MPS FAIR Hackathon IUPAC Gold Book Chemical Terminology

MPS FAIR Hackathon IUPAC Gold Book: Chemical Terminology Stuart J. Chalk Department of Chemistry, University of North Florida Titular Member, IUPAC Committee on Publications and Chemical Data Standards (CPCDS) schalk@unf. edu February 26 th, 2019

Outline IUPAC recommendations Development of the IUPAC Gold Book Compendium of Chemical Terminology IUPAC Project 2016 -046 -1 -024: Backup, Maintenance, and Redevelopment of the IUPAC Gold Book website Gold Book API The Future of the Gold Book

IUPAC Turns 100!

IUPAC Recommendations “IUPAC Recommendations are the output of IUPAC Projects or other studies on nomenclature, symbols, terminology, or conventions, and their purpose is to recommend unambiguous, uniform, and consistent nomenclature and terminology for specific scientific fields, usually presented as: glossaries of terms for specific chemical disciplines; definitions of terms relating to a group of properties; nomenclature of chemical compounds and their classes; terminology, symbols, and units in a specific field; classifications and uses of terms in a specific field; and conventions and standards of practice for presenting data in a specific field” – developed by chemical experts via consensus and through the formal IUPAC Inter-Divisional Committee on Terminology, Nomenclature and Symbols (ICTNS) process. https: //iupac. org/what-we-do/recommendations/

IUPAC Recommendations

IUPAC Recommendations

Development of the IUPAC Gold Book Initiated by Victor Gold in the early 1980’s Digital (XML) version of IUPAC Gold Book started in 2002 (Project 2001 -062 -2 -027) First version of the website in 2006 by Miloslav Nic, Jiri Jirat and Bedrich Kosata Last updated (before new project) in 2014

Current IUPAC Gold Book Website

Gold Book: Hydrocarbons

IUPAC Project 2016 -046 -1 -024: Backup, Maintenance, and Redevelopment of the IUPAC Gold Book website Dedicated administrator Files backed up at UNF and Git. Hub Update pages using PHP Scripts Correct any HTML formatting errors Convert pages to HTML 5 Cleanup/remove unnecessary code Update links for new content structure Add header metadata (dc ‘identifier’ & ‘description’) Add Google analytics tracking code

Anatomy of an IUPAC Gold Book Term From recommendations Preferred term Acronym Word class (4. ) Symbol Synonym Deprecated term Obsolete term Superseded term Definition of term Cross-referenced term Reference (related to definition) Note Example Related term(s) References (related to term) From the IUPAC Gold Book Contexts (’of’ or ‘in’) Also contains Related index Link map Digital Object Identifier (DOI) History of the term (online) Version https: //iupac. org/what-we-do/recommendations/guidelines-for-drafting-reports/

New Site – http: //dev. goldbook. iupac. org

IUPAC Project 2016 -046 -1 -024: Backup, Maintenance, and Redevelopment of the IUPAC Gold Book website REST API Machine-machine transfer/integration /terms/index/[all|A-W|XYZ]/[json|xml] /terms/view/[identifier]/[json/xml]/[download] /sources/index/[all]/[json|xml]/[download] /sources/view/[identifier]/[json/xml]/[download] Additional API endpoints will be added to serve the needs of the community

IUPAC Project 2016 -046 -1 -024: Backup, Maintenance, and Redevelopment of the IUPAC Gold Book website http: //dev. goldbook. iupac. org/terms/index/all/xml http: //dev. goldbook. iupac. org/terms/view/H 02889/json http: //dev. goldbook. iupac. org/terms/view/A 00381/xml http: //dev. goldbook. iupac. org/sources/index/all/xml http: //dev. goldbook. iupac. org/sources/view/106/json

The Future of the Gold Book Semantic Chemical Annotation Give meaning to chemical information Use the IUPAC Gold Book terms to define the meaning of things (knowledge representation)… …and allow reference to the meaning (DOI) Develop an IUPAC Chemical Ontology Build out the ontology with more terms from IUPAC Recommendations

Thanks to IUPAC Gold Book Project Task Group Greg Banik*, Brynn Hibbert, Mark Kinnan, Bonnie Lawlor, Leah Mc. Ewen*, Ron Weir* IUPAC Subcommittee on Cheminformatics Data Standards (SCDS) David Martinsen, Ian Bruno, Anthony Davies, Clàudio dos Santos, Chris Fellows, Jeremy Frey, Robert Lancashire, Andrey Yerin * Also on the SCDS

Questions? schalk@unf. edu Phone: 904 -620 -1938 Skype: stuartchalk Linked. In: https: //www. linkedin. com/in/stuchalk ORCID: http: //orcid. org/0000 -0002 -0703 -7776

Show and Tell on RDF Resource Description Framework Semantic Triples Subject (a thing) Predicate (relationship) Object (another thing OR literal) Basis of knowledge representation https: //www. w 3. org/RDF/

Java. Script Object Notation for Linked Data (JSON-LD) @context – aliases @id – unique id’s @type – data type @base – define the type of ‘thing’ that this file is about https: //www. w 3. org/TR/json-ld/

Equivalent RDF <http: //schema. org/Person/stuchalk> <http: //purl. org/dc/terms/identifier> "0000 -0002 -0703 -7776"^^<http: //www. w 3. org/2001/XMLSchema#string>. <http: //schema. org/Person/stuchalk> <http: //schema. org/name> "Stuart Chalk"^^<http: //www. w 3. org/2001/XMLSchema#string>. <http: //schema. org/Person/stuchalk> <http: //schema. org/worksfor> "University of North Florida"^^<http: //www. w 3. org/2001/XMLSchema#string>. <http: //schema. org/Person/stuchalk> <http: //xmlns. com/foaf/0. 1/mbox> "schalk@unf. edu"^^<http: //www. w 3. org/2001/XMLSchema#string>. https: //json-ld. org/playground/