Reporting Guidelines

No guidelines defined

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 links to assays and specific samples, and accepts direct submissions of sample information.

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ChEMBL
ChEMBL is an open, manually-curated, large-scale bioactivity database containing information from medicinal chemistry literature. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Information regarding the compounds tested (including their structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, allowing users to address a broad range of drug discovery questions.

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Molecular INTeraction database
MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT is an ELIXIR Core Resource.

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Identifiers.org Central Registry
The Identifiers.org Central Registry provides the necessary information for the generation and resolution of unique and perennial identifiers for life science data. Those identifiers are both in URI and compact form, and make use of Identifiers.org to provide direct access to the identified data records on the Web. Resource maintainers request an Identifiers.org prefix for their databases or services.

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Gene3D
Gene3D uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases. Sequence data from UniProtKB and Ensembl for domains with no experimentally determined structures are scanned against CATH HMMs to predict domain sequence boundaries and make homologous superfamily assignments.

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WikiPathways
WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.

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Protein Data Bank in Europe
The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. It is a founding member of the worldwide Protein Data Bank which collects, organises and disseminates data on biological macromolecular structures.

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The European Genome-phenome Archive
The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

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Reactome - a curated knowledgebase of biological pathways
The cornerstone of Reactome is a freely available, open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. Inferred orthologous reactions are available for 15 non-human species including mouse, rat, chicken, zebrafish, worm, fly, and yeast.

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Ensembl
Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. Ensembl is a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data.

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STRING
STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.

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Database of Protein Disorder
The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions are manually curated from literature. DisProt annotations cover both structural and functional aspects of disorder detected by specific experimental methods.

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IUPHAR/BPS Guide to PHARMACOLOGY
The information in the database is presented at two levels: the initial view or landing pages for each target family provide expert-curated overviews of the key properties and selective ligands and tool compounds available. For selected targets more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target. Recent extensions to the database provide specific portals for accessing data on immunopharmacology (IUPHAR Guide to IMMUNOPHARMACOLOGY; www.guidetoimmunopharmacology.org), and on malaria pharmacology (IUPHAR/MMV Guide to MALARIA PHARMACOLOGY; www.guidetomalariapharmacology.org). The database is enhanced with hyperlinks to additional information in other databases including Ensembl, UniProt, PubChem and ChEMBL, as well as curated chemical information and literature citations in PubMed.

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Human Protein Atlas
The Human Protein Atlas (HPA) portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in a number of different wild-type tissues, cancer types and human cell lines. The goal of the HPA is to map all the human proteins in cells, tissues and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. The HPA is composed of six parts: the Tissue Atlas, the Single Cell Type Atlas, the Pathology Atlas, the Blood Atlas, the Brain Atlas, and the Cell Atlas.

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HAMAP database of microbial protein families
HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.

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PROSITE
PROSITE is a database of protein families and domains. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.

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SWISS-MODEL Repository of 3D protein structure models
The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms.

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UniProt Knowledgebase
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").

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CATH
The CATH database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It provides a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor).

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Giga Science Database
GigaDB primarily serves as a repository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles. GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support an article or study.

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Protein Circular Dichroism Data Bank
The Protein Circular Dichroism Data Bank (PCDDB) is an open-access online repository for protein circular dichroism spectral- and meta-data. Users may freely extract and deposit validated data and the validation process is conveniently integrated into the deposition procedure. The PCDDB is a collaborative project between Birkbeck College, University of London and Queen Mary University of London and is funded by the U.K.'s Biotechnology and Biological Sciences Research Council.

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Global Biodiversity Information Facility
GBIF, the Global Biodiversity Information Facility, is an international open data infrastructure, funded by governments. It is not a data repository. Rather, GBIF indexes thousands of datasets shared freely by hundreds of institutions worldwide making it the biggest biodiversity database on the Internet. GBIF.org makes the data discoverable and citable, assigning each download a DOI and storing it for an extended period of time. More than 1 peer-reviewed research publication citing GBIF as a source of data is published every day, in studies spanning the impacts of climate change, the spread of pests and diseases, priority areas for conservation and food security. To share your data with GBIF follow this quick guide: http://www.gbif.org/publishing-data/quick-guide To deposit/host your data, it is recommended you use one of the trusted IPT data hosting centres (DHC) listed in FAIRsharing.org. The DHC will provide you with an account on their IPT, which will allow you to manage your own datasets and publish them through GBIF.org.

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FlyMine
FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides access to integrated data at a number of different levels, from browsing to construction of complex queries, which can be executed on either single items or lists.

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MobiDB
MobiDB is a database of intrinsically disordered regions (IDRs) and related features from various sources and prediction tools. Different levels of reliability and different features are reported as different and independent annotations. The database features three levels of annotation: manually curated, indirect and predicted. MobiDB annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined.

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Catalogue of Somatic Mutations in Cancer
The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data.

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Model Archive
The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in the corresponding manuscripts.

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DataMed
DataMed is a prototype biomedical data search engine. Its goal is to discover data sets across data repositories or data aggregators. In the future it will allow searching outside these boundaries. DataMed supports the NIH-endorsed FAIR principles of Findability, Accessibility, Interoperability and Reusability of datasets with current functionality assisting in finding datasets and providing access information about them. The data repositories covered in this initial release have been selected by the bioCADDIE team and represent only a small sample of biomedical data. DataMed indexes the core metadata available for most datasets, but it offers enhanced search functions when repositories provide additional metadata.

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MassBank Europe
MassBank is the first public repository of mass spectral data for sharing them among scientific research community. MassBank data are useful for the chemical identification and structure elucidation of chemical compounds detected by mass spectrometry.

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Ensembl Bacteria
Ensembl Bacteria is a browser for bacterial and archaeal genomes. These are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan).

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Ensembl Protists
Ensembl Protists stores protist genomes of interest, covering those involved in disease and of scientific interest. This includes genomes such as Plasmodium falciparum, Dictyostelium discoideum, Phytophthora infestans and Leishmania major. A majority of these genomes are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at EMBL-EBI, GenBank at the NCBI, and the DNA Database of Japan); in some cases, the annotation has been taken directly from the websites of the data generators

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Ensembl Fungi
Ensembl Fungi is a browser for fungal genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan); in some cases, the annotation has been taken directly from the websites of the data generators.

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Ensembl Metazoa
Ensembl Metazoa provides access to genomes of metazoans of interest in disease, environmental sciences, agriculture and economic concern. Extensive coverage exists of diptera, nematodes, lepidoptera and hymenoptera.

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Omics Discovery Index
The Omics Discovery Index (OmicsDI) provides dataset discovery across a heterogeneous, distributed group of Transcriptomics, Genomics, Proteomics and Metabolomics data resources, including both open and controlled access data resources. The resource provides a short description of every dataset, including accession, description, sample/data protocols biological evidences, and publication. Based on these metadata, OmicsDI provides extensive search capabilities, as well as identification of related datasets by metadata and data content where possible. In particular, OmicsDI identifies groups of related, multi-omics datasets across repositories by shared identifiers.

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FAIRsharing
FAIRsharing is a FAIR-supporting resource that provides an informative and educational registry on data standards, databases, repositories and policy, alongside search and visualization tools and services that interoperate with other FAIR-enabling resources. FAIRsharing guides consumers to discover, select and use standards, databases, repositories and policy with confidence, and producers to make their resources more discoverable, more widely adopted and cited. Each record in FAIRsharing is curated in collaboration with the maintainers of the resource themselves, ensuring that the metadata in the FAIRsharing registry is accurate and timely. Every record is manually reviewed at least once a year. Records can be collated into collections, based on a project, society or organisation, or Recommendations, where they are collated around a policy, such as a journal or funder data policy.

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Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.

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BridgeDb
BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interactions.

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database of Disease-Gene Associations with annotated Relationships
The database of Disease-Gene Associations with annotated Relationships (eDGAR) is a database for collecting and organizing the data on gene/disease associations as derived from OMIM, Humsavar and ClinVar. For each heterogeneous or polygenic disease, eDGAR provides information on the relationship among the proteins encoded by the involved genes, including transcription factors and protein-protein interactions.

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CHD7 Database
The CHD7 database contains locus-specific, anonymised mutation data on both published and unpublished variants of the CHD7 gene related to the CHARGE syndrome phenotype. It can be searched for patients and their clinical phenotype or for mutations. It can be used as a central, quick reference database for anyone who encounters a variant in the CHD7 gene. Mutations are numbered according to the current reference sequence (GenBank Accession no. NM017780.2).

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DEB Register
International Dystrophic Epidermolysis Bullosa Patient Registry (DEB Register) provides phenotypic and genotypic information on DEB and the related COL7A1 mutations. The registry is intended to aid in disease diagnosis, genetic counseling, and discovery of novel insights.

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International Microvillus Inclusion Disease Patient Registry
The international Microvillus Inclusion Disease Patient Registry contains anonymised data on both published and unpublished MVID patients, as well as their associated MYO5B, STX3 and STXBP2 mutations and genotypes, and clinical and molecular phenotypes.

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HumanMine
HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.

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Enzyme nomenclature database
ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. The database is complete and up to date. It is regularly updated to reflect updates and additions to the nomenclature.

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SynBioHub
SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources.

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COVID-19 Data Portal
The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. The portal includes relevant datasets submitted to EMBL-EBI as well as other major centres for biomedical data. The COVID-19 Data Portal is the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.

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NanoCommons Knowledge Base
The NanoCommons Knowledge Base is a data source provided by the NanoCommons project. It is based on the BioXM TM Knowledge Management Environment, developed over the last 15 years by Biomax Informatics AG and applied in multiple collaborative research projects and commercial environments. This database requires registration. NanoCommons provides a community framework and infrastructure for reproducible science and in-silico workflows for nanomaterials safety assessment

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WorkflowHub
The WorkflowHub is a registry of scientific workflows.

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iPPI-DB - Inhibitors of Protein-Protein Interaction Database
IPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents. A large variety of data is stored within IPPI-DB: structural, pharmacological, binding and activity profile, pharmacokinetic and cytotoxicity when available, as well as some data about the PPI targets themselves.

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AIP Mutation Database
The AIP Mutation Database collects variants (both pathogenic, non-pathogenic and with unknown significance) related to pituitary adenoma predisposition (PAP) and to familial isolated pituitary adenoma (FIPA) syndromes and their clinical information in order to understand better the molecular and clinical details of the disease. Variants are reported according to the GRCh37/hg19 assembly of the human genome and the reference sequence used is the AIP Locus Reference Genomic.

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bio.tools
bio.tools is a registry of information about bioinformatics software and data services. It was created to help researchers in biological and biomedical science to find and use such resources.

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Eukaryotic Ribosomal Internal Transcribed Spacer 1 Database
The Eukaryotic Ribosomal Internal Transcribed Spacer 1 Database (ITSoneDB) is a collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences. It is intended to provide a curated reference database aimed at ITS1-based metagenomic surveys. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive.

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National Inventory of Natural Heritage
The National Inventory of Natural Heritage (INPN) is a repository for data needed for the development of conservation strategies and the dissemination of information as well as national and international reports relating to the French natural heritage (plant and animal species, natural habitats and geological heritage). It was created to provide a national reference bank for French biodiversity.

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Paired Omics Data Platform
Paired Omics Data Platform (PoDP) was created to streamline access to paired omics data so humans and computers can access and read paired datasets as well as record and exploit validated links between BGCs and metabolites. The aim of the PoDP is to connect public metabolomics datasets to their genomic origins. The PoDP does not store any metabolomics or genomics datasets, but captures metadata defining pairs of omics datasets in existing public databases and platforms already validated and utilized by the genomics and metabolomics communities.

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BioImage Informatics Index
BioImage Informatics Index (BIII) is a bioimaging resource that describes software tools, training materials and imaging datasets with the aim of helping researchers find, identify and propagate image analysis tools or workflows. BIII aims to help biologists find any tool or workflow available for a particular image analysis problem; software and algorithm developers find missing tools (or components); and bioimaging analysts identify and edit workflows. It also helps raise awareness of bioimaging analysis solutions, even when they are not associated with a publication.

Record Maintainer