Tag: experimental measurement

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 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 ...

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 ...

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 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 ...

FASTQ is a text-based file format for sharing sequencing data combining both the sequence and an associated per base quality score.

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 ...

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made ...

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 ...

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.

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 ...

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 ...

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 ...

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 ...

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.

The mzQuantML standard format is intended to store the systematic description of workflows quantifying molecules (principally peptides and proteins) by mass spectrometry. A large number of different software packages are available that produce output ...

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 ...

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, ...

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.

The RDML file format is developed by the RDML consortium (http://www.rdml.org) and can be used free of charge. The RDML file format was created to encourage the exchange, publication, revision and re-analysis of raw qPCR data. The core of an RDML fil ...

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 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 ...

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 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 ...

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 ...

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 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 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 ...

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, ...

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, ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structur ...

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 ...

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.

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 ...

These guidelines for glyco(proteo)mics analyzed by capillary electrophoresis (CE) aim for standardized and high quality reporting of experimental conditions in the scientific literature. The guidelines cover all aspects of a glyco(proteo)mics CE expe ...

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.

EnzymeML is a free and open standard XML-based interchange format for data on enzyme-catalyzed reactions. The purpose of EnzymeML is to store and exchange enzyme kinetics data between instruments, software tools, and databases. EnzymeML will allow sc ...

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 ...

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 ...

The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. QUDT provide ...

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 ...

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 ...