Tag: experiment metadata

Found 57 sources
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Investigation Study Assay Tabular

General-purpose ISA-Tab file format - an extensible, hierarchical structure that focuses on the description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships).

IntAct molecular interaction database

IntAct provides a database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. IntAct (with MINT) is a Core Data Resource of ELIXIR. IntAct contains data from all ...

Minimum Information About a Microarray Experiment

MIAME is intended to specify all the information necessary for an unambiguous interpretation of a microarray experiment, and potentially to reproduce it. MIAME defines the content but not the format for this information.


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 ...

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 ...

Experimental Factor Ontology

The Experimental Factor Ontology provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anat ...


DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalogue published experimentally validated miRNA:gene interactions. DIANA-TarBase (v7.0), provides hundreds of thousands of high quality manually curated experimen ...

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 ...

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 ...

Evidence codes

Evidence and Conclusions Ontology (ECO) provides the terminology for describing scientific evidence from a variety of biological research types including laboratory studies, literature data mining or computational analysis. ECO uses both 'evidence an ...


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 ...


Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. It provides infrastructure and hosting for datasets.

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.

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 ...

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 ...

NCBI BioProject

A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that ...

BioProject XML Schema

This is a XML Schema specification of BioProject data. A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to f ...

Mimotope Database

Mimotope database, active site-mimicking peptides selected from phage-display libraries. It is a database which stores information on peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucle ...

Integrated Resource for Reproducibility in Macromolecular Crystallography

The Integrated Resource for Reproducibility in Macromolecular Crystallography includes a repository system and website designed to make the raw data of protein crystallography more widely available. Our focus is on identifying, cataloging and providi ...

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, ...

4DNucleome Data Portal

The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics d ...

Plant Experimental Condition Ontology

PECO is a structured, controlled vocabulary for the representation of plant experimental conditions. It describes the treatments, growing conditions, and/or study types used in various types of plant biology experiments.

Global Alliance for Genomics and Health Metadata Model

The metadata model for GA4GH, an international coalition of both public and private interested parties, formed to enable the sharing of genomic and clinical data.

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 ...

Manually Curated Database of Rice Proteins

‘Manually Curated Database of Rice Proteins’ (MCDRP) is a unique manually curated database based on published experimental data. Currently, the database has data for over 1800 rice proteins curated from > 4000 different experiments of over 400 resear ...

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 ...


MetaSRA is a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a ...

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 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 different ...


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. Crucially, all assets are related to the scientists that created them and the projects they originate from, so the model ...

FAANG metadata sample specification standard

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


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, ...

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 ...

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 ...

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.

Texas Data Repository

The Texas Data Repository is a platform for publishing and archiving datasets (and other data products) created by faculty, staff, and students at Texas higher education institutions. The repository is built in an open-source application called Datav ...

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 ...

VIVO Integrated Semantic Framework Ontology

VIVO is an open source platform for research discovery. The VIVO Integrated Semantic Framework ontology represents researchers in the context of their experience, outputs, interests, accomplishments, and associated institutions. VIVO-ISF provides a s ...

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 ...

China National GeneBank DataBase

The China National GeneBank database (CNGBdb) is a unified platform for biological big data sharing and application services. At present, CNGBdb has integrated a large amount of internal and external biological data from resources such as CNGB, NCBI, ...


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 ...

Neuroscience Information Framework Dysfunction

This ontology contains the former BIRNLex-Disease, version 1.3.2. -- The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental ...

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 ...

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 ...

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 ...

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 ...


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 ...

EBI BioSamples JSON Format

The EBI BioSamples JSON Format is a JSON schema used for submitting data to the EBI BioSamples database. This format can also be used to update or curate existing samples.

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. ...

Scientific Variables Ontology

The Scientific Variables Ontology (SVO) outlines the required and optional components for creating machine-interpretable scientific variable concepts. SVO comprises an upper ontology (SVU) that contains a set of modular conceptual categories and rela ...

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