Machine-Centric Science Transistor (https://transistor.fm) https://feeds.transistor.fm/machine-centric-science Stories about the FAIR principles in practice, for scientists who want to compound their impacts, not their errors. © 2025 Donny Winston 0756c418-0d3e-58e7-92ea-77bc02749e90 no What to expect from this podcast en-us Wed, 23 Jul 2025 10:34:48 -0400 Tue, 02 Dec 2025 18:45:18 -0500 https://img.transistor.fm/FfscbYjqNxIwHyFy7hPaeCuhvJ_cMULMJMYiMnFW7Sk/rs:fill:0:0:1/w:1400/h:1400/q:60/mb:500000/aHR0cHM6Ly9pbWct/dXBsb2FkLXByb2R1/Y3Rpb24udHJhbnNp/c3Rvci5mbS9zaG93/LzI4NTQ0LzE2NDU1/MzM1NjctYXJ0d29y/ay5qcGc.jpg Machine-Centric Science episodic Donny Winston Stories about the FAIR principles in practice, for scientists who want to compound their impacts, not their errors. Stories about the FAIR principles in practice, for scientists who want to compound their impacts, not their errors.. Donny Winston No No Sandra Gesing 28 28 Sandra Gesing full cf045c9b-8b20-4066-b0cb-ca0fe6258e9c https://podcast.polyneme.xyz/episodes/sandra-gesing 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.

]]> 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.

]]> Fri, 17 Feb 2023 14:42:09 -0500 Donny Winston Donny Winston 2481 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.

]]> No Christophe Blanchi 27 27 Christophe Blanchi full 0ef879bd-8ae2-4274-ab7b-681993253a6b https://podcast.polyneme.xyz/episodes/christophe-blanchi 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

]]> 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

]]> Wed, 18 Jan 2023 06:21:45 -0500 Donny Winston Donny Winston 4330 An interview with Christophe Blanchi, currently Executive Director of the DONA Foundation. An interview with Christophe Blanchi, currently Executive Director of the DONA Foundation. No Vineeth Venugopal 26 26 Vineeth Venugopal full e010ebe6-61d3-4a65-9816-7ddc9c0c960b https://podcast.polyneme.xyz/episodes/vineeth-venugopal https://en.wikipedia.org/wiki/Interatomic_potential

]]> https://en.wikipedia.org/wiki/Interatomic_potential

]]> Mon, 31 Oct 2022 04:46:46 -0400 Donny Winston Donny Winston 3559 Vineeth is a materials scientist working on creating a knowledge graph of materials. He is new to ontologies and the semantic web in general; he'd like to understand ontologies/taxonomies and what an ontologist/taxonomist does in general. I've agreed to let him barrage me with questions until hopefully some clarity is reached. Vineeth is a materials scientist working on creating a knowledge graph of materials. He is new to ontologies and the semantic web in general; he'd like to understand ontologies/taxonomies and what an ontologist/taxonomist does in general. I've agreed to l No walk-and-talk: DIKW pyramid/hierarchy 25 25 walk-and-talk: DIKW pyramid/hierarchy full 0c98f55c-2263-4495-858a-f622c71ea764 https://podcast.polyneme.xyz/episodes/walk-and-talk-dikw-pyramid-hierarchy DIKW pyramid / DIKW hierarchy - https://en.wikipedia.org/wiki/DIKW_pyramid

"Data becomes information when it is stored *in* a given *formation*."
From B. Fong and D. I. Spivak, “Seven Sketches in Compositionality: An Invitation to Applied Category Theory,” Ch. 3 - Databases, arXiv, Oct. 12, 2018. doi: 10.48550/arXiv.1803.05316.

"There are only three things we can do with data. We can accrete data by adding it to an existing collection, reduce data by discarding information from an existing collection, or reshape data by placing it in a different kind of collection."
From Z. Tellman, *Elements of Clojure*, Ch. 4 - Composition. Monee, IL: Lulu.com, 2019.

types of information: situational, methodological, philosophical (epistemological, axiological, ontological)
From Dorian Taylor, "2022-05-11 types of information", (May 11, 2022). Accessed: Sep. 27, 2022. [Online Video]. Available: https://www.youtube.com/watch?v=zNUNgZ6RTmQ

Inductions vs deductions vs abductions
Informed by M. K. Bergman, A Knowledge Representation Practionary: Guidelines Based on Charles Sanders Peirce. Cham: Springer International Publishing, 2018. doi: 10.1007/978-3-319-98092-8.

"programs must be written for people to read, and only incidentally for machines to execute."
From preface to first edition (and included in subsequent editions) of H. Abelson, G. J. Sussman, and J. Sussman, *Structure and interpretation of computer programs*, Cambridge, Mass.: MIT Press.

]]> DIKW pyramid / DIKW hierarchy - https://en.wikipedia.org/wiki/DIKW_pyramid

"Data becomes information when it is stored *in* a given *formation*."
From B. Fong and D. I. Spivak, “Seven Sketches in Compositionality: An Invitation to Applied Category Theory,” Ch. 3 - Databases, arXiv, Oct. 12, 2018. doi: 10.48550/arXiv.1803.05316.

"There are only three things we can do with data. We can accrete data by adding it to an existing collection, reduce data by discarding information from an existing collection, or reshape data by placing it in a different kind of collection."
From Z. Tellman, *Elements of Clojure*, Ch. 4 - Composition. Monee, IL: Lulu.com, 2019.

types of information: situational, methodological, philosophical (epistemological, axiological, ontological)
From Dorian Taylor, "2022-05-11 types of information", (May 11, 2022). Accessed: Sep. 27, 2022. [Online Video]. Available: https://www.youtube.com/watch?v=zNUNgZ6RTmQ

Inductions vs deductions vs abductions
Informed by M. K. Bergman, A Knowledge Representation Practionary: Guidelines Based on Charles Sanders Peirce. Cham: Springer International Publishing, 2018. doi: 10.1007/978-3-319-98092-8.

"programs must be written for people to read, and only incidentally for machines to execute."
From preface to first edition (and included in subsequent editions) of H. Abelson, G. J. Sussman, and J. Sussman, *Structure and interpretation of computer programs*, Cambridge, Mass.: MIT Press.

]]> Tue, 27 Sep 2022 11:41:15 -0400 Donny Winston Donny Winston 537 I walk in and around a park with my dog, talking about the the DIKW (Data, Information, Knowledge, Wisdom) class of models, eventually relating this to machine-centric science. I walk in and around a park with my dog, talking about the the DIKW (Data, Information, Knowledge, Wisdom) class of models, eventually relating this to machine-centric science. No I Fought the Law 24 24 I Fought the Law full c3796587-d7dd-411e-9942-245664d68569 https://podcast.polyneme.xyz/episodes/i-fought-the-law `.split()`s on strings and `filter`s on `None`
I fought the Law and the Law won
I fought the Law and the Law won
I needed spec compliance; I got none
I fought the Law and the Law won
I fought the Law and the Law won

I varied my output with the latest fad
Breakin' every downstream run
Needed Postel more than I ever had
I fought the Law and the Law won
I fought the Law and the

Scatterin' parsing like a shotgun
I fought the Law and the Law won
I fought the Law and the Law won
I lost robustness and I lost my fun
I fought the Law and the Law won
I fought the Law and the Law won

I varied my output with the latest fad
Breakin' every downstream run
Needed Postel more than I ever had
I fought the Law and the Law won
I fought the Law and the

]]> `.split()`s on strings and `filter`s on `None`
I fought the Law and the Law won
I fought the Law and the Law won
I needed spec compliance; I got none
I fought the Law and the Law won
I fought the Law and the Law won

I varied my output with the latest fad
Breakin' every downstream run
Needed Postel more than I ever had
I fought the Law and the Law won
I fought the Law and the

Scatterin' parsing like a shotgun
I fought the Law and the Law won
I fought the Law and the Law won
I lost robustness and I lost my fun
I fought the Law and the Law won
I fought the Law and the Law won

I varied my output with the latest fad
Breakin' every downstream run
Needed Postel more than I ever had
I fought the Law and the Law won
I fought the Law and the

]]> Wed, 07 Sep 2022 04:18:06 -0400 Donny Winston Donny Winston 72 "implementations should follow a general principle of robustness: be conservative in what you do, be liberal in what you accept from others" - Jon Postel, https://doi.org/10.17487/RFC0761, see also https://en.wikipedia.org/wiki/Robustness_principle "implementations should follow a general principle of robustness: be conservative in what you do, be liberal in what you accept from others" - Jon Postel, https://doi.org/10.17487/RFC0761, see also https://en.wikipedia.org/wiki/Robustness_principle No Martynas Jusevičius 23 23 Martynas Jusevičius full 56e90832-89cc-49f6-ab4a-c27cebb39834 https://podcast.polyneme.xyz/episodes/martynas-jusevicius - Linked Data
- Project Jupyter (Notebook, Lab, etc.)
- UI Blocks: Block Protocol
- Personal Knowledge Graphs: Roam, Logseq, Obsidian
- Solid: decentralized data stores
- Resource Description Framework (RDF)
- Twitter: Martynas, AtomGraph
- LinkedDataHub (Apache-2.0 license)
- AtomGraph: Website, GitHub

]]> - Linked Data
- Project Jupyter (Notebook, Lab, etc.)
- UI Blocks: Block Protocol
- Personal Knowledge Graphs: Roam, Logseq, Obsidian
- Solid: decentralized data stores
- Resource Description Framework (RDF)
- Twitter: Martynas, AtomGraph
- LinkedDataHub (Apache-2.0 license)
- AtomGraph: Website, GitHub

]]> Mon, 29 Aug 2022 09:40:11 -0400 Donny Winston Donny Winston 1799 "The RDF graph data model...seems like the only realistic implementation at this point for the FAIR principles." "To me, FAIR data is more or less equal to Linked Data." "The software has to be built around these principles. And that's maybe quite a radical idea because for a long time, data was just like an add-on to software, right? But essentially now it's the inverse. It's the data that is at the center -- that's the data-centric paradigm." "...there has to be some kind of paradigm shift, both in how researchers see this, but also for those who develop software for researchers, that what scientific publishing produces is not just PDFs...Through fair data, we can look at scientific publishing as this huge network of research artifacts that can be navigated, explored -- as a knowledge graph naturally -- but also recombined, reused and repurposed in different things." "The RDF graph data model...seems like the only realistic implementation at this point for the FAIR principles." "To me, FAIR data is more or less equal to Linked Data." "The software has to be built around these principles. And that's maybe quite a No FAIR-Enabling Services 22 22 FAIR-Enabling Services full 14dc15c7-9846-48bd-9823-07df01f64bea https://podcast.polyneme.xyz/episodes/fair-enabling-services Thu, 18 Aug 2022 22:10:55 -0400 Donny Winston Donny Winston 597 I was thinking about FAIR-enabling resources and wanted to distinguish between things that actually have to be running in order for data to be alive and for you to actually find it, access it, interoperate with it, and reuse it, versus "one-time" things that those services will need. I was thinking about FAIR-enabling resources and wanted to distinguish between things that actually have to be running in order for data to be alive and for you to actually find it, access it, interoperate with it, and reuse it, versus "one-time" things t No Stuck Data Mining Again (Lodi) 21 21 Stuck Data Mining Again (Lodi) full 2fd72ab9-192f-404b-9964-ecbcc2519d56 https://podcast.polyneme.xyz/episodes/stuck-data-mining-again-lodi Just about a week ago,
I set out to download.
Seekin' supplementary data,
lookin' for a pot of gold.

Things got bad, and things got worse,
I guess you will know the tune.
Oh lord, stuck data mining again.

Rode in on semantics,
I'll be hand-waving out if I go.
Trying controlled vocabularies,
must've been seven of 'em or more.
No corresponding authors
have replied to my emails yet.
Oh lord, I'm stuck data mining again.

The man from Stack Overflow
said I was on my way.
My code kept raising exceptions.
I was reading tracebacks for days.
I wanted to run a one-off benchmark.
Looks like my plans fell through.
Oh lord, stuck data mining again.

If I only had metadata
that was machine-actionable
every time I've had a dataset
that I's told was interoperable.
You know I'd catch the FAIR train
and breeze through my planned reuse.
Oh lord, I'm stuck data mining again.
Oh lord, I'm stuck data mining again.

]]> Just about a week ago,
I set out to download.
Seekin' supplementary data,
lookin' for a pot of gold.

Things got bad, and things got worse,
I guess you will know the tune.
Oh lord, stuck data mining again.

Rode in on semantics,
I'll be hand-waving out if I go.
Trying controlled vocabularies,
must've been seven of 'em or more.
No corresponding authors
have replied to my emails yet.
Oh lord, I'm stuck data mining again.

The man from Stack Overflow
said I was on my way.
My code kept raising exceptions.
I was reading tracebacks for days.
I wanted to run a one-off benchmark.
Looks like my plans fell through.
Oh lord, stuck data mining again.

If I only had metadata
that was machine-actionable
every time I've had a dataset
that I's told was interoperable.
You know I'd catch the FAIR train
and breeze through my planned reuse.
Oh lord, I'm stuck data mining again.
Oh lord, I'm stuck data mining again.

]]> Tue, 09 Aug 2022 14:32:55 -0400 Donny Winston Donny Winston 127 Things got bad, and things got worse. I guess you will know the tune. Things got bad, and things got worse. I guess you will know the tune. No Don't Silo Me In 20 20 Don't Silo Me In full c4ae3e92-9ca9-4d3d-8a3c-4824ccc71e91 https://podcast.polyneme.xyz/episodes/dont-silo-me-in Oh give me mappings, lots of mappings, with resolving URIs. Don’t silo me in.

Let me prance through semantics of namespaces that I love. Don’t silo me in.

Let me use an open protocol to access these bytes, and for metadata promise me you’ll keep on the lights. Authenticate me repeatedly, but give clear usage rights. Don’t silo me in.

Just give me data bare. Let me reuse my old CPUs and mint my URIs.

With my own software, let me wander over yonder with least surprise.

I want to probe the provenance of metadata rich and plural, and represent my knowledge to be machine actionable. And I can’t look at schemas if they’re not interoperable. Don’t silo me in.

]]> Oh give me mappings, lots of mappings, with resolving URIs. Don’t silo me in.

Let me prance through semantics of namespaces that I love. Don’t silo me in.

Let me use an open protocol to access these bytes, and for metadata promise me you’ll keep on the lights. Authenticate me repeatedly, but give clear usage rights. Don’t silo me in.

Just give me data bare. Let me reuse my old CPUs and mint my URIs.

With my own software, let me wander over yonder with least surprise.

I want to probe the provenance of metadata rich and plural, and represent my knowledge to be machine actionable. And I can’t look at schemas if they’re not interoperable. Don’t silo me in.

]]> Thu, 04 Aug 2022 15:19:53 -0400 Donny Winston Donny Winston 79 with apologies to Cole Porter and Robert Fletcher with apologies to Cole Porter and Robert Fletcher No Shreyas Cholia 19 19 Shreyas Cholia full 1f8d0988-76b7-4994-985f-b9c608fba9b2 https://podcast.polyneme.xyz/episodes/shreyas-cholia * [Materials Project](https://materialsproject.org/)

* [Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE)](https://ess-dive.lbl.gov/)

* [National Microbiome Data Collaborative (NMDC)](https://microbiomedata.org/)

* [W3C Provenance (PROV) specs](https://www.w3.org/TR/prov-overview/)

* [Research Equals (R=)](https://www.researchequals.com/)

* [JSON-LD](https://json-ld.org/)

* [Ecological Metadata Language (EML)](https://eml.ecoinformatics.org/)

* [DataCite](https://datacite.org/)

* [OSTI](https://www.osti.gov/)

* [DOI](https://www.doi.org/)

* schema.org

* [OAuth](https://oauth.net/2/)

* [OpenID Connect (OIDC)](https://openid.net/connect/)

* [OpenAPI](https://www.openapis.org/)

* [REST](https://en.wikipedia.org/wiki/Representational_state_transfer)

* [IGSN](https://www.igsn.org/)

* [Data Observation Network for Earth (DataONE)](https://www.dataone.org/)

* [Frictionless Data](https://frictionlessdata.io/)

]]> * [Materials Project](https://materialsproject.org/)

* [Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE)](https://ess-dive.lbl.gov/)

* [National Microbiome Data Collaborative (NMDC)](https://microbiomedata.org/)

* [W3C Provenance (PROV) specs](https://www.w3.org/TR/prov-overview/)

* [Research Equals (R=)](https://www.researchequals.com/)

* [JSON-LD](https://json-ld.org/)

* [Ecological Metadata Language (EML)](https://eml.ecoinformatics.org/)

* [DataCite](https://datacite.org/)

* [OSTI](https://www.osti.gov/)

* [DOI](https://www.doi.org/)

* schema.org

* [OAuth](https://oauth.net/2/)

* [OpenID Connect (OIDC)](https://openid.net/connect/)

* [OpenAPI](https://www.openapis.org/)

* [REST](https://en.wikipedia.org/wiki/Representational_state_transfer)

* [IGSN](https://www.igsn.org/)

* [Data Observation Network for Earth (DataONE)](https://www.dataone.org/)

* [Frictionless Data](https://frictionlessdata.io/)

]]> Fri, 29 Jul 2022 10:43:47 -0400 Donny Winston Donny Winston 1786 I interview Shreyas Cholia, currently at the Lawrence Berkeley National Laboratory in Berkeley, California. Topics we spoke about included: data lifecycles, edge computing for data firehoses, provenance, standards, broad versus detailed domain vocabularies, scope for common APIs, and identifier leveling. I interview Shreyas Cholia, currently at the Lawrence Berkeley National Laboratory in Berkeley, California. Topics we spoke about included: data lifecycles, edge computing for data firehoses, provenance, standards, broad versus detailed domain vocabul No Patrick Huck 18 18 Patrick Huck full e3729c81-6c66-4f55-9bba-c0c89614ddc9 https://podcast.polyneme.xyz/episodes/patrick-huck 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

]]> 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

]]> Thu, 21 Jul 2022 11:14:07 -0400 Donny Winston Donny Winston 3188 I interview Patrick Huck, currently staff on the Materials Project at the Lawrence Berkeley National Laboratory in Berkeley, California, United States. We talk about choices and considerations in implementing FAIR. I interview Patrick Huck, currently staff on the Materials Project at the Lawrence Berkeley National Laboratory in Berkeley, California, United States. We talk about choices and considerations in implementing FAIR. No FAIR Implementation Profile (FIP) Ontology 17 17 FAIR Implementation Profile (FIP) Ontology full 6a50f261-5e0d-4eb1-bea9-577f8a4115fb https://podcast.polyneme.xyz/episodes/fair-implementation-profile-fip-ontology The FAIR Implementation Profile (FIP) Ontology: https://w3id.org/fair/fip/terms/FIP-Ontology

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

]]> Fri, 15 Jul 2022 12:10:06 -0400 Donny Winston Donny Winston 583 A FAIR implementation profile is a way to communicate how you're implementing the FAIR principles. It's a way for people, communities of practice, to share how they're addressing the FAIR principles, the choices that they've made, or considerations they've made about those choices, what enabling resources they're using to make those choices or what challenges they have, what they're planning. Also, to associate themselves with a community of practice so that people can perhaps, in similar fields, adopt similar answers to some of the questions about how do you implement FAIR. A FAIR implementation profile is a way to communicate how you're implementing the FAIR principles. It's a way for people, communities of practice, to share how they're addressing the FAIR principles, the choices that they've made, or considerations they No R1.3: metadata and data meet domain-relevant community standards 16 16 R1.3: metadata and data meet domain-relevant community standards full 63908b83-400e-4be2-ad99-042664de0af3 https://podcast.polyneme.xyz/episodes/r1-3-metadata-and-data-meet-domain-relevant-community-standards 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/

]]> 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/

]]> Mon, 20 Jun 2022 17:02:42 -0400 Donny Winston Donny Winston 490 FAIR principle R1.3: meta(data) meet domain-relevant community standards. An overview of the fundamentals of relevance and ranking in your search for standards. FAIR principle R1.3: meta(data) meet domain-relevant community standards. An overview of the fundamentals of relevance and ranking in your search for standards. No R1.2: Metadata and data are associated with detailed provenance 15 15 R1.2: Metadata and data are associated with detailed provenance full e2f60a2b-0695-435b-a3a3-223288fa1c9b https://podcast.polyneme.xyz/episodes/r1-2-metadata-and-data-are-associated-with-detailed-provenance 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).

]]> 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).

]]> Thu, 02 Jun 2022 14:33:53 -0400 Donny Winston Donny Winston 449 The 14th of the 15 FAIR principles, R1.2: metadata and data are associated with detailed provenance. A dive into the World Wide Web Consortium (W3C) Provenance Data Model -- what are the different parts of provenance, and what are some terms that can be used in order to manage it? The 14th of the 15 FAIR principles, R1.2: metadata and data are associated with detailed provenance. A dive into the World Wide Web Consortium (W3C) Provenance Data Model -- what are the different parts of provenance, and what are some terms that can b No R1.1: Meta(data) are released with a clear and accessible data usage license 14 14 R1.1: Meta(data) are released with a clear and accessible data usage license full d6c48a7c-f821-4983-b4a8-ecebf979fda6 https://podcast.polyneme.xyz/episodes/r1-1-meta-data-are-released-with-a-clear-and-accessible-data-usage-license 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/>

]]> 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/>

]]> Wed, 25 May 2022 10:43:51 -0400 Donny Winston Donny Winston 705 FAIR Principle R1.1: Meta(data) are released with a clear and accessible data usage license. Overview of Creative Commons licenses for data and various licenses (BSD, MIT, GPL, oh my!) for code. FAIR Principle R1.1: Meta(data) are released with a clear and accessible data usage license. Overview of Creative Commons licenses for data and various licenses (BSD, MIT, GPL, oh my!) for code. No R1: (Meta)data are richly described with a plurality of accurate and relevant attributes 13 13 R1: (Meta)data are richly described with a plurality of accurate and relevant attributes full 2592c6cd-f51d-4550-9ec4-a7d82cbec8c6 https://podcast.polyneme.xyz/episodes/r1-meta-data-are-richly-described-with-a-plurality-of-accurate-and-relevant-attributes * 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/

]]> * 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/

]]> Wed, 18 May 2022 17:27:45 -0400 Donny Winston Donny Winston 552 The 12th of the 15 FAIR principles, R1: metadata and data are richly described with a plurality of accurate and relevant attributes. The 12th of the 15 FAIR principles, R1: metadata and data are richly described with a plurality of accurate and relevant attributes. No I3: (meta)data include qualified references to other (meta)data 12 12 I3: (meta)data include qualified references to other (meta)data full b4ad6552-f160-4fa4-a8eb-0d80c2b72c86 https://podcast.polyneme.xyz/episodes/i3-meta-data-include-qualified-references-to-other-meta-data 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

]]> 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

]]> Thu, 12 May 2022 02:42:29 -0400 Donny Winston Donny Winston 347 It's more powerful when our references are indexed by nature rather than by number. On the 11th of the 15 FAIR principles, I3: metadata and data include qualified references to other metadata and data. It's more powerful when our references are indexed by nature rather than by number. On the 11th of the 15 FAIR principles, I3: metadata and data include qualified references to other metadata and data. No I2: (Meta)data use vocabularies that follow the FAIR principles 11 11 I2: (Meta)data use vocabularies that follow the FAIR principles full 2423e379-fc08-45e0-be67-391b354f766a https://podcast.polyneme.xyz/episodes/i2-meta-data-use-vocabularies-that-follow-the-fair-principles 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

]]> 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

]]> Wed, 04 May 2022 18:32:42 -0400 Donny Winston Donny Winston 386 The 10th of the 15 FAIR principles, I2: metadata and data use vocabularies that follow the FAIR principles. The 10th of the 15 FAIR principles, I2: metadata and data use vocabularies that follow the FAIR principles. No I1: (Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation 10 10 I1: (Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation full d583e233-d8cb-430f-8f79-cfae07481731 https://podcast.polyneme.xyz/episodes/i1-meta-data-use-a-formal-accessible-shared-and-broadly-applicable-language-for-knowledge-representation GUPRIs, RDF, RDFS, OWL, SHACL, JSON, JSON-LD, JSON Schema, ActivityPub, "fediverse", XMPP, SMTP.

]]> GUPRIs, RDF, RDFS, OWL, SHACL, JSON, JSON-LD, JSON Schema, ActivityPub, "fediverse", XMPP, SMTP.

]]> Wed, 27 Apr 2022 18:33:57 -0400 Donny Winston Donny Winston 505 About the 9th of the 15 FAIR principles, I1: (Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation. You need controlled term sets, vocabularies, ontologies, thesauri, whatever you want to call it, ideally having globally unique, persistent, resolvable identifiers. And apart from these controlled vocabularies you need actual models, well-defined frameworks, to describe and structure the metadata according to those controlled vocabularies. About the 9th of the 15 FAIR principles, I1: (Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation. You need controlled term sets, vocabularies, ontologies, thesauri, whatever you want to call it, ide No A2. Metadata are accessible, even when the data are no longer available 9 9 A2. Metadata are accessible, even when the data are no longer available full 70162259-10c0-4934-b2d2-24cd17b538b8 https://podcast.polyneme.xyz/episodes/a2-metadata-are-accessible-even-when-the-data-are-no-longer-available Archival Resource Key (ARK) specification (section on policy metadata): https://datatracker.ietf.org/doc/html/draft-kunze-ark-34#section-5.1.1.

Permanence Levels and the Archives for NIH NLM's Permanent Web Documents: https://www.nlm.nih.gov/pubs/techbull/ma05/ma05_archive.html.

]]> Archival Resource Key (ARK) specification (section on policy metadata): https://datatracker.ietf.org/doc/html/draft-kunze-ark-34#section-5.1.1.

Permanence Levels and the Archives for NIH NLM's Permanent Web Documents: https://www.nlm.nih.gov/pubs/techbull/ma05/ma05_archive.html.

]]> Tue, 19 Apr 2022 11:31:04 -0400 Donny Winston Donny Winston 279 Data may be, or become, inaccessible by design, or on request, or by accident. While it was accessible, it may have been used by others. If someone has a reference to data by ID, can they minimally understand the nature and provenance of the data? Data may be, or become, inaccessible by design, or on request, or by accident. While it was accessible, it may have been used by others. If someone has a reference to data by ID, can they minimally understand the nature and provenance of the data? No A1.2: The protocol allows for authentication and authorisation where necessary 8 8 A1.2: The protocol allows for authentication and authorisation where necessary full 0cf4bd72-da4a-4e5f-b0ff-9ff10a4283cd https://podcast.polyneme.xyz/episodes/a1-2-the-protocol-allows-for-authentication-and-authorisation-where-necessary A brief dip into the world of HTTP auth. The Authorization request header. The WWW-Authenticate response header. Basic authentication. Bearer-based authentication. Authenticating securely. Shared secrets versus asymmetric encryption (for non-repudiation).

]]> A brief dip into the world of HTTP auth. The Authorization request header. The WWW-Authenticate response header. Basic authentication. Bearer-based authentication. Authenticating securely. Shared secrets versus asymmetric encryption (for non-repudiation).

]]> Wed, 13 Apr 2022 14:21:31 -0400 Donny Winston Donny Winston 304 FAIR does not mean open. You're certainly allowed to authenticate and to authorize. The HTTP protocol is pretty great for this. FAIR does not mean open. You're certainly allowed to authenticate and to authorize. The HTTP protocol is pretty great for this. No A1.1: The protocol is open, free and universally implementable 7 7 A1.1: The protocol is open, free and universally implementable full cc600d93-b062-4052-962d-d43cb8dc7afd https://podcast.polyneme.xyz/episodes/a1-1-the-protocol-is-open-free-and-universally-implementable Protocol versus implementation. HTTP, SMTP, Zulip.

]]> Protocol versus implementation. HTTP, SMTP, Zulip.

]]> Tue, 05 Apr 2022 16:24:26 -0400 Donny Winston Donny Winston 221 open -- free as in speech, free -- free as in beer, and universally implementable -- NOT free as in puppies. open -- free as in speech, free -- free as in beer, and universally implementable -- NOT free as in puppies. No A1: (Meta)data are retrievable by their identifier using a standardized communication protocol 6 6 A1: (Meta)data are retrievable by their identifier using a standardized communication protocol full 48847266-851e-41e9-a46f-aba54f0f3307 https://podcast.polyneme.xyz/episodes/a1-meta-data-are-retrievable-by-their-identifier-using-a-standardized-communication-protocol You want to avoid protocols with limited implementation, poor documentation, and, when possible, components involving human intervention.

It may not be possible to provide secure access through a fully mechanized protocol like HTTP, for example, for highly sensitive data. However, the protocol  must be clear and explicit in the metadata, whether it involves a verbal request, email, telephone number, Slack username, et cetera.

The important thing is that the communication protocol for how to access is explicit and clearly defined in the metadata, whether fully mechanized or not.

]]> You want to avoid protocols with limited implementation, poor documentation, and, when possible, components involving human intervention.

It may not be possible to provide secure access through a fully mechanized protocol like HTTP, for example, for highly sensitive data. However, the protocol  must be clear and explicit in the metadata, whether it involves a verbal request, email, telephone number, Slack username, et cetera.

The important thing is that the communication protocol for how to access is explicit and clearly defined in the metadata, whether fully mechanized or not.

]]> Tue, 29 Mar 2022 10:43:39 -0400 Donny Winston Donny Winston 168 So, you've identified a digital resource. Now it's time to retrieve it and/or its metadata record. TL;DR - Use HTTP(S) if possible. So, you've identified a digital resource. Now it's time to retrieve it and/or its metadata record. TL;DR - Use HTTP(S) if possible. No F4: (Meta)data are registered or indexed in a searchable resource 5 5 F4: (Meta)data are registered or indexed in a searchable resource full 733d3681-df4c-4398-9153-7c10cad20785 https://podcast.polyneme.xyz/episodes/f4-meta-data-are-registered-or-indexed-in-a-searchable-resource The goal here is leverage: increasing the ratio of machine action to user action in getting to the data that they want. Otherwise, your data is technically findable, but it's going to require a lot of user action. They might have to do a full data download, scan through a full table, scroll through a long webpage, and it's unlikely that they're going to actually find what they need, because they're just not going to put in that much effort. So you really want indexing. You want this leverage to have your machine help do some of the action that a user might otherwise do.

]]> The goal here is leverage: increasing the ratio of machine action to user action in getting to the data that they want. Otherwise, your data is technically findable, but it's going to require a lot of user action. They might have to do a full data download, scan through a full table, scroll through a long webpage, and it's unlikely that they're going to actually find what they need, because they're just not going to put in that much effort. So you really want indexing. You want this leverage to have your machine help do some of the action that a user might otherwise do.

]]> Tue, 22 Mar 2022 11:52:26 -0400 Donny Winston Donny Winston 402 Increasing leverage: the ratio of machine action to user action. Indexing as leverage via sorting. Increasing leverage: the ratio of machine action to user action. Indexing as leverage via sorting. No F3: Metadata clearly and explicitly include the identifier of the data they describe 4 4 F3: Metadata clearly and explicitly include the identifier of the data they describe full 9229e614-a7b8-459a-88bb-5334f50b71eb https://podcast.polyneme.xyz/episodes/f3-metadata-clearly-and-explicitly-include-the-identifier-of-the-data-they-describe Literature references with and without DOIs. Tables of data in articles with and without unique identifiers in each row for what that row is about. The magic of including identifiers in the metadata you share.

The Data Catalog (DCAT) Vocabulary: https://www.w3.org/TR/vocab-dcat-2/

]]> Literature references with and without DOIs. Tables of data in articles with and without unique identifiers in each row for what that row is about. The magic of including identifiers in the metadata you share.

The Data Catalog (DCAT) Vocabulary: https://www.w3.org/TR/vocab-dcat-2/

]]> Tue, 15 Mar 2022 15:15:02 -0400 Donny Winston Donny Winston 181 Literature references with and without DOIs. Tables of data in articles with and without unique identifiers in each row for what that row is about. The magic of including identifiers in the metadata you share. Literature references with and without DOIs. Tables of data in articles with and without unique identifiers in each row for what that row is about. The magic of including identifiers in the metadata you share. No F2: Data are described with rich metadata 3 3 F2: Data are described with rich metadata full f2cd896f-8119-4806-9f7c-bcc813700dd3 https://podcast.polyneme.xyz/episodes/f2-data-are-described-with-rich-metadata Kinds of metadata - "intrinsic" (machine-defined or machine-controlled; immutable) and "extrinsic" (user-defined or user-controlled). Other-than-technical interoperability. "Quality" in the eye of the beholder / data consumer. Analogy to web-browser feature detection, and application to search engine "rich results".

]]> Kinds of metadata - "intrinsic" (machine-defined or machine-controlled; immutable) and "extrinsic" (user-defined or user-controlled). Other-than-technical interoperability. "Quality" in the eye of the beholder / data consumer. Analogy to web-browser feature detection, and application to search engine "rich results".

]]> Tue, 08 Mar 2022 11:26:39 -0500 Donny Winston Donny Winston 193 "intrinsic" vs "extrinsic" metadata. Other-than-technical interoperability. Qualification vs. "Quality". Feature detection. Search-engine "rich results". "intrinsic" vs "extrinsic" metadata. Other-than-technical interoperability. Qualification vs. "Quality". Feature detection. Search-engine "rich results". No F1: (Meta)data have globally unique, persistent identifiers 2 2 F1: (Meta)data have globally unique, persistent identifiers full db619470-4b11-49bd-ae90-ce24c6d685d3 https://podcast.polyneme.xyz/episodes/f1-meta-data-have-globally-unique-persistent-identifiers
  • HTTP URLs
  •  orcid.org, doi.org, uniprot.org
  • archival resource keys (ARKs)
  • meta-resolvers: identifiers.org, n2t.net
    • ]]>
  • HTTP URLs
  •  orcid.org, doi.org, uniprot.org
  • archival resource keys (ARKs)
  • meta-resolvers: identifiers.org, n2t.net
    • ]]>     Tue, 01 Mar 2022 12:21:04 -0500 Donny Winston Donny Winston 417 Today, we'll be talking about the first of the FAIR principles, F1: Metadata are assigned globally unique and persistent identifiers. Today, we'll be talking about the first of the FAIR principles, F1: Metadata are assigned globally unique and persistent identifiers. No     What to expect from this podcast 1 1 What to expect from this podcast trailer f4292fd1-699a-4b7b-840c-fe7273cd3db1 https://podcast.polyneme.xyz/episodes/what-to-expect-from-this-podcast A rundown of what I'm planning: FAIRdowns, inside the Box, and FIP calls, oh my!

    ]]>     A rundown of what I'm planning: FAIRdowns, inside the Box, and FIP calls, oh my!

    ]]>     Mon, 21 Feb 2022 21:10:46 -0500 Donny Winston Donny Winston 70 A weekly podcast for scientific researchers getting far with FAIR. A weekly podcast for scientific researchers getting far with FAIR. No