This document describes the goals and activities of the Metadata Center project from 2014-2018. The project aimed to 1) map existing metadata standards, 2) develop methods for creating standardized metadata templates, and 3) develop tools and templates to make authoring metadata easier for researchers. The project would create a repository of populated metadata templates to facilitate discovery and reuse of experimental data. The goals were to analyze the templates to improve predictive data entry, link templates to publications and related experiments, and allow community feedback to enhance experimental descriptions. The project sought to leverage existing standards to make authoring high-quality metadata less burdensome for researchers.

1. metadatacenter.org
(2014
-­‐2018)

2. Mark
Musen,
Principal
Inves.gator
Steering
Commi2ee
Carol
Bean,
Project
Manager
Michel
Dumon8er
Olivier
Gevaert
Purvesh
Khatri
Steven
Kleinstein
Kei-­‐Hoi
Cheung
Jeffrey
Wiser
Susanna-­‐A
Sansone

3. Community-developed content standards
Including
minimum
informa*on
repor*ng
requirements,
or
checklists
to
report
the
same
core,
essen8al
informa8on
Including
controlled
vocabularies,
taxonomies,
thesauri,
ontologies
etc.
to
use
the
same
word
and
refer
to
the
same
‘thing’
Including
conceptual
model,
conceptual
schema
from
which
an
exchange
format
is
derived
to
allow
data
to
flow
from
one
system
to
another
• To
structure,
enrich
and
report
the
descrip8on
of
the
datasets
and
the
experimental
context
under
which
they
were
produced
• To
facilitate
discovery,
sharing,
understanding
and
reuse
of
datasets

4. ~
156
~
70
~
334
miame!
MIAPA!
MIRIAM!
MIQAS!
MIX!
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!
In the life sciences alone…..almost 600!

5. • Most
researchers
understand
the
value
of
standardized
descrip8ons,
when
using
third-­‐
party
datasets
• But
when
asked
to
structure
their
datasets,
they
view
requests
for
even
“minimal”
informa8on
as
burdensome
• There
is
an
urgent
need
to
lower
the
bar
for
authoring
good
metadata
Researchers hate standards!

6. • Most
researchers
understand
the
value
of
standardized
descrip8ons,
when
using
third-­‐
party
datasets
• But
when
asked
to
structure
their
datasets,
they
view
requests
for
even
“minimal”
informa8on
as
burdensome
Ø There
is
an
urgent
need
to
lower
the
bar
for
authoring
good
metadata
Researchers hate standards!

7. Our two initial uses cases

8. 1. Map the landscape of content standards

9. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta
Sansone www.ebi.ac.uk/net-project
Almost
600!

10. EXPLORE
Exploration and Reuse
of Datasets through
Metadata
ANNOTATE
Annotation of Data with
Metadata
STRUCTURE
Authoring of Metadata
Templates
Metadata
tempates
Template authors
define
Metadata
acquisition
forms
fill in search,
reuse
Scientists
contribute
Metadata
repository
2. Develop methods for creating templates

11. EXPLORE
Exploration and Reuse
of Datasets through
Metadata
ANNOTATE
Annotation of Data with
Metadata
STRUCTURE
Authoring of Metadata
Templates
Metadata
tempates
Template authors
define
Metadata
acquisition
forms
fill in search,
reuse
Scientists
contribute
Metadata
repository
2. Develop methods for creating templates
HCLS
WGs
use
‘elements’
from
content
standards
create
a
language
to
represent
rela*ons
among
‘elements’
use
exis*ng
examples
of
templates

12. EXPLORE
Exploration and Reuse
of Datasets through
Metadata
ANNOTATE
Annotation of Data with
Metadata
STRUCTURE
Authoring of Metadata
Templates
Metadata
tempates
Template authors
define
Metadata
acquisition
forms
fill in search,
reuse
Scientists
contribute
Metadata
repository
3. Develop methods to ease use of templates
• Enable
researchers
to
help
us
crea8ng
templates
appropriate
to
their
needs
• Help
researchers
to
find
and
use
these
templates
to
describe
their
experiments,
and
populate
them
with
appropriate
values
(e.g.
terms
from
ontologies)

13. EXPLORE
Exploration and Reuse
of Datasets through
Metadata
ANNOTATE
Annotation of Data with
Metadata
STRUCTURE
Authoring of Metadata
Templates
Metadata
tempates
Template authors
define
Metadata
acquisition
forms
fill in search,
reuse
Scientists
contribute
Metadata
repository
4. Create a repository of populated templates
CEDAR
repository
will:
• store
the
experimental
descrip8ons
• facilitate
submission
of
datasets
to
our
two
case
study
repositories
and
progressively
to
other
recognized
online
repositories

14. • Analyze
the
CEDAR
repository
to
reveal
pa<erns
in
the
metadata
that
will
enable
the
metadata
tools
to
use
predic*ve
data
entry
to
ease
the
task
of
filling
out
the
templates
• Augment
those
metadata
with
links
to
the
published
literature
(including
secondary
analyses
and
retrac8ons!)
• Augment
those
metadata
with
links
to
follow-­‐up
experiments
(in
online
databases
and
in
the
literature)
• Allow
the
scien8fic
community
to
comment
on
the
experiment
through
structured
metadata
Ø Learn
how
to
ease
the
authoring
of
metadata,
using
community
standards,
to
enhance
the
richness
of
the
experimental
descrip8ons
5. Exploring ways to enhance metadata

15. metadatacenter.org
(2014
-­‐2018)