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Data Curation and Management activities within the UCT Computational Biology Group. Dr Nicky Mulder. Outline. Activities at UCT: High-throughput biology data Sequence annotation DAS annotation development Issues we face A note on standards and ontologies. High-throughput biology data. - PowerPoint PPT Presentation
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Data Curation and Management activities within the UCT
Computational Biology Group
Dr Nicky Mulder
Outline
Activities at UCT:– High-throughput biology data– Sequence annotation– DAS annotation development
Issues we face A note on standards and ontologies
High-throughput biology data
Close ties with CPGR Microarray data storage –BASE Proteomics data:
– Annotation –pipeline required– Storage –LIMS required
BASE
BioArray Software Environment Open source database for storage of array-
type data Manages raw data (images) and annotations Has limited LIMS options Can include specifications for MIAME
compliance
BASE Sample Information
BASE Sample Information
BASE experimental info
Proteomics Data
Still in progress Peptide identification programs Additional cross-linking from results to public
database annotations Storage of experimental data and resulting
identifications Include MIAPE compliance Linking to genomics data –standards required
Sequence Annotation 1
Paeano pipeline for annotation of cDNAs from non-model organisms
Uses collection of publicly available and custom software
Results are stored under projects Links provided to array data in BASE
Sequence Annotation 2
Glossina (Tsetse) EST annotation project Held annotation jamboree at UWC Worked with Twiki tool developed by JBIRC Data to be submitted to public databases
Twiki system
Twiki system
DAS Annotation Tool
Distributed Annotation System –allows viewing of annotation from different sources
Can overlay your own data/annotation Facilitates information sharing without issue of updates Repositories distributed in different geographical
locations Extension of DASTy2 –developed at NBN Development of DAS annotation tool underway
DASTy
Links to other DAS viewers
DAS annotation tool
Collaborative visual annotation tool- Annotation- Comments
- Sequences - Features- Non positional features
- Methodology of trust on a collaborative annotation process
Data curation and management issues
HTB software licenses are expensive Open Source not always maintained Ensuring regular backups (data size) Keeping data up to date Researchers leave data after project –not updated to
new versions Privacy –researchers share data only with
collaborators, patient data is private Sharing and linking data
Standards and ontologies
Use a controlled vocabulary (controlled list of terms) or ontology (set of terms with relations)
Enables easy data retrieval and sharing Easy comparison of results from different labs Compatibility with other labs/databases world-
wide Ease of uploading data into public databases Unambiguous report of research
Open Biomedical Ontologies
Central location for accessing well-structured controlled vocabularies and ontologies for use in the biological and medical sciences
Provides simple format for ontologies Scope include anatomy, phenotype,
development, disease, “omics”, experiment, etc.
http://obo.sourceforge.net
Data exchange standards
Microarray standards –MIAME and MAGE Proteomics Standards Initiative (PSI) Systems Biology Markup Language (SBML) –
computer-readable format for representing models of networks
Biological Pathways Exchange (BioPAX) –format for representing pathways
Conclusions
Some tools in place for curation and management of different data types
Need better education of researchers to encourage this
Ontologies and standards are important in digital data curation and management, need to encourage compliance with international standards
Acknowledgements
Funding:
Collaborations:– CPGR– Researchers at UCT