithet": "lutris" } ``` Note that the following command should also produce the *exact* same results: </pre> <p>preston cat –remote https://linker.bio,https://zenodo.org/record/12112610/files/<br>hash://sha256/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7<br>| gunzip<br>| grep “Enhydra lutris”<br>| head -n1<br>| jq . ~~~</p> <p>and</p> <pre>preston cat --remote https://linker.bio,https://zenodo.org\ hash://sha256/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7\ | gunzip\ | grep "Enhydra lutris"\ | head -n1\ | jq .</pre> <p>and</p> <pre>preston cat --remote https://linker.bio,https://zenodo.org\ hash://md5/aa54d0c3587526e3da167cf93afa541f\ | gunzip\ | grep "Enhydra lutris"\ | head -n1\ | jq .</pre> <h1><a name="acknowledgements"></a>Acknowledgements</h1> <p>This work stands on the shoulders of contributors to open source software and openly accessible datasets. Thank you!</p> <h1><a name="bibliography"></a>References</h1> <div> <p>Ahyong, S., C. B. Boyko, N. Bailly, J. Bernot, R. Bieler, S. N. Brandão, M. Daly, et al. 2024. “World Register of Marine Species (WoRMS).” WoRMS Editorial Board. <a href="https://www.marinespecies.org/">https://www.marinespecies.org</a>. https://doi.org/10.14284/170</p> <p> </p> </div> <div> <p>Elliott, Michael J., Jorrit H. Poelen, and José A. B. Fortes. 2023. “Signing Data Citations Enables Data Verification and Citation Persistence.” <em>Scientific Data</em> 10 (1). <a href="https://doi.org/10.1038/s41597-023-02230-y">https://doi.org/10.1038/s41597-023-02230-y</a>.</p> </div> <div> <p> </p> <p>Maniatis, Petros, Mema Roussopoulos, Thomas J Giuli, David SH Rosenthal, and Mary Baker. 2005. “The LOCKSS Peer-to-Peer Digital Preservation System.” <em>ACM Transactions on Computer Systems (TOCS)</em> 23 (1): 2–50.</p> </div> <div> <p> </p> <p>Poelen, Jorrit H. (ed.). 2023. “Nomer Corpus of Taxonomic Resources hash://sha256 /12051b8aa59930d6561a3ed46b7cf3f67a31a98445a457d78 894f6b8a8e81641 hash://md5/1ff6b3628d7afc15b882cc0c9b1c3815.” Zenodo. <a href="https://doi.org/10.5281/zenodo.8326175">https://doi.org/10.5281/zenodo.8326175</a>.</p> </div> <p> </p> <p>Poelen, Jorrit, and José Augusto Salim. 2023. “Globalbioticinteractions/Nomer: 0.5.4.” Zenodo. <a href="https://doi.org/10.5281/zenodo.8329422">https://doi.org/10.5281/zenodo.8329422</a>.</p>
Рис. 4. РаспреΑеΛение рыб в верхнем и нижнем бьефе в периоΑ осенней миграции 2018 г. (а) и верхнем бьефе в весеннюю миграцию 2019 г. (б). Точками показаны места фиксации рыб эхоΛотом Fig. 4. Distribution of fish upstream and downstream of the reservoir during the autumn migration of 2018 (а) and upstream of the reservoir during the spring migration of 2019 (b). Points indicate the locations where fish were registered by echosounder in Dynamics and current status of the Amazar River ichthyofauna after the construction of the PPM «Polyarnaya» hydroelectric complex
Рис. 4. РаспреΑеΛение рыб в верхнем и нижнем бьефе в периоΑ осенней миграции 2018 г. (а) и верхнем бьефе в весеннюю миграцию 2019 г. (б). Точками показаны места фиксации рыб эхоΛотом Fig. 4. Distribution of fish upstream and downstream of the reservoir during the autumn migration of 2018 (а) and upstream of the reservoir during the spring migration of 2019 (b). Points indicate the locations where fish were registered by echosounder
Figure 1 in Newly registered tracks of Raccoon dogs (Nyctereutes procyonoides) indicate the presence of resident population in the region of Bolata dere (NE Bulgaria)
Figure 1. Schematic map of Bolata bay. The red dot indicates the position of the footprints of a Raccoon dog found on 16.04.2015. Abbreviations: N. p. tracks – Nyctereutes procyonoides tracks; r.n. - road north, r.s.- road south. Scale bar – 60 m.
BRAIN Journal-A Synoptic of Software Implementation for Shift Registers Based on 16th Degree Primitive Polynomials-Figure 4. Scheme for the polynomial with [16, 14, 13, 11] tap sequence
<p>A simulation program for the functioning on LFSR of the 16th degree for the Galois implementation was developed. In the following example an analysis for the 14 selected primitive polynomials will be presented. A list with the positions which will influence the future state is called tap sequence.</p> <p>This sequence can be represented by a polynomial mod 2, only with coefficients 1 and 0, called Feedback Polynomial or Characteristic Polynomial. For the above scheme this polynomial is: P(X)= X^16+X^14+X^13+X^11+1</p>
BRAIN Journal-A Synoptic of Software Implementation for Shift Registers Based on 16th Degree Primitive Polynomials-Figure 3. Galois implementation
<p>In Galois implementation there is a Shift Register, whose content is modified each step at a binary value sent to the output. In Galois configuration the single shifted out bit is XOR ed with several bits in the shift register and in conventional configuration each new bit input to the shift register is the XOR of several bits in the register.</p>
BRAIN Journal-A Synoptic of Software Implementation for Shift Registers Based on 16th Degree Primitive Polynomials-Figure 2. Fibonacci implementation
<p>A LFSR can be represented as a polynomial of variable x referred to as the generator polynomial or the characteristic polynomial. The input bit is given from a linear function of the initial status for a special shift register called Linear Feedback Shift Register (LFSR). The initial value of the register is called seed and the produced sequence is completely determined by the initial status. Because the register has a finite number of possible statuses, after a period the sequence will be repeated. If the feedback function is very well chosen, the produced sequence will be random and the cycle will be very long, called by Golomb (1967) maximum lengths shift register sequences. Goresky and Klapper (2004) show two possibilities to implement a LFSR: • Fibonacci Form • Galois. </p>
BRAIN Journal-A Synoptic of Software Implementation for Shift Registers Based on 16th Degree Primitive Polynomials-Figure 1. Basis scheme for a Feedback Shift Register
<p>Every LFSR works by taking the XOR of the selected bits in its internal state and any LFSR containing all zero bits will never move to any other state, so one possible state must be excluded from any cycle. A LFSR is composed of memory cells connected together as a shift register with linear feedback. In digital circuits a shift register is formed by flip-flops and EXOR gates chained together with a synchronous clock. Shift registers are a form of sequential logic like counters. Always the shift registers produce a discrete delay of a digital signal or waveform. Considering that a shift register has n stages, the waveform is delayed by n discrete clock times. Usually the naming of the shift register follows a type of convention shown normally in digital logic, with the least significant bit on the left. According to the communication protocol, the signals will be addressed, not the registers. There are n+1 signals for each n-bit register. Always the next state of an LFSR is uniquely determined from the previous one by the feedback network. Any LFSR will generate a sequence of different states starting with the initial one, called seed. A feedback shift register is composed of: - a shift register - a feedback function. </p>
BRAIN Journal-A Synoptic of Software Implementation for Shift Registers Based on 16th Degree Primitive Polynomials-Figure 10. Graphic containing the results for 1000 bits
<p>The distribution obtained depending on the length of the input string shows that time depends on the input length, but for lengths even closer together, the times are also close (this can be seen in Figure 8 for 20 bits inputs). Time does not change so much depending on which of the 14 different 16th degree primitive polynomials has been used. </p>
BRAIN Journal-A Synoptic of Software Implementation for Shift Registers Based on 16th Degree Primitive Polynomials-Figure 9. Graphic containing the results for 1000 bits
<p>The next two graphics show the obtained results from the execution of the main program for each of the 14 degrees, 16th primitive polynomials for three different situations depending on the lengths of the entrance data polynomial. The lengths of the input polynomials were 20. 30. 40, 50, 100 and 1000 bits. The maximum number of sequences is 216-1(Solomon, 1967). </p>
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