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Found 47 result(s)

Open Tree of Life

Tree of Life - Evolution

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The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in. Early release of the tree and tools will motivate data sharing and facilitate ongoing synthesis of knowledge.

LEPR - Library of Experimental Phase Relations

Library of Experimental Phase Relations and Trace element Distribution experimental database

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LEPR is a database of results of published experimental studies involving liquid-solid phase equilibria relevant to natural magmatic systems. TraceDs is a database of experimental studies involving trace element distribution between liquid, solid and fluid phases.

OrthoMCL

Ortholog Groups of Protein Sequences

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OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.

AmoebaDB

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AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first iteration (released in early 2010), AmoebaDB contains the genomes of three Entamoeba species (see below). AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining.

RAVE database

Radial Velocity Experiment Database

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RAVE (RAdial Velocity Experiment) is a multi-fiber spectroscopic astronomical survey of stars in the Milky Way using the 1.2-m UK Schmidt Telescope of the Anglo-Australian Observatory (AAO). The RAVE collaboration consists of researchers from over 20 institutions around the world and is coordinated by the Leibniz-Institut für Astrophysik Potsdam. As a southern hemisphere survey covering 20,000 square degrees of the sky, RAVE's primary aim is to derive the radial velocity of stars from the observed spectra. Additional information is also derived such as effective temperature, surface gravity, metallicity, photometric parallax and elemental abundance data for the stars. The survey represents a giant leap forward in our understanding of our own Milky Way galaxy; with RAVE's vast stellar kinematic database the structure, formation and evolution of our Galaxy can be studied.

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

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<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

Metlin

The original and most comprehensive MS/MS metabolite database

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METLIN represents the largest MS/MS collection of data with the database generated at multiple collision energies and in positive and negative ionization modes. The data is generated on multiple instrument types including SCIEX, Agilent, Bruker and Waters QTOF mass spectrometers.

The Monarch Initiative

Monarch Initiative

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As with most biomedical databases, the first step is to identify relevant data from the research community. The Monarch Initiative is focused primarily on phenotype-related resources. We bring in data associated with those phenotypes so that our users can begin to make connections among other biological entities of interest. We import data from a variety of data sources. With many resources integrated into a single database, we can join across the various data sources to produce integrated views. We have started with the big players including ClinVar and OMIM, but are equally interested in boutique databases. You can learn more about the sources of data that populate our system from our data sources page https://monarchinitiative.org/about/sources.

Barbara A. Mikulski Archive for Space Telescopes

MAST

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The Mikulski Archive for Space Telescopes (MAST) is a NASA funded project to support and provide to the astronomical community a variety of astronomical data archives, with the primary focus on scientifically related data sets in the optical, ultraviolet, and near-infrared parts of the spectrum. MAST is located at the Space Telescope Science Institute (STScI).

ClinVar

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ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible

Virus Pathogen Resource

ViPR

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<<<!!!<<< This repository is no longer available. >>>!!!>>> Migration of the data, tools, and services from IRD and ViPR to BV-BRC is complete! We are now in the sunsetting phase of the transition. Starting on October 31, 2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC home page. The current plan is to completely shut down IRD and ViPR by the end of this calendar year. Although it will still be possible to use those sites until shutdown, we strongly encourage you to start using BV-BRC now.

GiardiaDB

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Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains only 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems. Since the divergence of Giardia lamblia lies close to the transition between eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable, if not unique, model for gaining basic insights into genetic innovations that led to formation of eukaryotic cells. In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. A detailed study of its genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.

Comparative Welfare Entitlements Dataset

CWED

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The Comparative Welfare Entitlements Dataset (CWED) contains information about the structure and generosity of social insurance benefits in 33 countries around the world. The data contained here are an updated and extended version of CWED 1, which has been available since 2004. This web site allows you to download customized portions of the CWED 2 data, browse the Working Paper Series or access documentary material. For recent updates to this dataset, please see https://www.cwep.us/

The University of Pittsburgh English Language Institute Corpus

PELIC

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The University of Pittsburgh English Language Institute Corpus (PELIC) is a 4.2-million-word learner corpus of written texts. These texts were collected in an English for Academic Purposes (EAP) context over seven years in the University of Pittsburgh’s Intensive English Program, and were produced by over 1100 students with a wide range of linguistic backgrounds and proficiency levels. PELIC is longitudinal, offering greater opportunities for tracking development in a natural classroom setting.

The Microbial Protein Interaction Database

MPIDB

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>>>!!!<<< as stated 2017-06-09 MPIDB is no longer available under URL http://www.jcvi.org/mpidb/about.php >>>!!!<<< The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, protein complex membership, and 3D domain contacts (iPfam, 3did). We do not include (spoke/matrix) binary interactions infered from pull-down experiments.

Human Protein Reference Database

HPRD

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Human Protein Reference Database (HPRD) has been established by a team of biologists, bioinformaticists and software engineers. This is a joint project between the PandeyLab at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. HPRD is a definitive repository of human proteins. This database should serve as a ready reckoner for researchers in their quest for drug discovery, identification of disease markers and promote biomedical research in general. Human Proteinpedia (www.humanproteinpedia.org) is its associated data portal.

OpenWorm

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OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (C. elegans), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well studied in biology, this organism still eludes a deep, principled understanding of its biology. We are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so we are incorporating the data available in the scientific community into software models. We are engineering Geppetto and Sibernetic, open-source simulation platforms, to be able to run these different models in concert. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps All the code we produce in the OpenWorm project is Open Source and available on GitHub.

REBASE

The Restriction Enzyme Database

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The Restriction Enzyme Database is a collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations (dating back to 1952). REBASE is updated daily and is constantly expanding.

Coherent X-ray Imaging Data Bank

CXIDB

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Welcome to the Coherent X-ray Imaging Data Bank (CXIDB), a new database which offers scientists from all over the world a unique opportunity to access data from Coherent X-ray Imaging (CXI) experiments. CXIDB is dedicated to further the goal of making data from Coherent X-ray Imaging (CXI) experiments available to all, as well as archiving it.

Cultural Policy and the Arts National Data Archive

CPANDA

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<<<!!!<<< This repository is no longer available. >>>!!!>>> CPANDA, the Cultural Policy & the Arts National Data Archive, was the world's first interactive digital archive of policy-relevant data on the arts and cultural policy in the United States. It was founded in 2001. It was a collaborative effort of Princeton University's Firestone Library and the Princeton Center for Arts and Cultural Policy Studies. The Pew Charitable Trusts underwrote the original development of the archive. The National Endowment for the Arts completed transferring all data content in January 2016. Check at ICPSR https://www.icpsr.umich.edu/web/ICPSR/search/studies?q=cpanda, the National Archive of Data on Arts and Culture (NADAC) https://www.icpsr.umich.edu/web/NADAC/search/studies?q=cpanda. The old Cpanda URL http://www.cpanda.princeton.edu/ can be redirected to the zotero bibliography the data was moved to, https://www.zotero.org/bordelon/collections/3Q6Y9R6N. Confirm this is okay with Bobray Bordelon before implementing.

IAU Minor Planet Center

MPC

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The MPC is responsible for the designation of minor bodies in the solar system: minor planets; comets, in conjunction with the Central Bureau for Astronomical Telegrams (CBAT); and natural satellites (also in conjunction with CBAT). The MPC is also responsible for the efficient collection, computation, checking and dissemination of astrometric observations and orbits for minor planets and comets

AgBase

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AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models.

Immune Epitope Database

IEDB

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IEDB offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species. Epitopes involved in infectious disease, allergy, autoimmunity, and transplant are included. The IEDB also hosts tools to assist in the prediction and analysis of B cell and T cell epitopes.

CATH

CATH-Gene3D

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The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in the CATH hierarchy; Class, Architecture, Topology and Homologous superfamily.

The Data Hub

datahub

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the Data Hub is a community-run catalogue of useful sets of data on the Internet. You can collect links here to data from around the web for yourself and others to use, or search for data that others have collected. Depending on the type of data (and its conditions of use), the Data Hub may also be able to store a copy of the data or host it in a database, and provide some basic visualisation tools.