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Found 83 result(s)

CUAHSI

Universities Allied for Water Research

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CUAHSI's Hydrologic Information System (CUAHSI-HIS) provides web services, tools, standards and procedures that enhance access to more and better data for hydrologic analysis

NCBI

National Center for Biotechnology Information

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The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information

ImmPort

Immunology Database and Analysis Portal

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The Immunology Database and Analysis Portal (ImmPort) archives clinical study and trial data generated by NIAID/DAIT-funded investigators. Data types housed in ImmPort include subject assessments i.e., medical history, concomitant medications and adverse events as well as mechanistic assay data such as flow cytometry, ELISA, ELISPOT, etc. --- You won't need an ImmPort account to search for compelling studies, peruse study demographics, interventions and mechanistic assays. But why stop there? What you really want to do is download the study, look at each experiment in detail including individual ELISA results and flow cytometry files. Perhaps you want to take those flow cytometry files for a test drive using FLOCK in the ImmPort flow cytometry module. To download all that interesting data you will need to register for ImmPort access.

VEuPathDB

formerly: Eukaryotic Pathogen Database Resources

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EuPathDB (formerly ApiDB) is an integrated database covering the eukaryotic pathogens in the genera Acanthamoeba, Annacaliia, Babesia, Crithidia, Cryptosporidium, Edhazardia, Eimeria, Encephalitozoon, Endotrypanum, Entamoeba, Enterocytozoon, Giardia, Gregarina, Hamiltosporidium, Leishmania, Nematocida, Neospora, Nosema, Plasmodium, Theileria, Toxoplasma, Trichomonas, Trypanosoma and Vavraia, Vittaforma). While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all of these resources, and the opportunity to leverage orthology for searches across genera.

Federal Interagency Traumatic Brain Injury Research Informatics System

FITBIR

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The Federal Interagency Traumatic Brain Injury Research (FITBIR) informatics system was developed to share data across the entire TBI research field and to facilitate collaboration between laboratories, as well as interconnectivity with other informatics platforms. Sharing data, methodologies, and associated tools, rather than summaries or interpretations of this information, can accelerate research progress by allowing re-analysis of data, as well as re-aggregation, integration, and rigorous comparison with other data, tools, and methods. This community-wide sharing requires common data definitions and standards, as well as comprehensive and coherent informatics approaches.

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.

FungiDB

The Fungal and Oomycete Genomics Resource

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FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. FungiDB was first released in early 2011 as a collaborative project between EuPathDB and the group of Jason Stajich (University of California, Riverside). At the end of 2015, FungiDB was integrated into the EuPathDB bioinformatic resource center. FungiDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.

CU Scholar

University of Colorado Boulder's institutional repository

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CU Scholar is an open access institutional repository supporting the research and teaching mission of the University of Colorado Boulder. It is intended to serve as a platform for preserving the research activities of members of the CU Boulder community and for providing public access to that research. CU Scholar is maintained by the University Libraries.

ASU Library Research Data Repository

Arizona State University Dataverse

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The Arizona State University (ASU) Research Data Repository provides a platform for ASU-affiliated researchers to share, preserve, cite, and make research data accessible and discoverable. The ASU Research Data Repository provides a permanent digital identifier for research data, which complies with data sharing policies. The repository is powered by the Dataverse open-source application, developed and used by Harvard University. Both the ASU Research Data Repository and the KEEP Institutional Repository are managed by the ASU Library to ensure research produced at Arizona State University is discoverable and accessible to the global community.

MicrosporidiaDB

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MicrosporidiaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the phylum Microsporidia. In its first iteration (released in early 2010), MicrosporidiaDB contains the genomes of two Encephalitozoon species (see below). MicrosporidiaDB 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.

System for Earth Sample Registration

SESAR

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SESAR, the System for Earth Sample Registration, is a global registry for specimens (rocks, sediments, minerals, fossils, fluids, gas) and related sampling features from our natural environment. SESAR's objective is to overcome the problem of ambiguous sample naming in the Earth Sciences. SESAR maintains a database of sample records that are contributed by its users. Each sample that is registered with SESAR is assigned an International Geo Sample Number IGSN to ensure its global unique identification.

National Ecological Observatory Network

NEON

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Funded by the National Science Foundation (NSF) and proudly operated by Battelle, the National Ecological Observatory Network (NEON) program provides open, continental-scale data across the United States that characterize and quantify complex, rapidly changing ecological processes. The Observatory’s comprehensive design supports greater understanding of ecological change and enables forecasting of future ecological conditions. NEON collects and processes data from field sites located across the continental U.S., Puerto Rico, and Hawaii over a 30-year timeframe. NEON provides free and open data that characterize plants, animals, soil, nutrients, freshwater, and the atmosphere. These data may be combined with external datasets or data collected by individual researchers to support the study of continental-scale ecological change.

KBase

KBase: The U.S. Department of Energy Systems Biology Knowledgebase

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The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics. KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.

Ocean Observatories Initiative Data

Ocean Observatories Initiative Data Portal

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The Ocean Observatories Initiative (OOI) is a science-driven ocean observing network that delivers real-time data from more than 800 instruments to address critical science questions regarding the world’s ocean. OOI data are freely available online to anyone with an Internet connection.

Odum Institute Archive Dataverse

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The Odum Institute Archive Dataverse contains social science data curated and archived by the Odum Institute Data Archive at the University of North Carolina at Chapel Hill. Some key collections include the primary holdings of the Louis Harris Data Center, the National Network of State Polls, and other Southern-focused public opinion data. Please note that some datasets in this collection are restricted to University of North Carolina at Chapel Hill affiliates. Access to these datasets require UNC ONYEN institutional login to the Dataverse system.

TriTrypDB

kinetoplastid genomics resource

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TriTrypDB is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both Leishmania and Trypanosoma genera. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).

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.

Medical Imaging and Data Research Center

MIDRC

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MIDRC aims to develop a high-quality repository for medical images related to COVID-19 and associated clinical data, and develop and foster medical image-based artificial intelligence (AI) for use in the detection, diagnosis, prognosis, and monitoring of COVID-19.

VectorBase

Bioinformatics Resource for Invertebrate Vectors of Human Pathogens

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VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).

NCBI dbGaP

DataBase of Genotypes And Phenotypes

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The NCBI database of Genotypes and Phenotypes archives and distributes the results of studies that have investigated the interaction of genotype and phenotype, including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. The database provides summaries of studies, the contents of measured variables, and original study document text. dbGaP provides two types of access for users, open and controlled. Through the controlled access, users may access individual-level data such as phenotypic data tables and genotypes.

MaizeGDB

Maize Genetics and Genomics Database

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The Maize Genetics and Genomics Database focuses on collecting data related to the crop plant and model organism Zea mays. The project's goals are to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models. MaizeGDB also aims to make the Maize Newsletter available, and provide support services to the community of maize researchers. MaizeGDB is working with the Schnable lab, the Panzea project, The Genome Reference Consortium, and iPlant Collaborative to create a plan for archiving, dessiminating, visualizing, and analyzing diversity data. MMaizeGDB is short for Maize Genetics/Genomics Database. It is a USDA/ARS funded project to integrate the data found in MaizeDB and ZmDB into a single schema, develop an effective interface to access this data, and develop additional tools to make data analysis easier. Our goal in the long term is a true next-generation online maize database.aize genetics and genomics database.

brainlife

brainlife.io

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Brainlife promotes engagement and education in reproducible neuroscience. We do this by providing an online platform where users can publish code (Apps), Data, and make it "alive" by integragrate various HPC and cloud computing resources to run those Apps. Brainlife also provide mechanisms to publish all research assets associated with a scientific project (data and analyses) embedded in a cloud computing environment and referenced by a single digital-object-identifier (DOI). The platform is unique because of its focus on supporting scientific reproducibility beyond open code and open data, by providing fundamental smart mechanisms for what we refer to as “Open Services.”

WikiPathways

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WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.

NCBI Taxonomy

Entrez Taxonomy

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The NCBI Taxonomy database is a curated set of names and classifications for all of the organisms that are represented in GenBank. The EMBL and DDBJ databases, as well as GenBank, now use the NCBI Taxonomy as the standard classification for nucleotide sequences. Taxonomy Contains the names and phylogenetic lineages of more than 160,000 organisms that have molecular data in the NCBI databases. New taxa are added to the Taxonomy database as data are deposited for them. When new sequences are submitted to GenBank, the submission is checked for new organism names, which are then classified and added to the Taxonomy database.

TrichDB

Trichomonas vaginalis Sequence Database

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TrichDB integrated genomic resources for the eukaryotic protist pathogens Trichomonas vaginalis.