Data standards in bioinformatics
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This document discusses various data standards that are important for data integration in bioinformatics. It describes different types of data standards including data formats, controlled vocabularies, minimum information guidelines, and common identifiers. It also provides examples of popular data integration approaches, standard formats and schemas, ontology resources, minimum information guidelines, identifier mapping services, web services, and workflow management systems. The goal of data standards is to facilitate data sharing, comparison, analysis and integration across different biological databases and resources.
Data standards in bioinformatics
- 1. Data standards in bioinformatics Programmatic Access To Biological Databases (Perl) 1 – 4 October 2012 Rafael C. Jimenez [email protected]
- 2. DB I DB I DB I DB I DB I Database I User Molecular interaction information Ideally Reality Interface
- 3. Molecular Biology resources 13/12/2018 3 Genomics Databases (non-vertebrate) (17.9%) Protein sequence databases (12.9%) Human Genes and Diseases (9.8%) Structure Databases (9.7%) Metabolic and Signaling Pathways (9.3%) Nucleotide Sequence Databases (8.8%) Human and other Vertebrate Genomes (7.1%) Plant databases (7.1%) RNA sequence databases (4.9%) Microarray and other Gene Expression Databases (4.5%) Other Molecular Biology Databases (3.3%) Immunological databases (1.8%) Organelle databases (1.6%) Proteomics Resources (1.2%) Cell biology (0.2%) 1730 http://www.oxfordjournals.org/nar/database/c/
- 4. Pathway resources 13 December 2018 4 132 9 43 73 62 51 38 20 14 Pathway resource list Protein-Protein Interactions Genetic Interaction Networks Protein-Compound Interactions Metabolic Pathways Signaling Pathways Gene Regulatory Networks Pathway Diagrams Protein Sequence Focused Other http://www.pathguide.org/ 184 molecular interactions 442 pathway
- 5. Utility of Bioinformatics 13/12/2018 5 Scientificimpact Too little bioinformatics Too many databases Too diverse interfaces Tim Hubbard
- 6. Data integration DB I DB I DB I DB I Ideally Compromise Database InterfaceI User Combining data residing in different sources … providing users with a unified view of these data. DB I DB DB DB DB I Reality
- 7. Data integration problems Many data resources • Many to maintain • Databases change • New appearing • Some disappearing* • Not easy to find them Different query interfaces data integration? Variable results • Formats • Schemas • Controlled vocabularies • Minimum information guidelines * Merali Z. et all. Databases in peril. Nature 2005. • Inconsistency • Mapping problems • Records with not enough information • Redundancy
- 8. Nucleotide sequences INSDC EMBL DDBJ NCBI Molecular interactions IMEx IntAct InnateDB DIP MINT … Collaboration among data providers Agreement on data standards and data exchange • More data coverage • Less redundancy • Less inconsistency • Better data management Protein indentifications ProteomeXchange PRIDE PeptideAtlas GPMDB Tranche …
- 9. Data standards 13/12/2018 9 Integration AccessExchange Sharing Portability Interoperability Annotation Comparison Verification Reusability Representation Compliance Consistency Replication Web service API Submission Edition Conversion Comparison Visualization Analysis Integration Validation TOOLS
- 10. Data standards • Data format • File format • Format definition (schema) • Controlled vocabularies (ontologies) • Guidelines • Minimum information • Best practices • Common identifiers • Common query interfaces Schema Interfaces Guidelines Ontologies Format Identifiers Data Definition Representation Access
- 11. • Data format • File format • Format definition (schema) • Controlled vocabularies (ontologies) • Guidelines • Minimum information • Best practices • Common query interfaces • Common identifiers PSI-MI XSD PSICQUIC MIMIx PSI-MI CV XML UniProt Molecular interactions Definition Representation Access Data standards … molecular interactions
- 13. 1 3 5 Popular data integration approaches 4 6 2 ... Data centralization Data warehousing Dataset integration Hyperlinks Federated databases View integration
- 14. 13.12.2018 14 Warehousing vs. Federation Database Query InterfaceQI User Data warehousing Federated databases S i S i i S integration standardization
- 15. Warehousing vs. Federation • Data warehousing • Pull data from several resources into one resource. • Main features: • Data centralization • High maintenance • Data out of date • Modifications (schema, format, content, …) • Federated databases • Data residing in different sources using a common query interface. • Main features: • Fresh data (original) • Data redundancy • Data inconsistency
- 16. Heterogeneous data sources Same data types Data integration A B C 1 2 leverage B C A
- 17. Tools• Formats • DAS, PSI-MI, MzML , BioPAX , SBML , GFF3, CellML, … • Registry (~125): Biosharing • Controlled vocabularies • Gene Ontology, Sequence Ontology, Pathway Ontology, Molecular Interaction, … • Registries (~ 200 ontologies): Bioportal, OLS • Minimum information guidelines • i.e. MIAME, MIAPE , MIMIx , MIRIAM, … • Registry (~ 35 guidelines): MIBBI • ID Mapping services • PICR, David , CRONOS , BridgeDB, Biomart, DAS, … • API • Ensembl API, Uniprot API, Biomart API, … • Web Services • ClustalW, ArrayExpress, Blast, Emboss… • Registries (~ 2000 services): Biocatalogue, DAS registry, … • Workflow management systems • Taverna, Pegasys, Galaxy, …
- 18. Standard formats/schemas BioPAX PSI-MI SBML, CellML Genetic Interactions Molecular Interactions Pro:Pro All:All Interaction Networks Molecular Non-molecular Pro:Pro TF:Gene Genetic Regulatory Pathways Low Detail High Detail Database Exchange Formats Simulation Model Exchange Formats Rate Formulas Metabolic Pathways Low Detail High Detail Biochemical Reactions Small Molecules Low Detail High Detail Anatoly Sorokin
- 19. Formats, ontologies and guidelines http://biosharing.org
- 20. Controlled vocabularies • Ontology browser: http://www.ebi.ac.uk/ontology-lookup Ontology Lookup Service
- 22. • PSI: Proteomics Standards Initiative • Work group of the Human Proteome Organization • Defines community standards for data in proteomics • … facilitating data comparison, exchange and verification Minimum information guidelines 22 • MIAPE: The Minimum Information About a Proteomics Experiment • Data and metadata from proteomics experiments • Data: results • Metadata: data about the data • Where the samples came from • How the analysis were performed
- 23. Minimum information guidelines MIMIx • MIAPE document guideline for molecular interactions • 1. Manuscript information • 2. Experiment • 3. Interaction
- 24. ID Mapping services Logical xref (hyperlinked) Inactive xref Secondary Identifier Active xref (hyperlinked) Richard Cote Web services! • REST • SOAP http://www.ebi.ac.uk/Tools/picr/ Protein Identifier Cross-Reference Service
- 25. Web services
- 26. Web services
- 28. Workflow management systems Examples from myExperiment OLS PICR Biomart and Microarray analysis ChEBI