Machine-Centric Science – Details, episodes & analysis

An interview about FAIR software, workflows, and virtual research environments (VREs) / science gateways with Sandra Gesing, currently a Senior Research Scientist and Scientific Outreach and Diversity, Equity, and Inclusion (DEI) Lead at the Discovery Partners Institute at the University of Illinois, Chicago.

• https://galaxyproject.org/
• https://dpi.uillinois.edu/
• https://sciencegateways.org/
• https://www.rd-alliance.org/groups/fair-virtual-research-environments-wg

https://doi.org/20.500.14132/chris -->
https://doi.org/20.500.14132/chris?noredirect -->
https://www.dona.net/team/christophe-blanchi

Digital Object Identifier Resolution Protocol (DO-IRP): https://www.dona.net/sites/default/files/2022-06/DO-IRPV3.0--2022-06-30.pdf

Materials Project (MP) website: https://materialsproject.org/

Novel Materials Discovery (NOMAD) Laboratory: https://nomad-lab.eu/

Contributor Roles Taxonomy: https://credit.niso.org/

Authentication resources (FAIR A1.2):
- https://portier.github.io/using.html
- https://github.com/simov/grant
- https://docs.konghq.com/

U.S. Department of Energy resources:
- Office of Scientific and Technical Information (OSTI) Data ID Service: https://www.osti.gov/data-services
- https://www.energy.gov/science/office-science-pure-data-resources

Connecting with Patrick:
- https://www.linkedin.com/in/tschaume/
- https://twitter.com/tschaume
- https://appliedenergyscience.lbl.gov/people/patrick-huck

The FAIR Implementation Profile (FIP) Ontology: https://w3id.org/fair/fip/terms/FIP-Ontology

Linked Open Vocabularies (LOV): https://lov.linkeddata.es/dataset/lov/

FAIRSharing: https://fairsharing.org/

PageRank of Linked Open Vocabularies (LOV): https://donnywinston.com/posts/pagerank-of-linked-open-vocabularies-lov/

Principles of Open Scholarly Infrastructure (POSI): https://openscholarlyinfrastructure.org/

https://www.w3.org/TR/prov-dm/#dfn-provenance

# Component 1: Entities/Activities:
Type: Entity
Type: Activity
Relation: Generation/Invalidation (E-Act)
Relation: Usage (Act-E)
Relation: Communication (Act1-[E]-Act2)

Relation: Trigger/Starter of Start of Act (trigger E, starter Act)
Relation: Trigger/Ender of End of Act End of Act (trigger E, ender Act)

# Component 2: Derivations:
Relation: Derivation (E-E, E-Act)

Relation: Revision (E-E)
Relation: Quotation (E-E)
Relation: Primary Source (E-E)

# Component3 : Agents, Responsibility, and Influence
Type: Agent
Relation: Attribution (E-Agt)
Relation: Association (Act-Agt (role), Act-E (plan))
Relation: Delegation (Agt-Act) - acted on behalf of

Relation: Influencer/Influencee ({E,Act,Agt}-[usage,start,end,generation,invalidation,communication,derviation,attribution,association,delgation]-{E,Act,Agt})

3 core types: entities, activities, agents. “instantaneous events” are put in context of activities.
wrt "time instants":
- generation is at instant of completion of production
- usage is at instant of beginning of utilization
- start, when activity is deemed started, is an instant
- end, when activity is deemed ended, is an instant
- invalidation is at instant of start of destruction, cessation, or expiry

10 influencing relations (not including 3 included subtypes of derivation - (1) [was] revision [of], (2) quotation ("was quoted from"), (3) [had] primary source).

The Creative Commons suite of licenses: CC0, CC BY, CC BY-SA, CC-BY-ND, CC BY-NC, CC BY-NC-SA, CC BY-NC-ND.

Code licenses: Server Side Public License, Affero GPL (AGPL), Lesser GPL (LGPL), Mozilla Public License (MPL), Business Source License (used e.g. by Sentry, <https://github.com/getsentry/sentry/blob/master/LICENSE>), Elastic License (for Elasticsearch), Apache 2.0, BSD, MIT. Spectrum of user freedom and redistributor freedom.

"The CRAPL: An academic-strength open source license": <https://matt.might.net/articles/crapl/>

* https://queryunderstanding.com
* http://contentunderstanding.com
* https://www.w3.org/TR/json-ld11-framing/
* https://www.w3.org/TR/shacl/
* https://jasonformat.com/islands-architecture/
* https://www.hydra-cg.com/spec/latest/core/

In the W3C Provenance Ontology:
https://www.w3.org/TR/prov-o/#wasDerivedFrom

The HTML Anchor Element:
https://developer.mozilla.org/en-US/docs/Web/HTML/Element/a

Heather Hedden, "Foundation for a Knowledge Graph Taxonomy Design Best Practices", slides at https://zenodo.org/record/6510205

Teodora Petkova, "The Dialogic Potential of the Web of Data", slides at https://zenodo.org/record/6518557

https://en.wikipedia.org/wiki/Bohm_Dialogue

Tim Berners-Lee's bag of chips

https://www.w3.org/TR/vocab-dcat-2/#Class:Dataset

https://schema.org/Dataset