Tag: protocol

Found 55 sources
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Investigation Study Assay Tabular

Investigation Study Assay Tabular (ISA-Tab) describes the ISA Abstract Model reference implementation specified using the ISA-Tab format. ISA-Tab files are tab separated value (tsv) files, with specific labeled column structures. The ISA model consis ...


ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Expe ...


MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. The database is cross-species and cross-technique and it covers metabolite structures and their reference spectra as well as their biological ro ...

Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI fosters clear communication abo ...

Metabolomics Workbench

The Metabolomics Workbench serves as a national and international repository for metabolomics data and metadata and provides analysis tools and access to metabolite standards, protocols, tutorials, training, and more.


DIANA-TarBase is a reference database that indexes experimentally-supported microRNA (miRNA) targets. It integrates information on cell-type specific miRNA–gene regulation and includes miRNA-binding locations. The target data provided by DIANA-TarBas ...

Minimum Information About a Proteomics Experiment

MIAPE attempts to define the minimum set of information about whole proteomics experiments that would be required by a public repository.

Genomes OnLine Database

The Genomes Online Database provides access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing ...

Mass Spectrometry Virtual Interactive Environment

MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication ...

BioSamples at the European Bioinformatics Institute

The BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides lin ...

Open Microscopy Environment eXtensible Markup Language

OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community. The purp ...


The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range ...

Termini-Oriented Protein Function INferred Database

The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing sta ...


Synapse is a collaborative research platform that allows individuals and teams to share, track, and discuss their data and analysis in projects. Synapse allows researchers to share and describe data, analyses, and other content. Data and analyses can ...

Minimum Information about Plant Phenotyping Experiment

MIAPPE is a reporting guideline for plant phenotyping experiments. It comprises a checklist, i.e., a list of attributes to describe an experiment so that it is understandable and replicable. It should be consulted by people recording and depositing p ...

Experimental Conditions Ontology

The Experimental Conditions Ontology is designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.

CDISC Study/Trial Design Model

The CDISC Study/Trial Design Model in XML (SDM) is an extension of ODM and enables organizations to provide rigorous, machine-readable, interchangeable descriptions of the designs of their clinical studies, including treatment plans, eligibility and ...

CDISC Protocol Representation Model

The CDISC Protocol Representation Model (PRM) provides a standard for planning and designing a research protocol with focus on study characteristics such as study design, eligibility criteria, and requirements from the ClinicalTrials.gov, World Healt ...

Minimum Information Required for A Glycomics Experiment - Sample Preparation

MIRAGE (Minimum Information Required for A Glycomics Experiment) was created to improve the quality of glycomics data in the scientific literature. The sample preparation guidelines are designed to include all aspects of sample generation, purificati ...

Information Artifact Ontology

The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.

Statistics Ontology

STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of applications, and information needed or resulting from statistical methods, such as probability distributions, ...

eagle-i Research Resource Ontology

A unique feature of the eagle-i software is that the data collection and search tools are completely driven by ontologies. These ontologies are a set of modules that are written in the OWL language and edited and managed using Protégé. Beginning in 2 ...

GrainGenes, a Database for Triticeae and Avena

The GrainGenes website hosts a wealth of information for researchers working on Triticeae species, oat and their wild relatives. The website hosts a database encompassing information such as genetic maps, genes, alleles, genetic markers, phenotypic d ...

Collaborative Open Plant Omics

COPO is a portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. COPO can link your outputs to your ORCiD profile. By tracking unique id ...

Magnetic Resonance Dataset Acquisition Ontology

The OntoNeuroLOG Magnetic Resonance Dataset Acquisition (ONL-MR-DA) ontology is one of the modules in the OntoNeuroLOG ontology version 3.0, developed in the context of the NeuroLOG project., a French project supported by ANR (ANR-06-TLOG-024 grant) ...

Center for Expanded Data Annotation and Retrieval Workbench

The Center for Expanded Data Annotation and Retrieval (CEDAR) Workbench is a database of metadata templates that define the data elements needed to describe particular types of biomedical experiments. The templates include controlled terms and synony ...

EcoliWiki: A Wiki-based community resource for Escherichia coli

EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

Meta-omics Data and Collection Objects

The MOD-CO schema is a conceptual and procedural meta-omics schema developed as part of the MOD-CO project. The schema is represented in a number of different formats. MOD-CO is a generic and comprehensive schema providing specifications useful for l ...

Harvard Dataverse

Harvard Dataverse is a research data repository running on the open source web application Dataverse. Harvard Dataverse is fully open to the public, and allows upload and browsing of data from all fields of research, and is free for all researchers w ...

Ontology of Experimental Events

The Ontology of Experimental Events (OEEv) characterizes events that occur during an experiment; for example, moving of plants, dates of sowing, application of a given treatment, harvesting, measurements or sampling for ‐omic measurements, or any cat ...

Ontology for Experimental Phenotypic Objects

The Ontology for Experimental Phenotypic Objects (OEPO) describes objects involved in phenotyping experiments (e.g. infrastructure, devices, germplasm, scientific objects) and defines a hierarchy between them according to the specificities of the ins ...

Ontology of Experimental Variables and Values

The Ontology of Experimental Variables and Values (OoEVV) provides a lightweight representation of (a) the variables used to measure experimental properties and (b) the measurement scales that form the complex data types supporting that data. Many di ...

Standards for Reporting Enzymology Data Database

STRENDA DB is a storage and search platform supported by the Beilstein-Institut that incorporates the STRENDA Guidelines in a user-friendly, web-based system. If you are an author who is preparing a manuscript containing functional enzymology data, S ...

Just Enough Results Model Ontology

The JERM provides a framework to describe SEEK assets and the relationships between assets and the experiments that created them. All assets are related to the scientists that created them and the projects they originate from, so the model captures p ...


Metabolonote is a specialized database system that manages metadata for experimental data obtained through the study of Metabolomics. This system was developed with the aim of promoting the publication and utilization of Metabolomics data by simplify ...

Plant Experimental Assay Ontology

The Plant Experimental Assay Ontology (PEAO) was created to describe experimental procedures within plant research, regardless of the scientific questions that prompted the assays. This ontology models entities from three distinct realms (biological, ...

Protocol Registration Data Element Definitions

This standard describes the definitions for protocol registration data elements submitted to ClinicalTrials.gov for interventional studies (clinical trials) and observational studies.

AnaEE Thesaurus

The anaeeThes thesaurus aims at providing a controlled vocabulary for the semantic description of the study of continental ecosystems and their biodiversity. The thesaurus consists of concepts handled in different main thematic areas: abiotic (e.g. a ...

Minimal information for Chemosensitivity Assays

Minimal information for Chemosensitivity Assays (MICHA) is both a web tool to aid annotation of drug sensitivity screens and a guideline for defining the minimal information required to: capture critical drug sensitivity assay components, allow the F ...

Scholars Portal Dataverse

Scholars Portal Dataverse is a repository of research data in all fields of research. Researchers can share, publish, archive, find and cite data across all research fields. Researchers from subscribing institutions can use Dataverse to directly depo ...

Advanced Ecological Knowledge and Observation System

The Advanced Ecological Knowledge and Observation System from the Terrestrial Ecosystem Research Network (TERN AEKOS) focuses on ecological plot data that are generated by land-based ecosystem projects that use survey, monitoring and experimental stu ...

Access to Biological Collection Data DNA extension

ABCDDNA is a theme specific extension for ABCD (Access to Biological Collections Data) created to facilitate storage and exchange of data related to DNA collection units, such as DNA extraction specifics, DNA quality parameters, and data characterisi ...

Minimum Information Required for a Glycomics Experiment - Liquid Chromatography Analysis

Thes LC guidelines are intended to improve the reporting of liquid chromatography (LC) glycan data. The MIRAGE-LC module covers all aspects of instrument setup and modality of data handling and manipulation cross-linked with other MIRAGE recommentati ...

Cardiac Electrophysiology Ontology

The Cardiac Electrophysiology Ontology contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluo ...


heiDATA is Heidelberg University’s research data repository. It is managed by the Competence Centre for Research Data, a joint institution of the University Library and the Computing Centre. All researchers affiliated with Heidelberg University can u ...

Moorfields Eye Image Dataset Release 001

The Moorfields Eye Hospital Imaging and Ocular Phenotype Bio resource is a longitudinal eye imaging dataset from routinely collected data from MEH patients from 2004 to date. This dataset of > 10m images include a variety of high quality imaging typ ...

Moorfields AMD Dataset Release 002

The Moorfields AMD Dataset is a longitudinal dataset consisting of routinely collected imaging and clinical metadata from patients receiving treatment for age-related macular degeneration (AMD) at Moorfields, from 2004 to the present. This dataset ...

FAANG metadata analysis specification

The FAANG metadata analysis specification describes the specification for all analysis metadata as part of the larger FAANG metadata guidance project. Analysis metadata needs to contain the following process attributes: input data (a list of files us ...


ChemTHEATRE is an online resource for browsing and analyzing curated and user-contributed data sets of environmental contaminants. ChemTHEATRE also stores metadata of the samples and of the experimental methods.

DDBJ BioProject

The DDBJ BioProject resource organizes both the projects and the data from those projects which is deposited into several archival databases maintained by members of the INSDC. This allows searching by characteristics of these projects, using the pro ...

CyVerse Data Common Repository

The Data Commons provides services to manage, organize, preserve, publish, discover, and reuse data. Using our pipelines, you can easily publish data to the NCBI or directly to the CyVerse Data Commons. CyVerse Curated Data are stable and have DOIs. ...


CaltechDATA is an institutional data repository for Caltech. Caltech library runs the repository to preserve the accomplishments of Caltech researchers and share their results with the world. Caltech-associated researchers can upload data, link data ...

FAANG metadata experiment specification standard

The FAANG metadata experiment specification document describes the principles and structure for the FAANG metadata guidance. The main goal of the FAANG standards is to ensure all FAANG experiments are well described and that the description is well s ...

Investigation Study Assay JSON

Investigation Study Assay JSON (ISA-JSON) describes the ISA Abstract Model reference implementation specified using the JavaScript Object Notation (JSON) format, a text format for serializing structured data. The ISA model consists of three core enti ...

Open Data for Access and Mining Structural Metadata

Open Data for Access and Mining (ODAM) Structural Metadata is a format describing how the metadata should be formatted and what should be included to ensure ODAM compliance for a data set. To comply with this format, two metadata files in TSV format ...

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