GhoSST user manual

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Access to the GhoSST interface: http://ghosst-prod.obs.ujf-grenoble.fr/
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Access to the GhoSST interface: http://ghosst.osug.fr/
  
 
== General menu (upper left) ==
 
== General menu (upper left) ==
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:*; List (currently in Data)
 
:*; List (currently in Data)
 
 
-----
 
-----
 
  
 
=== Simple Search ===  
 
=== Simple Search ===  
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-----
 
-----
 +
 
=== Guided Search ===
 
=== Guided Search ===
  
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::*; Species relevance (list)
 
::*; Species relevance (list)
 
:::: choose one or more
 
:::: 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
 
  
 
-----
 
-----
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::::: - ‘fluorescence emission efficiency’:
 
::::: - ‘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:
 
:: They provide synthetic information on:
 
::: - '''''ID''''': product ID
 
::: - '''''ID''''': product ID
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:'''''Icons:'''''
 
:'''''Icons:'''''
 
:::- ''''''box' icon''''': allows to send directly the product in the 'shoping basket'
 
:::- ''''''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
 
:::- ''''''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)
  
 
-----
 
-----
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:*; Publication
 
:*; Publication
 
::: can filter by document type, publication state and year, author name, journal name, volume and first page, content and keyword
 
::: can filter by document type, publication state and year, author name, journal name, volume and first page, content and keyword
 +
 +
-----
  
 
=== Export ===
 
=== Export ===
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::: can filter by:
 
::: can filter by:
 
:::: - keyword name
 
:::: - keyword name
 +
 +
-----
  
 
=== Import ===
 
=== Import ===
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::*; Bandlist
 
::*; Bandlist
 
::: Import bandlists and bands
 
::: Import bandlists and bands
 +
 +
-----
  
 
=== Import history ===
 
=== Import history ===
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:: List all imported data with link
 
:: List all imported data with link
 
::: - Import type, data IDs, Date, producer name
 
::: - Import type, data IDs, Date, producer name
 +
 +
-----
  
 
=== Help ===
 
=== Help ===
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:: - edit and change users type and status
 
:: - edit and change users type and status
  
 +
-----
  
 
=== OpenEnums ===
 
=== OpenEnums ===
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::: - 'Create': create the attribute entered in 'Value'
 
::: - 'Create': create the attribute entered in 'Value'
 
::: - 'Cancel': exit the 'New' mode
 
::: - 'Cancel': exit the 'New' mode
 +
 +
-----
  
 
=== Import ===
 
=== Import ===
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::*; States
 
::*; States
 
::: Import molecule states
 
::: Import molecule states
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 +
-----
  
 
=== Import history ===
 
=== Import history ===
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::: - Your organization, Laboratory/Division (optional), address (optional), city, country (list)
 
::: - Your organization, Laboratory/Division (optional), address (optional), city, country (list)
 
::*; 'Register': to validate your registration
 
::*; 'Register': to validate your registration
 +
 +
-----
  
 
=== Login ===
 
=== Login ===
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::: - user + password
 
::: - user + password
  
 
+
-----
  
 
*; After login
 
*; After login
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:: Allow to change your personal information and login password
 
:: Allow to change your personal information and login password
+
 
 +
-----
 +
 
 
=== Export History ===
 
=== Export History ===
  
 
: Log of all exported data, with link
 
: Log of all exported data, with link
 
::: - Import type, data IDs, export date
 
::: - Import type, data IDs, export date
 +
 +
-----
  
 
=== Logout ===
 
=== Logout ===
  
 
:: Allow to logout
 
:: Allow to logout
 +
 +
-----
 +
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Latest revision as of 09:39, 2 September 2014

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

Contents

[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)
  • 'Register'
    to validate your registration

[edit] Login

To login as a registered user in Ghosst
- user + password

  • After login

[edit] Information

Allow to change your personal information and login password

[edit] Export History

Log of all exported data, with link
- Import type, data IDs, export date

[edit] Logout

Allow to logout


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