1 / 40

Nomenclature and Terminology - Standards for Materials and Processes

Nomenclature and Terminology - Standards for Materials and Processes. Jeremy G. Frey and Mark I. Borkum Chemistry, University of Southampton. Digital Chemistry. Reducing and Managing Uncertainty Chemistry 2.0 (or 3.0). Overview. Nomenclature & Terminology Materials and Processes

jbaxter
Download Presentation

Nomenclature and Terminology - Standards for Materials and Processes

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Nomenclature and Terminology - Standards for Materials and Processes Jeremy G. Frey and Mark I. Borkum Chemistry, University of Southampton

  2. Digital Chemistry Reducing and Managing Uncertainty Chemistry 2.0 (or 3.0)

  3. Overview • Nomenclature & Terminology • Materials and Processes • Human and Computer “readable” Jeremy Frey and Mark Borkum

  4. A Chemist’s Digital Aura http://mosaically.com/PhotoMosaic/3289771f-0bf3-49bf-bc8a-1810167096ff

  5. Definitions • Terminology • A set of names for things • Nomenclature • The rules for determining the name(s) for a given thing • Ontology • The rules for interpreting the name(s) for a given thing Jeremy Frey and Mark Borkum

  6. IUPAC Green Book Jeremy Frey and Mark Borkum

  7. Materials & Mixtures • Mixtures are complex • Process description • What went in • How was it processed • Characterization • Identify and describe final components • Related to two types of polymer nomenclature Jeremy Frey and Mark Borkum

  8. Computers and People • Computer must be able to process the descriptions • But also need to be consumable (if indirectly) by people Jeremy Frey and Mark Borkum

  9. Example #1 IUPAC InChI • Terminology • The set of expressible IUPAC InChIs • Nomenclature • Conversion of a chemical structure to an InChI • Ontology • Interpretation of an InChI as a chemical structure Jeremy Frey and Mark Borkum

  10. Example #2 RSC ChemSpider ID • Terminology • Natural numbers • Nomenclature • Given a chemical structure, usehttp://www.chemspider.com/Search.asmx?op=Mol2CSID • Ontology • Given an RSC ChemSpider ID, usehttp://www.chemspider.com/Search.asmx?op=GetCompoundInfo Jeremy Frey and Mark Borkum

  11. Example #3 IUPAC InChI  RSC ChemSpider ID • http://www.chemspider.com/InChI.asmx?op=InChIToCSID • RSC ChemSpider is a very large database, but it is not infinite • Some conversions fail because no matching database records are found • Other conversions fail because the IUPAC InChI is “invalid” Jeremy Frey and Mark Borkum

  12. Example #4 QRCode  HTTP-URL  RSC ChemSpider ID • http://www.chemspider.com/CSID Identity provider (resolution service) Identity token Jeremy Frey and Mark Borkum

  13. Overview • Nomenclature • Processes Jeremy Frey and Mark Borkum

  14. Definitions • Process • A directed graph of entities, activities and agents • Entities • A thing • Activity • A user and/or generator of an entity • Agent • A performer of an activity Jeremy Frey and Mark Borkum

  15. Examples of Processes • Scientific experimentation • Business • Art • Cooking Jeremy Frey and Mark Borkum

  16. Description • To describe a process, we have to fix our temporal perspective, either • Prospective • Forward looking; describing things that will happen (in the future); a plan • Retrospective • Backward looking; describing things that have happened (in the past); an enactment Jeremy Frey and Mark Borkum

  17. Provenance • The 7 W’s (see Zachman 1987, Goble 2002) • Agent-centred Who • Entity-centred What • Activity-centred Where, when, (w)how • Intent-centred Which, why Jeremy Frey and Mark Borkum

  18. W3C PROV http://www.w3.org/TR/prov-primer/images/key-concepts.png Jeremy Frey and Mark Borkum

  19. (I Can’t Get No) Satisfaction • Relating prospective and retrospective descriptions enables inference, e.g., • Does the retrospective description meet the requirements of the prospective description? • Does the retrospective description exceed the requirements of the prospective description? • Are there multiple retrospective descriptions for the same prospective description? Jeremy Frey and Mark Borkum

  20. Improvisation ≠ Deviation • Improvisation • A retrospective description that is not associated with a prospective description • Deviation • A retrospective description that is associated with, but does not comply with, a (possibly empty) prospective description Jeremy Frey and Mark Borkum

  21. Use Case #1 Risk Assessment • Idea • Use the prospective description of a scientific experiment to complete a risk assessment form • Requirements • Chemical information database • Health and safety information database Jeremy Frey and Mark Borkum

  22. Red square = Chemical substance Orange square = Mixture part Green square = PPE product, e.g., gloves Blue square = GHS hazard category Jeremy Frey and Mark Borkum

  23. 1) Load Web Application “Generate” button is disabled Jeremy Frey and Mark Borkum

  24. 2) Describe Scientific Experiment Dynamic searchwith auto-completion Jeremy Frey and Mark Borkum

  25. 2) Describe Scientific Experiment Selected product is added to list Link to Sigma-Aldrich product page Jeremy Frey and Mark Borkum

  26. 3) Select Template List of Templates Jeremy Frey and Mark Borkum

  27. 4) Accept Terms and Conditions “Generate” button is enabled Jeremy Frey and Mark Borkum

  28. Editable text fields for “Physical Form” and “Quantity” One row per product Editable text area for “Nature of Process” The University requires that assessment forms are printed and signed Jeremy Frey and Mark Borkum

  29. eCrystals • http://ecrystals.chem.soton.ac.uk • Repository for crystal structure determinations • Operated by EPSRC National Crystallography Service (NCS) • Based at the University of Southampton Jeremy Frey and Mark Borkum

  30. Plan for eCrystals • Structure determination workflow is described by a plan (right) • Available online @http://ecrystals.chem.soton.ac.uk/plan.rdf Jeremy Frey and Mark Borkum

  31. Jeremy Frey and Mark Borkum

  32. eCrystal #643 • Each eCrystals record contains: • Bibliographic metadata • Fundamental and derived data (excluding raw images) • Final structure solution Jeremy Frey and Mark Borkum

  33. eCrystal #643 (2) orechem:wasDerivedFrom Jeremy Frey and Mark Borkum

  34. SPARQL –“Raw, Derived and Reported” Jeremy Frey and Mark Borkum

  35. eCrystal #643 (3) ?run ?reported ?derived ?raw orechem:wasDerivedFrom Jeremy Frey and Mark Borkum

  36. Use Case #4 ELNs • Idea • An ELN as the front-end for a database of both prospective and retrospective descriptions of scientific experiments Jeremy Frey and Mark Borkum

  37. Vision LIMS Risk assessment (maps) Location Retrospective description of process (enactment) Instance Shopping basket Row ELN Product Prospective description of process (plan) Procurement Substance CIMS My PhD Risk assessment (forms) Health and safety Jeremy Frey and Mark Borkum

  38. Smart Tea Jeremy Frey and Mark Borkum

  39. Formulation • We can describe many (but not all) compounds. • We need to agree on a set of processing terms to describe the “formulation” process? • Map these to an “vocabulary” and possibly an ontology • But consider regulatory requirments Jeremy Frey and Mark Borkum

  40. Thank you for listening Trust me Mort - no electronic communications superhighway, no matter how vast and sophisticated, will ever replace the art of the schmooze

More Related