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WP6 – JRA1 - Interoperability

WP6 – JRA1 - Interoperability. WP6 – JRA1 - Interoperability. Data Models and XML Schema Dictionaries Query / Retrieval Languages Registries Other Documents. Data Models and XML Schema. XSAMS currently at v0.1.1 Now has Version Control (Subversion) Sourceforge repository:

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WP6 – JRA1 - Interoperability

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  1. WP6 – JRA1 - Interoperability

  2. WP6 – JRA1 - Interoperability • Data Models and XML Schema • Dictionaries • Query / Retrieval Languages • Registries • Other Documents

  3. Data Models and XML Schema • XSAMS currently at v0.1.1 • Now has Version Control (Subversion) • Sourceforge repository: http://xsams.svn.sourceforge.net/viewvc/xsams/ • Bug-tracking • Forum

  4. XSAMS version control nist-branch vamdc-working TRUNK Jan 2011 v0.1.1

  5. XSAMS version control v1.0 nist-branch vamdc-working TRUNK Jan 2011 v0.1.1

  6. Status at v0.1.1 (Nov 2010) Sources Methods • Sources • Methods • Functions • States • Atoms • Molecules • Solids • Particles • Processes • Radiative • Non-radiative • Collisions Functions Atoms Molecules Solids Particles Radiative Non-radiative Collisions

  7. Database compatibility with XSAMS v0.1.1 • HITRAN / HITEMP ✚ • VALD ✚ • BASECOL ✔ • CHIANTI ? • CDMS / JPL ✚ • TCSD – PAHdb✗ • Stark B ✚ • UDFA ✔ • NIST – Atoms ✔ • NIST – Diatomics / Triatomics✚

  8. XSAMS v0.1.1: What’s missing? • Line Broadening and Shifting • Environments • Absorption Cross Sections • Partition Functions • Molecular States (case-by-case?) • Molecular Structure • PAH Stuff: Normal Modes, Rotational Constants, etc.

  9. vamdc-working branch: XSAMS Proposal • Workshop #4: Vienna, Feb 16-18 2011 AsifAkram (UCAM) MishaDoronin (LPMAA) Christian Endres (Köln) Christian Hill (UCL) Theresa Lueftinger (Vienna) Thomas Marquart (UU) LjerkaNenadovic (LPMAA) Nikolai Piskunov (UU) Guy Rixon (UCAM) Tanya Ryabchikova (INASAN) Ken Smith (QUB)

  10. Database compatibility with XSAMS v0.1.1 • HITRAN / HITEMP ✚ • VALD ✚ • BASECOL ✔ • CHIANTI (✔) • CDMS / JPL ✚ • TCSD – PAHdb✗ • Stark B ✚ • UDFA ✔ • NIST – Atoms ✔ • NIST – Diatomics / Triatomics✚

  11. Database compatibility with vamdc-working • HITRAN / HITEMP ✔ • VALD ✔ • BASECOL ✔ • CHIANTI (✔) • CDMS / JPL ✔ • TCSD – PAHdb✚ • Stark B (✔) • UDFA (✔) • NIST – Atoms ✔ • NIST – Diatomics / Triatomics(✔)

  12. XSAMS – Future work • Implement for other databases • PAHs still need some work • Clean up and comment Schema documents • Documentation and examples • Test, debug, refine • Seek ratification by the XSAMS Steering Committee for v1.0 (by June?)

  13. Dictionaries • Keywords for: • RESTRICTABLES Quantities that can restrict a search (e.g. by species name, wavelength range, transition intensity) • RETURNABLES Quantities returned by a database query that map to the entires in a XSAMS document • Maintained by Thomas Marquart at: http://vamdc.tmy.se/dict/

  14. Dictionaries • Unique Species Identifier: InChI • InChI: IUPAC International Chemical Identifier – e.g. Ethanol: InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3 16O13O17O: InChI=1S/CO2/c2-1-3/i1+1,2+0,3+1 • Constructed in layers: 1. Main Layer: Chemical Formula, Atom connections, Hydrogen atoms 2. Charge Layer 3. Stereochemical Layer 4. Isotopic Layer

  15. Dictionaries • Unique Species Identifier: InChIKey– an SHA-256 hash on the InChI string: e.g. • 12CH4: InChI = 1S/CH4/h1H4/i1+0H4 InChIKey = VNWKTOKETHGBQD-XDMSWEHDSA-N • 13CH4: InChI = 1S/CH4/h1H4/i1+1H4 InChIKey = VNWKTOKETHGBQD-MRWQJCQWSA-N • 12CH3D: InChI = 1S/CH4/h1H4/i1+0DH3 InChIKey = VNWKTOKETHGBQD-DWJDBXPTSA-N

  16. Dictionaries – Future Work • Keywords for: • REQUESTABLES Refine what can be requested from a database node (e.g. Species, States, Collisions, RadiativeTransitions) • Dictionaries for quantities not dictated by the XSAMS Schema: • Meta-data explaining the meaning of and restrictions on molecular quantum numbers (case-by-case) • Allowed “OtherProperties” named by attribute and their meaning (e.g. AnharmonicityMatrix)

  17. Dictionaries – Future Work • Who will complete the dictionaries? • Standard VAMDC units for physical quantities

  18. Registry • Lists the VAMDC database nodes and their capabilities • Maintained by Guy Rixon at http://casx019-zone1.ast.cam.ac.uk/registry/main/index.jsp

  19. Query / Retrieval Languages • TAP-XSAMS and VSS1: VAMDC SQL Sub-set v.1 • Based on SQL92 syntax • MUST be a SELECT statement • MUST NOT contain ALTER, DROP, REPLACE, etc. statements • Database column names taken from the VAMDC dictionary of keywords • Implemented by VALD, HITRAN, BASECOL, CDMS, Chianti, …

  20. Query / Retrieval Languages – Future Work • VSS2: Implement REQUESTABLES • In development – RESTRICTABLE Prefixes e.g. reactant1.AtomIonCharge = +2 upper.StateEnergy < 10000 • How do we handle units?

  21. Future work for WP6 • Solid and surface spectroscopy… • Documentation • Implementation • Testing • Propose vamdc-working XSAMS to the IAEA XSAMS Steering Committee

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