SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data.
SSBD (https://ssbd.riken.jp) is a platform for the sharing and reuse of bioimaging data. As part of efforts to build a bioimaging data ecosystem, SSBD has recently been updated to a two-tiered data resource comprising SSBD:repository, a public repository for the sharing of all types of bioimaging data reported in journals, and SSBD:database, an added-value database for the sharing of curated, highly reusable, metadata-rich data. This update addresses the conflicting demands of rapid data publication and sharing of richly annotated data, thereby promoting bioimaging data sharing and reuse. With this update, SSBD is now positioned as a core repository and database within the foundingGIDE, an international consortium working to establish a global image data ecosystem. Harmonizing metadata between data resources enables cross-searching and data exchange with data resources from other countries and regions.
Pubmed ID: 39479781
Research resources used in this publication
- Biological Imaging Methods Ontology (RRID:SCR_010235) (ontology)
- CHEBI (RRID:SCR_002088) (data or information resource)
- UniProt (RRID:SCR_002380) (data or information resource)
- Ensembl (RRID:SCR_002344) (software resource)
- Experimental Factor Ontology (RRID:SCR_003574) (data or information resource)
- Cell Type Ontology (RRID:SCR_004251) (data or information resource)
- Gene Ontology (RRID:SCR_002811) (data or information resource)
- NCBITaxon (RRID:SCR_000479) (data or information resource)
- MeSH (RRID:SCR_004750) (data or information resource)
- UBERON (RRID:SCR_010668) (data or information resource)
- Ontology for Biomedical Investigations (RRID:SCR_006266) (data or information resource)
- Cell Line Ontology (RRID:SCR_005840) (data or information resource)
- Units of Measurement Ontology (RRID:SCR_010442) (ontology)
Additional research tools detected in this publication
None foundAntibodies used in this publication
None foundAssociated grants
- Agency: National Bioscience Database Center,
Id: JPMJND2201 - Agency: Core Research for Evolutional Science and Technology,
Id: JPMJCR1511 - Agency: Japan Society for the Promotion of Science,
Id: JP18H05412 - Agency: European Union,
Id: 101130216 - Agency: RIKEN Center for Biosystems Dynamics Research,
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This is a list of tools and resources that we have found mentioned in this publication.
Biological Imaging Methods Ontology (ontology)
RRID:SCR_010235
A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
View all literature mentionsCHEBI (data or information resource)
RRID:SCR_002088
Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
View all literature mentionsUniProt (data or information resource)
RRID:SCR_002380
Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.
View all literature mentionsEnsembl (software resource)
RRID:SCR_002344
Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsExperimental Factor Ontology (data or information resource)
RRID:SCR_003574
An application focused ontology modelling the experimental factors in ArrayExpress and Gene Expression Atlas. It has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology describes cross-product classes from reference ontologies in area such as disease, cell line, cell type and anatomy. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and ArrayExpress Atlas. You may also browse the EFO in the NCBO Bioportal. Term submissions are welcome.
View all literature mentionsCell Type Ontology (data or information resource)
RRID:SCR_004251
Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.
View all literature mentionsGene Ontology (data or information resource)
RRID:SCR_002811
Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
View all literature mentionsNCBITaxon (data or information resource)
RRID:SCR_000479
Ontology that is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.
View all literature mentionsMeSH (data or information resource)
RRID:SCR_004750
A controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world''''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.
View all literature mentionsUBERON (data or information resource)
RRID:SCR_010668
An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human.
View all literature mentionsOntology for Biomedical Investigations (data or information resource)
RRID:SCR_006266
An ontology for the description of biological and clinical investigations built with international, collaborative effort. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This includes a set of universal terms that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. Currently OBI is being built under the Basic Formal Ontology (BFO). This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project.
View all literature mentionsCell Line Ontology (data or information resource)
RRID:SCR_005840
A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan.
View all literature mentionsUnits of Measurement Ontology (ontology)
RRID:SCR_010442
Metrical units ontology for use in conjunction with PATO
View all literature mentions
