Prepared for RDA 8th Plenary Denver, 2016 Gary Berg-Cross

1. Domain Vocabulary Development, Standardization, Registration, Harmonization and Support BoF Breakout 8 – Saturday 17 Sept 11:00 - 12:30. Prepared for RDA 8th Plenary Denver, 2016 Gary Berg-Cross

2. Domain Vocabulary BoF Session Agenda • Facilitating Domain Vocabulary Development & Harmonization • A few words & illustrations about Conceptual Models & Tools - Gary Berg-Cross • Domain Discussion - Each domain group can provide a brief summary of their work such as: • Relevant vocabularies, models & ontologies, standards and • An illustrative use case such as harmonization and mappings between 2 or more vocabularies and issues involved. • Community discussion regarding the state of: • Vocabulary development, formalization, harmonization, infrastructure • Common interests such as vocabulary development & services, • issues and best practice solutions in the domain vocabulary space General Discussion & ideas in follow up work & plan for follow up virtual meetings and session at P9

3. Facilitating Domain Vocabulary Development & Harmonization      What Problem(s) are we trying to help with? Help systematize the already large body of domain definition work on terms and their meaning using a rationalized “consensus” knowledge of domain experts, especially as involved in RDA’s efforts. Part of this task is clarifying the alternate representation of implicit ideas in people's interpretation to reasonably reflect the types of entities found in reality. • Current vocabularies deal with data topics but we could extend the discussion Strategy - Start with a BoF to facilitate discussion and understanding of where groups are, what goals they have and what challenges we face. Leverage existing discussion and work such as vocabulary services to improve the quality of definitions and access e.g. common functionality for vocabulary publication services

4. General Heterogeneity Issue with Vocabularies There are some cases with dozens and dozens of local standards for data making integration a challenge Various types of standards are, for the most part, heterogeneous, meaning they: -are mostly fragmented and disconnected, describing things like surface or groundwater which: - lack a foundational grounding. – use the same or similar terms but with differences in semantics. (Illustrated in Simon's Key Note that included the term “soil”) – are described using different formal (or non-formal) languages. When pairwise mapping is attempted it runs into N2 issue. Something like a hub and spoke solution using a more expressive model/schema is desirable

5. Ontology and Vocabulary Space Vocabulary Knowledge of semantic relations between terms requires world knowledge about the relations between the objects that the terms refer to. You can't determine the semantic relations between the words “Denver” and “Colorado” unless you know that Denver is a part (a special part) of Colorado in the world. (“Standard”) Terms Metadata Tags/Annotations Ontologies Naming schemes often suggest some implied semantics. “Descriptions are more or less purposeful and theory-laden. Pharmacologists, for example, in their description of chemicals, emphasize the medical effects of chemicals, whereas "pure" chemists emphasis other things such as their structural properties.” Semantics and Knowledge Organization, Birger Hjørland

7. Other RDA work, GeoSpatial IG for example provides advice: “How open are we, really” by Gahegan & Adams Who can use it? Why was it made? Of Tasks and Domains What is it?

8. Illustrative Science Scenario: from BiG CZ SSI - all co-located soil microbial community and trace gas flux measurements  • In order to examine the relationship between soil microbial communities and trace gas fluxes across the soil-atmosphere interface, I want to collect all co-located measurements of these two kinds. • I want to limit my database to only those that were collected in the same ecosystem or vegetation type within 1 mile of each other, and within 2 years of each other. • If there are multiple measurements of both types, I want them paired by first closeness in terms of distance, and then by closeness in terms of time.....etc.

9. Finding Related Term and Concepts Some emerge during Science Scenario development Trace Gases list (sub-types Biotic and abiotic) “Trace gas flux” component “Flux NH+ 4” “Trace gas flux” component “Flux NO− 3” • ……………….methane, CH4, non-methane hydrocarbons (NMHCS), sulfur gases, Isoprene, Monoterpenes, Nitrous oxide,Ammonia, Carbonyl sulfide  (COS), DMS, C2H6, H2CO, CH3  …..

10. Additional Examples of Knowledge Sources“Trace Gas Emissions by Plants” Sharkey et al, 1991 Need NLP to extractrelevant “info/knowledge” from research articles.

11. Find Relevant Knowledge Base of Propositions -place like Cyc Microbes 101 which is Based in part on Carey et al, 2015 Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands and Dennis Baldocchi Lecture on Trace Gas Emissions from the Biosphere ESPM 228, Advanced Topics in Micrometeorology and Biometeorology April 27, 2012 • Soil microbial communities are an important component of ecosystem response to environmental change • Abiotic factors are non-biological factors & Abiotic soil properties are measured by observing soil moisture, temperature, pH, and inorganic N • Microbial functioning measured by nitrification and denitrification potentials & involves biotic factors, such as plant composition • plant-soil-atmosphere system interface is part of soil-atmosphere interface & soil microbial communities are part of the plant-soil-atmosphere system & play mediating ecosystem response roles • Biogenic trace gases emissions are caused by association with the biogeochemical cycles & Biogeochemical cycles subtypes [water and carbon, nitrogen, and sulfur compounds] cycles. • …..

12. Example- Attempts at Standard Radiation-Related Names atmosphere_clouds_radiation~incoming~shortwave__absorbed_energy_flux atmosphere_clouds_radiation~incoming~shortwave__absorptance atmosphere_clouds_radiation~incoming~shortwave__reflectance atmosphere_clouds_radiation~incoming~shortwave__reflected_energy_flux atmosphere_clouds_radiation~incoming~shortwave__transmittance atmosphere_clouds_radiation~incoming~shortwave__transmitted_energy_flux atmosphere_clouds_radiation~outgoing~longwave__emittance atmosphere_clouds_radiation~outgoing~longwave~downward__energy_flux atmosphere_clouds_radiation~outgoing~longwave~upward__energy_flux

13. Semanticscience Integrated Ontology (SIO)for research & knowledge discovery An ‘object’ is an ‘entity’ that occupies space and is fully identifiable by its characteristics at any moment in time in which it exists. A ‘process’ is an ‘entity’ that unfolds in time and has temporal parts. A ‘quality’ (intrinsic attribute), ‘capability’ (action specification) or ‘role’ (behavior, right and obligation)

14. SIO View of CSDMS Model Radiation-Related Names atmosphere_aerosol_radiation~incoming~shortwave__absorbed_energy_flux

15. Example of SIO Elements