cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7758090
title: SANTOS Benchmark for Table Union Search

description: This record contains the datasets released with SIGMOD 2023 paper entitled "SANTOS: Relationship-based Semantic Table Union Search". We release two new tabular benchmarks to evaluate the table union search problem over the data lakes. Furthermore, we also release relabeled ground truth for an existing TUS benchmark by taking the binary relationship between the columns into account. Please visit our paper for further details.

If you use our dataset for your work, please cite our paper as:

Aamod Khatiwada, Grace Fan, Roee Shraga, Zixuan Chen, Wolfgang Gatterbauer, Renée J. Miller, and MirekRiedewald. 2023. SANTOS: Relationship-based Semantic Table Union Search. SIGMOD Conference 2023, ACM

@article{DBLP:journals/pacmmod/KhatiwadaFSCGMR23,  author       = {Aamod Khatiwada and                  Grace Fan and                  Roee Shraga and                  Zixuan Chen and                  Wolfgang Gatterbauer and                  Ren{\'{e}}e J. Miller and                  Mirek Riedewald},  title        = {{SANTOS:} Relationship-based Semantic Table Union Search},  journal      = {Proc. {ACM} Manag. Data},  volume       = {1},  number       = {1},  pages        = {9:1--9:25},  year         = {2023},  doi          = {10.1145/3588689},}

You can find SANTOS implementation at: https://github.com/northeastern-datalab/santos

You can find the original TUS benchmark at: https://github.com/RJMillerLab/table-union-search-benchmark

Abstract: Existing techniques for unionable table search define unionability using metadata (tables must have the same or similar schemas) or column-based metrics (for example, the values in a table should be drawn from the same domain). In this work, we introduce the use of semantic relationships between pairs of columns in a table to improve the accuracy of union search. Consequently, we introduce a new notion of unionability that considers relationships between columns, together with the semantics of columns, in a principled way. To do so, we present two new methods to discover semantic relationship between pairs of columns: The first uses an existing knowledge base (KB), the second (which we call a “synthesized KB”) uses knowledge from the data lake itself. We adopt an existing Table Union Search benchmark and present new (open) benchmarks that represent small and large real data lakes. We show that our new unionability search algorithm called SANTOS outperforms a state-of-the-art union search that uses a wide variety of column-based semantics, including word embeddings and regular expressions. We show empirically in all benchmarks that our synthesized KB improves the accuracy of union search by representing relationship semantics that may not be contained in an available KB. This result hints at a promising future of creating a synthesized KBs from data lakes with limited KB coverage and using them for union search.
DOI: 10.5281/zenodo.7758091
title: SANTOS Benchmark for Table Union Search

description: This record contains the datasets released with SIGMOD 2023 paper entitled "SANTOS: Relationship-based Semantic Table Union Search". We release two new tabular benchmarks to evaluate the table union search problem over the data lakes. Furthermore, we also release relabeled ground truth for an existing TUS benchmark by taking the binary relationship between the columns into account. Please visit our paper for further details.

If you use our dataset for your work, please cite our paper as:

Aamod Khatiwada, Grace Fan, Roee Shraga, Zixuan Chen, Wolfgang Gatterbauer, Renée J. Miller, and MirekRiedewald. 2023. SANTOS: Relationship-based Semantic Table Union Search. SIGMOD Conference 2023, ACM

@article{DBLP:journals/pacmmod/KhatiwadaFSCGMR23,  author       = {Aamod Khatiwada and                  Grace Fan and                  Roee Shraga and                  Zixuan Chen and                  Wolfgang Gatterbauer and                  Ren{\'{e}}e J. Miller and                  Mirek Riedewald},  title        = {{SANTOS:} Relationship-based Semantic Table Union Search},  journal      = {Proc. {ACM} Manag. Data},  volume       = {1},  number       = {1},  pages        = {9:1--9:25},  year         = {2023},  doi          = {10.1145/3588689},}

You can find SANTOS implementation at: https://github.com/northeastern-datalab/santos

You can find the original TUS benchmark at: https://github.com/RJMillerLab/table-union-search-benchmark

Abstract: Existing techniques for unionable table search define unionability using metadata (tables must have the same or similar schemas) or column-based metrics (for example, the values in a table should be drawn from the same domain). In this work, we introduce the use of semantic relationships between pairs of columns in a table to improve the accuracy of union search. Consequently, we introduce a new notion of unionability that considers relationships between columns, together with the semantics of columns, in a principled way. To do so, we present two new methods to discover semantic relationship between pairs of columns: The first uses an existing knowledge base (KB), the second (which we call a “synthesized KB”) uses knowledge from the data lake itself. We adopt an existing Table Union Search benchmark and present new (open) benchmarks that represent small and large real data lakes. We show that our new unionability search algorithm called SANTOS outperforms a state-of-the-art union search that uses a wide variety of column-based semantics, including word embeddings and regular expressions. We show empirically in all benchmarks that our synthesized KB improves the accuracy of union search by representing relationship semantics that may not be contained in an available KB. This result hints at a promising future of creating a synthesized KBs from data lakes with limited KB coverage and using them for union search.
DOI: 10.15468/dl.4cyfcf
title: Occurrence Download

description: A dataset containing 4480 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Coccothraustes abeillei (Lesson, 1839)"
 ]
}

 The dataset includes 4480 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013089-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4mksc3
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "GadmGid is CAN.11_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Vermivora chrysoptera (Linnaeus, 1766)",
 "Year 1990-2024"
 ]
}

 The dataset includes 12 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013090-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4azc4j
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "GadmGid is CAN.11_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Antrostomus vociferus (A.Wilson, 1812)",
 "Year 1990-2024"
 ]
}

 The dataset includes 33 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013092-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jhdscq
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coccothraustes abeillei abeillei"
 ]
}

 The dataset includes 68 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013091-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9rru2q
title: Occurrence Download

description: A dataset containing 30221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-108.502 20.282,-99.43 20.282,-99.43 34.179,-108.502 34.179,-108.502 20.282))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Euphagus cyanocephalus (Wagler, 1829)"
 ]
}

 The dataset includes 30221 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013093-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5sq7fp
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Micaria pallipes (Lucas, 1846)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-29 36, 42 36, 42 70, -29 70, -29 36))"
 ]
}

 The dataset includes 33 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013094-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.27004724
title: Phylogenetic analysis and morphological characteristics of laccate <i>Ganoderma</i> specimens in Finland

description: The <i>Ganoderma lucidum</i> complex includes fungi with similar morphologies but which are thought to represent different species. The lack of available type material and associated absence of multiple locus sequence data has complicated identification of these fungi. The aim of this study was to clarify the identity of the laccate <i>Ganoderma</i> species occurring in Finland by inferring a phylogeny using DNA sequences from available boreal-temperate material. DNA from Finnish isolates together with an older <i>G. lucidum</i> isolate originating from the United Kingdom was sequenced, and the morphological features of the Finnish specimens were examined. The phylogenetic analysis of the internal transcribed spacer region (ITS), the elongation factor 1-α (<i>tef1</i>), RNA polymerase II subunit (<i>rpb2</i>), and partial β-tubulin (<i>β-tub</i>) genes revealed that the <i>G. lucidum</i> isolate from the United Kingdom did not fall within a well-supported clade with other <i>G. lucidum</i> sequences or related species. The Finnish isolates were closely related to the <i>G. tsugae</i> lineage in <i>tef1, rpb2</i>, and <i>β-tub</i> phylogenies. However, <i>G. tsugae</i> appears morphologically distinct from the Finnish material. The results suggest that <i>G. tsugae</i>, or a species phylogenetically closely related to it, may occur in Finland. But further investigation into the relationship between <i>G. tsugae</i> and <i>G. lucidum</i> from Europe will be needed to clarify the identity of the laccate <i>Ganoderma</i> species in Finland.
DOI: 10.6084/m9.figshare.27004724.v1
title: Phylogenetic analysis and morphological characteristics of laccate <i>Ganoderma</i> specimens in Finland

description: The <i>Ganoderma lucidum</i> complex includes fungi with similar morphologies but which are thought to represent different species. The lack of available type material and associated absence of multiple locus sequence data has complicated identification of these fungi. The aim of this study was to clarify the identity of the laccate <i>Ganoderma</i> species occurring in Finland by inferring a phylogeny using DNA sequences from available boreal-temperate material. DNA from Finnish isolates together with an older <i>G. lucidum</i> isolate originating from the United Kingdom was sequenced, and the morphological features of the Finnish specimens were examined. The phylogenetic analysis of the internal transcribed spacer region (ITS), the elongation factor 1-α (<i>tef1</i>), RNA polymerase II subunit (<i>rpb2</i>), and partial β-tubulin (<i>β-tub</i>) genes revealed that the <i>G. lucidum</i> isolate from the United Kingdom did not fall within a well-supported clade with other <i>G. lucidum</i> sequences or related species. The Finnish isolates were closely related to the <i>G. tsugae</i> lineage in <i>tef1, rpb2</i>, and <i>β-tub</i> phylogenies. However, <i>G. tsugae</i> appears morphologically distinct from the Finnish material. The results suggest that <i>G. tsugae</i>, or a species phylogenetically closely related to it, may occur in Finland. But further investigation into the relationship between <i>G. tsugae</i> and <i>G. lucidum</i> from Europe will be needed to clarify the identity of the laccate <i>Ganoderma</i> species in Finland.
DOI: 10.6084/m9.figshare.27046090
title: Phylogenetic analyses show the Select Agent <i>Coniothyrium glycines</i> represents a single species that has significant morphological and genetic variation

description: Soybean red leaf blotch (RLB), caused by the fungus <i>Coniothyrium glycines</i>, represents a foliar disease of soybean that is thus far restricted to Africa. The fungus is listed as a Select Agent by the Federal Select Agent Program because it could pose a severe threat to plant health were it to establish in the United States. Previous work uncovered tremendous molecular diversity at the internal transcribed spacer region, suggesting that there may be multiple species causing RLB. To determine whether multiple species cause RLB, we reconstructed the phylogeny of <i>C. glycines</i> and taxonomic allies using sequence data from four genes. We included 33 <i>C. glycines</i> isolates collected from six African countries and determined that all isolates form a well-supported, monophyletic lineage. Within this lineage there are at least six well-supported clades that largely correspond to geography, with one clade exclusively composed of isolates from Ethiopia, another exclusively composed of isolates from Uganda, and four composed of isolates from southern Africa. However, we did not detect any concordance for these clades between the four genes, indicating that all isolates included in this analysis are representative of a single species. Isolates in the Ethiopia clade are morphologically distinct from isolates in the other clades, as they produce larger sclerotia and smaller pycnida and more sclerotia in planta. Additionally, ancestral range estimations suggest that the <i>C. glycines</i> lineage emerged in southern Africa. These results show that there is significantly more genetic and morphological diversity than was initially suspected with this high-consequence fungal plant pathogen.
DOI: 10.6084/m9.figshare.27046090.v1
title: Phylogenetic analyses show the Select Agent <i>Coniothyrium glycines</i> represents a single species that has significant morphological and genetic variation

description: Soybean red leaf blotch (RLB), caused by the fungus <i>Coniothyrium glycines</i>, represents a foliar disease of soybean that is thus far restricted to Africa. The fungus is listed as a Select Agent by the Federal Select Agent Program because it could pose a severe threat to plant health were it to establish in the United States. Previous work uncovered tremendous molecular diversity at the internal transcribed spacer region, suggesting that there may be multiple species causing RLB. To determine whether multiple species cause RLB, we reconstructed the phylogeny of <i>C. glycines</i> and taxonomic allies using sequence data from four genes. We included 33 <i>C. glycines</i> isolates collected from six African countries and determined that all isolates form a well-supported, monophyletic lineage. Within this lineage there are at least six well-supported clades that largely correspond to geography, with one clade exclusively composed of isolates from Ethiopia, another exclusively composed of isolates from Uganda, and four composed of isolates from southern Africa. However, we did not detect any concordance for these clades between the four genes, indicating that all isolates included in this analysis are representative of a single species. Isolates in the Ethiopia clade are morphologically distinct from isolates in the other clades, as they produce larger sclerotia and smaller pycnida and more sclerotia in planta. Additionally, ancestral range estimations suggest that the <i>C. glycines</i> lineage emerged in southern Africa. These results show that there is significantly more genetic and morphological diversity than was initially suspected with this high-consequence fungal plant pathogen.
DOI: 10.6084/m9.figshare.27115258
title: <i>Fusarium</i> species associated with <i>Euwallacea xanthopus</i> in South Africa, including two novel species

description: Ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) are small wood-boring insects that live in an obligate symbiosis with fungi, which serve as their primary food source. Beetles residing in the genus <i>Euwallacea</i> have evolved a unique association with a clade of <i>Fusarium</i> that falls within the aptly named Ambrosia <i>Fusarium</i> Clade (AFC). The discovery of the invasive polyphagous shot hole borer, <i>E. fornicatus</i>, in South Africa, has heightened awareness of ambrosia beetles and their symbionts in the country. In this study, we investigated the <i>Fusarium</i> symbionts of three species of <i>Euwallacea</i> in South Africa, with a specific focus on those associated with <i>E. xanthopus</i>. Isolations of <i>Fusarium</i> strains from both living and dissected beetles yielded nearly 100 isolates. Using multigene phylogenetic analyses, these isolates were identified as six different <i>Fusarium</i> species. <i>Fusarium hypothenemi</i> and <i>F. euwallaceae</i> have previously been reported from South Africa. <i>Fusarium pseudensiforme</i> and <i>Fusarium</i> AF-6 are new records for the country. The remaining two species are new to science and are described here as <i>F. rufum</i> sp. nov. and <i>F. floriferum</i> sp. nov. Targeted fungal isolation from specific beetle body parts revealed that the AFC species collected were typically associated with the dissected beetle heads and helped us identify the likely nutritional symbiont of <i>E. xanthopus</i>. This study highlights the understudied diversity of fungal associates of ambrosia beetles present in South Africa.
DOI: 10.6084/m9.figshare.27115258.v1
title: <i>Fusarium</i> species associated with <i>Euwallacea xanthopus</i> in South Africa, including two novel species

description: Ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) are small wood-boring insects that live in an obligate symbiosis with fungi, which serve as their primary food source. Beetles residing in the genus <i>Euwallacea</i> have evolved a unique association with a clade of <i>Fusarium</i> that falls within the aptly named Ambrosia <i>Fusarium</i> Clade (AFC). The discovery of the invasive polyphagous shot hole borer, <i>E. fornicatus</i>, in South Africa, has heightened awareness of ambrosia beetles and their symbionts in the country. In this study, we investigated the <i>Fusarium</i> symbionts of three species of <i>Euwallacea</i> in South Africa, with a specific focus on those associated with <i>E. xanthopus</i>. Isolations of <i>Fusarium</i> strains from both living and dissected beetles yielded nearly 100 isolates. Using multigene phylogenetic analyses, these isolates were identified as six different <i>Fusarium</i> species. <i>Fusarium hypothenemi</i> and <i>F. euwallaceae</i> have previously been reported from South Africa. <i>Fusarium pseudensiforme</i> and <i>Fusarium</i> AF-6 are new records for the country. The remaining two species are new to science and are described here as <i>F. rufum</i> sp. nov. and <i>F. floriferum</i> sp. nov. Targeted fungal isolation from specific beetle body parts revealed that the AFC species collected were typically associated with the dissected beetle heads and helped us identify the likely nutritional symbiont of <i>E. xanthopus</i>. This study highlights the understudied diversity of fungal associates of ambrosia beetles present in South Africa.
DOI: 10.6084/m9.figshare.27391804
title: <i>Tuber cumberlandense and T. canirevelatum</i>, two new edible <i>Tuber</i> species from eastern North America discovered by truffle-hunting dogs

description: Ectomycorrhizal fungi in the genus <i>Tuber</i> form hypogeous fruiting bodies called truffles. Many <i>Tuber</i> species are highly prized due to their edible and aromatic ascomata. Historically, there has been attention on cultivating and selling European truffle species, but there is growing interest in cultivating, wild-harvesting, and selling species of truffles endemic to North America. North America has many endemic <i>Tuber</i> species that remain undescribed, including some that have favorable culinary qualities. Here, we describe two such <i>Tuber</i> species from eastern North America. Maximum likelihood and Bayesian phylogenetic analyses of ITS (internal transcribed spacer), <i>tef1</i> (translation elongation factor 1-alpha), and <i>rpb2</i> (second largest subunit of RNA polymerase II) sequences were used to place these species within a phylogenetic context. We coupled these data with morphological analyses and volatile analyses based on gas chromatography–mass spectrometry. <i>Tuber cumberlandense</i>, sp. nov. (previously referred to as <i>Tuber</i> sp. 66), is a member of the Rufum clade that has been opportunistically harvested for commercial sale from <i>T. melanosporum</i> orchards across eastern North America. <i>Tuber canirevelatum</i>, sp. nov. belongs in the Macrosporum clade and thus far is only known from eastern Tennessee, USA. Both new species were discovered with the assistance of trained truffle dogs. The volatile profiles of <i>T. canirevelatum</i> and <i>T. cumberlandense</i> were measured in order to characterize aromas based on the chemical compounds produced by these fungi. Ascomata from both species were enriched in acetone, dimethyl sulfide, 1-(methylthio)-1-propene, and 1-(methylthio)propane. In this work, we celebrate and encourage the use of trained truffle-hunting dogs for fungal biodiversity discovery and research.
DOI: 10.6084/m9.figshare.26615336
title: Four new species of <i>Candolleomyces</i> (Psathyrellaceae) from the Punjab Plains, Pakistan

description: The purpose of this study is to explore the genus <i>Candolleomyces</i> from Pakistan. Fungal surveys were conducted in different sites of the Punjab plains during the 2016–2022 period. Several specimens belonging to the family Psathyrellaceae were collected. Traditional morphology and multigene phylogenetic analyses confirmed the novelty and placement of the species in genus <i>Candolleomyces</i>. The phylogenetic study of the nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) and partial 28S rRNA regions confirmed the distinct positions of four new taxa, <i>Candolleomyces iqbalii, C. kotadduensis, C. pakistanicus</i>, and <i>C. parvipileus</i>, in the genus. Currently, the genus consists of 43 species worldwide. However, with the inclusion of these four species, the total number has risen to 47. Detailed descriptions, phylogeny, comparisons, and illustrations are provided.