Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage
Nature Methods,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 13, 2025
Abstract
The
Human
BioMolecular
Atlas
Program
(HuBMAP)
aims
to
construct
a
3D
Reference
(HRA)
of
the
healthy
adult
body.
Experts
from
20+
consortia
collaborate
develop
Common
Coordinate
Framework
(CCF),
knowledge
graphs
and
tools
that
describe
multiscale
structure
human
body
(from
organs
tissues
down
cells,
genes
biomarkers)
use
HRA
characterize
changes
occur
with
aging,
disease
other
perturbations.
v.2.0
covers
4,499
unique
anatomical
structures,
1,195
cell
types
2,089
biomarkers
(such
as
genes,
proteins
lipids)
33
ASCT+B
tables
65
Objects
linked
ontologies.
New
experimental
data
can
be
mapped
into
using
(1)
type
annotation
(for
example,
Azimuth),
(2)
validated
antibody
panels
or
(3)
by
registering
tissue
spatially.
This
paper
describes
user
stories,
terminology,
formats,
ontology
validation,
unified
analysis
workflows,
interfaces,
instructional
materials,
application
programming
flexible
hybrid
cloud
infrastructure
previews
atlas
usage
applications.
Language: Английский
Digital evolution: Novo Nordisk’s shift to ontology-based data management
Journal of Biomedical Semantics,
Journal Year:
2025,
Volume and Issue:
16(1)
Published: March 22, 2025
The
amount
of
biomedical
data
is
growing,
and
managing
it
increasingly
challenging.
While
Findable,
Accessible,
Interoperable
Reusable
(FAIR)
principles
provide
guidance,
their
adoption
has
proven
difficult,
especially
in
larger
enterprises
like
pharmaceutical
companies.
In
this
manuscript,
we
describe
how
leverage
an
Ontology-Based
Data
Management
(OBDM)
strategy
for
digital
transformation
Novo
Nordisk
Research
&
Early
Development.
Here,
include
both
our
technical
blueprint
approach
organizational
change
management.
We
further
discuss
such
OBDM
ecosystem
plays
a
pivotal
role
the
organization's
aspirations
federation
discovery
fuelled
by
artificial
intelligence.
Our
aim
paper
to
share
lessons
learned
order
foster
dialogue
with
parties
navigating
similar
waters
while
collectively
advancing
efforts
fields
management,
semantics
driven
drug
discovery.
Language: Английский
Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph for Linked Open Data
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Dec. 23, 2024
Abstract
The
Human
Reference
Atlas
(HRA)
for
the
healthy,
adult
body
is
developed
by
a
team
of
international,
interdisciplinary
experts
across
20+
consortia.
It
provides
standard
terminologies
and
data
structures
describing
specimens,
biological
structures,
spatial
positions
experimental
datasets
ontology-linked
reference
anatomical
(AS),
cell
types
(CT),
biomarkers
(B).
We
introduce
HRA
Knowledge
Graph
(KG)
as
central
resource
v2.2,
supporting
cross-scale,
queries
to
Resource
Description
Framework
graphs
using
SPARQL.
In
December
2024,
KG
covered
71
organs
with
5,800
AS,
2,268
CTs,
2,531
Bs;
it
had
10,064,033
nodes,
171,250,177
edges,
size
125.84
GB.
comprises
13
Digital
Objects
(DOs)
Common
Coordinate
Ontology
standardize
core
concepts
relationships
DOs.
(1)
provide
code
construction;
(2)
detail
deployment
Linked
Open
Data
principles;
(3)
illustrate
usage
via
application
programming
interfaces,
user
products.
A
companion
website
at
https://cns-iu.github.io/hra-kg-supporting-information
.
Language: Английский