ASOV Janvier 2012

Development of a Solid Spectroscopy Data Model (SSDM) and the GhoSST DataBase

GhoSST “Grenoble Astrophysics and Planetology Solid Spectroscopy and Thermodynamics" database service

Bernard Schmitt, Damien Albert, Philippe Bollard, Lydie Bonal, Maria Gorbacheva, (Pierre Volcke) and the SSDM Expert group*

Institut de Planétologie et Astrophysique de Grenoble (former LPG), CNRS / UJF

Task “New databases” of IDIS/Europlanet (WP25)

+ interoperability/deployment of VAMDC (WP6 / WP4)

Laboratory spectroscopic databases for solids :

- Develop a Solid spectroscopy data model (SSDM)

- Develop a generic database infrastructure (+ some tools) for spectroscopic data of solids (intended to be available to other data producers, in a second step).

- Generate a first new database (GhoSST) covering :- UV-to-FIR transmission spectroscopy of ices and simple organics

- UV-to-NIR bidirectional reflection spectroscopy of solid surfaces (planetary materials; minerals and ices, meteorites, organics, adsorption, processed, …)

- Raman and Fluorescence micro-spectrometry (minerals, meteorites, organics…)

- Infrared micro-spectroscopy- Band list of molecular solids and adsorbed molecules

prototype delivery: July 2011

VO compliant infrastructure

Why a Solid Spectroscopy Data Model ?

• For efficient interoperability (cross search …) we develop

an uniform and as complete as possible description of the solid samples, instruments & techniques used and of the spectral data (spectra and band list) produced by experimentalist of this field.

Development of a “Solid Spectroscopy Data Model” (SSDM) that we intend to propose to be, at least, an European standard, and possibly an international one.

Include in the data model schema, up to some limited complexity level, the requirements of most of the European solid spectroscopy data producers (SSDM Expert Group*)

General aims and (current) limitations

To describe:

- Most Solid samples and their internal structure, up to some degree of complexity, from layers down to atoms

- synthetic and natural materials, simple to complex

- adsorption on / absorption in solids, processed solids, …

- All spectroscopic techniques from VUV up to mm

- absorption, reflection (all types), emission, Raman, fluorescence,

micro-spectrometry, ellipsometry, ATR, …

- All associated types of spectra and their products

- from raw calibrated spectra (level 1) to, e.g., optical constants (level 4)

- Individual vibration bands of molecules and molecular ions in molecular solids and ad/absorbed on/in other solids (no mineral/rocks except as substrate)

Types of planetary / astrophysical solids

- Molecular solids : ices, volatile molecules, hydrates, clathrates, …

- Organic materials : simples, polymers, macromolecular, … - Minerals, salts, hydrated minerals, rocks, …

- Natural and extraterrestrial samples (meteorites, IDP's, Stardust, Lunar, ...)

- Solids with adsorbed and/or absorbed molecules (H2O, …)

- Processed solids with various type of energy sources (UV, ions, …)

- Optical components (windows, filters, fibers, reflectors, radiators, ...)

SSDM General Structure

SAMPLE INSTRUMENT

EXPERIMENT

PUBLICATIONS

BAND LIST

SPECIES MATTERS OBJECTS

SSDM General Structure

SAMPLE INSTRUMENT

EXPERIMENT

PUBLICATIONS

BAND LIST

SPECIES MATTERS MineralsMeteorites, …

Lab spectraObservations

Transmission, Reflection, Raman, Fluo, Microscopy

FTIR, Gonio, Raman, Fluo, Microscope, …

Ices, Minerals, OrganicsMeteorites, Adsorption…

MoleculesMineralsAtoms

Ices, simple OrganicsAdsorption…

Processings: thermal, pressure, chemical, irradiation, …

OBJECTS Meteorites, IDPs, …

Sample description

The most complex part for solids !!!

LAYERS superposition

MATERIALS (grains: simple or complexe)

mixing

CONSTITUENTS (phases)

arrangement

SPECIES (molecular, mineral)

combinations

- pure solid, molecular mixture, - polymer, clathrate, hydrate, …- adsorption, absorption, …

- heterogeneous polycrystal, - coated grains, …- crystal with adsorbed molecule

SAMPLE

Layer 2

Layer 1

nn

ATOMS(isotopes)

n

n

MATTER Sample Description

MATTER Object Description

1

1

n

n

- complex mix of constituents or species- macro-species, …

simpleco

mplex

n

Mineral

rock

- Meteorites, natural organics, …- rocks, …

Layers organization - layers_number

- layer_addition

Layer 2

Layer 1 Sample

n n

Sample-Layers-Materials description

Name + references - name - parent_sample

Physical characteristics

- thickness

- thickness_error

- mass, …

Sample processingsThermal processing

- temperature

- temperature_error

- annealing_temperature

- annealing_timePressure processing

Fluid processing

Irradiation processing

Layer organization - layer_order

- layer_type

Layer abundance

- thickness

- mass

Formation conditions

- deposition_rate

- deposition_condition

- deposition_temperature

Materials mixing

- materials_number

- materials_mixing

- Materials_list

Material type

- matter_origin

- matter_family

Material abundance

- mass

- mass_fraction, …

Formation conditions (synthetic)

Precursor materials and mixing

- precursors_list + _mixing

Precursors materials processing

- processing_method

- processing_temperature

- processing_fluid

Material texture

- grain size distribution

- grain texture

LAYERS MATERIALS SAMPLE

Physical characteristics

- density - porosity …

Material type

- matter_origin

- matter_family

Material abundance

- mass

- mass_fraction, …

Formation conditions (synthetic)

Precursor materials and mixing

- precursors_list + _mixing

Precursors materials processing

- processing_method

- processing_temperature

- processing_fluid

Material texture

- grain_size_distribution

- grain_texture

MATERIALS

Materials-Constituents-Species descriptionCONSTITUENTS SPECIES

n n

Constituent organization

- constituents_number

- constituents_mixing

- constituents_list

Constituent type + orga

- family  

- arrangement  

Constituent abundance

- mass_fraction

- mole_fraction

Constituent state

- phase_type

- phase

- texture

Species organization

- number

- compound_type

- species_list

Matters and Species type

- family

- compound_state

Species abundance

- mass_fraction

- mole_fraction

Molecule composition

- structural_formula

- atom_list + number

- isotopic composition

Molecule name + identifier

- iupac_name

- inchi

- inchikey

Instruments and Techniques

- The instrument is defined by “instrument and technique descriptions” and by "spectral parameters".

Depending on the instrument and technique there are also additional or optional "spatial parameters", "angular parameters", "polarization parameters", and/or "Raman source parameters".

Measurement technics - absorption, reflection (bidirectional, directional-hemispheric, specular)- emission (hemispheric, directional, …)

- Raman, fluorescence, infrared microscopy

Spectral / Angular / Spatial - range - resolution - sampling, …

polarization, …

Experiment

An Experiment is defined as one or a series of spectrum measurement(s) of a single sample with an unique instrument and one of its technique.

During an experiment :

- several types of instrument (measurements) parameters can be changed (e.g. goniometer angles, spectral range, …) without limitation.

- a sample can be subjected to simple changes of a single parameter.

Spectral products: spectra

The spectroscopic data consist of a spectrum file and some "file and spectrum information". The spectrum is linked with an "experiment" which connect to the "sample" and the "instrument parameters" used.

Case of transmission spectroscopy:

o Transmission spectrum (level 1)

o Normalized absorbance spectrum (level 2)

o Absorption coefficient spectrum (level 3)

o Optical constants spectrum (level 4)

- reflection spectra, polarized spectra, BRDF, spectral scattering functions

- emission spectra, spectral emissivity, …

- Raman, Fluorescence, micro-spectroscopy, …

Spectral products: spectra

- Absorbance spectra (level. 2) Optical constants (level. 4)

Spectral products: vibrations band list

A band list contains individual information on each known vibration bands of one particular species inside a constituent in a given phase and physical conditions.

This band information may have different and complementary origins in term of measurement type (absorption, reflection, emission, Raman, …)

- Description of the molecule in its constituent, and the physical conditions

- Description of the vibration band:

- Frequency [+ uncertainty]- Width (FWHM) [+ uncertainty]- Peak Intensity (abs. coeff., or k) [+ uncertainty]- Integrated intensity (abs. coeff., or k) [+ uncertainty]- Vibration mode (ex: 21 + 2 + 3 3)- Vibration mode type (ex: O-H stretching)- Reference list (1st measurement/attribution)

Spectral products: molecular parameters list

The molecular parameters list contain quantum numbers and interaction parameters on defined molecular solid.

Derived from the analysis and attribution of the known absorption bands and allow to calculate the band position (and intensity ?) of the fundamental, overtone and combination internal vibration modes, measured or not.

This band information may have different and complementary origins in term of measurement type (absorption, reflection, emission, Raman, …)

- Description of the molecule in its constituent, and the physical conditions

- Description of the vibration parameters:

- Fundamental modes - Vibration parameters and band position equation- Reference list (model, parameter)

Dictionary of the Solid Spectroscopy Data Model (SSDM version 0.3.4e).

SSDM implementation schema

SampleBand list

Material

Species

Publis

ExperimentInstrumentSpectra

Opt. Cte

User

Exp. Param.

GhoSST Prototype

• Samples: Layers/Material/Constituents Stable Done• Species:

– Molecular and atomic Done Done

– Minerals Done TBD soon

• Matters: – Minerals / Rocks Done TBD soon

– Meteorites Draft TBC TBD

• Instruments/techniques:– Transmission + reflection Done Done

– Emission + Raman/Fluo Done Done

• Spectra and products:– Transmission Done Done

– Reflection Done Done

– Emission + Raman/Fluo Done Done

• Band lists– Molecular solids + adsorption in progress TBD

• Publications Done in progress

SSDM + GhoSST Implementation : planning

For prototype of GhoSST

•Samples: Layers/Material/Constituents Test set + TBD•Species:

– Molecular and atomic Partly Done + TBC

– Minerals TBD

•Matters: – Minerals TBD

– Meteorites TBD

•Spectra and products:– Transmission / molecular solids Test set + TBD

– Reflection / ices (H2O, CO2) Test set + TBD

– Reflection / minerals + adsorption Test set + TBD

– Raman / Meteorites TBD

•Band lists– Molecular solids + adsorption TBD

Data feeding: planning

Extensions of SSDM• Completion of the band list DM (vibration modes of solids, …)• Development of “matters” data model: meteorites• Gas phase (XSAMS) and solid phase (SSDM) datamodels Mapping

Data validation• Scientific validation of spectra (quality, errors, analysis, metadata, …)• Band list : Analysis of spectra, bibliography compilations, …• Tools for determination of vibration modes in solids & bands prediction

Feeding GhoSST database• Species: molecules (continued), minerals• Matters: mineral samples, meteorites, • Spectra: samples, instruments, spectra (transmission, reflection,

Raman) • Band list: lab data + critical biblio compilation

Still a lot of work to be done!

Public version of GhoSST: July 2012

Ongoing developments: SSDM

GhoSST: data import and validation• Administration tools for database feeding interface (data import & survey)• Metadata validation by logical checks on parameters• Update and correction tools• Generic database: adaptation to other data producers

GhoSST: data query, comparison and delivery• User tools for data consultation (favorites, download history, email warning…)• Advanced data visualization and comparison tools• Export in different formats + conversions• Development of VO data access layer

GhoSST: development of “Band list” interface• Database feeding tools• Query and visualization tools – links with spectra• Delivery formats• Integration in the VO layer

Public version of GhoSST: July 2012

Ongoing developments: GhoSST