How to cite this record FAIRsharing.org: Bioschemas; Bioschemas; DOI: https://doi.org/10.25504/FAIRsharing.20sbr9; Last edited: Nov. 23, 2018, 11:27 a.m.; Last accessed: Dec 12 2018 1:16 a.m.
Record added: Feb. 5, 2018, 2:10 p.m.
Record updated: Feb. 5, 2018, 2:59 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.20sbr9' by 'The FAIRsharing Team' at 14:59, 05 Feb 2018 (approved): 'related_databases' has been modified: Before: After: biodbcore-000008|BioSample at the European Bioinformatics Institute biodbcore-000550|CATH Protein Structure Classification biodbcore-000328|The European Genome-phenome Archive biodbcore-001004|FAIRsharing biodbcore-000595|Giga Science Database biodbcore-000398|Guide to Pharmacology biodbcore-000411|Human Protein Atlas biodbcore-000649|MobiDB biodbcore-000544|UniProt Knowledgebase biodbcore-000015|ChEMBL: a large-scale bioactivity database for drug discovery biodbcore-000068|Identifiers.org Registry biodbcore-000322|Protein Data Bank in Europe Added: biodbcore-000008|BioSample at the European Bioinformatics Institute biodbcore-000550|CATH Protein Structure Classification biodbcore-000328|The European Genome-phenome Archive biodbcore-001004|FAIRsharing biodbcore-000595|Giga Science Database biodbcore-000398|Guide to Pharmacology biodbcore-000411|Human Protein Atlas biodbcore-000649|MobiDB biodbcore-000544|UniProt Knowledgebase biodbcore-000015|ChEMBL: a large-scale bioactivity database for drug discovery biodbcore-000068|Identifiers.org Registry biodbcore-000322|Protein Data Bank in Europe Removed:
No XSD schemas defined
Conditions of UseApplies to: Database software
No publications available
No guidelines defined
No semantic standards defined
Models and Formats
No identifier schema standards defined
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 an specific samples, and accepts direct submissions of sample information.
The core of the Registry is a catalogue of data collections (corresponding to e.g. controlled vocabularies, databases), their URIs and the corresponding physical URLs (or resources). These resources are monitored daily to ensure data accessibility and the validity of the resolution mechanism.
Protein Data Bank in Europe
The Protein Data Bank in Europe is a founding member of the worldwide Protein Data Bank which collects, organises and disseminates data on biological macromolecular structures.
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).
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. The database is enhanced with hyperlinks to additional information in other databases including Ensembl, UniProt, PubChem, ChEMBL and DrugBank, as well as curated chemical information and literature citations in PubMed.
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 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").
CATH Protein Structure Classification
The CATH database is 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). This collection is concerned with superfamily classification.
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.
A database of protein disorder and mobility annotations. MobiDB was designed to offer a centralized resource for annotations of intrinsic protein disorder. The database features three levels of annotation: manually curated, indirect and predicted. Manually curated data is extracted from the DisProt database. Indirect data is inferred from PDB structures that are considered an indication of intrinsic disorder. The 10 predictors currently included (three ESpritz flavors, two IUPred flavors, two DisEMBL flavors, GlobPlot, VSL2b and JRONN) enable MobiDB to provide disorder annotations for every protein in absence of more reliable data. The new version also features a consensus annotation and classification for long disordered regions. In order to complement the disorder annotations, MobiDB features additional annotations from external sources. Annotations from the UniProt database include post-translational modifications and linear motifs. Pfam annotations are displayed in graphical form and are link-enabled, allowing the user to visit the corresponding Pfam page for further information. Experimental protein–protein interactions are also classified for disorder content.
A manually curated, searchable portal that maps metadata standards, databases/data repositories and data policies across disciplines, describing both the resources and the relationships between them. 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. FAIRsharing is also a community activity under the Research Data Alliance (RDA), Force11 and ELIXIR, among other global and discipline specific initiatives.
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