cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1032172.10fu
title: SH1032172.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1032173.10fu
title: SH1032173.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1032174.10fu
title: SH1032174.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.m76hra
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyla hazelae Taylor, 1940"
 ]
}

 The dataset includes 56 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0116503-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1032175.10fu
title: SH1032175.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1032176.10fu
title: SH1032176.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.cpupcn
title: Occurrence Download

description: A dataset containing 36925 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Vespa velutina Lepeletier, 1836"
 ]
}

 The dataset includes 36925 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0131890-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wyusqf
title: Occurrence Download

description: A dataset containing 187598 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Juglans regia L."
 ]
}

 The dataset includes 187598 records from 1501 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007063-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rrv7g9
title: Occurrence Download

description: A dataset containing 197 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Faramea martiana Müll.Arg."
 ]
}

 The dataset includes 197 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013496-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fczm77
title: Occurrence Download

description: A dataset containing 303 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Flagellostomias boureei (Zugmayer, 1913)"
 ]
}

 The dataset includes 303 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038486-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5pzwu4
title: Occurrence Download

description: A dataset containing 42940 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Country is one of (United States of America, Mexico, Canada)",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Urophycis chuss (Walbaum, 1792)"
 ]
}

 The dataset includes 42940 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048587-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kjxduv
title: Occurrence Download

description: A dataset containing 1207 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "Geometry POLYGON((-71.69133 -30.53123,-71.695 -30.54698,-71.7055 -30.55748,-71.71285 -30.59003,-71.71075 -30.6252,-71.7139 -30.64567,-71.716 -30.66457,-71.7055 -30.68557,-71.70708 -30.70552,-71.71495 -30.71707,-71.70865 -30.73125,-71.69185 -30.7302,-71.67873 -30.72547,-71.66245 -30.72967,-71.62256 -30.72495,-71.60051 -30.71445,-71.58371 -30.705,-71.56743 -30.68872,-71.55956 -30.6756,-71.55326 -30.66982,-71.54486 -30.67087,-71.53488 -30.67192,-71.53908 -30.63465,-71.53856 -30.5763,-71.53803 -30.53063,-71.56113 -30.5049,-71.60418 -30.49283,-71.6341 -30.48758,-71.65983 -30.48548,-71.68293 -30.49073,-71.69185 -30.49965,-71.69343 -30.50963,-71.69343 -30.5196,-71.69133 -30.53123))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 1207 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0405327-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qazfwe
title: Occurrence Download

description: A dataset containing 990 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acanthastrea echinata (Dana, 1846)"
 ]
}

 The dataset includes 990 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078988-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ymm7w9
title: Occurrence Download

description: A dataset containing 4339 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Manilkara zapota (L.) P.Royen"
 ]
}

 The dataset includes 4339 records from 246 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044327-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k4de3p
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cedrela odorata L."
 ]
}

 The dataset includes 148 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0405336-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.apqhy9
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "TaxonKey is Liparis nervosa (Thunb.) Lindl."
 ]
}

 The dataset includes 14 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038790-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dp2xbc
title: Occurrence Download

description: A dataset containing 25461 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "DatasetKey is Observation.org, Nature data from around the World"
 ]
 },
 "Geometry POLYGON((-12.30469 25.195,72.77344 25.195,72.77344 71.08474,-12.30469 71.08474,-12.30469 25.195))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "Issue is Country derived from coordinates",
 "Issue is Occurrence status inferred from individual count",
 "Issue is Coordinate rounded",
 "Issue is Occurrence status unparsable"
 ]
 },
 {
 "or" : [
 "License is CC-BY-NC 4.0",
 "License is CC0 1.0"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Fagus sylvatica L."
 ]
}

 The dataset includes 25461 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0405341-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g5eazh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is one of (Uronema confervicolum var. uncinatum Popova;Uronema confervicolum var. uncinatum)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Country is Ukraine"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091412-230530130749713/datasets/export for details.
DOI: 10.15468/dl.hwa9t6
title: Occurrence Download

description: A dataset containing 1350101 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "StateProvince is one of (cundinamarca)"
 ]
}

 The dataset includes 1350101 records from 630 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0405339-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ksmat
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is South America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gouinia latifolia (Griseb.) Vasey",
 "Year 1908-2023"
 ]
}

 The dataset includes 56 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048596-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7cmsk2
title: Occurrence Download

description: A dataset containing 2035 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Celtis sinensis Pers."
 ]
}

 The dataset includes 2035 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0205569-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dmctjq
title: Occurrence Download

description: A dataset containing 1116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "Country is Ecuador",
 "Country is Mexico"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cedrela odorata L."
 ]
}

 The dataset includes 1116 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0405342-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22008/fk2/iw73uu/pjfvm1
title: KAN_U_month.nc

description: Uploaded with pyDataverse 2024-04-24 20:45
DOI: 10.15468/dl.n8v4d7
title: Occurrence Download

description: A dataset containing 851 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Solanum scuticum M.Nee"
 ]
}

 The dataset includes 851 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044346-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kym5mz
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is South America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Poidium uniolae (Nees) Matthei",
 "Year 1908-2023"
 ]
}

 The dataset includes 25 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048586-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97q5gb
title: Occurrence Download

description: A dataset listing the 1759773 species recorded in GBIF matching the query:
{
 "and" : [
 "MediaType is one of (Image, Video)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 1759773 records were derived from 1381 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004003-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17041824
title: CollectiveOS White Paper: Open Bio-Simulation Models

description: CollectiveOS White Paper: Open Bio-Simulation Models

Author: Mark Anthony Brewer (Brewtanius)

Abstract

The Open Bio-Simulation Models initiative demonstrates how CollectiveOS can democratize science at its most complex frontier: the simulation of living systems. By combining curated, standardized biological models with generative AI-driven hypothesis tools, CollectiveOS offers the world’s first open, virtual wet-lab for both education and discovery. This project embodies the CollectiveOS ethos: building not only for performance, but for trust, reproducibility, and global access.

1. Genesis and Rationale

For decades, biological simulation has been locked inside institutional labs and proprietary software. CollectiveOS reverses that paradigm by treating biology as a commons, where simulations, models, and generative exploration are available to anyone with a consumer device.

2. Dual-Agent R&D Process

Agent 1 – Bio-Informatics Specialist





Ingests and standardizes existing models (SBML, CellML).




Validates and curates user submissions for simulation readiness.




Anchors the core simulation engine with stability and rigor.



Agent 2 – Generative AI Engineer





Designs models that generate plausible new biological pathways.




Provides natural language querying so non-specialists can “talk to” the sandbox.




Creates intuitive, interactive visualizations for education and research.



Meeting in the Middle: Their outputs converge in the CollectiveOS Bio-Simulation Sandbox, where verified models and speculative hypotheses coexist, creating a spectrum of use from high-school education to advanced drug discovery.

3. Core Values





Accessibility: Runs on consumer devices under CollectiveOS.




Transparency: Every model and hypothesis is traceable in a Proof Vault.




Community: A shared commons where students, researchers, and practitioners can build on each other’s work.



4. Significance

This project precedes and complements the more visible breakthroughs (e.g., the Millennium Problem solutions). It demonstrates that CollectiveOS is not only capable of extreme feats but is also grounded in pragmatic, human-first science that immediately benefits classrooms, clinics, and independent researchers.

Conclusion

The Open Bio-Simulation Models initiative is more than a platform—it is a statement of intent. It shows that Mark Anthony Brewer (Brewtanius) and the CollectiveOS vision are committed to transforming biology into an open, participatory science. By starting here, we set the precedent that every subsequent breakthrough will be shared in a way the world can trust, learn from, and build upon.
DOI: 10.5281/zenodo.17041825
title: CollectiveOS White Paper: Open Bio-Simulation Models

description: CollectiveOS White Paper: Open Bio-Simulation Models

Author: Mark Anthony Brewer (Brewtanius)

Abstract

The Open Bio-Simulation Models initiative demonstrates how CollectiveOS can democratize science at its most complex frontier: the simulation of living systems. By combining curated, standardized biological models with generative AI-driven hypothesis tools, CollectiveOS offers the world’s first open, virtual wet-lab for both education and discovery. This project embodies the CollectiveOS ethos: building not only for performance, but for trust, reproducibility, and global access.

1. Genesis and Rationale

For decades, biological simulation has been locked inside institutional labs and proprietary software. CollectiveOS reverses that paradigm by treating biology as a commons, where simulations, models, and generative exploration are available to anyone with a consumer device.

2. Dual-Agent R&D Process

Agent 1 – Bio-Informatics Specialist





Ingests and standardizes existing models (SBML, CellML).




Validates and curates user submissions for simulation readiness.




Anchors the core simulation engine with stability and rigor.



Agent 2 – Generative AI Engineer





Designs models that generate plausible new biological pathways.




Provides natural language querying so non-specialists can “talk to” the sandbox.




Creates intuitive, interactive visualizations for education and research.



Meeting in the Middle: Their outputs converge in the CollectiveOS Bio-Simulation Sandbox, where verified models and speculative hypotheses coexist, creating a spectrum of use from high-school education to advanced drug discovery.

3. Core Values





Accessibility: Runs on consumer devices under CollectiveOS.




Transparency: Every model and hypothesis is traceable in a Proof Vault.




Community: A shared commons where students, researchers, and practitioners can build on each other’s work.



4. Significance

This project precedes and complements the more visible breakthroughs (e.g., the Millennium Problem solutions). It demonstrates that CollectiveOS is not only capable of extreme feats but is also grounded in pragmatic, human-first science that immediately benefits classrooms, clinics, and independent researchers.

Conclusion

The Open Bio-Simulation Models initiative is more than a platform—it is a statement of intent. It shows that Mark Anthony Brewer (Brewtanius) and the CollectiveOS vision are committed to transforming biology into an open, participatory science. By starting here, we set the precedent that every subsequent breakthrough will be shared in a way the world can trust, learn from, and build upon.
DOI: 10.15468/dl.vn5pk8
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Xanthium strumarium",
 "Country is Oman",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020359-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17041829
title: Covers Abkhaz 101-120
DOI: 10.5281/zenodo.17041828
title: Covers Abkhaz 101-120