GhoSST user manual

Latest revision as of 10:39, 2 September 2014

Access to the GhoSST interface: http://ghosst.osug.fr/

[edit] General menu (upper left)

[edit] Before login

[edit] Home

To go back to home page [Future: with a simple search]

[edit] Search

Guided

Step by step search (2 starting options, 7 fields)

Advanced

Search with 27 optional fields

[edit] Login

To login as a registered user in Ghosst

[edit] After login

[edit] Home

To go back to home page [Future: with a simple search]

[edit] Search

Guided

Step by step search (2 starting options, 7 fields)

Advanced

Search with 27 optional fields

[edit] Data

List

To search all used data in the database by categories and with a few filters

Export

To download the selected data

[edit] Producer (restr.)

(access restricted to data providers)

Full Search

To search all data entered in the database by categories with a few filters

Import (in the database)

Matters

To import matters

Sample

To import samples

Experiment & Spectra

To import experiments and their spectra

Bandlist

To import bandlists and their bands

Import history

Log of the data import

Help

Gives access (wiki) to all documents and files necessary for import data

[edit] Manager (restr.)

(access restricted to database managers)

Users

To list and manage user profiles

OpenEnums

To list and manage attributes of OpenEnums

Import (in the database)

Species

To import fundamental species (atoms, molecules, chemical functions, minerals, …)

Instrument & Lab.

To import instruments, laboratories, experimentalists

Publications

To import publications

States

To import molecular states

Import history

Log of the data import

[edit] User

Information

To change your personal information and login password

Export history

Log of the user data export

Logout

To logout as an external user from Ghosst

[edit] Information menu (Bottom of page)

[edit] Documentation

Various documentation (GhoSST, data use, SSDM, experimental systems, …)

[edit] Contact

To give feedback on interface and data (question, comment, error report, user case..)

[edit] History

Provides an history of the development of SSDM datamodel and GhoSST interface

[edit] Credits

List of contributors, financial support and technical components used

[edit] Statistics

Provides user & database content & download statistics, and link to a stat engine

[edit] Search

3 levels available [future: 4 levels]

Simple

[future (also in ‘home’)]

Guided

Advanced

List (currently in Data)

[edit] Simple Search

[Future]

Search on: species formula or name, phase type ?, spectral range type, spectrum type

[edit] Guided Search

2 different search options in 7 steps:

by spectrum type

Starts by “Instrument type” field

by species

Starts by “species type” field

Add next field

to add the next selection field

View results

to display the list of selected spectra

Reset

to reset the search to the first step (set to --All--)

Tips:

- Select one or several choices by left Clic (first), Ctrl+Clic (next), shift+Clic (range), deselect by Ctrl+Clic. No choice = '-- All --'

- The list of choices adjusts depending on the data available with your filters

- The next field open or refresh automatically after your choice

- You can force to go to next field with the 'Add next field' buttom

- After each step the number of spectra satisfying your filters is displayed (upper right)

Fields:

Instrument type (list)

choose one or more

Instrument technique (list)

choose one or more

Spectral range type (list)

either choose a typical range or set to 'Custom'

Spectral range unit (list)

choose a wavenumber / wavelength / frequency unit

Spectral range min/max

set one or both limits (min and/or max) in the above unit

Matter family (list)

choose one or more

Species type (list)

choose one or more

Species name

write a molecule or mineral name (after the 2 first letters it will propose you a list of relevant choices)

Species formula

write a molecule or mineral formula, or just any part of it (after the 2 first letters it will propose you a list of relevant choices)

Species relevance (list)

choose one or more

[edit] Advanced Search

27 different optional selection fields

View results

to display the list of selected spectra

Reset

to reset the search to the first step (set to --All--)

Tips:

- Select one or several choices by left Clic (first), Ctrl+Clic (next), shift+Clic (range), deselect by Ctrl+Clic. No choice: '-- All --'

- After each choice the number of products (spectra and band lists) satisfying your filters is displayed (upper right)

Fields:

--- Species ---

Species type (list)

family: 'atomic'

- ‘atom’

- ‘atomic ion’

family: 'molecular'

- ‘molecule’

- ‘molecular ion’

- ‘free radical’

family: 'mineral'

- ‘native element’

- ‘silicate’

- ‘non-silicate mineral’

- ‘organic mineral’

Species formula

write a molecule or mineral formula (for isotopes type ‘13C,18O2’ for 13C18O2), or just any part of it

(You will be proposed a list of matching molecules after the second character)

Species name and code

write a molecule or mineral name, or its code (InChI key or CAS number)

(You will be proposed a list of matching molecules after the second character)

Species relevance (list)

Flag telling the origin of the species [default = 'main']

- ‘main’: all species, except impurities, present in the sample at the beginning of an experiment

- ‘precursor’: precursor species used for synthetic material formation, or pre-processing of natural matters. Flagged ‘precursor’ only in the precursor material.

- ‘product’: species producted in the sample subjected to a processing during the experiment

- ‘impurity’: species not wanted but present in synthetic materials, or minor unwanted mineral species in natural mineral matters, or others matters.

- ‘unknown’: if origin of the species is not clear: ‘impurity’ or ‘product’ ?

--- Layer/Material ---

Matter origin

general origin of the matter constituting the material

- ‘terrestrial’: natural matter colleted on Earth

- ‘extraterrestrial’: natural matter coming from extraterrestrial bodies

- ‘synthesized’: material or matter synthesized in laboratory

- ‘commercial’: matter synthesized by a factory

- ‘simulated’: material defined for a numerical simulation

Material name

write a material name

(You will be proposed a list of matching molecules after the second character)

Material family

Type of material family depending on the species and matters that constitute the material

- ‘atomic’: simple synthetic material made of atomic species

- ‘molecular’: simple synthetic material made of molecular species

- ‘mineral’: simple natural or synthetic material made of minerals

- ‘molecular-mineral’: simple synthetic material made of a mixture of molecular species and minerals

- ‘mineral matter’: natural or synthetic matter made of minerals including ‘rock’: natural matter made of assemblage of minerals

- ‘fluid matter’: natural or synthetic matter made of molecular liquid or gas

- ‘organic-carbonaceous matter’: complex natural or synthetic matter made of complex molecular species or of a macromolecular structure

- ‘inorganic matter’: synthetic matter made of inorganic molecular species

- ‘meteorite matter’: complex extraterrestrial matter made of organics and minerals coming from a meteorite

- ‘solar system dust matter’: complex extraterrestrial matter made of organics and minerals coming from extraterrestrial dust

- ‘snow matter’: terrestrial matter made of natural water snow or ice with mineral/organic impurities

Layers number

Number of different materials mixed in the layer

Layer texture

Layer macroscopic texture (at scale above material grains)

type: ‘granular’:

- ‘muddy’: wet earthy or pulverulent powder

- ‘earthy’: Dull, clay-like texture (< 2 µm) with no visible crystalline affinities

- ‘pulverulent’: very fines grains (< 50 µm) without, or with very weak aggregation

- ‘loose granular’: no or weak mechanical links between grains, large open porosity

- ‘sintered granular’: grains moderately to strongly linked together without another material between them, open porosity

- ‘porous cemented granular’: grains with another material linking them, open porosity

- ‘compact cemented granular’: grains with another material linking them forming a compact medium, no or little porosity

- ‘mixed granular’: mixture of two or more of the above texture

type: ‘compact film’ and ‘compact slab’:

- ‘compact glassy’: vitreous without bubble

- ‘compact glassy with bubbles’: vitreous with isolated bubbles (closed porosity)

- ‘compact poor grained’: compact layer with very fine grains grains (< 50 µm)

- ‘compact porous poor grained’: compact layer with very fine grains (< 50 µm), presence of open porosity

- ‘compact fine grained’: compact layer with fine grains (< 1 mm)

- ‘compact porous fine grained’: compact layer with fine grains (< 1 mm), presence of open porosity

- ‘compact coarse grained’: compact layer with coarse grains (> 1 mm)

- ‘compact porous coarse grained’: compact layer with coarse grains (> 1 mm), presence of open porosity

- ‘compact lamellar’: distinctly foliated fine-grained forms.

- ‘compact fibrous’: distinctly fibrous fine-grained forms.

- ‘compact crystal’: compact layer with a single, or a few, monocrystals

- ‘compact mixed’: several (at least 2) different textures are present

type: ‘single grain’:

- ‘single grain’: single individual grain (its texture will be described in ‘material_texture’)

type: ‘aerosols’:

- ‘isolated aerosols’: individual aerosols particles in suspension in fluid

- ‘aggregated aerosols’: agregated aerosols particles in suspension in fluid

type: ‘clusters’:

- ‘clusters’: molecular or atomic clusters in jet or vacuum

type: ‘fluid’:

- ‘liquid’: liquid

- ‘gaseous’: gas

type: ‘other’:

- ‘other’: not one described in the list, will be defined in “comments”

- ‘unknown’: unknown texture

--- Constituent ---

Constituent mixing

Describe how the constituents are mixed at the sub-grain level in the material grains

- ‘single phase’: only one constituent in the grains (but possibly several crystals)

- ‘multi-phases’: limited number of phases coexisting in the grains without specific organization

- ‘endmembers polyphase’: intimate mixing (at microscopic level) of endmember phases within a solid solution phase (equivalent to a single solid solution of intermediate composition)

- ‘matrix with inclusions’: mix of phases with a matrix-inclusions organization: individual phase(s) isolated in a continuous matrix.

- ‘grains with inclusions’: the grains are mostly one single phase but with small inclusions of another phase (solid, liquid, or gas) fully embedded inside the grains

- ‘filled agglomerate’: aggregate or agglomerate of one phase (or more) with their pores filled by another phase

- ‘coated grains’: the grains have their core made of one phase and an external shell of another phase (the coating)

- ‘concentric zoning’: concentric organization of several phases inside grains

- ‘sector zoning’: sector organization of several phases inside grains

- ‘layer zoning’: layered organization of several phases inside grains

- ‘complex mixing’: complex mixture of phases (numerous or indicernable and/or very heterogeneous) without clear topologic organization’

- ‘multi-adsorbed phases’: when several adsorbed phases (constituents) co-exist but are not adsorbed on the same adsorbat constituent.

Constituent family

Family of the constituent

- ‘molecular solid’: single molecular solid phase

- ‘molecular liquid’: single molecular liquid phase

- ‘molecular gas’: single molecular gas phase

- ‘atomic-molecular sorbed’: atomic and molecular species adsorbed on, or in interlayer in other solids

- ‘atomic-molecular clusters’: atomic and molecular species forming Van der Walls aggregates of 2 to 100 000 atoms/molecules

- ‘organic solid’: solid constituent made of (a mixture of) large organic species: oligomer solid, polymers, …. Intermediate between organic ‘molecular solids’ and ‘complex organic’

- ‘complex organic’: solid constituent made of a complex mixture of molecular species or of a macromolecular structure

- ‘mineral’: single mineral phase (include crypto-polyminerals)

- ‘covalent solid’: single covalent solid phase (except minerals)

- ‘covalent liquid’: single covalent liquid phase

- ‘ionic solid’: single ionic solid phase (except minerals)

- ‘ionic liquid’: single ionic liquid phase (salts)

- ‘metallic solids’: single metal phase (including metallic minerals)

- ‘metallic liquid’: single liquid metallic phase

- ‘complex mix’: complex mixture of molecular, organic, ionic, … and/or mineral constituents

- ‘other’: when family of constituent cannot be described by one of above words

- ‘unknown’: when family of constituent is unknown

Phase type

Type of phase of the constituent (solid, liquid, gas)

- ‘crystalline’: with a well defined crystalline structure

- ‘Hypocrystalline’: partially crystalline, with crystals embedded in an amorphous or glassy matrix

- ‘metamict’: disordered crystalline structure due to some external effects (irradiation, …)

- ‘quasi-amorphous’: nanocrystalline solids

- ‘amorphous’: solid lacking the long-range order characteristic of a crystal.

- ‘glassy’: amorphous solid that transforms into a liquid upon heating through the glass transition

- ‘adsorbed’: phase of adsorbed molecules, or films, at the surface or in pores (macro/meso/micro) of another material

- ‘interlayer’: phase of the interlayer molecular layer (generally H2O) inside minerals (phylosilicates)

- ‘adsorbed+interlayer’: when it is not possible to distinguish the adsorbed and interlayer phases

- ‘mono-multimers’: Van der Walls aggregates up to 4 molecules

- ‘cluster’: Van der Walls aggregates of 5 to 100 000 molecules

- ‘supercooled liquid’: liquid phase under the freezing point

- ‘liquid’ : liquid phase

- ‘gas’: gaseous phase

- ‘other’: when phase of constituent cannot be described by one of above words

- ‘unknown’: when phase of constituent is unknown

Species compound

Type of solid compound composing the constituent. It tells how the species are mixed at the molecular level

For molecular solids:

- ‘molecular solid’: molecular isotopic species or natural isotopic mixture condensed as a solid

- ‘molecular solid solution’: solid-state solution of one or more molecules (solutes) in another (solvent) forming a single homogeneous crystalline phase having the crystal structure of the solvent.

- ‘clathrate hydrate’: clathrate structure formed with H2O (host)

- ‘clathrate’: clathrate structure formed with other host molecules

- ‘solid hydrate’: solid stoichiometric hydrate containing water molecules combined in a definite ratio as an integral part of the crystal

For ionic solids (synthetic, excluding minerals),

- ‘ionic solid’: Ex: NaCl

- ‘ionic liquid’: Ex:

- ‘ionic solution’: ionic solid (solute) dissolved in water or other solvent

For covalent solids (synthetic, excluding minerals),

- ‘covalent solid’: Ex: Si, Ge, …

- ‘covalent liquid’: Ex:

For metallic solids (synthetic),

- ‘metallic solid’: Ex: Fe, Cu, Al, …

- ‘metallic liquid’: Ex: Hg, Ga,

- ‘metallic alloy’: Ex: Fe-Ni

For minerals:

- ‘mineral’: single mineral species

- ‘mineral solid solution’: mineral solid solution

- ‘crypto-polymineral’: exsolution at the nanometer-submicrometer scale of generaly 2 mineral species from a solid solution

- ‘complex mineral mix’: complex mixture of minerals minerals too numerous, too intermixed or at a scale difficult to separate them

For organic solids:

- ‘solid oligomers’: Solid of molecules made of a small number of monomer units, up to a few dozen.

- ‘homopolymer’: mixture of macromolecules composed of the same unique repeating structural unit.

- ‘copolymer’: mixture of macromolecules composed of several repeating structural units.

For complex organic matters:

- ‘Insoluble Organic Matter’ (IOM) : insoluble mixture of macromolecules composed of various and non-repeating structural units.

- ‘Soluble Organic Matter’ (SOM): soluble mixture of macromolecules composed of various and non-repeating structural units.

- ‘complex macromolecular mixture’ (IOM+SOM): mixture of soluble and insoluble macromolecules composed of various and non-repeating structural units.

For complex organic+mineral matter:

- ‘complex organic-mineral mix’: complex mixture of organic solids/matter and minerals too numerous, too intermixed or at a scale difficult to separate them

For adsorbed molecular or atomic species (molecules/radicals/ions/atoms):

- ‘physically adsorbed atomic phase’: natural or isotopic atomic species physically adsorbed on a solid, in its (micro)porosity or in its porous structure.

- ‘chemically adsorbed atomic phase’: natural or isotopic atomic species chemically adsorbed on a solid, in its (micro)porosity or in its porous structure

- ‘physically adsorbed molecular phase’: natural or isotopic molecular species physically adsorbed on a solid, in its (micro)porosity or in its porous structure.

- ‘chemically adsorbed molecular phase’: natural or isotopic molecular species chemically adsorbed on a solid, in its (micro)porosity or in its porous structure

For interlayer atomic or molecular species in solids:

- ‘atomic interlayer phase’: natural or isotopic atomic species adsorbed in the interlayer space of a solid (mostly clay minerals)

- ‘molecular interlayer phase’: natural or isotopic molecular species adsorbed in the interlayer space of a solid (mostly clay minerals)

For atomic and molecular clusters:

- ‘atomic clusters’: Van der Walls aggregates of 2 to 100 000 atoms

- ‘molecular clusters’: Van der Walls aggregates of 2 to 100 000 molecules

For molecular liquids and gases:

- ‘molecular gas’: molecular isotopic species or a natural isotopic mixture in a gas

- ‘molecular liquid’: molecular isotopic species or a natural isotopic mixture in a liquid

- ‘liquid solution’: molecular species (solute) dissolved in another species in the liquid state (solvent)

Others compounds and complex mixtures

- ‘other complex mix’: complex mixture of compounds too numerous, too intermixed or at a scale difficult to separate them

- ‘other compound’: compounds which cannot be described by one of the above words (include some mixtures such as atomic+molecular clusters)

- ‘unknown’: unknown compound

Compound state

State of the species inside its compound

For molecular compounds and in some cases for ions in ionic compounds, and atoms in covalent and metallic compounds

- ‘pure’: only one species forms the compound (also gas, liquid and clusters)

- ‘mixed’: more than one species forms the compound and the species state cannot be described with one of the next compound (also gas, liquid and clusters)

- ‘matrix’: the species largely dominates the compound (mole fraction > 95%).

- ‘monomers’: the species is fully isolated in minor abundance in the compound (generally when mole fraction < 0.1 %), or in clusters. Also used for precursor monomers of polymers

- ‘dimers’: the species occurs as isolated pairs of species without chemical bond (generally when mole fraction < 1 %), or in clusters.

- ‘multimers’: isolated small group of species without chemical bond and with limited size: 1 to 4 monomers (generally when mole fraction < 5 %), or in clusters.

- ‘solute’: molecule diluted in a liquid or solid solution (or atom in alloy)

- ‘solvent’: molecule that dilute the solute in a liquid or solid solution (or main element of the alloy)

- ‘solid solution’: for mineral or molecular solid solution when at least 2 mole fractions are > 0.1 (solute ~ solvent).

- ‘clathrate network’: host molecule forming the clathrate structure (Ex: H2O for clathrate hydrate)

- ‘clathrate guest’: guest molecule occupying the cages of the clathrate structure

- ‘hydration’: H2O molecules in solid stoichiometric hydrate

- ‘hydrated’*^: species that are form with water a solid stoichiometric hydrate

For minerals:

- (‘pure’): mineral (or solid solution mineral) without replacement and/or substitution elements (follow its nominal formula).

- (‘matrix’): mineral with replacement and/or substitution elements

- (‘solvent’): mineral solid solution with replacement and/or substitution elements

- (‘mixed’): for crypto-polyminerals exsolved at constituent scale

For molecular or atomic species adsorbed at the surface, in (micro)pores or in interlayer:

- ‘physically adsorbed’: physical adsorption at surface and in porosities (macro-, micro-)

- ‘chemically adsorbed’: chemical adsorption at surface and in porosities (macro-, micro-)

- ‘interlayer physically adsorbed’: physical adsorption in interlayer spaces of solids (mostly clay minerals)

For complex organic matter, mineral mixtures and other complex mixtures:

- ‘complex’: complex or too numerous state(s) of the species

- ‘unknown’: unknown state of the species

Others compounds

- ‘other’: species state in a compound which cannot be described by one of the above words

--- Temperature ---

Temperature min / max (K)

Sample temperature

you can set one or both limits

--- Spectral range ---

Unit (list)

- wavenumber (cm-1 or m-1)

- wavelength (mm, µm, nm, or Angstrom)

- frequency unit (Khz, MHz or Ghz)

Type (list)

either choose a typical spectral range or set to 'Custom'

- ‘EUV’: Extreme Ultraviolet (10-120 nm)

- ‘VUV’: Vacuum Ultraviolet (120-200 nm)

- ‘UV’: Ultraviolet (200-400 nm)

- ‘UV-Vis’: Ultraviolet-Visible (200-800 nm)

- ‘Vis_blue’: Visible Blue (400-600 nm)

- ‘Vis’: Visible (400-1000 nm)

- ‘Vis_red’: Visible-Red (600-800 nm)

- ‘Vis-NIR’: Visible Near-IR (400-5000nm)

- ‘NIR’: Near-InfraRed (1-5 µm)

- ‘NIR-MIR’: Near+Mid-IR (1-25 µm)

- ‘MIR’: Mid-InfraRed (2.5-25 µm)

- ‘FIR’: Far-InfraRed (15-500 µm)

- ‘sub-mm’: Sub-millimeter (300-1000 µm)

- ‘mm’: millimeter (1-10 mm)

Custom min./max.

set one or both limits (min and/or max) in the above unit

--- Instrument ---

Type

Type of instrument or model

- ‘FTIR spectrometer’:

- ‘grating spectrometer’:

- ‘AOTF spectrometer’:

- ‘CRDS spectrometer’:

- ‘laser diode spectrometer’:

- ‘SWIFT spectrometer’:

- ‘narrow-band filters spectrometer’:

- ‘grating spectro-imager’:

- ‘narrow-band filters imager’:

- ‘spectro-gonio radiometer’:

- ‘Raman spectrometer’:

- ‘Raman micro-spectrometer’:

- ‘FTIR micro-spectrometer’:

- ‘ellipsometer’:

- ‘radiative transfer simulation’:

- ‘quantum mechanical simulation’:

Technique

[Future: Choice will depend on the instrument type]

For FTIR, grating, CRDS, ... spectrometers:

- ‘transmission (absorption)’

- ‘(surface) bidirectional reflection’

- ‘(surface) biconical reflection’

- ‘(surface) directional-hemispheric reflection’

- ‘(surface) hemispheric-directional reflection’

- ‘(surface) specular reflection’

- ‘(surface) thermal emission’

- ‘ATReflection’

- ‘(grains) scattering’

- ‘(grains) thermal emission’

For spectro-gonio radiometers:

- ‘(surface) bidirectional reflection’

For Raman spectrometers:

- ‘fluorescence emission’

- ‘raman scattering’

For ellipsometers:

- ‘ellipsometry’

Laboratory

Laboratory who has copyright on the spectrum (where it has been recorded, and/or laboratory of the visiting experimetalists)

--- Spectrum ---

Type

Type(s) of spectra – depends on the instrument type

For transmission spectroscopy

- ‘transmission’:

- ‘absorbance’:

- ‘normalized absorbance’:

- ‘optical density’:

- ‘absorption coefficient’:

- ‘optical constants’:

For Atenuated Total Reflection spectroscopy

- ‘ATR transmission’:

- ‘ATR absorbance’:

- ‘corrected ATR absorbance’:

For reflection spectroscopy

- ‘reflectance’:

- ‘bidirectional reflectance’:

- ‘hemispheric-directional reflectance’:

- ‘directional-hemispheric albedo’:

- ’SBRDF ’:

- ‘(BRDF)’:

- ‘scattering coefficients’:

For thermal emission spectroscopy

- ‘thermal emission’:

- ‘thermal emittance’:

- ‘directional thermal emissivity’:

- ‘hemispheric thermal emissivity’:

- ‘SDEDF’:

- ‘(DEDF)’:

For Raman spectroscopy

- ‘raman scattering’:

- ‘normalized raman scattering’:

- ‘raman scattering efficiency’:

For fluorescence spectroscopy

- ‘fluorescence emission’:

- ‘normalized fluorescence emission’:

- ‘fluorescence emission efficiency’:

[edit] Search result Tables

The search results are displayed in 2 tables 'Spectrum' and 'Bandlist'

They provide synthetic information on:

- ID: product ID

- Type: product type

- Title: product title describing its major features (composition, temperature, spectral range, ...)

- Sample (for spectrum): description of the sample

- Primary constituent (for bandlist): composition of the constituent containing the primary molecular species of the bandlist

- Primary species (for bandlist): the band list contains the bands information of this specific (isotopic) species in the above constituent

- Spectral range min./max.: limits of validity of the product (in the unit you specified in search)

- Sample temperature: in K

- Species (for spectrum): list of the species contained in the sample

Icons:

- 'box' icon: allows to send directly the product in the 'shoping basket'

- 'magnifer' icon (for spectrum): display a small plot of the spectrum

- 'table' icon: go to product informations with interactive display of spectrum

[edit] Spectrum graph & info

accessed from the 'table icon' in the search result table

[edit] Graph

display the graph in its original unit

Legend:

Settings:

- Errors:

- Infos:

- Unit:

- Color(s): 'intensity' or 'n' and 'k'

Zooms:

- Full range

- Valid range

Navigation:

- Vertical zoom: Click + Mouse move (Up or Down)

- Horizontal zoom: Click + Mouse move (Left or Right)

- Zoom out: Click

- Zoom reset: Double Click

- Pan: [SHIFT] + Click + Mouse move (Up, Down, Left or Right)

[edit] Spectrum info

[edit] Sample info

the sample info is structured in several levels:

Sample

Layer(s)

Material(s)

Constituent(s)

Specie(s)

[edit] Data

[edit] List

Allow to search all used data in the database by categories and with a few filters

[edit] Species

Molecules

can filter by type, formula, name, InChI / CAS. Can exclude isotopes

Minerals

can filter by type, formula, name, class, code and crystal system. Can restrict to hydrated minerals

[edit] Sample data

Samples

can filter by name, layer type, matter origin and family, constituent phase type and compound, species type, formula, name, code and relevance

Materials

can filter by name, matter origin and family, constituent phase type and compound, species type, formula, name, code and relevance

Matters

can filter by main type (currently mineral or fluid), name, reference, origin. Mineral family, type, rock type and texture. Fluid family and type.

[edit] Spectral data

Spectra

can filter by ID, type, update date, publication state, sample ID. Can include parent/sons spectra.

Band lists

can filter by type and title, sample name, constituent name, family, phase and arrangement, Species type, formula, name, code and relevance.

[edit] Bibliography

Publication

can filter by document type, publication state and year, author name, journal name, volume and first page, content and keyword

[edit] Export

Allow to export the selected spectra and associated information (spectrum, sample, experiment, instrument)

[future: export of band list]

Table of selected spectra

- display ID, spectrum type, file title, spactral range min/max, sample species, date

Parameters

- Wavenumber/Wavelength/Frequency: unit, format, number of digits and decimals

- Spectral range: whole range, valid range only, user defined min/max

- Value/Intensity: format, number of digits and decimals

- Spectra data file: type and format

- Export archive file: filename, compression type

[edit] Producer

Restricted to data provider

[edit] Full search

Allow to search all data in the database: fundamental data, sample data and publications

[edit] Species and Matters data

Atoms

can filter by ID, UID, type, symbol, name, mass number A, and atomic number Z. Can exclude isotopes

Chemical functions

can filter by ID, UID, type, formula, and name

Molecules

can filter by ID, UID, type, formula, name, and InChI / CAS. Can exclude isotopes

Minerals

can filter by ID, UID, type, formula, name, class, code and crystal system. Can restrict to hydrated minerals

Matters

can filter by ID, UID, main type (currently mineral or fluid), name, reference, origin. Mineral family, type, rock type and texture. Fluid family and type.

Solutions

can filter by ID, UID, type and name

[edit] Sample data

Samples

can filter by sample ID, UID, name, generic and processing type; Layer type and formation mode; Material ID, matter origin and family; Constituent ID, phase type and compound; Species type, formula, name, code and relevance

Layers

can filter by layer ID, UID, type, texture, formation mode; Material number and mixing

Materials

can filter by material ID, UID, name; Matter origin and family; Constituent phase type and compound; Species type, formula, name, code and relevance

Constituents

can filter by constituent ID, UID, name, family, phase type and compound; Species type, formula, name, code and relevance

[edit] Spectral data

Experiments

can filter by:

- experiment ID and UID. Can include parent/sons experiments

- sample ID and UID. Can include parent/sons sample

- spectrum ID and UID. Can include parent/sons spectra

- experimentalist ID, UID and name

Spectra

can filter by:

- spectrum ID, UID, type, level, original file name. Can include parent/sons spectra

- spectrum dates: creation, update and validation

- validator name

- publication state

- sample ID

Band lists

can filter by:

- bandlist ID, UID, type and title,

- sample ID, UID and name

- constituent ID, UID, name, family, phase and arrangement

- species ID, UID, type, formula, name, code and relevance

[edit] Instrument data

Instruments

can filter by:

- instrument ID, UID, name, type, technique

- laboratory

Laboratories

can filter by:

- laboratory ID, UID, name/acronym

Experimentalists

can filter by:

- experimentalists ID, UID, name, status

- laboratory

[edit] Bibliography

Publications

can filter by:

- publication ID, UID, document type, publication state and year;

- author name;

- journal name, volume and first page

- publication content and keywords

[edit] Other data

OpenEnum

can filter by:

- keyword name

[edit] Import

Use specially formatted XML files for data import

- various validity checks are performed: xml format, enumerations, mandatory keywords, ...

- The simulation mode allow the debug of the file before import

Matter

Import matter(s)

Sample

Import a sample

Experiment & Spectra

Import an experiment and its spectra

Bandlist

Import bandlists and bands

[edit] Import history

List all imported data with link

- Import type, data IDs, Date, producer name

[edit] Help

go to 'Data providers documentation' page in wiki

- How to prepare step by step the XML files for the import of data in the GhoSST database

- General rules to fill data XML files

- How to import data with XML files

- XML import files: repository of the xml templates for:

Fundamental data imports

Species
Matters
Objects (for meteorites)
States (for bandlist)
Publications
Laboratory / Experimentalists
Instruments

Data imports

Samples
Experiments + instrument parameters + spectra
Band lists / bands

[edit] Manager

Restricted to database manager

[edit] Users

Allow to:

- list the users information: ID, name, organization, laboratory, city, country, users type and status

- edit and change users type and status

[edit] OpenEnums

Management of the attribute of the OpenEnumerations

Search: list the attributes of the selected OpenEnum 'Keyword(s)'

- keyword, attribute value

Reset: unselect the 'Keyword(s)'
New: to create a new attribute of the selected OpenEnum 'Keyword'

- 'Create': create the attribute entered in 'Value'

- 'Cancel': exit the 'New' mode

[edit] Import

Use specially formatted XML files for data import

- various validity checks are performed: xml format, enumerations, mandatory keywords, ...

- the simulation mode allow the debug of the file before import

Species

Import fundamental species (atoms, molecules, minerals, chemical functions, solutions)

Instruments & labs

Import instruments, laboratories and experimentalists

Publications

Import publications

States

Import molecule states

[edit] Import history

List all imported data with link

- Import type, data IDs, Date, producer name

[edit] User

Before login

[edit] Register

Allow to register as a GhoSST user

Ask for

- e-mail address and new password

- your first and last names

- Your organization, Laboratory/Division (optional), address (optional), city, country (list)

@@ Line 1: / Line 1: @@
-Access to the GhoSST interface: http://ghosst-prod.obs.ujf-grenoble.fr/
+Access to the GhoSST interface: http://ghosst.osug.fr/
 == General menu (upper left) ==
@@ Line 192: / Line 192: @@
 ::*; Species relevance (list)
 :::: choose one or more
-:'''''Results Tables:'''''
-:: The results are displayed in 2 tables ''''Spectrum'''' and ''''Bandlist''''
-:: They provide synthetic information on:
-::: - '''''ID''''': product ID
-::: - '''''Type''''': product type
-::: - '''''Title''''': product title describing its major features (composition, temperature, spectral range, ...)
-::: - '''''Sample''''' (for spectrum): description of the sample
-::: - '''''Primary constituent''''' (for bandlist): composition of the constituent containing the primary molecular species of the bandlist
-::: - '''''Primary species''''' (for bandlist): the band list contains the bands information of this specific (isotopic) species in the above constituent
-::: - '''''Spectral range min./max.''''': limits of validity of the product (in the unit you specified in search)
-::: - '''''Sample temperature''''': in K
-::: - '''''Species''''' (for spectrum): list of the species contained in the sample
-:'''''Icons:'''''
-:::- ''''''box' icon''''': allows to send directly the product in the 'shoping basket'
-:::- ''''''magnifer' icon''''' (for spectrum): display a *** of the spectrum
-:::- ''''''table' icon''''': go to product informations with interactive display of spectrum
 -----
@@ Line 596: / Line 577: @@
 ::::: -	‘fluorescence emission efficiency’:
+-----
-:'''''Results Tables:'''''
+=== Search result Tables ===
-:: The results are displayed in 2 tables ''''Spectrum'''' and ''''Bandlist''''
+:: The search results are displayed in 2 tables ''''Spectrum'''' and ''''Bandlist''''
 :: They provide synthetic information on:
 ::: - '''''ID''''': product ID
@@ Line 613: / Line 595: @@
 :'''''Icons:'''''
 :::- ''''''box' icon''''': allows to send directly the product in the 'shoping basket'
-:::- ''''''magnifer' icon''''' (for spectrum): display a *** of the spectrum
+:::- ''''''magnifer' icon''''' (for spectrum): display a small plot of the spectrum
 :::- ''''''table' icon''''': go to product informations with interactive display of spectrum
+-----
+=== Spectrum graph & info ===
+: accessed from the 'table icon' in the search result table
+==== Graph ====
+: display the graph in its original unit
+::* Legend:
+::* Settings:
+:::: - Errors:
+:::: - Infos:
+:::: - Unit:
+:::: - Color(s): 'intensity' or 'n' and 'k'
+::* Zooms:
+:::: - Full range
+:::: - Valid range
+::* Navigation:
+:::: - Vertical zoom: Click + Mouse move (Up or Down)
+:::: - Horizontal zoom: Click + Mouse move (Left or Right)
+:::: - Zoom out: Click
+:::: - Zoom reset: Double Click
+:::: - Pan: [SHIFT] + Click + Mouse move (Up, Down, Left or Right)
+==== Spectrum info ====
+-----
+=== Sample info ===
+: the sample info is structured in several levels:
+::*; Sample
+::*; Layer(s)
+::*; Material(s)
+::*; Constituent(s)
+::*; Specie(s)
 -----
@@ Line 913: / Line 943: @@
 :: Allow to logout
+-----
+-----

GhoSST user manual

Latest revision as of 10:39, 2 September 2014

Contents

[edit] General menu (upper left)

[edit] Before login

[edit] Home

[edit] Search

[edit] Login

[edit] After login

[edit] Home

[edit] Search

[edit] Data

[edit] Producer (restr.)

[edit] Manager (restr.)

[edit] User

[edit] Information menu (Bottom of page)

[edit] Documentation

[edit] Contact

[edit] History

[edit] Credits

[edit] Statistics

[edit] Search

[edit] Simple Search

[edit] Guided Search

[edit] Advanced Search

[edit] Search result Tables

[edit] Spectrum graph & info

[edit] Graph

[edit] Spectrum info

[edit] Sample info

[edit] Data

[edit] List

[edit] Species

[edit] Sample data

[edit] Spectral data

[edit] Bibliography

[edit] Export

[edit] Producer

[edit] Full search

[edit] Species and Matters data

[edit] Sample data

[edit] Spectral data

[edit] Instrument data

[edit] Bibliography

[edit] Other data

[edit] Import

[edit] Import history

[edit] Help

[edit] Manager

[edit] Users

[edit] OpenEnums

[edit] Import

[edit] Import history

[edit] User

[edit] Register

[edit] Login

[edit] Information

[edit] Export History

[edit] Logout

Personal tools

Namespaces

Variants

Views

Actions

Search

Navigation

Toolbox