Non-composition Data

This section addresses:

:USDA #9:

Support input and storage of various non-composition data types (metabolomic profiles; DNA barcodes; taxonomic information; and chromatographic and spectral profiles).

Attention

This section applies to USDA prime data, not to USDA select data. For explanation of USDA prime and USDA select data, see Deposition Workflow

Table of Contents

Chromatographic and Spectral Profiles

Ontomatica deposition service integrates the following terms for use by investigators € when depositing chromatographic and spectral profiles.

The Physico-chemical methods and properties ontology (FIX) has been parsed and each term below is referenceable. The HUPO Proteomics Mass Spectrometry ontology (MS) has not been parse. Instead, Ontomatica uses the Essepuntato Live OWL Documentation Service (LODE) to display the MS ontology. Be patient while the LODE service parses the MS ontology OWL file. Once displayed, each facet term code below is searchable.

Ontomatica deposition service will enable investigators € to deposit data like this data from USDA:

In the table below a Section is upper case bold and a Topic € is upper case italic. The spectral term is lower case and associated with its facet term code.

Spectral Profile Information

Ontology Term

Deposit Accession

EDAM:data_2091

Deposit Title

dc:title

Analysis Date

Time

Deposit Creation, Last Modification Date

Time

Authors and Affiliations of Deposit

vCard

Creative Commons License of Re-use of Deposit

Creative Commons

Copyright of Deposit

Creative Commons

Reference to Spectral Data

CHEMINF_000302

—

—

Chemical Compound Information

Name of Chemical Compound Analyzed

CHEMINF_000140

Category of Chemical Compound

ChEFS

Molecular Formula of Chemical Compound

CHEMINF_000037

Monoisotopic Mass of Chemical Compound

CHEMINF_000218

SMILES String

CHEMINF_000020

IUPAC International Chemical Identifier (InChIKey)

CHEMINF_000059

Biological Sample Information

Identity of Biological Species

EDAM:data_1875

—

—

Method of Analysis Information

Instrument model

MS_1000031

Ion analyzer type

chromatography by separation mechanism

FIX_0000610

capillary electrophoresis

FIX_0000836

gas chromatography

FIX_0000098

liquid chromatography

FIX_0000608

Ionization methods

MS_1000008

atmospheric pressure ionization mass spectrometry

FIX_0000908

atmospheric pressure photoionization mass spectrometry

FIX_0000907

electron ionization mass spectrometry

FIX_0000089

electrospray ionization mass spectroscopy

FIX_0000079

fast atom bombardment mass spectrometry

FIX_0000086

matrix-assisted laser desorption/ionization mass spectrometry

FIX_0000081

APCI

MS_1000070

APPI

MS_1000382

EI

MS_1000389

ESI

MS_1000073

B

MS_1000080

IT

MS_1000264

Q

MS_1000081

TOF

MS_1000084

Fourier transformation

Fourier transform-ion cyclotron resonance mass spectrometry

FIX_0000083

Ion trap analyzer

ion trap mass spectrometry

FIX_0000917

Data Type

MSn spectrum

MS_1000580

precursor ion spectrum

MS_1000341

Polarity of Ion Detection

positive thermal ionization mass spectrometry

FIX_0000914

positive thermal ionization mass spectrometry

MS_1000030

negative thermal ionization mass spectrometry

FIX_0000915

negative thermal ionization mass spectrometry

MS_1000129

Ion mode

MS_1000465

Collision Energy for Dissociation

collision energy

MS_1000045

Name of Collision Gas

ChEFS

collision gas

MS_1000419

Flow Rate of Desolvation Gas

ion desolvation

MS_1000390

flow rate array

MS_1000820

Temperature of Desolvation Gas

temperature array

MS_1000822

Matrix Used in MALDI

MALDI matrix application

MS_1000832

Name of Reagent Gas

ChEFS

Retention Time on Chromatography

Retention time

MS_1000016

—

—

Mass Spectral Data Description

m/z of Base Peak

base peak

MS_1000210

Molecular Formula of Derivative

PubChem

Mass of Derivative

PubChem

Type of Focused Ion

see footnote 1

m/z of Precursor Ion in MSn spectrum

msPrefix precursor recalculation

MS_1000781

precursor m/z

MS_1000504

Type of Precursor Ion in MSn

Precursor type

MS_ 1000792

Precursor type

see footnote 2

—

—

Mass Spectral Peaks Information

Data Processing Method of Peak Detection

Data processing

MS_1000543

Peak Detection

selected ion detection

MS_1000091

peak picking

MS_1000035

Total Number of Peaks

number of matched peaks

MS_1001121

Footnotes

1

Type of Focused Ion. Available types are:

[M]+, [M]+*, [M+H]+, [2M+H]+, [M+Na]+, [M-H+Na]+, [2M+Na]+, [M+2Na-H]+, [(M+NH3)+H]+, [M+H-H2O]+, [M+H-C6H10O4]+, [M+H-C6H10O5]+, [M]-, [M-H]-, [M-2H]-, [M-2H+H2O]-, [M-H+OH]-, [2M-H]-, [M+HCOO-]-, [(M+CH3COOH)-H]-, [2M-H-CO2]- and [2M-H-C6H10O5]-

2

Precursor type. Available types are:

[M]+, [M]+*, [M+H]+, [2M+H]+, [M+Na]+, [M-H+Na]+, [2M+Na]+, [M+H-C6H10O4]+, [M-H+OH]-, [M+2Na-H]+, [M+H-C6H10O5]+, [2M-H]-, [M+HCOO-]-, [M]-, [(M+NH3)+H]+, [M+H-H2O]+, [M-H]-, [M-2H+H2O]-, [M-2H]-, [(M+CH3COOH)-H]-, [2M-H-CO2]- and [2M-H-C6H10O5]-

Metabolomic Profiles

From Wikipedia:

Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the “systematic study of the unique chemical fingerprints that specific cellular processes leave behind”, the study of their small-molecule metabolite profiles. The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes. mRNA gene expression data and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell. One of the challenges of systems biology and functional genomics is to integrate proteomic, transcriptomic, and metabolomic information to provide a better understanding of cellular biology.

Ontomatica Coverage

ChEMATIC discussion here

Taxonomic Information

Replay taxonomic data in several production databases.

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