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By selecting “Show samples” from the left panel, a list of available molecular entries appears.
Each entry is hyperlinked; selecting the molecular name provides access to its associated dataset.
For targeted searches, the query box (located at the top of the interface) accepts either full or partial molecular formulas and/or common names.
Once the results are displayed, the dataset may be ordered by interacting with the column headers (e.g., name, version identifier, or acquisition date).
Multiple dataset versions may exist for a single molecule. These versions may arise from distinct experimental measurements, modifications to the experimental conditions, or alternative post-processing and analysis procedures (“Versions”).
The availability of datasets is conditional upon the user’s access level. By default, only data published in peer-reviewed literature is accessible.
Trusted users having committed to a non-disclosure agreement may be allowed to see also preliminary/unpublished datasets.
At the top-left of each molecular entry page, a drop-down menu lists all dataset versions associated with the selected species. Each version corresponds to a distinct set of molecular data, structured across multiple tabs.
Version identifiers follow the notation:
"X.Y.Z commentary" with
X - experimental dataset
Y - data reduction (e.g., continuum subtraction)
Z - spectral band analysis
Commentary - optional annotation (e.g., Reference)
The “info” panel provides general metadata about the selected dataset, including:
Species under analysis
Instrument and settings used
Sample information
Date and location of the measurements
Responsible for measurements
Etc…
Additional details may be revealed/hidden by clicking on "Information" or "Instruments".
This panel displays a 3D representation of the selected molecule.
This panel grants access to the full recorded spectra across all experimental temperatures.
A single representative spectrum is displayed by default, more are shown by clicking on “Show full spectra for all temperatures”. If multiple temperatures are present, it can be changed here. This change will also affect the “over-plot” spectrum.
This table lists the vibrational bands which have been analysed in detail. The label corresponds to the wavenumber range of the band. It can be hidden if empty. For example, theoretical data may not have analysis.
Selecting a specific wavenumber provides access to the corresponding band analysis.
Each band is displayed as a function of temperature, with spectra color-coded from low (blue) to high (red) temperatures.
A results table provides information on the outcomes of the multi-components fits, including the evolution of position and of full width at half maximum (FWHM), and integrated area across temperatures.
Below the table, we found spectra of this band and their decomposition across temperatures. Components can be interactively shown or hidden via checkboxes.
A summary of the empirical anharmonicity parameters χ (as defined in Pech et al., A&A 388, 639–651 (2002)) for each band is reported. It can be hidden if no analysis is present as, for example, for some theoretical data.
The Over-plot tab enables spectral comparison by overlaying selected spectrum (at the temperature selected in the "Full spectrum panel") with:
Other datasets within this database (use URL)
The Theoretical Spectral Database of Polycyclic Aromatic Hydrocarbons (use URL)
NASA AMES PAH IR Spectroscopic Database (use URL)
User-uploaded spectra or mode files
When a mode file accompanies the spectrum, vibrational mode assignments are automatically displayed, with the option to toggle their visibility.
It is also possible to get the URL of the figure to save it.
The dimension can be changed by dragging the “+” at the bottom-right corner of the figure.
The label threshold is here to limit the number of vibrational modes displayed. The FWHM is used to convolve spectra constituted of a list of vibrational mods.
Scaling factor is used to realign spectra.
Data may be exported through the "Export" panel. After selecting the desired elements, the user may click on "download". That produces a compressed archive (.zip). This archive typically contains:
AstroModel files: inputs for modeling applications (only if presents),
Anharmonicity tables: tables with empirical anharmonicity parameters,
Infos file: metadata associated with the dataset,
Fullspectra folder: recorded spectra across experimental temperatures,
Bands folder: organized by wavenumber, each containing the results file and associated spectra.
Alternatively, data may be retrieved manually:
Template on the "infos" panel for the metadata,
Fullspectra from the panel "Full spectrum" --> "Show full spectra for all temperatures", zip link,
Bands spectra/results from "Analysis bands & multi-fit" --> click on a wavenumber, zip link.
Public datasets can also be extracted programmatically using structured URLs of the form:
https://www.cosmicpah-irdb.ovgso.fr/science/<Molecule name>/<Phase>/<TYPE>/file/<Flags>
<Molecule name> Like Pyrene
<Phase> Gas, Solid...
<Type> “Experimental” or “e” for experimental data else theoretical data
<Flags> Composed of 5 letters: First for full spectra, second for bands spectra, third for detailed band analyes, fourth for anharmonicity tables, and fifth for astroModels. Exemple: .../Pyrene/Gas/0/file/ttttt for downloading everything; .../Pyrene/Gas/0/file/tffff only the full spectra
The data extracted will be the one marked as "Reference" version or a public version if no "Reference" is found.
JSON file is generated if the required dataset exist
https://www.cosmicpah-irdb.ovgso.fr/machine/<Molecule>/<Phase>/<Type>/<Name>
<molecule> chemical formula: C16H10 ; or name of the molecule;chemical formula: Pyrene;C16H10.
<Phase> Gas, Solid ... or All.
<Type> “Experimental” or “e” for experimental data else theoretical data
<Name> Must start with Reference or Publication. The name corresponds to the version commentary to specify a publication the specific commentary can be written.
Example: https://www.cosmicpah-irdb.ovgso.fr/machine/C16H10/e/Publication
If <Name> is 0, a list of molecules and their links is returned. All the fields can be filled with 0 to generate a list of all the entries and then all fields can be added as filters.
Example: https://www.cosmicpah-irdb.ovgso.fr/machine/0/0/e/0
Return all the experimental entries available in the following format:
{<Molecule_Name >;<Molecule_formula >:{<Phase >/<Type >:{<Version >:<MachineURL >},
{<Version2>:<MachineURL2>}},
{<Phase2>/<Type2>:{<Version3>:<MachineURL3>}}},
{<Molecule_Name2>;<Molecule_formula2>:{<Phase3>/<Type3>:{<Version4>:<MachineURL4>}}}
Data ingestion requires user authentication. The ability to create or modify entries depends on the assigned access level:
Guest - Editing private entries if explicitly designated as an editor.
Contributor - Same as Guest + Adding new dataset versions to existing entries
Collaborator - Same as Contributor + adding new species, new versions, new instruments
Administrator - unrestricted access to all data, including private entries; full editing rights for species and instruments.
Requests for access-level changes must be directed to system support see contact.
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Collaborators must first ensure that all instruments are correctly registered in the database. If an instrument is absent, it must be added manually, or support should be contacted to modify existing records.
Metadata is divided into two categories:
Extrafield: variables of the instruments. Separator must be ", "
Fixedfield: static instrument attributes. Format must follow: "FieldName: Value" and separator still is ", " so no "," is allowed on FieldName or Value.
Extrafield containing file in the name will accept the ingestion of the file. More specifically the “Output file” is designed for AnharmoniCaOs proclogfile.
New molecular species can be introduced. In the case where the species to be added already exists a new version will be created instead.
For the following step it is the same as for contributors so see below.
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Contributors are authorized to add new dataset versions to existing species. This is achieved via the Version button at the top of the entry page.
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Editors of a private dataset, can update the information on this datasets.
Structure- requires a link to a picture to be shown
Phase- select an existing phase or define a new one via "New phase"
Editors- the list of editors can be updated, while clicking on this entry a list of users appears. Users can be searched by tapping some letters on the keyboard.
Visibility- must remain on Private until all entries are complete and validated. Edition is only possible on Private for most of the entries
Instruments- added via the "Add instrument".
All modifications must be saved by using the Update button.
In case of inconsistencies, contact support.
The 3D model is automatically queried from the theoretical spectral database of polycyclic aromatic hydrocarbons. But if the structure is not correct or a different conformer is wanted, it can be updated by uploading a file or giving the .cml URL of the structure. .xyz and .cml are accepted.
To edit the spectra, click on "Full spectrum" → "Show full spectra for all temperatures" → upload your file of raw data in .dpt or .txt. The filenames must follow the format: <name>_<temperature>K_<comentary>.txt.
Example: pyrene_2021_100K_v1.dpt.
The minimum required is _<temperature>K.txt
Multiple files can be deposited at once. The uploaded file will be saved no additional updates are required. Uploaded file can be downloaded just after.
Navigation to the previous page can be done by clicking on the name of the molecule on top of the page. The displayed (Over-plot) and default (Anharmonicity parameters) temperatures can be changed from this previous page
To add a band: enter the band wavenumber and click "Add"; Click on the band wavenumber to access the band's analysis.
Upload of the band spectra and the results file is possible with "Click here to Upload…" The files must end with .dpt or .txt,
<name>_<temperature>K_<commentary>.txt Example: pyrene_2021_100K_v1.dpt. The minimum required is _<temperature>K.txt
The results file must be in .csv. Each new results file erased the previous version.
All files can be uploaded at the same time.
The update is made immediately after the upload. No additional update is required.
The molecule name can be used as a link to the previous page.
All information may be ingested at the same time by uploading a structured zip file or all individual files at the same time by using "Click here to upload everything...".
A template is proposed on the main page of any molecule. This template is a summary of the "infos" panel. Fields can be modified in this file, but the filename must remain unchanged.
To upload all the spectra from here, the file names must follow the same format as before. For band spectra the <name> must start with 'B<wavenumber>' or 'b<wavenumber>' as in 'B711'. So for full spectrum the name must not start with 'b' or 'B'.
Example: Full spectra: Pyrene_C16H10_ID10_323K.txt; Band spectra B711_Pyrene_C16H10_ID10_323K.txt.
The minimums are: Full spectra _<temperature>K.txt; Band spectra: B<wavenumber>_<temperature>K.txt;
Uploaded result files of all bands must be in the format results_B<wavenumber>_<name>.csv .
For example: "results_B711_Pyrene_C16H10_ID10.csv"
The structure of the zip file is free as long as there is no other txt/dpt/csv file in the zip file and the format names are respected.
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