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72 results for “Biological databases”
BioReCer Main biological feedstock flows database
<p>BioReCer aims at assessing and complementing current certification schemes for biological resources according to the new EU sustainability goals to enhance bio-based circular systems.</p> <p>This will be achieved by including new criteria that align with EU taxonomy and EU corporate due diligence regulations into guidelines for certifying biological resources’ sustainability, origin, tracking and traceability (T&T), and by ensuring applicability at EU and global scale.</p> <p>By promoting the sustainability and trade of biological resources, BioReCer will increase the added value, use, as well as social acceptance of bio-based products.</p> <p>Part of the specific objectives of the project is to map the current European biomass flows in 4 main sectors:</p> <ol> <li>Fishery</li> <li>Urban waste and wastewater</li> <li>Agriculture</li> <li>Forestry</li> </ol> <p>This database presents information on over 30 biomass feedstocks from across this sectors and is estimated to cover approx. 90% of the available secondary biological feedstocks in the EU. </p> <p>Table 1 shows the amount of secondary biomass produced by feedstock and their fates.</p> <p>Table 2 shows the amount of primary biomass prodused, imported and exported to and from Europe.</p> <p>This database is based on the work done for derivable 2.1 - Main biological feedstocks flows.</p>
Linked collectors and determiners for: Marine Biological Sample Database, JAMSTEC.
Natural history specimen data linked to collectors and determiners held within, "Marine Biological Sample Database, JAMSTEC". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/3c1a56f8-b63a-492f-bb77-babb497204fb">https://bionomia.net/dataset/3c1a56f8-b63a-492f-bb77-babb497204fb</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3c1a56f8-b63a-492f-bb77-babb497204fb">https://gbif.org/dataset/3c1a56f8-b63a-492f-bb77-babb497204fb</a>. Formatted as a Frictionless Data package.
Biological invasions: a field synopsis, systematic review, and database of the literature
Species introductions of anthropogenic origins are a major aspect of rapid ecological change globally. Research on biological invasions has generated literature on many different aspects of this phenomenon. This literature is enormous and has grown rapidly since the mid‐twentieth century. Therefore, we created this dataset in order to describe and categorize some aspects of this literature, to better understand what has been studied and what we know, mapping well‐studied areas and important gaps. To do so, we employed the techniques of systematic reviewing widely adopted in other scientific disciplines. We identified 2398 relevant studies in a field synopsis of the biological invasions literature. The purpose of the field synopsis was to map and categorize the scope of available information (and what is not known) from the literature addressing a fundamental understanding of biological invasions. We then examined 1537 papers in greater detail in a systematic review. The systematic review addressed the state of our knowledge about the mechanisms that permit species to invade novel environments. We carried this out by attempting to identify and characterize the literature, including what hypotheses have been tested, and what organisms and systems have been studied. A secondary goal of our work was to create a publicly accessible database of this literature for future research.
Database including meta data and R script for bachelor thesis biology on ground beetles as bioindicator 2017
<p>Database including meta data and R script for bachelor thesis biology on ground beetles as bioindicator 2017</p>
Selected biological journal names and sample bibliography databases
<p>This 3rd version contains a full backup of X Dong's bibliographic files entered in BiBTeX format; it also includes an update of the three journal name database files (with over 4800 multidisciplinary journal names). Each of the bibliographic files is a collection of references under a certain topic, but sometimes the references were gathered in a specific file just for convenience of writing a specific manuscript. One may combine all the bibliographic files (with about 4000 references) into one .bib file, but beware that sometimes there are duplications, which can lead to LaTeX to complain during compilation. To prevent that from happening again, one may go back to remove the duplicated entries. Like the previous versions, for journal articles, only the nicknames of the respective journals are used in all of the bibliographic files. This assumes the bibliographic files will be used along with one of the three journal name database files (always list the journal name database file first; see description of Version 1).</p> <p>### <br>compens -- references related to root water uptake compensation<br>cotton_drought -- related to plant drought tolerance, in particular of cotton <br>cover -- related to cover crops<br>Ghg -- related to greenhouse gas flux/management/measurement etc., from natural or managed ecosystems<br>Ghg_Ai -- additional references related to greenhouse gas<br>gpr -- related to ground penetrating radar application to agriculture<br>guayule -- related to the study of guayule, a natural rubber plant native to the Chihuahuan desert<br>hemp -- related to industrial hemp, esp. physiology and agronomy<br>JLong -- the journal name database with full journal names <br>Jshort -- the journal name database with abbreviated journal names <br>Jshort_dod -- the journal name database with abbreviated journal names and a period<br>leaf_wax -- related to leaf wax<br>Mycorr -- related to mycorrhizae<br>onion_water -- related to water stress and irrigation scheduling of onion<br>opt1 -- related to optimization, esp. mathematical modeling applications in biology and agriculture<br>pv -- related to pressure-volume curves for studying plant water relations<br>RainPulse -- related to variations of rainfall in natural ecosystems<br>Root-dist -- related to plant root distribution<br>Stat_Mod -- related to statistical modeling and its applications in biology and agriculture<br>XDref -- a collection of miscellaneous references </p> <p> </p> <p> </p> <p> </p> <p> </p>
Compound activity data sets for 15 biological targets compiled from the ChEMBL and PubChem databases.
<p>Compound activity data sets for the 15 biological targets are deposited, along with structure-activity relationship matrices IDs. Active compounds were extracted from the ChEMBL database and inactive were from the PubChem database. Details of the data sets are described in the original publication. and the summary of the data sets is given in the readme.txt file. </p>
Addressing Sex Imbalance In EGA And dbGaP Biological Databases: A Roadmap For Better Practices
<p>Data extracted from EGA and dbGaP analyzed in<strong> "Addressing Sex Imbalance In EGA And dbGaP Biological Databases: A Roadmap For Better Practices"</strong></p>
Supplementary tables for the paper: "Comprehensive Mapping of the AOP-Wiki Database: Identifying Biological and Disease Gaps"
<p><strong>Supplementary tables for the paper: "Comprehensive Mapping of the AOP-Wiki Database: Identifying Biological and Disease Gaps"</strong></p> <p><em>Original Research Article</em><br><strong>Frontiers in Toxicology</strong>, March 8, 2024<br>Section: Regulatory Toxicology<br><strong>Volume 6 - 2024</strong> | <a href="https://doi.org/10.3389/ftox.2024.1285768" target="_new" rel="noopener">https://doi.org/10.3389/ftox.2024.1285768</a></p> <p><strong>Authors</strong>:<br>Thomas Jaylet, Thibaut Coustillet, Nicola M. Smith, Barbara Viviani, Birgitte Lindeman, Lucia Vergauwen, Oddvar Myhre, Nurettin Yarar, Johanna M. Gostner, Pablo Monfort-Lanzas, Florence Jornod, Henrik Holbech, Xavier Coumoul, Dimosthenis A. Sarigiannis, Philipp Antczak, Anna Bal-Price, Ellen Fritsche, Eliska Kuchovska, Antonios K. Stratidakis, Robert Barouki, Min Ji Kim, Olivier Taboureau, Marcin W. Wojewodzic, Dries Knapen, Karine Audouze</p>
A dark side of conservation biology: protected areas fail in representing subterranean biodiversity. Databases.
<p>We obtained distribution data for leiodids by digitizing the information provided by Fresneda and Salgado (2017). This information was updated and expanded with additional data from several sampling campaigns (unpublished data). For subterranean spiders, we included the entirety of the Alps range extending from France in the east westward through Switzerland, Italy, Liechtenstein, Austria, Germany, and Slovenia, by integrating available data in Global Biodiversity Information Facility (GBIF), Spider of Europe), Araneae.it and other literature sources.</p>
Supplemental Files to "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs"
<p>These are supplemental files to the manuscript, "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs". Supplements contain excel spreadsheets, DNA alignments, Newick tree files, FigTree files, and csv files.</p>
Supplementary material 2 from: Senderov V, Georgiev T, Penev L (2016) Online direct import of specimen records into manuscripts and automatic creation of data papers from biological databases . Research Ideas and Outcomes 2: e10617. https://doi.org/10.3897/rio.2.e10617
This spreadsheet contains the information about the specimen API's of GBIF, BOLD Systems, iDigBio, and PlutoF. It lists the endpoints and the documentation URLs in the sheet named "APIs". In the sheet named "Mappings" it lists how to map the non-DwC compliant APIs (BOLD and PlutoF) to DwC-terms.
Supplementary material 3 from: Senderov V, Georgiev T, Penev L (2016) Online direct import of specimen records into manuscripts and automatic creation of data papers from biological databases . Research Ideas and Outcomes 2: e10617. https://doi.org/10.3897/rio.2.e10617
This archive contains XSLT transformations from EML v. 2.1.1 and v. 2.1.0 to Pensoft data paper format.
Database of Incidence per reef and región of the research "Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) for capturing the biological diversity of two coral reefs in the Yucatán Península, México"
<p><strong>*Corresponding autor: </strong>edlinguerra@gmail.com</p> <p>This database contains information of specimens of the cryptofauna assemblages identified by experts of each Phyla per reef and región and is a complementary material of the research “Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) to estimate cryptic diversity in two coral reefs of the Yucatan Península, México”. For the present research, animals of the appropriate species and quality were selected and the minimum number required to obtain scientifically valid results were considered, all animals were anesthetized and deposited in National Collections: Colección Regional de Crustáceos de la Península de Yucatán (SEMARNAT number: YUC-CC-255-11), Colección Regional de Moluscos de la Península de Yucatán (SEMARNAT number: YUC. -INV-240-01-11), Colección Regional de Equinodermos de la Península de Yucatán (SEMARNAT number: DGVS-CC-307-18), Colección Regional de Ascidias de la Península de Yucatán (SEMARNAT number: DGVS-CC-306-18), Colección Regional de Briozoos de la Península de Yucatán (SEMARNAT number: DGVS-CC-308-18), Colección Regional de Cnidarios de la Península de Yucatán (SEMARMAT number: YUC-CC-254-11), Colección Regional de Policládidos de la Península de Yucatán (105 Collection CONABIO) and Colección Nacional del Phyla Porifera “Gerardo Green” of Universidad Nacional Autónoma de México, Facultad de Ciencias, Sisal, Mexico (UMDI-Sisal) and within accordance with scientific collection permits: PPF/DGOPA: 295/17, 300/17, 294/17, 293/17, PPF/DGOPA-076/19 issued by Mexico’s State Secretaria de Agricultura, Ganaderia, Desarrollo Rural, Pesca y Alimentación (SAGARPA).</p> <p><strong>CC-BY-NC-N</strong></p>
BOLD Insecta and Araneae data files for "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs"
<p>These are the BOLD Insecta and Araneae DWC files for use with the automated scripting procedure from "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs".</p>
Clinico-biological Database in Patients Treated With Metabolic Radiotherapy in the Nuclear Medicine Department
ClinicalTrials.gov study NCT04104529. IPD Sharing: YES. Countries: 1. Publications: 25.
Development of a Clinical and Biological Database in Rectum Cancer
ClinicalTrials.gov study NCT04006951. IPD Sharing: NO. Countries: 1. Publications: 1.
Development of a Cinical and Biological Database in Ovarian, Fallopian Tube and Peritoneal Cancers
ClinicalTrials.gov study NCT03976999. IPD Sharing: NO. Countries: 1. Publications: 4.
Clinical Database Associated With a Biological Banking Accessible to Initiate Epidemiological and Translational Collaborative Researches in Kidney Transplantation
ClinicalTrials.gov study NCT02900040. IPD Sharing: Not stated. Countries: 1. Publications: 2.
National Clinical and Biological Sarcoma Database : An Initiative of the French Sarcoma Group
ClinicalTrials.gov study NCT03978039. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
Development of a Autoimmune Hepatitis Patient's Database Linked to a Biological Sample Storage
ClinicalTrials.gov study NCT06078098. IPD Sharing: NO. Countries: 1. Publications: 7.
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.