Tag: experimentally determined

Found 24 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 ...

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 ...


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.

Open Microscopy Environment - Tagged Image File Format

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 ...

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 ...

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.

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 ...

Network of Cancer Genes

The Network of Cancer Genes (NCG) contains information on duplicability, evolution, protein-protein and microRNA-gene interaction, function, expression and essentiality of cancer genes from manually curated publications . NCG also provides informatio ...

Human Transcriptional Regulation Interactions database

The Human Transcriptional Regulation Interactions database (HTRIdb) is a repository of experimentally verified interactions among human transcription factors (TFs) and their respective target genes. It has been constructed to be an open-access and us ...

Integrated Resource for Reproducibility in Macromolecular Crystallography

The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) was created to make the raw data of protein crystallography more widely available. The IRRMC identifies, catalogs and provides metadata related to datasets that cou ...


CollecTF is a database of transcription factor binding sites (TFBS) in the Bacteria domain. It aims at becoming a reference, highly-accessed database by relying on its ability to customize navigation and data extraction, its relevance to the communit ...

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.

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 ...

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, ...

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 ...

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. ...

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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