cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/trp-3cy-cft
title: Hemicypris Sars, 1903

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p1t-8f9-0ld
title: Aretopsis amabilis De Man, 1910

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fjl-79z-3bh
title: Polybius pusillus (Leach, 1816)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h1p-5cr-xwb
title: Parabetaeus euryone (De Man, 1910)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3f9-4ww-3gw
title: Corystes cassivelaunus (Pennant, 1777)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mlm-cne-wwe
title: Gilvossius tyrrhenus (Petagna, 1792)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/59h-s93-trr
title: Balanus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j6g-cxv-ssx
title: Macropodia rostrata (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3cq-fzx-hdg
title: Pachylasmatidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4vj-kll-hbp
title: Pseudocandona Kaufmann, 1900

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/95z-647-xz8
title: Chthamalus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yte-h6k-2cb
title: Candonidae Kaufmann, 1900

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bcj-s5c-n79
title: Gammarus locusta (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a0d-xlw-tyb
title: Abludomelita obtusata (Montagu, 1813)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vgk-pq6-bvy
title: Gammarus wautieri A. L. Roux, 1967

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7rv-12a-lkz
title: Cystisoma pellucida (Willemöes-Suhm, 1873)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3gv-sct-gp9
title: Calappa Weber, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nld-z7d-x29
title: Talitroides topitotum (Burt, 1934)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kk3-nvs-k39
title: Camposcia retusa (Latreille, 1829)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zpf-6lr-fne
title: Podophthalmus vigil (Fabricius, 1798)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7mk-7gr-qtq
title: Eualus cranchii (Leach, 1817)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/erv-8dt-4xp
title: Thalamita sexlobata Miers, 1886

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ndj-3zg-ke9
title: Pollicipes

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.n67h45
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leucas lavandulifolia Sm.",
 "Country is Solomon Islands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104343-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/2wk-2b3-bh5
title: Latreutes fucorum (J. C. Fabricius, 1798)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q7h-7w6-c8l
title: Peltogaster

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e63-y6c-m3e
title: Caridina nilotica (P. Roux, 1833)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yw4-6vp-lq7
title: Xanthidae MacLeay, 1838

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hn3-546-532
title: Balanidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.18176365
title: General Description of Project - AIRPRO
DOI: 10.5281/zenodo.18176366
title: General Description of Project - AIRPRO
DOI: 10.5281/zenodo.15244644
title: ProtCLIP: Function-Informed Protein Multi-Modal Learning

description: Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were still unable to replicate the extraordinary success of language-supervised visual foundation models due to the ineffective usage of aligned protein-text paired data and the lack of an effective function-informed pre-training paradigm. To address these issues, this paper curates a large-scale protein-text paired dataset called ProtAnno with a property-driven sampling strategy, and introduces a novel function-informed protein pre-training paradigm. Specifically, the sampling strategy determines selecting probability based on the sample confidence and property coverage, balancing the data quality and data quantity in face of large-scale noisy data. Furthermore, motivated by significance of the protein specific functional mechanism, the proposed paradigm explicitly model protein static and dynamic functional segments by two segment-wise pre-training objectives, injecting fine-grained information in a function-informed manner. Leveraging all these innovations, we develop ProtCLIP, a multi-modality foundation model that comprehensively represents function-aware protein embeddings. On 22 different protein benchmarks within 5 types, including protein functionality classification, mutation effect prediction, cross-modal transformation, semantic similarity inference and protein-protein interaction prediction, our ProtCLIP consistently achieves SOTA performance, with remarkable improvements of 75% on average in five cross-modal transformation benchmarks, 59.9% in GO-CC and 39.7% in GO-BP protein function prediction. The experimental results verify the extraordinary potential of ProtCLIP serving as the protein multi-modality foundation model.

This repository contains the ProtAnno dataset and model weights for ProtCLIP.
DOI: 10.5281/zenodo.15244645
title: ProtCLIP: Function-Informed Protein Multi-Modal Learning

description: Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were still unable to replicate the extraordinary success of language-supervised visual foundation models due to the ineffective usage of aligned protein-text paired data and the lack of an effective function-informed pre-training paradigm. To address these issues, this paper curates a large-scale protein-text paired dataset called ProtAnno with a property-driven sampling strategy, and introduces a novel function-informed protein pre-training paradigm. Specifically, the sampling strategy determines selecting probability based on the sample confidence and property coverage, balancing the data quality and data quantity in face of large-scale noisy data. Furthermore, motivated by significance of the protein specific functional mechanism, the proposed paradigm explicitly model protein static and dynamic functional segments by two segment-wise pre-training objectives, injecting fine-grained information in a function-informed manner. Leveraging all these innovations, we develop ProtCLIP, a multi-modality foundation model that comprehensively represents function-aware protein embeddings. On 22 different protein benchmarks within 5 types, including protein functionality classification, mutation effect prediction, cross-modal transformation, semantic similarity inference and protein-protein interaction prediction, our ProtCLIP consistently achieves SOTA performance, with remarkable improvements of 75% on average in five cross-modal transformation benchmarks, 59.9% in GO-CC and 39.7% in GO-BP protein function prediction. The experimental results verify the extraordinary potential of ProtCLIP serving as the protein multi-modality foundation model.
DOI: 10.5281/zenodo.15245558
title: ProtCLIP: Function-Informed Protein Multi-Modal Learning

description: Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were still unable to replicate the extraordinary success of language-supervised visual foundation models due to the ineffective usage of aligned protein-text paired data and the lack of an effective function-informed pre-training paradigm. To address these issues, this paper curates a large-scale protein-text paired dataset called ProtAnno with a property-driven sampling strategy, and introduces a novel function-informed protein pre-training paradigm. Specifically, the sampling strategy determines selecting probability based on the sample confidence and property coverage, balancing the data quality and data quantity in face of large-scale noisy data. Furthermore, motivated by significance of the protein specific functional mechanism, the proposed paradigm explicitly model protein static and dynamic functional segments by two segment-wise pre-training objectives, injecting fine-grained information in a function-informed manner. Leveraging all these innovations, we develop ProtCLIP, a multi-modality foundation model that comprehensively represents function-aware protein embeddings. On 22 different protein benchmarks within 5 types, including protein functionality classification, mutation effect prediction, cross-modal transformation, semantic similarity inference and protein-protein interaction prediction, our ProtCLIP consistently achieves SOTA performance, with remarkable improvements of 75% on average in five cross-modal transformation benchmarks, 59.9% in GO-CC and 39.7% in GO-BP protein function prediction. The experimental results verify the extraordinary potential of ProtCLIP serving as the protein multi-modality foundation model.
DOI: 10.5281/zenodo.15245588
title: ProtCLIP: Function-Informed Protein Multi-Modal Learning

description: Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were still unable to replicate the extraordinary success of language-supervised visual foundation models due to the ineffective usage of aligned protein-text paired data and the lack of an effective function-informed pre-training paradigm. To address these issues, this paper curates a large-scale protein-text paired dataset called ProtAnno with a property-driven sampling strategy, and introduces a novel function-informed protein pre-training paradigm. Specifically, the sampling strategy determines selecting probability based on the sample confidence and property coverage, balancing the data quality and data quantity in face of large-scale noisy data. Furthermore, motivated by significance of the protein specific functional mechanism, the proposed paradigm explicitly model protein static and dynamic functional segments by two segment-wise pre-training objectives, injecting fine-grained information in a function-informed manner. Leveraging all these innovations, we develop ProtCLIP, a multi-modality foundation model that comprehensively represents function-aware protein embeddings. On 22 different protein benchmarks within 5 types, including protein functionality classification, mutation effect prediction, cross-modal transformation, semantic similarity inference and protein-protein interaction prediction, our ProtCLIP consistently achieves SOTA performance, with remarkable improvements of 75% on average in five cross-modal transformation benchmarks, 59.9% in GO-CC and 39.7% in GO-BP protein function prediction. The experimental results verify the extraordinary potential of ProtCLIP serving as the protein multi-modality foundation model.

This repository contains the ProtAnno dataset and model weights for ProtCLIP.
DOI: 10.15468/dl.qjtf4c
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cussonia spicata",
 "Country is Malawi",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007388-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hytu4g
title: Occurrence Download

description: A dataset containing 857 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Persicaria odorata)",
 "DecimalLatitude is greater than or equal to 0"
 ]
}

 The dataset includes 857 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007994-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bcd9pa
title: Occurrence Download

description: A dataset containing 20948 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The dataset of bat (Chiroptera, Mammalia) occurrences in Ukraine collected by the Ukrainian Bat Rehabilitation Center (2011-2022)"
 ]
}

 The dataset includes 20948 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007992-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3y28fa
title: Occurrence Download

description: A dataset containing 14554 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((2.7315 43.56154,10.98209 43.56154,10.98209 49.10466,2.7315 49.10466,2.7315 43.56154))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lynx lynx",
 "Year 2015-2025"
 ]
}

 The dataset includes 14554 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007993-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hyuh5d
title: Occurrence Download

description: A dataset containing 13737 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhamnus saxatilis Jacq.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 13737 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055835-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bfux3f
title: Occurrence Download

description: A dataset containing 444 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epitonium albidum (d'Orbigny, 1842)"
 ]
}

 The dataset includes 444 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086950-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6mmaam
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is IDN",
 "TaxonKey is Theobroma cacao L."
 ]
}

 The dataset includes 42 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037608-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q3373x
title: Occurrence Download

description: A dataset containing 1799 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helcogramma decurrens McCulloch & Waite, 1918"
 ]
}

 The dataset includes 1799 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055836-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2dk2bg
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-87.6832617999999968 41.7646967000000018, -87.6832617999999968 41.7694057400000034, -87.6832617999999968 41.7719564599999984, -87.6832617999999968 41.7752920300000028, -87.6832617999999968 41.7776465500000000, -87.6832617999999968 41.7801972800000030, -87.6832617999999968 41.7837290499999980, -87.6832617999999968 41.7866721999999982, -87.6775573799999961 41.7866721999999982, -87.6724430799999936 41.7866721999999982, -87.6669353700000045 41.7866721999999982, -87.6635914000000014 41.7866721999999982, -87.6635914000000014 41.7831404200000023, -87.6635914000000014 41.7790200199999973, -87.6635914000000014 41.7760768699999971, -87.6635914000000014 41.7737223499999999, -87.6635914000000014 41.7707791999999998, -87.6635914000000014 41.7670512199999990, -87.6635914000000014 41.7646967000000018, -87.6689024100000012 41.7646967000000018, -87.6748035300000055 41.7646967000000018, -87.6801145400000053 41.7646967000000018, -87.6832617999999968 41.7646967000000018))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 57 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086940-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mp2sgn
title: Occurrence Download

description: A dataset containing 806 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficus tonduzii Standl.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 806 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037609-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dja8z3
title: Occurrence Download

description: A dataset containing 2391 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhodothamnus chamaecistus (L.) Rchb.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2391 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055866-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfkup4
title: Occurrence Download

description: A dataset containing 306 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phlegmariurus fordii (Baker) Ching",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 306 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0199700-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nffaex
title: Occurrence Download

description: A dataset containing 54533 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Jardín Botánico de Córdoba: Herbarium COA"
 ]
}

 The dataset includes 54533 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037623-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xcwpj5
title: Occurrence Download

description: A dataset containing 65795 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhinanthus alectorolophus (Scop.) Pollich",
 "HasCoordinate is true"
 ]
}

 The dataset includes 65795 records from 316 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055837-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8kwf7x
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epitonium babylonia (Dall, 1889)"
 ]
}

 The dataset includes 14 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086957-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.knqwhc
title: Occurrence Download

description: A dataset containing 710 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centropyge fisheri (Snyder, 1904)"
 ]
}

 The dataset includes 710 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037610-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fnstbd
title: Occurrence Download

description: A dataset containing 635 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epitonium angulatum (Say, 1831)"
 ]
}

 The dataset includes 635 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086953-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w2kh52
title: Occurrence Download

description: A dataset containing 106 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Opistognathus robinsi Smith-Vaniz, 1997"
 ]
}

 The dataset includes 106 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055867-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.