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This standard
...
(nano-TAB)
...
specifies
...
the
...
format
...
for
...
representing
...
and
...
sharing
...
information
...
about
...
nanomaterials,
...
small
...
molecules
...
and
...
biological
...
specimens
...
along
...
with
...
their
...
assay
...
characterization
...
data
...
(including
...
metadata,
...
and
...
summary
...
data)
...
using spreadsheet or TAB-delimited
...
files
...
.
Prerequisites
Familiarity with the fields of nanotechnology and nanomedicine is a pre-requisite for this specification. An understanding of ISA-TAB is recommended but not required as the nano-TAB specification provides descriptive information on ISA-TAB as applied to nanotechnology.
1. nano-TAB Introduction
1.1 Rationale
Nanobioinformatics has been largely recognized as an essential element of our nation’s competitiveness in nanotechnology and a rational approach to employ weight-of-the-evidence
...
strategies
...
that
...
ensure
...
its
...
safe
...
development
...
according
...
to
...
the
...
National
...
Nanotechnology
...
Initiative,
...
2006.
...
The
...
ability
...
to
...
manipulate
...
matter
...
at
...
the
...
atomic
...
scale
...
will
...
enable
...
a
...
broad
...
range
...
of
...
beneficial
...
applications
...
in
...
the
...
electronics,
...
healthcare
...
(e.g.
...
nanomedicine,
...
imaging,
...
and
...
diagnostics),
...
cosmetics,
...
technologies
...
and
...
engineering
...
industries.
...
Pertinent
...
to
...
the
...
development
...
of
...
promising
...
biomedical
...
nanotechnologies
...
and
...
to
...
the
...
safety
...
of
...
nanoscale
...
materials
...
in
...
general,
...
is
...
a
...
thorough
...
understanding
...
of
...
nanomaterial-biological
...
interactions.
...
However,
...
a
...
rational
...
approach
...
must
...
be
...
employed
...
early
...
on
...
in
...
nanotechnology
...
evolution
...
to
...
direct
...
the
...
safe
...
development
...
of
...
novel
...
nanotechnologies
...
and
...
provide
...
accurate
...
predictions
...
of
...
nanomaterial-biological
...
interactions
...
based
...
on
...
weight-of-the-evidence
...
(Dahl
...
et
...
al.,
...
2007;
...
McKenzie
...
and
...
Hutchison,
...
2004).
...
This
...
inevitably
...
will
...
require
...
data
...
mining
...
and
...
computer
...
simulation
...
for
...
visualization
...
of
...
the
...
important
...
parameters
...
in
...
an
...
almost
...
infinite
...
set
...
of
...
data
...
from
...
global
...
research
...
efforts
...
in
...
nanoscience
...
and
...
nanotechnology
...
(Teeguarden
...
et
...
al.,
...
2007).
...
To
...
date,
...
the
...
lack
...
of
...
standardization
...
has
...
been
...
one
...
of
...
the
...
most
...
significant
...
barriers
...
to
...
data
...
sharing.
...
The nanotechnologies (nano)
...
tab-delimited
...
(TAB)
...
format
...
is
...
a
...
general
...
purpose
...
framework
...
that
...
provides
...
a
...
standard
...
means
...
to
...
communicate
...
metadata
...
(
...
i.e.
...
,
...
study
...
details,
...
material
...
characteristics,
...
assay
...
measurements
...
etc.
...
),
...
data
...
on
...
nanomaterial
...
physicochemical
...
properties,
...
as
...
well
...
as
...
data
...
from
...
in
...
vitro
...
and
...
in
...
vivo
...
experiments
...
of
...
nanomaterials.
...
The
...
nano-TAB
...
standard
...
specification
...
will
...
enable
...
the
...
submission
...
and
...
exchange
...
of
...
nanomaterials
...
to/from
...
nanotechnology
...
resources
...
like
...
the
...
NCI’s
...
caNanoLab
...
nanotechnology
...
portal
...
and
...
the
...
Oregon
...
State
...
University’s
...
Nanomaterial-Biological
...
Interactions
...
(NBI)
...
knowledgebase;
...
empower
...
organizations
...
to
...
adopt
...
standards
...
for
...
representing
...
data
...
in
...
nanotechnology
...
publications;
...
and
...
provide
...
researchers
...
with
...
guidelines
...
for
...
representing
...
nanomaterials
...
and
...
characterizations
...
to
...
achieve
...
cross-material
...
comparison.
...
nano-TAB’s
...
extended
...
structure
...
is
...
built
...
on
...
the
...
need
...
to
...
capture
...
the
...
complexity
...
inherent
...
to
...
nanomaterials
...
and
...
their
...
evaluation
...
in
...
many
...
disparate
...
model
...
systems.
...
The nano-TAB
...
effort
...
is
...
collaboration
...
between
...
a
...
variety
...
of
...
organizations
...
including
...
the
...
NCI,
...
Washington
...
University,
...
Oregon
...
State
...
University,
...
ONAMI,
...
NIOSH,
...
Stanford
...
University,
...
and
...
ISA-TAB.
...
nano-TAB
...
is
...
registered
...
as
...
an
...
ASTM
...
Work
...
Item
...
(ASTM
...
WK28974),
...
which
...
facilitates
...
broad
...
community
...
outreach
...
and
...
input
...
to
...
the
...
development
...
of
...
nano-TAB
...
and
...
other
...
standards
...
needed
...
to
...
support
...
nanomedicine.
...
1.2
...
nano-TAB
...
Development
...
Process
...
nano-TAB
...
is
...
based
...
on
...
existing
...
standards
...
developed
...
by
...
the
...
European
...
Bioinformatics
...
Institute
...
(EBI)
...
and
...
the
...
Investigation/Study/Assay
...
(ISA-TAB)
...
file
...
format,
...
which
...
represents
...
a
...
variety
...
of
...
assays
...
and
...
technology
...
types.
...
The
...
nano-TAB
...
specification
...
leverages
...
ISA-TAB
...
files
...
for
...
describing
...
investigations,
...
studies,
...
and
...
assays
...
and
...
provides
...
extensions
...
to
...
support
...
nanomaterial
...
chemical
...
and
...
structural
...
information
...
and
...
assay
...
measurements.
...
The
...
development
...
of
...
nano-TAB
...
is
...
being
...
facilitated
...
through
...
the
...
use
...
of
...
knowledge
...
that
...
is
...
represented
...
in
...
the
...
NanoParticle
...
Ontology
...
(NPO).
...
The
...
development
...
of
...
nano-TAB
...
extensions
...
is
...
a
...
community
...
driven
...
initiative
...
established
...
under
...
the
...
caBIG®
...
Nano
...
Working
...
Group
...
(WG).
...
Nano
...
WG
...
team
...
members
...
met
...
on
...
a
...
weekly
...
basis
...
during
...
the
...
initial
...
development
...
of
...
nano-TAB
...
extensions
...
and
...
will
...
continue
...
to
...
meet
...
on
...
a
...
scheduled
...
basis
...
once
...
nano-TAB
...
extensions
...
have
...
been
...
formalized
...
with
...
the
...
community.
...
nano-TAB
...
is
...
a
...
registered
...
ASTM
...
Work
...
Item
...
(ASTM
...
WK28974)
...
and
...
it
...
is
...
expected
...
that
...
community
...
feedback
...
will
...
be
...
received
...
through
...
the
...
caBIG
...
Nano
...
WG,
...
pilot
...
efforts
...
with
...
the
...
NCI
...
Cancer
...
Centers
...
of
...
Nanotechnology
...
Excellence
...
(CCNEs),
...
and
...
the
...
ASTM
...
nanotechnology
...
community.
...
1.3
...
NanoParticle
...
Ontology
| Wiki Markup |
|---|
The NanoParticle Ontology (NPO) is an ontology that is designed and developed within the framework of the Basic Formal Ontology (BFO) and implemented in the Ontology Web Language (OWL) \[Thomas et al, JBI 2010; \[http://www.nano-ontology.org\]\]. It is being developed to represent the knowledge underlying the description, preparation and characterization of nanomaterials. NPO development began with the representation of knowledge underlying the chemical composition, preparation, physiochemical and functional / biological characterization of nanoparticles that are formulated and tested for applications in cancer diagnostics and therapeutics.
\\ |
...
The
...
NPO
...
is
...
being
...
further
...
developed
...
for
...
the
...
following
...
purposes:
...
1)
...
to
...
provide
...
terms
...
for
...
annotating
...
data
...
generated
...
from
...
research
...
in
...
nanotechnology,
...
2)
...
to
...
provide
...
the
...
knowledge
...
framework
...
required
...
for
...
developing
...
data
...
sharing
...
models
...
and
...
standards
...
in
...
nanomedicine,
...
3)
...
to
...
enable
...
semantic
...
integration
...
of
...
data
...
by
...
providing
...
the
...
terms
...
and
...
relationships
...
for
...
data
...
annotation,
...
4)
...
to
...
enable
...
unambiguous
...
interpretation
...
of
...
data
...
pertaining
...
to
...
the
...
description
...
and
...
characterization
...
of
...
nanomaterials,
...
and
...
5)
...
to
...
enable
...
knowledge-based
...
searching
...
of
...
the
...
data
...
for
...
accessing
...
and
...
retrieving
...
relevant
...
information,
...
which
...
in
...
turn
...
facilitates
...
comparison
...
of
...
nanomaterial
...
descriptions
...
and
...
characterization
...
results,
...
leading
...
towards
...
knowledge
...
enhancement
...
and
...
discovery.
...
The
...
NanoParticle
...
Ontology
...
was
...
primarily
...
developed
...
by
...
...
...
in
...
collaboration
...
with
...
...
...
and
...
...
...
. The NPO development was supported by the NIH through grants U54 CA119342 and U54 HG004028.
2. nano-TAB v0.5 Structure Overview
2.1 nano-TAB Structure
nano-TAB leverages and extends the ISA-TAB file structure to capture nanotechnology metadata (Figure 2-1).
|
The ISA-TAB file structure relies on three primary files - Investigation, Study, and Assay files. Data files specific to each assay can also be provided to capture assay specific measurements. nano-TAB leverages and extends ISA-TAB by introducing a Materials file for representing the structural composition of the nanomaterial. nano-TAB extends the ISA-TAB Study file which traditionally provides a mapping between studies and biological specimens, by referencing the Material file for mapping the study to nanomaterials or small molecules.
Each file has a defined structure and is described throughout this section. Detailed descriptions of the contents of each file with nanotechnology examples are provided in Section 4 and Appendix A.
2.2 nano-TAB file Development Process
Figure 2-2 describes the nano-TAB file development process. Typically, the Investigation file is developed first and describes the overall investigation and associated studies. The Investigation file is a text file with a naming convention of “i_xxx.txt”, where xxx can be any name provided by the investigator. Once the Investigation file has been completed, one or more Study files (following the convention “s_xxx.txt”) can be created. The Study file describes any samples (biospecimens, nanomaterials, small molecules) leveraged in the study. The Material file describes the nanomaterial (or small molecule) and its components including structural information and follows the naming convention “m_xxx.txt”. The Material file provides valuable information allowing for cross-particle comparison across nanotechnology resources. Assay files (following the convention “a_xxx.txt”) are created for all assays performed. Assay files include associated data files that are specific to the assay type being performed.
Once the nano-TAB files have been created, the files can be validated and submitted into nanotechnology resources that support the nano-TAB specification. It is anticipated that validation of the files may occur via a validation service that leverages a modified version of the ISA-TAB validator. It is also anticipated that nanotechnology resources like caNanoLab, the NBI, and other resources will provide facilities for importing/exporting nano-TAB files as the nano-TAB specification evolves.
3. Relationship to Other Standards
3.1 ISA-TAB
| Wiki Markup |
|---|
nano-TAB file format leverages and extends the investigation, study, and assay files of the ISA-TAB (Investigation/Study/Assay-TAB delimited) format. The ISA-TAB format is a general purpose framework for sharing metadata and data from omics-based experiments \[ref\]. The ISA-TAB Investigation file is used for three purposes: 1) to record all declarative information referenced in other files; 2) to relate Assay files to Study files; and 3) to group multiple Study files that are part of the same investigation. The ISA-TAB Study file is used to record information about the source, sampling methodology, treatment, preparation, and characteristics of the subjects (biospecimens) studied using one or more assays under an investigation. The nano-TAB format includes an additional type of file called the Material file which is used to record information about the chemical and structural descriptions of the nanomaterial formulations and other types of chemical samples (e.g., drug formulations). The ISA-TAB Assay file is used to record information about the assay protocols and references to data files. |
...
3.2
...
NanoParticle
...
Ontology
...
(NPO)
...
Section
...
1.3
...
provides
...
a
...
brief
...
overview
...
of
...
the
...
NanoParticle
...
Ontology
...
(NPO).
...
The
...
NPO
...
will
...
provide
...
the
...
terms
...
and
...
relationships
...
for
...
the
...
description
...
and
...
characterization
...
of
...
nanomaterials
...
in
...
the
...
nano-TAB
...
file
...
format.
...
NPO
...
also
...
provides
...
the
...
knowledge
...
framework
...
for
...
developing
...
and
...
using
...
the
...
Material
...
file
...
format.
...
3.3
...
LS
...
DAM
...
The
...
caBIG
...
Life
...
Sciences
...
Domain
...
Analysis
...
Model
...
(LS
...
DAM)
...
provides
...
a
...
shared
...
view
...
of
...
the
...
semantics
...
of
...
the
...
life
...
sciences
...
domains
...
that
...
are
...
represented
...
by
...
the
...
different
...
workspaces
...
in
...
the
...
caBIG
...
infrastructure.
...
It
...
has
...
a
...
nano
...
sub
...
domain,
...
which
...
was
...
developed
...
based
...
on
...
caNanoLab
...
object
...
model
...
and
...
NPO
...
terms.
...
LS
...
DAM
...
makes
...
a
...
distinction
...
between
...
biospecimens
...
(e.g.,
...
cell
...
line,
...
tissue
...
samples,
...
body
...
fluid
...
samples,
...
organ
...
parts)
...
and
...
materials
...
that
...
are
...
not
...
derived
...
from
...
a
...
cell,
...
tissue,
...
organ
...
or
...
body
...
(e.g.,
...
nanoparticle
...
formulations,
...
drug
...
formulations,
...
solvent,
...
etc.).
...
This
...
motivated
...
the
...
use
...
of
...
the
...
term
...
“material
...
sample”
...
in
...
the
...
nano-TAB
...
material
...
file.
