ISMB Workshop 2014

1. What was the plan? A role for data standards, models and computational workﬂows in scholarly data publishing Alejandra González-Beltrán, PhD Philippe Rocca-Serra, PhD Oxford e-Research Centre, University of Oxford {alejandra.gonzalezbeltran,philippe.rocca-serra}@oerc.ox.ac.uk ISMB Workshop:What Bioinformaticians need to know about digital publishing beyond the PDF2 July15th, 2014 Boston, USA

2. Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment The experimental workﬂow

3. Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment The experimental workﬂow metadata

4. Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment The experimental workﬂow metadata

5. Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment Data Interoperability The experimental workﬂow Reproducibility Data Review

6. The experimental workﬂow Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment Data Reusability

7. The experimental plan - life sciences case experimental design! sample characteristic(s)! experimental variable(s)! 2-week systemic rat study using male Wistar rats (N=15 per dose group) 14 proprietary drug candidates from participating companies and 2 reference toxic compounds InnoMed PredTox Project

8. The experimental plan - life sciences case experimental design! sample characteristic(s)! experimental variable(s)! technology(s)! measurement(s)! protocols(s)! data ﬁle(s)! …!

9. 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.

10. genome assembly algorithm genome size Predictor Variables! (Factor Name, Factor Type) The experimental plan - computational case

11. genome assembly algorithm genome size SOAPdenovo2 SOAPdenovo1 ALL-PATHS-LG Predictor Variables! (Factor Name, Factor Type) The experimental plan - computational case

12. genome assembly algorithm genome size SOAPdenovo2 SOAPdenovo1 ALL-PATHS-LG bacterial genome insect genome human genome Predictor Variables! (Factor Name, Factor Type) The experimental plan - computational case

13. genome assembly algorithm genome size SOAPdenovo2 SOAPdenovo1 ALL-PATHS-LG bacterial genome insect genome human genome bacterial genome insect genome human genome bacterial genome insect genome human genome Predictor Variables! (Factor Name, Factor Type) 3x3 factorial design 9 study groups The experimental plan - computational case

14. genome assembly algorithm genome size SOAPdenovo2 SOAPdenovo1 ALL-PATHS-LG bacterial genome insect genome human genome bacterial genome insect genome human genome bacterial genome insect genome human genome Predictor Variables! (Factor Name, Factor Type) The experimental plan - computational case S. aureus R. sphaeroides B. impatiens Chinese Han genome (or YH genome)

15. genome assembly algorithm genome size SOAPdenovo2 SOAPdenovo1 ALL-PATHS-LG bacterial genome insect genome human genome bacterial genome insect genome human genome bacterial genome insect genome human genome Predictor Variables! (Factor Name, Factor Type) The experimental plan - computational case Response Variables! genome coverage computation run time memory consumption

16. http://www.ama-rochester.org/WP/wp-content/uploads/2013/01/three-pillars.png

17. 17 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 signatures ! • environmental health • environmental genomics • metabolomics • metagenomics • nanotechnology • proteomics

18. 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 !

19. H. Sapiens H. Sapiens H. Sapiens H1 H1 H2 35 35 33 Years Years Years H1.sample1 H1.sample2 H2.sample1 Labeling Labeling H1.sample1.labeled H2.sample1.labeled h1-s1.cel h1-s2.cel h2-s1.cel Scanning Scanning Scanning ... H. Sapiens 33 Years H1 H2 H1.sample1 H1.sample2 H2.sample1 Labeling Labeling H1.sample1.labeled H2.sample1.labeled h1-s1.cel h1-s2.cel h2-s1.cel H. Sapiens 35 Years Scanning Scanning Scanning ... ... ...

20. H. Sapiens H. Sapiens H. Sapiens H1 H1 H2 35 35 33 Years Years Years H1.sample1 H1.sample2 H2.sample1 Labeling Labeling H1.sample1.labeled H2.sample1.labeled h1-s1.cel h1-s2.cel h2-s1.cel Scanning Scanning Scanning ... H. Sapiens 33 Years H1 H2 H1.sample1 H1.sample2 H2.sample1 Labeling Labeling H1.sample1.labeled H2.sample1.labeled h1-s1.cel h1-s2.cel h2-s1.cel H. Sapiens 35 Years Scanning Scanning Scanning ... ... ... obi:material entity obi:material sample obi:material processing obi:processed material obi:planned process isa:raw data ﬁle bfo:derives from

21. http://gigasciencejournal.com http://gigadb.org/dataset/100035

22. http://gigasciencejournal.com http://gigadb.org/dataset/100035

23. Experimental metadata or structured component (in-house curated, machine-readable formats) Article or narrative component (PDF and HTML) 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

24. SOAPdenovo2 http://isa-tools.github.io/soapdenovo2

25. SOAPdenovo2 http://isa-tools.github.io/soapdenovo2

26. SOAPdenovo2 http://isa-tools.github.io/soapdenovo2 Galaxy workﬂows to re-enact the data analysis

27. http://isa-tools.github.io/soapdenovo2 SOAPdenovo2 Nanopub: represents structured data along with its provenance in a single publishable and citable entity

28. http://isa-tools.github.io/soapdenovo2 SOAPdenovo2 ResearchObject: enables the aggregation of the digital resources contributing to ﬁndings of computational research, including results, data and software, as citable compound digital objects

29. Reproducing SOAPdenovo2 results Galaxy workﬂows S. aureus pipeline

30. Reproducing SOAPdenovo2 results Galaxy workﬂows

31. Reproducing SOAPdenovo2 results Galaxy workﬂows

32. 2241 400 30 119.0 11 106 24 68 0 Reproducing SOAPdenovo2 results Galaxy workﬂows

33. “genome coverage increased over the human data when comparing SOAPdenovo2 against SOAPdenovo1”! Response Variables! genome coverage memory consumption

34. OntoMaton:(a(Bioportal(powered( Ontology(widget(for(Google( Spreadsheets( Maguire(et(al,((2013( Bioinforma?cs( widget for ontology annotation and tagging on Google spreadsheets relying on BioPortal and Linked Open Vocabularies services

35. OntoMaton:(a(Bioportal(powered( Ontology(widget(for(Google( Spreadsheets( Maguire(et(al,((2013( Bioinforma?cs( widget for ontology annotation and tagging on Google spreadsheets relying on BioPortal and Linked Open Vocabularies services NanoMaton https://github.com/ISA-tools/NanoMaton Ontology for Biomedical Investigations SemanticsScience Integrated Ontology

36. Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment Findable, Accessible, Interoperable, Reusable!FAIR data

37. Contributing to ! Metabolights and ISA • BBRSC UK-China Award & BGI funded Hackathon! • venue: BGI Hong-Kong! • Participants:! • Metabolights/BGI/ISA/Birmingham/Hong-Kong University! • Outcome: ! • ISAtab web viewer code! • Functional Specifications & Code for DoE Wizard API! • 4 datasets coded in ISA format! • Conversion Metabolights datasets to RDF

38. 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 Tak-wah Lam, University of Hong Kong

39. Questions? You can email us... isatools@googlegroups.com View our blog http://isatools.wordpress.com Follow us onTwitter @isatools View our websites View our Git repo & contribute http://github.com/ISA-tools Thanks for your attention!

ISMB Workshop 2014

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