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BioSharing - RDA Plenary 6 - Metadata Standards Catalog WG and BioSharing WG Joint session

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BioSharing - RDA Plenary 6 - Metadata Standards Catalog WG and BioSharing WG Joint session

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An introduction to the metadata landscape in the life sciences. Covering metadata standards, the databases that implement them and the policies that endorse/recommend both standards and databases in the life sciences.

An introduction to the metadata landscape in the life sciences. Covering metadata standards, the databases that implement them and the policies that endorse/recommend both standards and databases in the life sciences.

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BioSharing - RDA Plenary 6 - Metadata Standards Catalog WG and BioSharing WG Joint session

  1. 1. BioSharing – mapping the metadata standards in the life sciences BioSharing – mapping the metadata standards in the life sciences Peter McQuilton, PhD BioSharing Content Lead
  2. 2. Outline 1. The sea of standards in the life sciences 1. What is BioSharing? 2. Work in progress 3. BioSharing WG and potential collaborations
  3. 3. miame MIAPA MIRIAM MIQASMIX MIGEN ARRIVE MIAPE MIASE MIQE MISFISHIE…. REMARK CONSORT MAGE-Tab GCDML SRAxml SOFT FASTA DICOM MzML SBRML SEDML… GELML ISA-Tab CML MITAB AAO CHEBI OBI PATO ENVO MOD BTO IDO… TEDDY PRO XAO DO VO There are more than 600 standards in the life sciences There are more than 600 standards in the life sciences Databases and tools implementing Standards; also training material on and around standards
  4. 4. Mapping Standards and Databases in the Life Sciences “Which standard should I use for this data, considering I’d like to publish in X journal? “Are we using the most up-to-date version of this standard?” “My data is in X format, which databases take that format?
  5. 5. 5 (2008) (2009) (2011) (2015) • registry development, • content collection, • community engagement, • funds raising • creation of a WG in RDA and Force11; Advisory Board • links with ELIXIR and NIH BD2K
  6. 6. A$web$based,$curated and$searchable.registry.ensuring$that$biological standards and$databases are$registered,$informative and$discoverable5$ also$monitoring$the$development$and$evolution$of$standards,$their$use$in$ databases$and$the$adoption$of$both$in$data$policies.$
  7. 7. Researchers,$developers and$curators lack$support$and$guidance$on$how$to$best$navigate$and$ select$content$standards,$understand$their$maturity,$or$find$databases$that$implement$them5$ Funders,$journals and$librarians do$not$have$enough$information$to$make$informed$decisions$ on$which$content$standards$or$database$to$recommended$in$policies,$or$fund$or$implement Our mission: To help people make the right choice
  8. 8. Three interlinked registries
  9. 9. STANDARD DATABASE Standards and databases cross-linked
  10. 10. Terminologies linked to NCBO BioPortal
  11. 11. The$ International$ Conference$ on$Systems$Biology$ (ICSB),$22J28$ August,$2008$ $$$$$$Susanna$Assunta. Sansone www.ebi.ac.uk/netJproject Tracking evolution, e.g. deprecations and substitutions
  12. 12. The$ International$ Conference$ on$Systems$Biology$ (ICSB),$22J28$ August,$2008$ $$$$$$Susanna$Assunta. Sansone www.ebi.ac.uk/netJproject Tracking evolution, e.g. deprecations and substitutions
  13. 13. Core.functionalities: • search$and$filtering,$e.g.$by$ funder,$domain,$type$of$ standard • Refine$by$publication,$ maintainer$etc. • add$new$records,$edit$ existing$records • “claim”$records • person’s$profile$(as$ maintainer$of$records)$ associated$to$the$ORCID$ profile$(for$credit) • visualization$and$views$of$ content$and$linking Annotation.Sources: • 4$axis:$(material,$process,$ quality,$information) • NIF,OBI,CL,GO,IAO,EDAM Search filter, refineSearch filter, refine
  14. 14. Create your own CollectionCreate your own Collection
  15. 15. 1..Maximize$categorization$to$improve$searching,$continue$curation,$add$ records,$increase$maintainers/vetting$of$records 2..Schema$views:$progressively$visualize$formats$and$reporting$guidelines$ as$tested$for$terminologies$(via$BioPortal)$ 3..Export$of$metadata$elements:$as$part$of$ WIP – surveys, advisory board & WGsWIP – surveys, advisory board & WGs
  16. 16. The relationship among popular standard formats for pathway information. Demir, et al., The BioPAX community standard for pathway data sharing, NatBiotech.2010. 4.$Create$relation$or$“usage$maps$and$guides”,$e.g.:$ 5.$Metrics$of$maturity,$usability$and$popularity,$kickJstarted$by$ Tenenbaum,$Sansone,$Haendel.$$A$sea$of$standards$for$omics$data:$sink$or$ swim?$J Am7Med7Inform7Assoc (2014). 6.$Embed$in$the$ecosystem$of$complementary$registries WIP – surveys, advisory board & WGsWIP – surveys, advisory board & WGs
  17. 17. Green.=..0.$ 6.months WG7is7just7starting The products are • principles for linking information about databases, content standards and journal / funder policies in the life sciences • and a curated registry to access and cross-search the information, on which a variety of stakeholders can base their decisions This is a joint WG The work will benefit from the existing also part of
  18. 18. Key points: • We all provide information to those seek guidance to use, do or recommend something (databases, tools, standards, training material etc.) • Designed with a slightly different focus and user needs; focus on curating/cataloguing certain information • Have different entry points and UIs to fit the specific scope/user needs is good, so federation is key, e.g. cross-referencing • Pool resources where appropriate Collaboration and communication
  19. 19. Proponents, core WG members and adoptersOperational Team – based at the Philippe Rocca-Serra, PhD Alejandra Gonzalez-Beltran, PhD Milo Thurston, PhD Peter McQuilton, PhD Allyson Lister, PhD Eamonn Maguire, DPhil / Contractor David Johnson, PhD Susanna Sansone, PhD WED - Session1 • RDA/WDS PublishingData Workflows THUR - Session6 • Jointmeeting ofIGMetadata,WGMetadata Standards Catalog & WGBioSharingRegistry:Connectingdata policies,standards & databases in life sciences" FRI - Sessions 8 and 9 • Jointmeeting ofIGELIXIR Bridging Force & WG BioSharingRegistry:Life Sciences and SensitiveData” • Jointmeeting ofIGDomain Repositories,IGAgriculture Data InterestGroup (IGAD),WGBioSharingRegistry,IG RDA/CODATA Materials Data,Infrastructure & Interoperability & WGWheatData Interoperability" Where we are and present

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