cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14997297
title: O'Hare, et al., 2025, Neuron

description: Data and code to reproduce results in O'Hare et al., 2025 (Neuron). 

Everything in this folder is self-contained. Wherever you unzip it, you should run things exclusively from within it.

 

Contents:

1. Jupyter notebook (made in Jupyter Lab) to reproduce all analytical plots

2. plotting_utils Python module to assist Jupyter notebook

3. lab Python module to illustrate operations for template-based event detection and plateau potential classification

4. Conda environment for all code. See instructions below. You'll need 1.33 GB to unpack this environment.

 

To get going:

1. Unpack conda environments (locally, no need to permanently link to your conda install!)

   a.  ohare2025 needs to be unpacked from .tar.gz file. to do so:

      i. cd /path/to/folder/OHare2025_code/envs

      ii. mkdir ohare2025

      iii. tar -xzf ohare2025-env.tar.gz -C ohare2025 #unpack into empty ohare2025 folder. may take a while.

 

2. Register the ohare2025 env as a Python kernel in your jupyter lab/notebook distribution.

   a. open whatever conda environment you normally use to run jupyter

   b. install ipykernel if you don't have it: pip install ipykernel #do NOT use conda install here!

   c. conda deactivate #unless running jupyter from base, in which case skip this command

   d. source /path/to/folder/OHare2025_code/envs/ohare2025/bin/activate #activates the conda env in-place

   e. python -m ipykernel install --prefix /path/to/jupyterlab_env --name ohare2025 --display-name "Python 2.7 (OHare2025)"

   f. exit the ohare2025 env

      deactivate #don't use conda here

      source ~/.bashrc #if you still see ohare2025 hanging around in your command prompt

   g. return to your jupyter env and verify kernel installed: 

      conda activate <env_you_use_for_jupyter>

      jupyter kernelspec list #you should see it here, located in its conda env, e.g. ~/miniconda3/envs/jupyter/share/jupyter/kernels/ohare2025

 

3. Launch jupyter lab/notebook.

   a. cd /path/to/folder/OHare2025_code #this is critical

   b. launch jupyter lab:

       jupyter lab #or jupyter notebook, if that's your jam

   c. open O'Hare_2025_Figs.ipynb from the file explorer tab and select the new OHare2025 kernel you created.

 

Enjoy!

Code is shown exactly as used to produce each data figure in our manuscript. Feel free to explore the datasets further - they are stored as Pandas DataFrames in .pkl files and are thoroughly annotated, e.g. with animal ID, dendrite type, dendrite order, dendrite path distance to soma, dendrite parent soma, ROI genotype, etc. Enjoy!

*Note: The Jupyter notebook was created in JupyterLab to enable toggling by figure. It may also function in a classical Jupyter notebook with nbextensions enabled. Without toggling, these notebooks will be unwieldy.
DOI: 10.15468/dl.r8py29
title: Occurrence Download

description: A dataset containing 58104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aedes aegypti (Linnaeus, 1762)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 58104 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006230-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kgxh27
title: Occurrence Download

description: A dataset containing 189 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mactra chinensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 189 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008858-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e5wzez
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinanga javana"
 ]
}

 The dataset includes 29 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008859-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmwzg4
title: Occurrence Download

description: A dataset containing 1161575 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia",
 "Year 2010-2023"
 ]
}

 The dataset includes 1161575 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008839-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tx4x8e
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-44.7674 -22.53342,-44.49246 -22.53342,-44.49246 -22.31847,-44.7674 -22.31847,-44.7674 -22.53342))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cyatheaceae"
 ]
}

 The dataset includes 78 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008862-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rczfgm
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ridolfia segetum",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 30 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008863-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5tux6
title: Occurrence Download

description: A dataset containing 589 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ridolfia segetum",
 "Country is Spain",
 "HasCoordinate is true"
 ]
}

 The dataset includes 589 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008864-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.36e3m5
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Material citation",
 "Country is Peru",
 "Geometry POLYGON((-81.89351 -20.55372,-65.22900 -20.55372,-65.22900 -13.89159,-81.89351 -13.89159,-81.89351 -20.55372))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Eurhomalea lenticularis"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008861-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pxct9e
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinanga javana"
 ]
}

 The dataset includes 29 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008865-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5a3n6z
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinanga javana"
 ]
}

 The dataset includes 29 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008866-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mvw668
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mactra cuneata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008867-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ujrvzn
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Seseli campestre",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 29 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008868-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnb3vc
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mactra glabrata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 41 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008869-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dvuqg6
title: Occurrence Download

description: A dataset containing 1013 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Smyrnium perfoliatum",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1013 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008871-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ba7gdy
title: Occurrence Download

description: A dataset containing 194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Smyrnium perfoliatum",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 194 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008870-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dt8y7x
title: Occurrence Download

description: A dataset containing 477 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Smyrnium perfoliatum",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 477 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008872-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pzjjug
title: Occurrence Download

description: A dataset containing 447 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Inga edulis"
 ]
}

 The dataset includes 447 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008873-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.393n2b
title: Occurrence Download

description: A dataset listing the 4069759 species recorded in GBIF matching the query:
{
 "OccurrenceStatus" : [
 "is Present"
 ]
}

 The dataset's 4069759 records were derived from 76459 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008846-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wr4s7e
title: Occurrence Download

description: A dataset containing 530 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mactra glauca",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 530 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008874-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4cnxc3
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Colombia, Mexico, Costa Rica)",
 "TaxonKey is Melpomene peruviana"
 ]
}

 The dataset includes 21 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008875-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p6p4mb
title: Occurrence Download

description: A dataset containing 519 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Smyrnium perfoliatum",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 519 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008877-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5unjg9
title: Occurrence Download

description: A dataset containing 494 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Smyrnium perfoliatum",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 494 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008878-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wdqf48
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ptychococcus paradoxus"
 ]
}

 The dataset includes 148 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008876-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6nh4w6
title: Occurrence Download

description: A dataset containing 1113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Smyrnium perfoliatum",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1113 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008879-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11096333
title: Key dataset used in the paper of "Emergent constraints reveal lower estimates of global river flow"

description: This dataset includes key data used in the emergent constraint approach for refined partitioning of global water cycle components.
DOI: 10.5281/zenodo.11096334
title: Key dataset used in the paper of "Emergent constraints reveal lower estimates of global river flow"

description: This dataset includes key data used in the emergent constraint approach for refined partitioning of global water cycle components.
DOI: 10.5281/zenodo.17138406
title: Conjunto de dados com filmes, séries, videoclipes e outras produções audiovisuais que representam bibliotecários, bibliotecas ou biblioteconomia

description: Planilha .xlsx contendo 1 aba denominada CONJUNTO DE DADOS, com 150 registros de produções audiovisuais que representam bibliotecários, bibliotecas ou biblioteconomia em cenas ou diálogos contendo título, tipo de obra audiovisual, ano, temporada/episódio, minutagem aproximada e observações.
DOI: 10.5281/zenodo.17138407
title: Conjunto de dados com filmes, séries, videoclipes e outras produções audiovisuais que representam bibliotecários, bibliotecas ou biblioteconomia

description: Planilha .xlsx contendo 1 aba denominada CONJUNTO DE DADOS, com 150 registros de produções audiovisuais que representam bibliotecários, bibliotecas ou biblioteconomia em cenas ou diálogos contendo título, tipo de obra audiovisual, ano, temporada/episódio, minutagem aproximada e observações.
DOI: 10.15468/dl.y8m9sf
title: Occurrence Download

description: A dataset containing 98 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhopaloblaste ledermanniana"
 ]
}

 The dataset includes 98 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008882-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eh9pb8
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dipterocarpus cinereus"
 ]
}

 The dataset includes 9 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008883-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bhdmnb
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mactra grandis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 37 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008884-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.786vgf
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhopaloblaste ceramica"
 ]
}

 The dataset includes 53 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008885-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmkrd2
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((252.58280 -14.54926,290.49553 -14.54926,290.49553 0.60748,252.58280 0.60748,252.58280 -14.54926))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bostrycapulus calyptraeiformis"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008886-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uf785k
title: Occurrence Download

description: A dataset containing 45821 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Placopecten magellanicus",
 "Year 2000-2025"
 ]
}

 The dataset includes 45821 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008887-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mdpczy
title: Occurrence Download

description: A dataset containing 1916 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Smyrnium perfoliatum",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1916 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008888-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z8tq4h
title: Occurrence Download

description: A dataset containing 20170 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'SZ'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence."year" &gt;= 2001 AND occurrence."year" &lt;= 2025)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 20170 records were derived from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008860-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.