Publicación de Datos en Acción BioSharing y la infraestructura ISA Alejandra González-Beltrán, PhD Oxford e-Research Centre, University of Oxford [email protected]@alegonbel Centro Internacional Franco-Argentino de Ciencias de la Información y Sistemas (CIFASIS) 19 de diciembre 2014 Rosario, Argentina
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Publicación de Datos en Acción BioSharing y la infraestructura ISA
Alejandra González-Beltrán, PhD Oxford e-Research Centre, University of Oxford
A growing ecosystem of over 30 public and internal resources using the ISA metadata tracking framework (ISA-Tab and/or tools) to facilitate standards-compliant collection, curation, management and reuse of investigations in an increasingly diverse set of life science domains, including: !
• stem cell discovery • system biology • transcriptomics • toxicogenomics • also by communities working to build a library of cellular
General-purpose, configurable format designed to support: !• description of the experimental metadata, making the annotation explicit and discoverable !• provenance tracking !
• use of community standards, such as minimal reporting guidelines and terminologies !• designed to be converted to - a growing number of - other metadata formats, e.g. used by the European Bioinformatics Institute (EBI) repositories !
Evaluation of SOAPdenovo2 tool for the de novo assembly of genomes from small DNA segments reads by next generation sequencing, implementing improvements over SOAPdenovo1 assembler.
The experimental plan - computational case
•open peer-review •availability of
•data •analysis scripts •documentation
Evaluation of SOAPdenovo2 tool for the de novo assembly of genomes from small DNA segments reads by next generation sequencing, implementing improvements over SOAPdenovo1 assembler.
The experimental plan - computational case
•open peer-review •availability of
•data •analysis scripts •documentation
Evaluation of SOAPdenovo2 tool for the de novo assembly of genomes from small DNA segments reads by next generation sequencing, implementing improvements over SOAPdenovo1 assembler.
unambiguously identify electronic resources, such as are records from public repositories, by providing their official identifiers be explicit about experimental design and experimental variables, identifying the goal of the experiment, independent and response variables remain neutral and report all findings of similar importance with the same weight
report the results with respect to all the identified response variables
A new online-only publication for descriptions of scientifically valuable datasets in the life, environmental and biomedical sciences, but not limited to these!
Credit for sharing your data
Focused on reuse and reproducibility
Peer reviewed, curated
Promoting Community Data Repositories
Open Access
Data Scientist
Visualization
Analysis
Planning
Data Management
Data CollectionPublication
Use existing data
Perform new experiment
Findable, Accessible, Interoperable, Reusable!FAIR data
http://goo.gl/tWRjYI
Our areas of research:!Data capture and curation!Data (nano)publication !Data provenance !Open, community ontologies and standards!Semantic web!Software development!Training
Communities we work with/for:!
As part of:!UK, European and international consortia!Pre-competitive informatics public-private partnerships!Standardisation initiatives!
!Some of the groups we engage with incl.:!
eTRIKS – european Translational Information and Knowledge management Services Consortium of academic (Imperial College, CNRS, Un of Luxemburg) and pharmas (Janssen, Merck, AZ, Lilly, Lundbeck, Pfizer, Roche, Sanofi, Bayer, GSK) building a sustainable, open translational research informatics platform
• Nature Publishing Group‘s Scientific Data • BioMedCentral and BGI‘s GigaScience • F1000 Research • Oxford University Press
StatO – Statistics Ontology
CEDAR – Centre for Expanded Data Annotation and Retrieval BioCADDIE – Biomedical and healthCAre Data Discovery and Indexing Ecosystem
COPO – Collaboratively Open Plant Omics Consortium of academic (TGAC, EBI, Oxford, Warwick) building a sustainable, open research informatics platform for plant science
funders
acknowledgements
Scott Edmunds, GigaScience
Peter Li, GigaScience
Jun Zhao, Lancaster University
María Susana Avila García, Oxford University
Marco Roos, Leiden University
Mark Thompson, Leiden University
Ruibang Luo, University of Hong Kong Tin-Lap Lee, Chinese University of Hong Kong