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Bioschemas

Bioschemas aims to improve data interoperability in life sciences. It does this by encouraging people in life science to use schema.org markup, so that their websites and services contain consistently structured information. This structured information then makes it easier to discover, collate and analyse distributed data. The main outcome of Bioschemas is a collection of specifications that provide guidelines to facilitate a more consistent adoption of schema.org markup within the life sciences. This collection identifies those resources known to have Bioschemas markup.

This record is maintained by: ajggray ORCID

Record added: June 22, 2020, 11:27 a.m..
Record updated: June 22, 2020, 9:14 p.m. by ajggray.

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Edits to 'https://fairsharing.org/bsg-c000072' by 'ajggray' at 21:14, 22 Jun 2020 (approved):

	'databases' has been modified:
		Before:
			BioSamples at the European Bioinformatics Institute
			ChEMBL
			Molecular INTeraction database
			Identifiers.org Central Registry
			The European Genome-phenome Archive
			Reactome - a curated knowledgebase of biological pathways
			Database of Protein Disorder
			IUPHAR/BPS Guide to PHARMACOLOGY
			Human Protein Atlas
			HAMAP database of microbial protein families
			PROSITE
			SWISS-MODEL Repository of 3D protein structure models
			UniProt Knowledgebase
			CATH Protein Structure Classification
			Giga Science Database
			Protein Circular Dichroism Data Bank
			Global Biodiversity Information Facility
			FlyMine
			MobiDB
			Catalogue of Somatic Mutations in Cancer
			Model Archive
			DataMed
			Ensembl Genomes
			Omics Discovery Index
			FAIRsharing
			Alliance of Genome Resources
			database of Disease-Gene Associations with annotated Relationships
			Scientific Data ISA-explorer
			CHD7 Database
			DEB Register
			International Microvillus Inclusion Disease Patient Registry
			HumanMine
			Enzyme nomenclature database
			SynBioHub
		After:
			BioSamples at the European Bioinformatics Institute
			ChEMBL
			Molecular INTeraction database
			Identifiers.org Central Registry
			Protein Data Bank in Europe
			The European Genome-phenome Archive
			Reactome - a curated knowledgebase of biological pathways
			Database of Protein Disorder
			IUPHAR/BPS Guide to PHARMACOLOGY
			Human Protein Atlas
			HAMAP database of microbial protein families
			PROSITE
			SWISS-MODEL Repository of 3D protein structure models
			UniProt Knowledgebase
			CATH Protein Structure Classification
			Giga Science Database
			Protein Circular Dichroism Data Bank
			Global Biodiversity Information Facility
			FlyMine
			MobiDB
			Catalogue of Somatic Mutations in Cancer
			Model Archive
			DataMed
			Ensembl Genomes
			Omics Discovery Index
			FAIRsharing
			Alliance of Genome Resources
			database of Disease-Gene Associations with annotated Relationships
			Scientific Data ISA-explorer
			CHD7 Database
			DEB Register
			International Microvillus Inclusion Disease Patient Registry
			HumanMine
			Enzyme nomenclature database
			SynBioHub
		Added:
			Protein Data Bank in Europe
		Removed:

Edits to 'https://fairsharing.org/bsg-c000072' by 'ajggray' at 21:11, 22 Jun 2020 (approved):

	'databases' has been modified:
		Before:
		After:
			BioSamples at the European Bioinformatics Institute
			ChEMBL
			Molecular INTeraction database
			Identifiers.org Central Registry
			The European Genome-phenome Archive
			Reactome - a curated knowledgebase of biological pathways
			Database of Protein Disorder
			IUPHAR/BPS Guide to PHARMACOLOGY
			Human Protein Atlas
			HAMAP database of microbial protein families
			PROSITE
			SWISS-MODEL Repository of 3D protein structure models
			UniProt Knowledgebase
			CATH Protein Structure Classification
			Giga Science Database
			Protein Circular Dichroism Data Bank
			Global Biodiversity Information Facility
			FlyMine
			MobiDB
			Catalogue of Somatic Mutations in Cancer
			Model Archive
			DataMed
			Ensembl Genomes
			Omics Discovery Index
			FAIRsharing
			Alliance of Genome Resources
			database of Disease-Gene Associations with annotated Relationships
			Scientific Data ISA-explorer
			CHD7 Database
			DEB Register
			International Microvillus Inclusion Disease Patient Registry
			HumanMine
			Enzyme nomenclature database
			SynBioHub
		Added:
			BioSamples at the European Bioinformatics Institute
			ChEMBL
			Molecular INTeraction database
			Identifiers.org Central Registry
			The European Genome-phenome Archive
			Reactome - a curated knowledgebase of biological pathways
			Database of Protein Disorder
			IUPHAR/BPS Guide to PHARMACOLOGY
			Human Protein Atlas
			HAMAP database of microbial protein families
			PROSITE
			SWISS-MODEL Repository of 3D protein structure models
			UniProt Knowledgebase
			CATH Protein Structure Classification
			Giga Science Database
			Protein Circular Dichroism Data Bank
			Global Biodiversity Information Facility
			FlyMine
			MobiDB
			Catalogue of Somatic Mutations in Cancer
			Model Archive
			DataMed
			Ensembl Genomes
			Omics Discovery Index
			FAIRsharing
			Alliance of Genome Resources
			database of Disease-Gene Associations with annotated Relationships
			Scientific Data ISA-explorer
			CHD7 Database
			DEB Register
			International Microvillus Inclusion Disease Patient Registry
			HumanMine
			Enzyme nomenclature database
			SynBioHub
		Removed:

36 records in view

Name	Abbreviation	Type	Subject	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
Alliance of Genome Resources	Alliance of Genome Resources	Database	Life Science	Gene name Genome map Functional association Disease process modeling Gene Plus 1 more...	Caenorhabditis Danio rerio Drosophila Homo sapiens Mus musculus Plus 2 more...	FlyBase SGD WormBase GOA RGD Plus 2 more...	DOID GO	None	Bioschemas
BioSamples at the European Bioinformatics Institute	BioSD	Database	Biology	Biological sample Experiment metadata Disease Genotype Phenotype Plus 1 more...	All	ArrayExpress ENA PRIDE Cellosaurus COVID-19 Data Portal	EFO ChEBI SampleTab BioProject XML Schema FAANG metadata sample specification standard Plus 6 more...	MNI Open Research UCL Child Open Health Research HRB Open Research AAS Policy Gates Open Research Data Guidelines Plus 2 more...	Bioschemas ELIXIR Core Data Resources and Deposition Databases
Bioschemas	Bioschemas	Standard	Computer Science Life Science	Annotation	Not applicable	BioSD Identifiers.org Central Registry PDBe EGA Guide to Pharmacology Plus 6 more...	Schema.org	None	Bioschemas Toxicology
Catalogue of Somatic Mutations in Cancer	COSMIC	Database	Biomedical Science Life Science	Genome annotation Somatic mutation Cancer	Homo sapiens	NCG neXtProt CCGD	None	Nature Publishing Group - Nature Genetics - Availability of Data and materials Nature Publishing Group - Nature Materials - Availability of Data and materials Nature Publishing Group - Nature Chemical Biology - Availability of Data and materials Nature Publishing Group - Nature Biotechnology - Availability of Data and materials Nature Publishing Group - Nature Cell Biology - Availability of Data and materials	Bioschemas
CATH Protein Structure Classification	CATH domain	Database	Life Science	Annotation Classification Curated information Protein Structure	All	FunTree MACiE ProtoNet STAP Gene3D Plus 8 more...	Bioschemas PDB FASTA GO	None	Bioschemas ELIXIR Core Data Resources and Deposition Databases ELIXIR UK node resources
CHD7 Database	CHD7 Database	Database	Biology Biomedical Science Genetics Life Science Molecular biology	Gene expression data Disease phenotype Gene Genotype Mutation Plus 1 more...	Homo sapiens	None	CHD	None	Bioschemas
ChEMBL	ChEMBL	Database	Biochemistry Drug Discovery Medicinal Chemistry	Chemical structure Bioactivity Drug Small molecule	All	BindingDB GPCRDB Guide to Pharmacology PubChem Cellosaurus Plus 9 more...	ChEBI BTO CHEMINF UO BAO Plus 5 more...	MNI Open Research UCL Child Open Health Research HRB Open Research AAS Policy Advanced Genetics Plus 4 more...	Toxicology Data Citation Implementation Bioschemas ELIXIR Core Data Resources and Deposition Databases Advanced Genetics
database of Disease-Gene Associations with annotated Relationships	eDGAR	Database	Biomedical Science Life Science	Protein interaction Transcription factor Disease Gene-disease association	Homo sapiens	Reactome Ensembl HGNC STRING BioGRID Plus 4 more...	GO	None	Bioschemas
Database of Protein Disorder	DisProt	Database	Biomedical Science	Intrinsically disordered proteins Protein structure Disease Protein	Archaea Bacteria Eukaryota Viruses	MobiDB	FASTA	None	Bioschemas RDA Covid-19 WG Resources
DataMed	DataMed	Database	Biomedical Science	FAIR	All	None	DATS Schema.org	None	Bioschemas bioCADDIE
DEB Register	DEB Register	Database	Biomedical Science Life Science	Gene Gene-disease association Genetic disorder Mutation	Homo sapiens	MVID	None	None	Bioschemas
Ensembl Genomes	Ensembl Genomes	Database	Comparative Genomics	DNA sequence data Genome alignment Genome annotation Genome visualization Genome	Bacteria Eukaryota Fungi Plantae Vertebrata	TarBase PHI-base Gramene ENA Ensembl Plus 9 more...	NCBITAXON	None	Bioschemas ELIXIR Core Data Resources and Deposition Databases RDA Covid-19 WG Resources
Enzyme nomenclature database	ENZYME	Database	Biology Life Science	Classification Enzyme Commission number Catalytic activity Enzyme	All	Rhea IntEnz ExplorEnz TargetMine	EC Number	None	Bioschemas
FAIRsharing	FAIRsharing	Database	Agriculture Biomedical Science Earth Science Environmental Science Humanities Plus 2 more...	FAIR	All	None	Schema.org BioDBCore Bioschemas SRAO DOI Plus 2 more...	MNI Open Research UCL Child Open Health Research Elsevier's Data Policy PLOS Recommended Repositories EMBO Recommended Databases and Data Standards Plus 12 more...	Bioschemas ELIXIR Recommended Interoperability Resources ELIXIR UK node resources Advanced Genetics
FlyMine	FlyMine	Database	Genomics Life Science	Protein interaction Gene Protein	Anopheles gambiae Caenorhabditis elegans Drosophila melanogaster	FlyBase IntAct modMine GenomeRNAi BDGP Plus 21 more...	SO GO FASTA GFF3 OBO Format Plus 2 more...	None	Bioschemas InterMine
Giga Science Database	GigaDB	Database	Computational Biology Genetics Genomics Life Science Proteomics	Gene expression data Imaging Sequencing Software	All	None	ISA-Tab Bioschemas NCBITAXON	PLOS Recommended Repositories eLife Data Policy BioMed Central - Minimum Standards of Reporting Checklist GigaScience - Minimum Standards of Reporting Checklist	Data Citation Implementation Bioschemas RDA Covid-19 WG Resources
Global Biodiversity Information Facility	GBIF	Database	Biodiversity Bioinformatics Life Science	Taxonomic classification	All	Scratchpads Brazilian Flora 2020 REFLORA ALA IPT - GBIF Australia Repository GBIF Spain IPT - GBIF Spain Repository Plus 29 more...	DwC EML ABCD TAPIR	PLOS Recommended Repositories Open Research Data and Data Management Plans - Information for ERC grantees by the ERC Scientific Council eLife Data Policy SciData Data Policy BioMed Central - Minimum Standards of Reporting Checklist Plus 1 more...	Data Citation Implementation Bioschemas Global Biodiversity Information Facility (GBIF) international open data infrastructure
HAMAP database of microbial protein families	HAMAP	Database	Life Science	Amino acid sequence Sequence annotation Protein	All	InterPro TIGRFAMs PROSITE Genome Properties	GO FASTA	None	Bioschemas
HumanMine	HumanMine	Database	Genomics Life Science	Single nucleotide polymorphism Disease Gene Homologous Molecular interaction Plus 2 more...	Homo sapiens Mus musculus	InterPro Reactome HGNC HPA RGD Plus 16 more...	None	None	Bioschemas InterMine
Human Protein Atlas	HPA	Database	Biomedical Science Life Science Transcriptomics	Biological imaging Medical imaging Protein expression Cell line Cellular localization Plus 6 more...	Homo sapiens	FunCoup MitoMiner neXtProt CRC Atlas HumanMine	SNOMEDCT TFClass Bioschemas	None	Euro-BioImaging Bioschemas ELIXIR Core Data Resources and Deposition Databases RDA Covid-19 WG Resources
Identifiers.org Central Registry	Identifiers.org Central Registry	Database	Life Science	Resource metadata Centrally registered identifier	All	PC	Compact Identifier Format Bioschemas MIRIAM	None	Bioschemas ELIXIR Recommended Interoperability Resources Systems Medicine
International Microvillus Inclusion Disease Patient Registry	MVID	Database	Biomedical Science Cell Biology Life Science Pediatrics	Disease Gene-disease association Genetic disorder Mutation	Homo sapiens	DEB Register	None	None	Bioschemas
IUPHAR/BPS Guide to PHARMACOLOGY	Guide to Pharmacology	Database	Immunology Life Science Pharmacology	Drug interaction Receptor Channel Ligand Malaria Plus 1 more...	Homo sapiens Plasmodium falciparum	ChEMBL DrugBank Ensembl PubChem PubMed Plus 4 more...	NIFSTD Bioschemas	None	Bioschemas ELIXIR UK node resources COVID-19 Resources RDA Covid-19 WG Resources
MobiDB	MobiDB	Database	Life Science	Intrinsically disordered proteins Curated information Protein Structure	All	ELM IDEAL Pfam Gene3D InterPro Plus 8 more...	Bioschemas PDB UniProtKB XML Format FASTA	None	Bioschemas
Model Archive	Model Archive	Database	Structural Biology	Mathematical model Computational predictions Protein structure Molecular structure Modeling and simulation Plus 2 more...	All	MMDB SWISS-MODEL ModBase	PDB DOI	None	Bioschemas RDA Covid-19 WG Resources
Molecular INTeraction database	MINT	Database	Life Science	Protein interaction Molecular interaction	All	IntAct APID Interactomes STRING VirHostNet iRefWeb Plus 10 more...	PSI-MI CV MITAB GO PSI-MI XML FASTA Plus 1 more...	Elsevier's Data Policy EMBO Recommended Databases and Data Standards Cold Spring Harbor Lab Press - Genome Research Elsevier - Current Opinion in Cell Biology - Guide for Authors Cell Press - Current Biology - Information for Authors Plus 1 more...	International Molecular Exchange Consortium (IMEx) Bioschemas ELIXIR Core Data Resources and Deposition Databases ELIXIR Non-CDR and Non-Deposition Database
Omics Discovery Index	OmicsDI	Database	Data Integration Genomics Life Science Metabolomics Proteomics Plus 1 more...	Data identity and mapping	All	Expression Atlas MTBLS ArrayExpress BioModels PRIDE Plus 7 more...	Schema.org OmicsDI XML format	None	Bioschemas RDA Covid-19 WG Resources
PROSITE	PROSITE	Database	Life Science	Protein domain Protein identification Functional domain Protein Structure	All	ProtoNet PlantTFDB InterPro HAMAP Genome Properties	FASTA	MNI Open Research UCL Child Open Health Research HRB Open Research AAS Policy Gates Open Research Data Guidelines Plus 2 more...	Bioschemas ELIXIR Non-CDR and Non-Deposition Database RDA Covid-19 WG Resources
Protein Circular Dichroism Data Bank	PCDDB	Database	Life Science	Protein circular dichroism spectroscopic data Molecular structure Protein	All	None	None	Elsevier's Data Policy Springer Nature Research Data Policy Type 1 PLOS Recommended Repositories Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 4 Plus 6 more...	Bioschemas Data Citation Implementation
Protein Data Bank in Europe	PDBe	Database	Bioinformatics Structural Biology	Drug structure Protein structure X-ray diffraction Deoxyribonucleic acid Electron density map Plus 5 more...	All	2P2Idb SNAPPI-DB CCD Europe PMC PDBsum Plus 20 more...	Bioschemas PDBx/mmCIF PDB ChEBI GO	MNI Open Research UCL Child Open Health Research Elsevier's Data Policy HRB Open Research AAS Policy Plus 17 more...	Bioschemas ELIXIR Core Data Resources and Deposition Databases RDA Covid-19 WG Resources
Reactome - a curated knowledgebase of biological pathways	Reactome	Database	Epidemiology Life Science Virology	Drug interaction Protein interaction Reaction data Biological regulation Curated information Plus 5 more...	Bos taurus Caenorhabditis elegans Canis familiaris Danio rerio Dictyostelium discoideum Plus 11 more...	IntAct Rhea WikiPathways CTD APID Interactomes Plus 20 more...	BioPAX ChEBI SBGN MITAB GO Plus 6 more...	MNI Open Research UCL Child Open Health Research HRB Open Research Cold Spring Harbor Lab Press - Genome Research AAS Policy Plus 4 more...	Open Science Prize Bioschemas ELIXIR Non-CDR and Non-Deposition Database Systems Medicine COVID-19 Resources Plus 1 more...
Scientific Data ISA-explorer	Scientific Data ISA-explorer	Database	None	Resource metadata	All	None	ISA-Tab	None	Bioschemas Systems Medicine
SWISS-MODEL Repository of 3D protein structure models	SWISS-MODEL	Database	Life Science	Mathematical model Protein structure Protein Structure	All Viruses	PDBe STRING RCSB PDB Model Archive	PDB	None	Bioschemas ELIXIR Non-CDR and Non-Deposition Database COVID-19 Resources RDA Covid-19 WG Resources
SynBioHub	SBH	Database	Bioengineering Synthetic Biology	Deoxyribonucleic acid Protein	Not applicable	VPR	SBOL SBOL Visual	None	Bioschemas Systems Medicine
The European Genome-phenome Archive	EGA	Database	Biomedical Science Genomics Life Science	DNA sequence data Genetic polymorphism Genome Genotype Phenotype	Homo sapiens	ENA EVA DGVa OmicsDI COVID-19 Data Portal	FASTQ Sequence and Sequence Quality Format BAM OmicsDI XML format MIxS Schema.org Plus 2 more...	MNI Open Research UCL Child Open Health Research Springer Nature Research Data Policy Type 1 PLOS Recommended Repositories Springer Nature - Research Data Policies Plus 29 more...	Data Citation Implementation National Child Development Study (UK) Bioschemas ELIXIR Core Data Resources and Deposition Databases Advanced Genetics Plus 2 more...
UniProt Knowledgebase	UniProtKB	Database	Functional Genomics Life Science	Annotation Biocuration Function analysis Gene expression data Gene functional annotation Plus 9 more...	All	DAMPD LegumeIP MitoMiner Pfam ProtoNet Plus 83 more...	ChEBI ECO NCBITAXON GO FASTA Plus 12 more...	MNI Open Research UCL Child Open Health Research Elsevier's Data Policy Springer Nature Research Data Policy Type 1 PLOS Recommended Repositories Plus 48 more...	NIH-supported data repositories Data Citation Implementation Open Science Prize International Molecular Exchange Consortium (IMEx) Bioschemas Plus 4 more...

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