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BioSharing – mapping the metadata
standards in the life sciences
BioSharing – mapping the metadata
standards in the life sciences
Peter McQuilton, PhD
BioSharing Content Lead
Outline
1. The sea of standards in the life sciences
1. What is BioSharing?
2. Work in progress
3. BioSharing WG and potential collaborations
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
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
(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
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.$
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$implement
Our mission: To help people make
the right choice
Three interlinked registries
STANDARD DATABASE
Standards and databases cross-linked
Terminologies linked to NCBO BioPortal
The$ International$ Conference$ on$Systems$Biology$ (ICSB),$22J28$ August,$2008$ $$$$$$Susanna$Assunta.
Sansone www.ebi.ac.uk/netJproject
Tracking evolution, e.g. deprecations and substitutions
The$ International$ Conference$ on$Systems$Biology$ (ICSB),$22J28$ August,$2008$ $$$$$$Susanna$Assunta.
Sansone www.ebi.ac.uk/netJproject
Tracking evolution, e.g. deprecations and substitutions
Core.functionalities:
• search$and$filtering,$e.g.$by$
funder,$domain,$type$of$
standard
• Refine$by$publication,$
maintainer$etc.
• add$new$records,$edit$
existing$records
• “claim”$records
• person’s$profile$(as$
maintainer$of$records)$
associated$to$the$ORCID$
profile$(for$credit)
• visualization$and$views$of$
content$and$linking
Annotation.Sources:
• 4$axis:$(material,$process,$
quality,$information)
• NIF,OBI,CL,GO,IAO,EDAM
Search filter, refineSearch filter, refine
Create your own CollectionCreate your own Collection
1..Maximize$categorization$to$improve$searching,$continue$curation,$add$
records,$increase$maintainers/vetting$of$records
2..Schema$views:$progressively$visualize$formats$and$reporting$guidelines$
as$tested$for$terminologies$(via$BioPortal)$
3..Export$of$metadata$elements:$as$part$of$
WIP – surveys, advisory board & WGsWIP – surveys, advisory board & WGs
The relationship among
popular standard formats
for pathway information.
Demir, et al., The BioPAX
community standard for
pathway data sharing,
NatBiotech.2010.
4.$Create$relation$or$“usage$maps$and$guides”,$e.g.:$
5.$Metrics$of$maturity,$usability$and$popularity,$kickJstarted$by$
Tenenbaum,$Sansone,$Haendel.$$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
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
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
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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