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Click here for ISA-TAB-Nano

OVERVIEW

PRESENTATION

|https://ncisvn.nci.nih.gov/svn/isa

-

tab-nano/trunk/presentations/ISA-TAB-Nano_Overview.ppt] \-

a

great

place

to

start

\

!

Click

for

each

File

type

template:

[

Investigation |

https://ncisvn.nci.nih.gov/svn/isa-tab-nano/trunk/templates/i_xxxx.xls] \| [

Study |

https://ncisvn.nci.nih.gov/svn/isa-tab-nano/trunk/templates/s_xxxx.xls] \| [

Material |

https://ncisvn.nci.nih.gov/svn/isa-tab-nano/trunk/templates/m_xxxx.xls] \| [Assay |https://ncisvn.nci.nih.gov/svn/isa-tab-nano/trunk/templates/a_xxxx.xls] See each File pages for more information and links to examples and glossaries. h2. Scope This standard

Assay

See each File pages for more information and links to examples and glossaries.

Scope

This standard (ISA-TAB-Nano)

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.

h2. Prerequisites Familiarity with the fields of nanotechnology and nanomedicine is a

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

ISA-TAB-Nano

specification

provides

descriptive

information

on

ISA-TAB

as

applied

to

nanotechnology.

{column}\\ {section} h2.


ISA-TAB-Nano

...

Introduction

...

Rationale

The field of nanomedicine faces many challenges in the development of standards to support meaningful data submission and information exchange. Nanomaterial characterization requires numerous physico-chemical,

...

in-vitro,

...

and

...

in-vivo

...

assays

...

where

...

measurements

...

mostly

...

depend

...

on

...

non-standardized

...

protocols

...

and

...

diverse

...

technology

...

types.

...

Unfortunately,

...

information

...

describing

...

the

...

nanomaterial,

...

including

...

functionalizing

...

entities

...

and

...

three-dimensional

...

(3D)

...

structure,

...

is

...

often

...

represented

...

in

...

an

...

undisciplined

...

fashion.

...

In

...

addition,

...

there

...

has

...

been

...

no

...

standard

...

way

...

to

...

associate

...

this

...

information

...

with

...

the

...

data

...

and

...

metadata

...

from

...

characterization

...

studies

...

This

...

lack

...

of

...

standardization

...

has

...

been

...

a

...

significant

...

deterrent

...

to

...

meaningful

...

data

...

sharing

...

across

...

the

...

nanotechnology

...

community;

...

few

...

publications

...

contain

...

sufficient

...

information

...

to

...

enable

...

adequate

...

interpretation

...

of

...

results

...

and

...

successful

...

achievement

...

of

...

experimental

...

reproducibility.

...

Furthermore,

...

there

...

has

...

been

...

very

...

limited

...

success

...

in

...

using

...

non-standardized

...

data

...

to

...

represent

...

or

...

derive

...

structure-activity-relationships

...

(SARs)

...

that

...

are

...

critical

...

for

...

understanding

...

the

...

effects

...

of

...

nanomaterial

...

structure

...

on

...

biological

...

activity

...

in

...

nanomedicine.

...

Significance

The ISA-TAB-Nano

...

specification

...

is

...

intended

...

to

...

facilitate

...

the

...

submission

...

and

...

exchange

...

of

...

nanomaterial

...

descriptions

...

and

...

characterization

...

data

...

(metadata

...

and

...

summary

...

data)

...

along

...

with

...

the

...

other

...

files

...

(raw/derived

...

data

...

files,

...

image

...

files,

...

protocol

...

documents,

...

etc.)

...

among

...

individual

...

researchers

...

and

...

to/from

...

nanotechnology

...

resources

...

like

...

the

...

NCI’s

...

cancer

...

Nanotechnology

...

Laboratory

...

(caNanoLab)

...

portal

...

[

...

https://cananolab.nci.nih.gov/caNanoLab]

...

and

...

the

...

Nanomaterial-Biological

...

Interactions

...

(NBI)

...

knowledgebase

...

[

...

http://nbi.oregonstate.edu/

...

Wiki Markup
{multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}

...

].

...

ISA-TAB-Nano

...

also

...

serves

...

to

...

empower

...

organizations

...

to

...

adopt

...

standard

...

methods

...

for

...

representing

...

data

...

in

...

nanotechnology

...

publications;

...

and

...

to

...

provide

...

researchers

...

with

...

guidelines

...

for

...

representing

...

nanomaterials

...

and

...

characterizations

...

to

...

achieve

...

cross-material

...

comparison.

...

ISA-TAB-Nano

...

Development

...

The

...

ISA-TAB-Nano

...

project

...

is

...

an

...

effort

...

of

...

the

...

National

...

Cancer

...

Institute

...

(NCI)

...

Cancer

...

Biomedical

...

Informatics

...

Grid

...

(caBIG®)

...

Nanotechnology

...

Informatics

...

Working

...

Group

...

(Nano

...

WG).

...

ISA-TAB-Nano

...

Standards

...

Re-Use

...

ISA-TAB

...

The

...

ISA-TAB-Nano

...

format

...

specification

...

is

...

based

...

on

...

an

...

existing

...

specification

...

developed

...

by

...

the

...

ISA-commmunity

...

(

...

http://www.isa-tools.org

...

Wiki Markup
{multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}
),

...

namely,

...

the

...

investigation/study/assay

...

(ISA-TAB)

...

format

...

specification.

...

The

...

ISA-TAB

...

format

...

(

...

http://isatab.sourceforge.net/

...

Wiki Markup
{multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}
)

...

is

...

used

...

by

...

the

...

‘omics’

...

(proteomics,

...

genomics,

...

metabolomics,

...

and

...

transcriptomics)

...

communities

...

to

...

share

...

data

...

and

...

metadata

...

associated

...

with

...

different

...

assays

...

and

...

technology

...

types

...

in

...

their

...

experiments.

...

The

...

ISA-TAB

...

file

...

structure

...

relies

...

on

...

three

...

primary

...

files---investigation,

...

study,

...

and

...

assay

...

(ISA)

...

files.

...

Raw/derived

...

data

...

files

...

and

...

any

...

other

...

files

...

(e.g.,

...

image

...

files,

...

protocol

...

documents)

...

specific

...

to

...

each

...

assay

...

are

...

shared

...

along

...

with

...

the

...

three

...

primary

...

ISA-TAB

...

files

...

if

...

the

...

data

...

files

...

are

...

referenced

...

in

...

the

...

primary

...

ISA-TAB

...

files.

...

ISA-TAB

...

does

...

not

...

provide

...

format

...

specification

...

for

...

files

...

other

...

than

...

the

...

investigation,

...

study,

...

and

...

assay

...

files.

...

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.

...

National

...

Cancer

...

Institute

...

Enterprise

...

Vocabulary

...

Service

...

(NCI

...

EVS)­

...

The

...

NCI

...

EVS

...

is

...

a

...

project

...

of

...

the

...

NCI

...

Center

...

for

...

Biomedical

...

Informatics

...

and

...

Information

...

Technology

...

(CBIIT).

...

EVS

...

provides

...

controlled

...

terminologies

...

and

...

ontologies

...

in

...

support

...

of

...

the

...

biomedical

...

research

...

and

...

informatics

...

activities

...

of

...

the

...

NCI

...

and

...

its

...

partners,

...

including

...

the

...

caBIG^®^ community.

...

The

...

activities

...

of

...

the

...

EVS

...

include

...

development

...

of

...

terminologies,

...

development

...

of

...

terminology-related

...

software,

...

and

...

operations

...

support

...

to

...

address

...

the

...

broad

...

spectrum

...

of

...

terminology

...

needs

...

in

...

the

...

cancer

...

research

...

enterprise.

...

Among

...

the

...

vocabularies

...

that

...

EVS

...

supports

...

is

...

the

...

NanoParticle

...

Ontology

...

(NPO),

...

by

...

providing

...

terminology

...

development

...

facilities

...

and

...

terminology

...

servers,

...

which

...

are

...

made

...

available

...

both

...

via

...

the

...

web

...

and

...

programmatically

...

through

...

EVS

...

server

...

APIs.

...

Additionally,

...

the

...

NPO

...

is

...

presented

...

to

...

the

...

public

...

by

...

EVS

...

both

...

in

...

a

...

standalone

...

format

...

and

...

as

...

a

...

component

...

of

...

the

...

NCI

...

Metathesaurus,

...

where

...

its

...

concepts

...

are

...

mapped

...

to

...

the

...

concepts

...

of

...

other

...

vocabularies

...

used

...

by

...

the

...

NCI

...

community.

...

Also,

...

the

...

EVS-managed

...

NCI

...

Thesaurus

...

(NCIt)

...

includes

...

nanotechnology

...

concepts

...

that

...

have

...

been

...

utilized

...

in

...

the

...

development

...

of

...

the

...

NCI

...

caNanoLab.

...

Data

...

from

...

caNanoLab

...

has

...

been

...

utilized

...

in

...

the

...

ISA-TAB-Nano

...

example

...

files.

...

Life

...

Sciences

...

Domain

...

Analysis

...

Model

...

(LS

...

DAM)

...

The

...

caBIG®

...

(cancer

...

Bioinformatics

...

Grid)

...

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

...

nanotechnolog

...

subdomain,

...

which

...

was

...

developed

...

based

...

on

...

caNanoLab

...

object

...

model

...

and

...

NPO

...

terms.

...

LS

...

DAM

...

makes

...

a

...

distinction

...

between

...

biospecimens

...

(for

...

example,

...

cell

...

line,

...

tissue

...

samples,

...

body

...

fluid

...

samples,

...

organ

...

parts)

...

and

...

materials

...

that

...

are

...

not

...

derived

...

from

...

a

...

cell,

...

tissue,

...

organ,

...

or

...

body

...

(for

...

example,

...

nanoparticle

...

formulations,

...

drug

...

formulations,

...

solvent,

...

and

...

so

...

forth).

...

This

...

motivated

...

the

...

use

...

of

...

the

...

term

...

“material

...

sample”

...

in

...

the

...

ISA-TAB-Nano

...

material

...

file.

...

Weekly

...

Nano

...

WG

...

web-conferencing

...

was

...

used

...

to

...

ensure

...

the

...

alignment

...

of

...

ISA-TAB-Nano

...

with

...

the

...

LS

...

DAM.

...

NanoParticle

...

Ontology

...

(NPO)

...

Like

...

ISA-TAB,

...

ISA-TAB-Nano

...

provides

...

fields

...

for

...

entering

...

and

...

referencing

...

terms

...

selected

...

from

...

ontologies

...

and

...

standard

...

terminologies.

...

The

...

ontologies

...

are

...

available

...

at

...

BioPortal

...

(

...

http://www.bioontology.org

...

Wiki Markup
{multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}
),

...

which

...

is

...

maintained

...

by

...

the

...

National

...

Center

...

for

...

Biomedical

...

Ontologies.

...

Though

...

the

...

investigator

...

may

...

use

...

alternative

...

ontology

...

and

...

vocabulary

...

sources,

...

the

...

ability

...

to

...

evaluate

...

and

...

share

...

data

...

require

...

that

...

all

...

parties

...

have

...

access

...

to

...

those

...

being

...

used

...

(they

...

should

...

be

...

available

...

to

...

the

...

investigators).

...

All

...

terms

...

and

...

fields

...

used

...

in

...

this

...

standard

...

utilize

...

the

...

NCI

...

EVS

...

(

...

http://evs.nci.nih.gov

...

)

...

and

...

NanoParticle

...

Ontology

...

elements.

...

NanoParticle

...

Ontology

...

(NPO)

...

[

...

http://www.nano-ontology.org

...

Wiki Markup
{multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}

...

]

...

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).

...

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

...

provided

...

the

...

knowledge

...

framework

...

for

...

developing

...

the

...

ISA-TAB-Nano

...

material

...

file

...

format.

...

The

...

NPO

...

provides

...

a

...

subset

...

of

...

the

...

terms

...

and

...

relationships

...

for

...

the

...

description

...

and

...

characterization

...

of

...

nanomaterials

...

in

...

the

...

ISA-TAB-Nano

...

file

...

format.

...

The

...

NPO

...

is

...

being

...

further

...

developed

...

for

...

the

...

following

...

purposes:

...

(1)

...

to

...

provide

...

terms

...

for

...

annotating

...

nanotechnology

...

research

...

data;

...

(2)

...

to

...

provide

...

the

...

knowledge

...

framework

...

required

...

for

...

developing

...

data-sharing

...

models

...

and

...

standards

...

in

...

nanomedicine;

...

(3)

...

to

...

enable

...

semantic

...

integration

...

of

...

data;

...

(4)

...

to

...

enable

...

unambiguous

...

interpretation

...

of

...

the

...

description

...

and

...

characterization

...

of

...

nanomaterials;

...

and

...

(5)

...

to

...

enable

...

knowledge-based

...

searching

...

and

...

comparison

...

of

...

nanomaterial

...

descriptions

...

and

...

characterization

...

results.

...

ISA-TAB-Nano

...

Extensions

...

to

...

ISA-TAB

...

ISA-TAB-Nano

...

extension

...

to

...

ISA-TAB--

...

-

...

While

...

ISA-TAB-Nano

...

leverages

...

the

...

three

...

primary

...

ISA-TAB

...

files,

...

it

...

extends

...

ISA-TAB

...

by

...

providing

...

specification

...

for

...

a

...

fourth

...

file

...

(called

...

the

...

material

...

file)

...

for

...

representing

...

the

...

composition

...

and

...

characteristics

...

of

...

nanoparticle

...

formulations

...

and

...

small

...

molecules.

...

Raw/

...

derived

...

data

...

files

...

and

...

any

...

other

...

files

...

(for

...

example,

...

image

...

files,

...

protocol

...

documents)

...

specific

...

to

...

each

...

assay

...

have

...

to

...

be

...

shared

...

along

...

with

...

the

...

four

...

primary

...

ISA-TAB-Nano

...

files.

...

ISA-TAB-Nano

...

does

...

not

...

provide

...

any

...

specification

...

for

...

how

...

to

...

format

...

files

...

other

...

than

...

the

...

four

...

primary

...

files:

...

investigation,

...

study,

...

assay

...

and

...

material

...

files.

...

Although

...

ISA-TAB-Nano

...

adopts

...

ISA-TAB

...

field

...

names

...

and

...

their

...

definition

...

in

...

the

...

investigation,

...

study,

...

and

...

assay

...

files,

...

some

...

of

...

the

...

definitions

...

are

...

modified

...

and

...

additional

...

fields

...

are

...

introduced.

...

These

...

modifications

...

and

...

extensions

...

are

...

required

...

to

...

expand

...

the

...

scope

...

of

...

information

...

captured

...

from

...

nanotechnology

...

data

...

sets

...

into

...

the

...

ISA-TAB-Nano

...

files.

...

Distinction

...

between

...

biological

...

and

...

non-biological

...

samples

...

In

...

nanotechnology,

...

samples

...

from

...

biological

...

and

...

non-biological

...

sources

...

can

...

be

...

the

...

primary

...

subjects

...

of

...

a

...

study.

...

Therefore,

...

in

...

ISA-TAB-Nano,

...

samples

...

derived

...

from

...

biological

...

sources

...

are

...

called

...

biological

...

specimens

...

or

...

biospecimens

...

(for

...

example,

...

cell

...

line,

...

body

...

fluids,

...

organs,

...

etc.).

...

Whereas,

...

samples

...

derived

...

from

...

non-biological

...

sources

...

are

...

simply

...

called

...

material

...

samples

...

(for

...

example,

...

nanomaterials,

...

nanoparticle

...

formulations,

...

small

...

molecules).

...

For

...

physico-chemical

...

characterizations

...

of

...

nanomaterials,

...

the

...

sample

...

is

...

the

...

nanomaterial.

...

For

...

in-vitro

...

and

...

in-vivo

...

characterizations,

...

the

...

sample

...

is

...

the

...

biological

...

specimen

...

(cell

...

line,

...

animal,

...

and

...

so

...

forth).

...

Hence,

...

in

...

ISA-TAB-Nano,

...

the

...

concept

...

of

...

a

...

sample

...

(as

...

used

...

in

...

ISA-TAB

...

specification)

...

is

...

redefined

...

to

...

include

...

both

...

biological

...

specimens

...

and

...

material

...

samples.

...

The

...

ISA-TAB

...

study

...

file

...

can

...

only

...

be

...

used

...

to

...

record

...

the

...

source

...

and

...

characteristics

...

of

...

biospecimens

...

studied

...

in

...

an

...

assay,

...

and

...

cannot

...

support

...

the

...

representation

...

of

...

materials.

...

Therefore,

...

in

...

ISA-TAB-Nano,

...

the

...

material

...

file

...

is

...

used

...

to

...

describe

...

material

...

samples,

...

while

...

the

...

study

...

file

...

is

...

used

...

to

...

describe

...

biospecimens.

...

ISA-TAB-Nano

...

File

...

Structure

...

ISA-TAB-Nano

...

uses

...

the

...

three

...

primary

...

files

...

of

...

ISA-TAB-

...

-

...

investigation

...

file,

...

study

...

file,

...

and

...

assay

...

file;

...

and,

...

introduces

...

a

...

fourth

...

file

...

called

...

the

...

material

...

file

...

(FIG

...

1).

...

Other

...

files

...

such

...

as

...

raw/derived

...

data

...

files,

...

image

...

files,

...

protocol

...

documents,

...

etc.,

...

referenced

...

in

...

the

...

ISA-TAB-Nano

...

files

...

have

...

to

...

be

...

shared

...

along

...

with

...

the

...

ISA-TAB-Nano

...

files.

...

FIG

...

1.

...

ISA-TAB-Nano

...

File

...

Structure
diagram of file structureImage Added

ISA-TAB

...

specifies

...

that

...

the

...

names

...

of

...

the

...

primary

...

files

...

end

...

with

...

.txt

...

extensions.

...

ISA-TAB-Nano

...

file

...

names

...

may

...

end

...

in

...

either

...

.txt

...

or

...

.xls

...

extensions.

...

The

...

ISA-TAB-Nano

...

files

...

used

...

as

...

examples

...

in

...

this

...

document

...

were

...

prepared

...

in

...

excel

...

spreadsheets,

...

and

...

so

...

their

...

filenames

...

have

...

the

...

.xls

...

extension.

...

In

...

FIG

...

2,

...

the

...

ISA-TAB-Nano

...

file

...

development

...

process

...

is

...

described.

...


Typically,

...

the

...

investigation

...

file

...

is

...

developed

...

first

...

and

...

describes

...

the

...

overall

...

investigation,

...

associated

...

studies

...

and

...

assays.

...

The

...

investigation

...

file

...

is

...

a

...

text

...

file

...

with

...

a

...

naming

...

convention

...

of

...

“i_xxx.txt”

...

or

...

“i_xxx.xls,”

...

in

...

which

...

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”

...

or

...

“s_xxx.xls”)

...

can

...

be

...

created.

...

Similarly,

...

one

...

or

...

more

...

material

...

files

...

can

...

be

...

created.

...

The

...

material

...

file

...

describes

...

the

...

nanomaterial

...

(or

...

small

...

molecule)

...

and

...

its

...

components

...

including

...

structural

...

information

...

and

...

follows

...

the

...

naming

...

convention

...

“m_xxx.txt”

...

or

...

“m_xxx.xls”.

...

Assay

...

files

...

(following

...

the

...

convention

...

“a_xxx.txt”

...

or

...

“a_xxx.xls”)

...

are

...

created

...

for

...

all

...

assays

...

performed.

...

Each

...

assay

...

is

...

defined

...

by

...

the

...

endpoint

...

measured

...

and

...

the

...

technique

...

used

...

to

...

measure

...

that

...

endpoint.

...

Data

...

files

...

(raw

...

or

...

derived)

...

specific

...

to

...

each

...

type

...

of

...

assay

...

can

...

be

...

associated

...

to

...

the

...

respective

...

assay

...

files

...

by

...

referencing

...

the

...

names

...

of

...

the

...

data

...

files

...

in

...

the

...

assay

...

files.

...

FIG

...

2.

...

ISA-TAB-Nano

...

File

...

Development

...

Process
diagram of file development processImage Added

When sharing primary ISA-TAB-Nano

...

files,

...

other

...

files

...

referenced

...

in

...

these

...

files

...

have

...

to

...

be

...

shared

...

along

...

with

...

the

...

primary

...

files.

...

It

...

is

...

anticipated

...

that

...

content

...

management

...

systems

...

will

...

become

...

available

...

to

...

facilitate

...

the

...

sharing

...

and

...

exchange

...

of

...

files.

...

Until

...

then,

...

these

...

files

...

could

...

be

...

bundled

...

together

...

in

...

a

...

folder

...

and

...

shared

...

as

...

a

...

zip

...

file.

...

Once

...

the

...

ISA-TAB-Nano

...

files

...

have

...

been

...

created,

...

the

...

files

...

can

...

be

...

validated

...

and

...

submitted

...

into

...

nanotechnology

...

resources

...

that

...

support

...

the

...

ISA-TAB-Nano

...

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

...

[

...

http://isatab.sourceforge.net/validator.html

...

Wiki Markup
{multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}
.

...

It

...

is

...

also

...

anticipated

...

that

...

nanotechnology

...

resources

...

like

...

caNanoLab

...

(

...

https://cananolab.nci.nih.gov/caNanoLab/

...

),

...

the

...

Nanomaterial-Biological

...

Interactions

...

(NBI)

...

knowledgebase

...

(

...

http://nbi.oregonstate.edu/

...

Wiki Markup
{multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}
),

...

and

...

other

...

resources

...

will

...

provide

...

facilities

...

for

...

importing/exporting

...

ISA-TAB-Nano

...

files

...

as

...

the

...

ISA-TAB-Nano

...

specification

...

evolves.

...

ISA-TAB-Nano

...

File

...

Templates

...

Templates

...

for

...

each

...

ISA-TAB-Nano

...

file

...

are

...

provided

...

below:

...

...

A definition of terms in each file are available in ISA-TAB-Nano

...

Glossary

...

Files

...

.

ISA-TAB-Nano

...

Example

...

Files

...

Below

...

are

...

example

...

ISA-TAB-Nano

...

files

...

for

...

nanotechnology

...

investigations

...

involving

...

physico-chemical,

...

in

...

vitro,

...

and

...

in

...

vivo

...

characterization

...

studies.

...

Investigation

...

Title:

...

Nanotechnology

...

Characterization

...

Laboratory

...

(NCL)

...

Dendrimer-Based

...

MRI

...

Contrast

...

Agent

Investigation Description:

...

The

...

objective

...

of

...

this

...

investigation

...

is

...

to

...

characterize

...

a

...

PAMAM

...

dendrimer

...

with

...

an

...

associated

...

gadolinium

...

chelate

...

MRI

...

contrast

...

agent.

...

The

...

nanomaterials

...

submitted

...

for

...

testing

...

at

...

the

...

NCL

...

were

...

(NCL20)

...

G4

...

tris

...

(hydroxyl)

...

terminated

...

PAMAM

...

dendrimer,

...

(NCL21)

...

G4

...

pyrrolidinone

...

terminated

...

PAMAM

...

dendrimer,

...

(NCL22)

...

G4.5

...

COONa

...

terminated

...

PAMAM

...

dendrimer,

...

(NCL23)

...

G4.5

...

COONa

...

terminated

...

PAMAM

...

dendrimer-Magnevist®

...

complex,

...

(NCL25)

...

G4

...

tris

...

(hydroxyl)

...

terminated

...

PAMAM

...

dendrimer-Magnevist®

...

complex,

...

and

...

(NCL26)

...

G4

...

pyrrolidinone

...

terminated

...

PAMAM

...

dendrimer-Magnevist®

...

complex.

...

Commercially

...

available

...

Magnevist®

...

(NCL24)

...

was

...

used

...

as

...

a

...

control.

...

NCL

...

studies

...

addressed

...

in

...

this

...

report

...

can

...

be

...

divided

...

into

...

three

...

main

...

categories:

...

physicochemical

...

characterization;

...

immunotoxicology;

...

in

...

vitro

...

toxicology.

...



Example Files:

...

...

...

ISA-TAB-Nano XML Specification

An XML specification for ISA-TAB-Nano was derived from the
ISA-TAB-Nano Object Model to assist in validating the ISA-TAB-Nano file format.