Tag: study design

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 ...

A reporting guideline composed of 32 criteria for qualitative research interviews and focus groups.

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.

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 ...

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 ...

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 ...

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 ...

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

OME-TIFF is a standardized file format for multidimensional image data. OME-TIFF was created to maximize the respective strengths of OME-XML and TIFF. It takes advantage of the metadata defined in OME-XML while retaining the pixels in multi-page TIFF ...

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 Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has fun ...

The Open Science Framework (OSF) is a free and open source project management tool that supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery. Features include automated versioning, logging of all actions, c ...

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 ...

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 ...

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 ...

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.

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.

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, ...

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 ...

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.

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 ...

The UK Stem Cell Bank (UKSCB) facilitates the use and sharing of quality-controlled stem cell lines to support scientific research and clinical development of stem cell therapies. The work of the UK Stem Cell Bank covers three main areas: banking for ...

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 ...

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 ...

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 ...

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 ...

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 ...

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, ...

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

Data Documentation Initiative (DDI-Codebook, DDI-C) is a more light-weight version of DDI-Lifecycle, intended primarily to document simple survey data. Originally DTD-based, DDI-C is now available as an XML Schema. The freely available international ...

Data Documentation Initiative (DDI) Lifecycle (DDI-Lifecycle, DDI-L) is designed to document and manage data across the entire life cycle, from conceptualization to data publication, analysis and beyond. The freely available international DDI standar ...

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 ...

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 ...

Ascomycete Phenotype Ontology is a structured controlled vocabulary for the phenotypes of Ascomycete fungi.

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 ...

The IBP Crop Research Ontology describes experimental design, environmental conditions and methods associated with the crop study/experiment/trait and their evaluation. It has been adapted from the database management system (DMS) and germplasm manag ...

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 ...

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 ...