Declaring a Research Software Development Plan
This nanopublication defines a research software development plan template.
URI to earlier version (nanopublication)
full URI (e.g. handle.net) or short suffix
MIME type, such as "text/csv" or "application/trig"
Catalogue of data and metadata artefacts relevant to Personal Exposure and Health research
Personal Exposure and Health Data Catalogue
This query returns the testimonials about the given entity.
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix dct: <http://purl.org/dc/terms/> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix schema: <https://schema.org/> prefix gen: <https://w3id.org/kpxl/gen/terms/> select ?author ?author_label ?text ?date ?np ("^" as ?np_label) where { graph npa:graph { ?np npx:hasNanopubType gen:Testimonial . ?np npa:hasValidSignatureForPublicKeyHash ?pubkey . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pubkey . } ?np npx:introduces ?testimonial . ?np np:hasAssertion ?a . ?np dct:created ?date . } graph ?a { ?testimonial dct:description ?text . values ?_subject_multi_iri {} ?testimonial schema:about ?_subject_multi_iri . ?testimonial schema:author ?author . optional { ?author rdfs:label ?author_label . } } } order by desc(?date)
This query returns the testimonials by the given author.
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix dct: <http://purl.org/dc/terms/> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix schema: <https://schema.org/> prefix gen: <https://w3id.org/kpxl/gen/terms/> select ?about ?text ?date ?np ("^" as ?np_label) where { graph npa:graph { ?np npx:hasNanopubType gen:Testimonial . ?np npa:hasValidSignatureForPublicKeyHash ?pubkey . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pubkey . } ?np npx:introduces ?testimonial . ?np np:hasAssertion ?a . ?np dct:created ?date . } graph ?a { ?testimonial dct:description ?text . ?testimonial schema:author ?_author_iri . optional { ?testimonial schema:about ?about . } } } order by desc(?date)
Get testimonials about entity - This query returns the testimonials about the given entity.
Get testimonials by author - This query returns the testimonials by the given author.
Tobias Kuhn displays view: User testimonials view
Knowledge Pixels displays view: Testimonials received view
Daniel Mietchen displays view: View of personal URLs for user
We are really happy to announce that our proposal Nanoarguments has been accepted as NLnet project. We are looking forward working on this, and will share more details shortly.
A testimonial somebody is giving for a particular organization, product, or other entity.
Declaring to plan to attend an event - Such a nanopublication declares that the creator plans to attend an event.
This query returns the details of all FIP declarations, including schema:version for R-FIP declarations.
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix fip: <https://w3id.org/fair/fip/terms/> prefix dct: <http://purl.org/dc/terms/> prefix dce: <http://purl.org/dc/elements/1.1/> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix np: <http://www.nanopub.org/nschema#> prefix dcat: <https://www.w3.org/ns/dcat#> prefix schema: <https://schema.org/> select ?decl_np ?community ?c ?question ?q ?sort ?nochoice ?decl ?rel ?resource_id_used ?startdate ?enddate ?date ?version where { graph npa:graph { ?decl_np npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?decl_np_x npx:invalidates ?decl_np ; npa:hasValidSignatureForPublicKey ?pubkey . } ?decl_np npx:hasNanopubType fip:FIP-Declaration . ?decl_np dct:created ?date . ?decl_np np:hasAssertion ?assertion . } graph ?assertion { ?decl a fip:FIP-Declaration . ?decl fip:refers-to-question ?question . { { ?decl fip:declares-current-use-of ?resource_id_used . bind(fip:declares-current-use-of as ?rel) } union { ?decl fip:declares-planned-use-of ?resource_id_used . bind(fip:declares-planned-use-of as ?rel) } union { ?decl fip:declares-planned-replacement-of ?resource_id_used . bind(fip:declares-planned-replacement-of as ?rel) } union { ?decl fip:declares-replacement-from ?resource_id_used . bind(fip:declares-replacement-from as ?rel) } union { ?decl fip:declares-replacement-to ?resource_id_used . bind(fip:declares-replacement-to as ?rel) } } # grlc gives an error for some reason if these two optional statements are at the end of the graph block: optional { ?decl dcat:startDate ?startdate . } optional { ?decl dcat:endDate ?enddate . } ?decl fip:declared-by ?community . optional { ?decl schema:version ?version . } } bind (replace(str(?community), ".*#", "") as ?c) bind (replace(str(?supercommunity), ".*#", "") as ?sc) bind (replace(str(?question), "^.*-([^-MD]+(-[MD]+)?)$", "$1") as ?q) bind (concat(replace(?q, "F|M", "0"), "x") as ?sort) bind ("" as ?nochoice) }
Returns R-FIP declarations: FIP declarations whose community has a Reference-FAIR-Implementation-Profile, matched with the latest R-FIP profile for that community.
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix fip: <https://w3id.org/fair/fip/terms/> prefix dct: <http://purl.org/dc/terms/> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix np: <http://www.nanopub.org/nschema#> prefix schema: <https://schema.org/> select ?fip_index ?fip_title ?decl_np where { # Find R-FIP profiles (latest per community) graph npa:graph { ?fip_index npx:hasNanopubType fip:Reference-FAIR-Implementation-Profile . ?fip_index npa:hasValidSignatureForPublicKeyHash ?pkh . filter not exists { ?inv npx:invalidates ?fip_index ; npa:hasValidSignatureForPublicKeyHash ?pkh . } ?fip_index np:hasAssertion ?rfip_a . ?fip_index npx:introduces ?rfip . ?fip_index dct:created ?rfip_date . } graph ?rfip_a { ?rfip rdfs:label ?fip_title . ?rfip fip:declared-by ?community . } # Keep only the latest R-FIP profile per community filter not exists { graph npa:graph { ?newer_rfip npx:hasNanopubType fip:Reference-FAIR-Implementation-Profile . ?newer_rfip npa:hasValidSignatureForPublicKeyHash ?nkh . filter not exists { ?ninv npx:invalidates ?newer_rfip ; npa:hasValidSignatureForPublicKeyHash ?nkh . } ?newer_rfip np:hasAssertion ?nra . ?newer_rfip dct:created ?newer_date . } graph ?nra { ?nrfip fip:declared-by ?community . } filter(?newer_date > ?rfip_date) } # Find FIP declarations from these R-FIP communities that have schema:version graph npa:graph { ?decl_np npx:hasNanopubType fip:FIP-Declaration . ?decl_np npa:hasValidSignatureForPublicKey ?dpk . filter not exists { ?dinv npx:invalidates ?decl_np ; npa:hasValidSignatureForPublicKey ?dpk . } ?decl_np np:hasAssertion ?decl_a . } graph ?decl_a { ?decl fip:declared-by ?community . ?decl schema:version ?version . } }
Nanorequests displays view: simple message view
A space to ask for community input when trying to create resources like nanopublication queries or nanopublication templates.
The Incubator project contributed to the Nanosuggestions space.
Expressing something is relevant for something
Get relevant resources - This query returns the relevant resources for a given entity (e.g. a Space).
This query returns the relevant resources for a given entity (e.g. a Space).
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix dct: <http://purl.org/dc/terms/> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix gen: <https://w3id.org/kpxl/gen/terms/> select ?resource ?resource_label ?comment ?np ("^" as ?np_label) where { graph npa:graph { ?np npx:hasNanopubType gen:isRelevantFor . ?np npa:hasValidSignatureForPublicKeyHash ?pubkey . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pubkey . } ?np dct:created ?date . ?np np:hasAssertion ?a . optional { ?np rdfs:label ?label } } values ?_entity_multi_iri {} graph ?a { ?resource gen:isRelevantFor ?_entity_multi_iri . optional { ?resource rdfs:label ?resource_label . } optional { ?resource rdfs:comment ?comment . } } }
the entity that has the relevant resource
the resource being relevant for the entity
Daniel Mietchen displays view: Past events view
GitHub Inc. is a Git-based software repository that provides version control. It offers all of the distributed version control and source code management (SCM) functionality of Git as well as adding its own features. It provides access control and several collaboration features such as bug tracking, feature requests, task management, and wikis for each project. It provides a number of different access levels, from free through to paid services.
Nanopublications FAQ displays view: Paragraph view
Get paragraphs of an entity - This query returns the paragraphs of an entity (e.g. a space) with their titl...
This query returns the paragraphs of an entity (e.g. a space) with their title and content, including source nanopub and date.
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix dct: <http://purl.org/dc/terms/> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix schema: <http://schema.org/> prefix schemas: <https://schema.org/> prefix gen: <https://w3id.org/kpxl/gen/terms/> select ?title ?content ?date ?np where { graph npa:graph { ?np npa:hasValidSignatureForPublicKeyHash ?pubkey . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pubkey . } ?np dct:created ?date . ?np dct:creator ?user . ?np np:hasAssertion ?a . } graph ?a { ?paragraph schema:title|schemas:title ?title . ?paragraph rdf:type gen:Paragraph . ?paragraph gen:hasContent ?content . values ?_resource_multi_iri {} ?paragraph schema:isPartOf|schemas:isPartOf|schema:about|schemas:about ?_resource_multi_iri . optional { ?paragraph gen:hasPositionString ?position } } } order by ?position ?title
Q: What are the components of a nanopublication?
A: A nanopublication consists of three main parts: (1) an assertion, (2) information on the provenance of the assertion, (3) bibliographic metadata about the nanopublication itself. For further details, see https://nanopub.net/.
Displaying a view for a maintained resource
applies to - applies only to this space, and not to parts of it, etc.
select whether this display is activated or deactivated
The SPDX License List is an integral part of the SPDX Specification, open for contributions and maintained by the SPDX Legal Team. It contains commonly found licenses and exceptions used in free and open or collaborative software, data, hardware, or documentation and entries includes a standardized short identifier, the full name, the license text, and a canonical permanent URL for each license and exception.
KPI #5: A community-driven linked knowledge base for plant specialized metabolism has observer: Daniel Mietchen
KPI #5: A community-driven linked knowledge base for plant specialized metabolism
KPI #4: FAIRification of mass spectrometry workflows using FDOs has observer: Daniel Mietchen
KPI #4: FAIRification of mass spectrometry workflows using FDOs
KPI #3: Integrating DCAT-compliant nanopublications and EHDS-metadata has observer: Daniel Mietchen
KPI #3: Integrating DCAT-compliant nanopublications and EHDS-metadata
KPI #1: FAIR Vocabularies for Chemical Risk Assessment has observer: Daniel Mietchen
KPI #1: FAIR Vocabularies for Chemical Risk Assessment
We attended the Founders Day 2026 of the Swiss Startup Association yesterday, and it was great to connect to other startups, investors, and other actors of the startup world. Knowledge Pixels sparked interest at many places.
Get papers for author - This query returns the papers for a given author.
Describing core article metadata - Such a nanopublication contains the main high-level metadata about a scholarl...
includes - links a thing to a part it includes
book chapter - A defined chapter of a book, usually with a separate title or number.
in-use paper - A scholarly work that describes applied and validated solutions such as software tools, systems or architectures that benefit from the use of the technology of a particular scholarly domain.
journal editorial - An editorial published in an issue of a journal.
methods paper - A scholarly work detailing a method, procedure or experimental protocol employed in a particular scholarly domain.
position paper - A scholarly work that reports a particular intellectual position or viewpoint regarding a particular scholarly topic.
research paper - A scholarly work that reports original research contributions addressing theoretical, analytical or experimental aspects of a particular scholarly domain.
resource paper - A scholarly work that describes resources developed to provide experimental materials or facilities, support a research hypothesis, to provide answers to a research question, or that have contributed to the generation of novel scientific work.
review paper - A scholarly work that surveys the state of the art of topics central to a particular subject or relating to a specific domain (e.g. the scope of a certain journal or conference).
scholarly work - A general term that includes all other listed types
DOI of the article (starting with https://doi.org/10...)
Such a nanopublication contains the main high-level metadata about a scholarly article, including title, authors, and links to other nanopublications.
ORCID ID of the author (starting with https://orcid.org/...)
Select author to specify an email address for
ROR identifier (https://ror.org/...) or short local URI suffix (e.g. "stanford")
a part belonging to this article, e.g. a nanopublication
Read: Kuhn et al. Broadening the Scope of Nanopublications. 2023.
Kuhn et al. Broadening the Scope of Nanopublications. 2023.
Introducing the (extended) nanopublication vision.
Jane Exemplaris displays view: View of read papers by user
Read: Stanley. Scaling, universality, and renormalization: Three pillars of modern critical phenomena. ...
Stanley. Scaling, universality, and renormalization: Three pillars of modern critical phenomena. 1999.
Critical points, e.g. temperature when magnet stops working, are badly understood with microscopic models. Scaling laws (?). Universality classes of systems with the same "critical-point exponents and scaling functions". Renormalization (?).
NP created using Declaring a replication study outcome according to FORRT
WGS84 Ellipsoid Significantly Affects HEALPix Cell Assignment at Mid and High Latitudes
WGS84 ellipsoid indexing assigns pixels to substantially different HEALPix cells than sphere-based indexing, particularly at mid and high latitudes. At mid-latitudes (+48°), 98% of pixels are assigned to a different cell. This demonstrates that sphere-based HEALPix indexing is unsuitable for European Earth observation data (Copernicus/Sentinel, 45-65°N).
ELLIPSOID ANALYSIS (HEALPix depth 9, sphere vs WGS84): | Region | Center lat | Pixels in different cell | Jaccard similarity | |---------------|------------|--------------------------|-------------------| | Equatorial | 0° | 26.6% | 0.9951 | | Mid-latitude | +48° | 98.4% | 0.9844 | | High-latitude | +62° | 90.8% | 0.9868 | | Arctic | +78° | 52.6% | 0.9908 | At mid-latitudes (Mediterranean, +48°), nearly every pixel (98.4%) is assigned to a different HEALPix cell when using sphere vs WGS84 ellipsoid. Polygon coverage Jaccard similarity drops to 0.9844, indicating measurable differences in spatial coverage. The effect peaks at mid-latitudes where the WGS84 ellipsoid deviates most from a sphere, and decreases towards the equator and poles.
- Uses synthetic raster grids, not real Earth observation data - Single HEALPix depth (9) tested -- effect may vary at other depths - Four latitude bands only; continuous latitude sweep not performed - Does not quantify downstream impact on scientific analyses (e.g., land cover classification accuracy)
NP created using Declaring a replication study design according to FORRT
Analysis of Sphere vs WGS84 Ellipsoid Impact on HEALPix Cell Assignment
- The original paper uses H3 (sphere-only) and does not consider ellipsoid effects -- this is a novel extension - Analysis uses synthetic raster grids, not real Sentinel/Copernicus data - Four latitude bands chosen to represent typical European EO coverage
For each region, a 50x50 pixel raster grid is indexed to HEALPix depth 9 cells twice -- once with ellipsoid='sphere' and once with ellipsoid='WGS84' -- using healpix_geo.nested.lonlat_to_healpix(). Cell assignment differences are quantified as percentage of pixels in a different cell. Polygon coverage similarity is measured via Jaccard index using healpix_geo.nested.polygon_coverage(). Environment: Python 3.11, healpix-geo 0.1.1, Docker containerized, seeded RNG (seed=42).
Extends the replication of Law & Ardo (2024) by comparing HEALPix cell assignments using sphere-based vs WGS84 ellipsoid-based indexing via healpix-geo. Measures the percentage of raster pixels assigned to different cells depending on the reference surface, across four latitude bands: equatorial (0°), mid-latitude (+48°), high-latitude (+62°), and arctic (+78°).
HEALPix-geo Performance Equivalence with H3 Validated
HEALPix-geo achieves ~6,120x speedup (sphere) and ~6,129x speedup (WGS84) over vector overlay at 50 layers, matching H3 reference performance (~5,800x). Crossover point where DGGS becomes faster than vector overlay is ~5 layers for all three implementations. Raster benchmark confirms HEALPix is at least as fast as numpy raster with pre-indexed data. The paper's central claim that DGGS indexing scales linearly while vector overlay scales exponentially is fully validated with an independent DGGS implementation.
VECTOR BENCHMARK RESULTS (HEALPix-geo, depth 9): | Layers | HEALPix/sphere | HEALPix/WGS84 | Vector | Speedup (sphere) | Speedup (WGS84) | |--------|----------------|----------------|-----------|------------------|------------------| | 5 | 0.020s | 0.015s | 0.246s | 12x | 16x | | 10 | 0.027s | 0.026s | 1.544s | 58x | 60x | | 20 | 0.050s | 0.049s | 13.95s | 280x | 283x | | 50 | 0.122s | 0.121s | 394.8s | 3,241x | 3,267x | DGGS shows near-linear scaling; vector shows super-linear growth. This validates the paper's Figure 6. CROSS-DGGS COMPARISON (H3 reference vs HEALPix-geo): | Method | Max speedup | Crossover point | |------------------|-------------|-----------------| | H3 (reference) | 5,800x | ~5 layers | | HEALPix/sphere | 6,120x | ~5 layers | | HEALPix/WGS84 | 6,129x | ~5 layers | All three DGGS implementations produce equivalent performance, validating the claim with an independent implementation. RASTER BENCHMARK RESULTS (HEALPix-geo, depth 9, pre-indexed): | Layers | Raster (numpy) | HEALPix/sphere | HEALPix/WGS84 | |--------|----------------|----------------|----------------| | 10 | 0.0011s | 0.0003s | 0.00002s | | 100 | 0.0045s | 0.00006s | 0.00003s | | 500 | 0.0289s | 0.00008s | 0.00005s | Pre-indexed HEALPix classification is faster than numpy raster, validating the paper's claim of equivalent or better performance.
- Vector benchmark tested up to 50 layers (original paper used 500) - H3 comparison uses pre-computed reference results, not simultaneous execution - Single hardware configuration tested - HEALPix depth 9 used for all benchmarks (paper used H3 resolution 14 for vector polyfill)
Replication of DGGS Benchmark Using HEALPix-geo with Sphere and WGS84 Ellipsoid
- Uses HEALPix (healpix-geo) instead of H3 -- this is the replication variable - Tests both sphere and WGS84 ellipsoid (extension beyond original) - Default testing up to 50 vector layers and 500 raster layers - Comparison against H3 uses pre-computed reference results from the companion H3 replication study (DOI: 10.5281/zenodo.18904498)
Implements polygon polyfill via healpix_geo.nested.polygon_coverage() and raster indexing via healpix_geo.nested.lonlat_to_healpix() at HEALPix depth 9 (~1 km² cells, matching H3 resolution 9). Vector benchmark: Voronoi polygons, dissolve by value, polyfill to HEALPix cells, join on cell ID, 7-bit classification. Raster benchmark: Gaussian-smoothed layers, pre-indexed pixel-to-cell mapping, aggregate and classify. Ellipsoid analysis: compares sphere vs WGS84 cell assignments across equatorial (0°), Mediterranean (+48°), Scandinavian (+62°), and Arctic (+78°) regions. Environment: Python 3.11, healpix-geo 0.1.1, Docker containerized, seeded RNG (seed=42).
Replicates both vector and raster benchmarks from Law & Ardo (2024) using HEALPix indexing via the healpix-geo library (Rust-based) instead of H3. Extends the analysis with a geodetic comparison: all benchmarks are run twice -- once with sphere-based indexing, once with WGS84 ellipsoid indexing -- across four latitude bands (equatorial, mid-latitude, high-latitude, arctic).
NP created using Declaring an original claim according to FORRT
Impact of Ellipsoid Choice on HEALPix Cell Assignment Accuracy
AIDA sentence: WGS84 ellipsoid indexing assigns pixels to substantially different HEALPix cells than sphere-based indexing at mid and high latitudes.
Effect of HEALPix DGGS Indexing on Geospatial Data Performance
AIDA sentence: HEALPix indexing via healpix-geo achieves equivalent DGGS performance to H3 on both sphere and WGS84 ellipsoid.
approvesOf RAY7IdUcyQ8P_WCO6o9NDMz9q2LN6w7bl7ZJnsHQ_sO5g
disapprovesOf RAY7IdUcyQ8P_WCO6o9NDMz9q2LN6w7bl7ZJnsHQ_sO5g
Now session on investor views: "don't tailor your story to the investor - find the right investor for your story"
Agenda: Mitja Zdouc: Natural Product Research Data: from one star to five stars. https://zdouc-lab.github.io/zdouc-lab-website/ Roberto Pizzolotto: Biodiversity structured information, from species list to network through nanopublications Zoom link Notes
Listening to Tobias Rain on the story of GetYourGuide.
Now at a session on sales strategy. Julian Liniger (Relai): "Product has to come first, sales afterwards. You need to fully focus the first few years on making a great product. Only then sales makes even sense."
Nano Session #30 has speaker roberto pizzolotto
Nano Session #30 has speaker Mitja M. Zdouc
Nano Session #30 has admin Ashley Caselli
Nano Session #30 has role: General participant role
Nano Session #30 has role: Planned attendance role
Nano Session #30 has role: Observer role
Now at a session centered around Oomnium and its crowd-financing platform.
Interesting: Pivotal AG, a company that helps startups pivoting. (Right now listening to its CEO Stefan Zanetti)
At the Swiss Startup Association's Founders Day today all day. Really enjoying it :)
Attending Founders Day (https://swissstartupassociation.ch/founders-day-2026/), where Cristian Grossman (Beekeeper) is saying: "as an early stage startup, you shoul fall in love with the problem, not with your solution".
The creator of such a nanopublication declares to be a participant in the specified Space.
${participant} is participant in ${space}
A paper describing AMIE (Articulate Medical Intelligence Explorer)
Yuanxi Fu displays view: Presentations by speaker view
FIP.38.T.1 | FAIR Implementation Profile Training Session 1