cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.22qrwt
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-141.60762 54.11934,-127.92517 54.11934,-127.92517 60.70685,-141.60762 60.70685,-141.60762 54.11934))",
 "HasGeospatialIssue is false",
 "TaxonKey is Buxbaumia viridis (Moug. ex DC.) Brid. ex Moug. & Nestl."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019997-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2sw859
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.01927 -18.03005,-69.71623 -18.03005,-69.71623 -13.76638,-75.01927 -13.76638,-75.01927 -18.03005))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Busarellus nigricollis (Latham, 1790)",
 "Year 2021-2025"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019999-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zex2r8
title: Occurrence Download

description: A dataset containing 2310 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepus saxatilis F.Cuvier, 1823"
 ]
}

 The dataset includes 2310 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019998-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60635/c3k02z
title: Barro Colorado Island, Clearing_Air Temperature

description: Air temperature, electronic sensor, interval max/min/avg
 Barro Colorado Island (BCI),Clearing ('El Claro')
 Location: 9°9'47.21"N, 79°50'17.64"W
 The Clearing Station was established in 1972. It is a small, fenced in area with nearby forest on two sides and open spaces on the other two. The surrounding vegetation if periodically pruned to prevent that significant changes to the local micro-climate. The station consists of a Stevenson screen with max/min thermometers, air pressure sensor and electronic temperature/humidity sensor. Two manual rain gauges and evaporation sensors are located at various locations close to the screen.
 Historical datasets can be located here: https://smithsonian.figshare.com/articles/dataset/Barro_Colorado_Island_Clearing_Air_Temperature/10042451
DOI: 10.60635/c3f61d
title: Barro Colorado Island, Clearing_Air Pressure

description: Air pressure, interval avg
 Barro Colorado Island (BCI),Clearing ('El Claro')
 Location: 9°9'47.21"N, 79°50'17.64"W
 The Clearing Station was established in 1972. It is a small, fenced in area with nearby forest on two sides and open spaces on the other two. The surrounding vegetation if periodically pruned to prevent that significant changes to the local micro-climate. T0he station consists of a Stevenson screen with max/min thermometers, air pressure sensor and electronic temperature/humidity sensor. Two manual rain gauges and evaporation sensors are located at various locations close to the screen.
 Historical datasets can be located here: https://smithsonian.figshare.com/articles/dataset/Barro_Colorado_Island_Clearing_Air_Pressure/10042436
DOI: 10.15468/dl.wvs92c
title: Occurrence Download

description: A dataset containing 899 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Academy of Natural Sciences Entomology Collection – OrthopNet",
 "Issue is Recorded date invalid"
 ]
}

 The dataset includes 899 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020001-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/0b3609ac248cc5ff04b45aeafcdc1548
title: Double-crested Cormorant (Nannopterum auritum) nesting colony and environmental data in Biscayne National Park, Florida, USA (2009-2024)

description: Double-crested Cormorant (DCCO) nesting data were collected from colonies in Biscayne National Park (BISC) by the South Florida/Caribbean Inventory and Monitoring Network as part of the Colonial Nesting Birds vital sign monitoring program. Nesting data collected from 2010 to 2023 are included in this dataset. Salinity, chlorophyll, and ammonia data were acquired from sites monitored in the Surface Water Quality Monitoring Program managed by the Miami-Dade County Division of Environmental Management’s Department of Regulatory and Economic Resources (RER-DERM). Seagrass data were acquired from sites monitored by RER-DERM as a part of the Biscayne Bay Benthic Habitat Monitoring Program. Mangrove fish and epifauna data were acquired from the U.S. National Oceanic and Atmospheric Administration's (NOAA) Integrated Biscayne Bay Ecological Assessment and Monitoring Project (IBBEAM). Environmental data (salinity, chlorophyll, ammonia, seagrass, mangrove fish, and epifauna) were manipulated in order to examine the relationship between DCCO nesting trends and the BISC ecosystem. This data package is completed. Code included is pertinent to the methods described in "Assessment of ecosystem health in Biscayne National Park, Florida according to Double-crested Cormorant (Nannopterum auritum) nesting trends" by Taylor et al. 2025, currently submitted to and under review by Ecological Indicators.
DOI: 10.5281/zenodo.15359483
title: Data IJEBEG

description: Survey data conducted to 377 batik industry
DOI: 10.5281/zenodo.15359484
title: Data IJEBEG

description: Survey data conducted to 377 batik industry
DOI: 10.60635/c39g76
title: Barro Colorado Island, Clearing_Relative Humidity

description: Interval avg/max/min electronic sensor Relative HumidityBarro Colorado Island (BCI),Clearing ('El Claro')Location: 9°9'47.21"N, 79°50'17.64"WThe Clearing Station was established in 1972. It is a small, fenced in area with nearby forest on two sides and open spaces on the other two. The surrounding vegetation if periodically pruned to prevent that significant changes to the local micro-climate. The station consists of a Stevenson screen with max/min thermometers, air pressure sensor and electronic temperature/humidity sensor. Two manual rain gauges and evaporation sensors are located at various locations close to the screen.Historical datasets can be located here: https://smithsonian.figshare.com/articles/dataset/Barro_Colorado_Island_Clearing_Relative_Humidity_manual/10042457
DOI: 10.15468/dl.xxa572
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cattleya lawrenceana Rchb.f."
 ]
}

 The dataset includes 53 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020002-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60635/c35p6n
title: Barro Colorado Island, Clearing_Electronic Precipitation

description: Precipitation, electronic, Interval totals
 Barro Colorado Island (BCI),Clearing ('El Claro')
 Location: 9°9'47.21"N, 79°50'17.64"W
 The Clearing Station was established in 1972. It is a small, fenced in area with nearby forest on two sides and open spaces on the other two. The surrounding vegetation if periodically pruned to prevent that significant changes to the local micro-climate. The station Consists of a Stevenson screen with max/min thermometers, air pressure sensor and electronic temperature/humidity sensor. Two manual rain gauges and evaporation sensors are located at various locations close to the screen.
 Historical datasets can be located here: https://smithsonian.figshare.com/articles/dataset/Barro_Colorado_Island_Clearing_Precipitation/10042463
DOI: 10.60635/c32029
title: Barro Colorado Island, Clearing_Precipitation, manual

description: Manual Precipitation, daily
 Barro Colorado Island (BCI),Clearing ('El Claro')
 Location: 9°9'47.21"N, 79°50'17.64"W
 The Clearing Station was established in 1972. It is a small, fenced in area with nearby forest on two sides and open spaces on the other two. The surrounding vegetation if periodically pruned to prevent that significant changes to the local micro-climate. The station consists of a Stevenson screen with max/min thermometers, air pressure sensor and electronic temperature/humidity sensor. Two manual rain gauges and evaporation sensors are located at various locations close to the screen.
 Historical datasets can be located here: https://smithsonian.figshare.com/articles/dataset/Barro_Colorado_Island_Clearing_Precipitation_manual/10042502
DOI: 10.15468/dl.pa8f8n
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-72.4589 -14.16587,-70.35788 -14.16587,-70.35788 -11.93761,-72.4589 -11.93761,-72.4589 -14.16587))",
 "HasGeospatialIssue is false",
 "TaxonKey is Hesperomeles Lindl."
 ]
}

 The dataset includes 126 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020003-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15359522
title: Supplementary Table 2

description: Rice accession used in this study and their metadata
DOI: 10.5281/zenodo.15359523
title: Supplementary Table 2

description: Rice accession used in this study and their metadata
DOI: 10.15468/dl.zsg69y
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stenocactus zacatecasensis (Britton & Rose) A.Berger ex A.W.Hill"
 ]
}

 The dataset includes 13 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020005-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.84984v
title: Occurrence Download

description: A dataset containing 768 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-73.15856 -16.95598,-69.28647 -17.58296,-69.28647 -13.77643,-73.72322 -13.77643,-75.14056 -15.48291,-73.15856 -16.95598))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Daptrius Vieillot, 1816",
 "Year 2021-2025"
 ]
}

 The dataset includes 768 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020004-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n94qy6
title: Occurrence Download

description: A dataset containing 17673 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Procyon lotor (Linnaeus, 1758)"
 ]
}

 The dataset includes 17673 records from 187 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020006-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/36a-ntj-y81
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qw1-5ab-a1l
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v4m-bb8-qkp
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pd1-9db-cjm
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r25-zm9-vlg
title: †Nummulites Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wm0-n6p-eyy
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/aa3-87f-r2b
title: Amphistegina lessonii d'Orbigny in Deshayes, 1830

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h65-frl-jf1
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1z2-jhr-pyy
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tyv-6q1-9dt
title: Globigerina bulloides d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rgy-k7a-r2s
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vp5-wqt-0pq
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2xw-6ey-zge
title: Globigerina

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/egp-mps-re2
title: †Camerina discoidea Caudri, 1934

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ys7-099-mjj
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5hs-zza-pqa
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kka-xeq-y6n
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/40k-9kp-ae8
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fl4-pax-wwx
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.14029554
title: Supplemental tables for 'Pan-microalgal dark proteome mapping via interpretable deep learning and synthetic chimeras'

description: Distinguishing genuine microbial proteins from contaminants remains a major bottleneck in genomics, particularly for environmental and non-model organisms where conventional homology-based tools are slow, resource-intensive, and leave large fractions of the "dark proteome" unclassified. LA4SR offers a scalable, interpretable framework that classifies algal and bacterial proteins directly from translated sequence data, achieving near-complete recall while accelerating inference by ~ 10,000-fold relative to BLASTP. By revealing that internal sequence features alone can drive robust classification, LA4SR bypasses the need for complete gene models or perfect annotations—opening new opportunities for analyzing complex microbial communities and metagenomes. Interpretability methods further link emergent amino acid signatures to evolutionary and ecological features, highlighting the potential of language models not only to accelerate genomics workflows but also to uncover new biological insights.

 

Table S1 | External spreadsheet. This spreadsheet contains LA4SR performance metrics, technical performance estimations, and BLAST results and runtimes of genomes comprising the algal training data. 

Table S2 | External spreadsheet. Captum attributions for 100 sequences each of algal and bacterial origin obtained using the LayerIntegratedGradients function.

Table S3 | External spreadsheet. Influential motifs found with the DeepMotifMinerPro software introduced in this work (see Data S3).

Table S4 | External spreadsheet. LA4SR and Diamond BLAST results for data from new assemblies from seen species (Fig. S7), contaminated assemblies from unseen genera (Fig. S7), and clean assemblies from unseen genera (Fig. 8). For the LA4SR results for genome assemblies from unseen genera, the genomes were published after the model was trained, and the genera shown were not included in the training dataset. Newly sequenced genomes uploaded to NCBI SRA accession SUB14799921.
DOI: 10.5281/zenodo.16901165
title: Supplemental tables for 'Pan-microalgal dark proteome mapping via interpretable deep learning and synthetic chimeras'

description: Distinguishing genuine microbial proteins from contaminants remains a major bottleneck in genomics, particularly for environmental and non-model organisms where conventional homology-based tools are slow, resource-intensive, and leave large fractions of the "dark proteome" unclassified. LA4SR offers a scalable, interpretable framework that classifies algal and bacterial proteins directly from translated sequence data, achieving near-complete recall while accelerating inference by ~ 10,000-fold relative to BLASTP. By revealing that internal sequence features alone can drive robust classification, LA4SR bypasses the need for complete gene models or perfect annotations—opening new opportunities for analyzing complex microbial communities and metagenomes. Interpretability methods further link emergent amino acid signatures to evolutionary and ecological features, highlighting the potential of language models not only to accelerate genomics workflows but also to uncover new biological insights.

 

Table S1 | External spreadsheet. This spreadsheet contains LA4SR performance metrics, technical performance estimations, and BLAST results and runtimes of genomes comprising the algal training data. 

Table S2 | External spreadsheet. Captum attributions for 100 sequences each of algal and bacterial origin obtained using the LayerIntegratedGradients function.

Table S3 | External spreadsheet. Influential motifs found with the DeepMotifMinerPro software introduced in this work (see Data S3).

Table S4 | External spreadsheet. LA4SR and Diamond BLAST results for data from new assemblies from seen species (Fig. S7), contaminated assemblies from unseen genera (Fig. S7), and clean assemblies from unseen genera (Fig. 8). For the LA4SR results for genome assemblies from unseen genera, the genomes were published after the model was trained, and the genera shown were not included in the training dataset. Newly sequenced genomes uploaded to NCBI SRA accession SUB14799921.
DOI: 10.15468/dl.f5e7zx
title: Occurrence Download

description: A dataset containing 114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hypnea musciformis",
 "Country is Ghana",
 "HasCoordinate is true"
 ]
}

 The dataset includes 114 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022750-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/79j-ysk-s2p
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5vn-e7d-x11
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lqr-bz1-4ps
title: †Nummulites Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/64s-8ct-d1k
title: Spiroloculina depressa d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m0n-d6y-r39
title: Cibicides refulgens Montfort, 1808

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rla-0ea-rjx
title: †Lepidosemicyclina bifida (Rutten, 1912)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4g3-h95-3wl
title: †Nummulites Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c8l-mf4-vcn
title: †Spiroclypeus Douvillé, 1905

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cja-7jm-7c5
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vpr-0tn-hlp
title: †Rotalia Lamarck, 1804

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0v8-v2y-52n
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1y7-aw9-kr8
title: Asteroidea de Blainville, 1830

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b09-y0a-mrw
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m50-y7r-fpz
title: Amphistegina d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/krm-5q4-gp3
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/04k-49f-pyj
title: †Belorussiella textilarioides (Reuss, 1863)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0px-n80-njn
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bkw-y9m-yml
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ftf-w02-e2b
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lpp-av7-fvg
title: †Nummulites Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kcx-y01-db7
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.tab8tw
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"TUR.59.1_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007152-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.acqf5c
title: Occurrence Download

description: A dataset containing 1881 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acacia macracantha Humb. & Bonpl. ex Willd."
 ]
}

 The dataset includes 1881 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031457-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.