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BigDAWG version 0.1

Vijay Gadepally, Kyle O'Brien, Adam Dziedzic, Aaron Elmore, Jeremy Kepner, Samuel Madden, Tim Mattson, Jennie Rogers, Zuohao She, Michael Stonebraker
<span title="">2017</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/v67j4hwzdjcu3csnvox3vnxiry" style="color: black;">2017 IEEE High Performance Extreme Computing Conference (HPEC)</a> </i> &nbsp;

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<span title="2017-07-03">2017</span> <span class="release-stage" >pre-print</span> <span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1707.00721v1">arXiv:1707.00721v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6zivpbknbraxbp74psgwhjqv4e">fatcat:6zivpbknbraxbp74psgwhjqv4e</a> </span>
BigDAWG (Big Data Working Group) is our reference implementation of a polystore system. In this paper, we describe the current BigDAWG software release which supports PostgreSQL, Accumulo and SciDB.  ...  We describe the overall architecture, API and initial results of applying BigDAWG to the MIMIC II medical dataset.  ...  In this paper we described the open source release of our polystore system, BigDAWG version 0.1.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/hpec.2017.8091077">doi:10.1109/hpec.2017.8091077</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/hpec/GadepallyODEKMM17.html">dblp:conf/hpec/GadepallyODEKMM17</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3zrqpgqocfgi3p6izhovutjauu">fatcat:3zrqpgqocfgi3p6izhovutjauu</a> </span>
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Vijay Gadepally, Kyle O'Brien, Adam Dziedzic, Aaron Elmore, Jeremy Kepner, Samuel Madden, Tim Mattson, Jennie Rogers, Zuohao She, Michael Stonebraker. "BigDAWG version 0.1." 2017 IEEE High Performance Extreme Computing Conference (HPEC) (2017) 1-7

High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility

Kazutoyo Osoegawa, Lisa E. Creary, Gonzalo Montero-Martín, Kalyan C. Mallempati, Sridevi Gangavarapu, Stacy J. Caillier, Adam Santaniello, Noriko Isobe, Jill A. Hollenbach, Stephen L. Hauser, Jorge R. Oksenberg, Marcelo A. Fernández-Viňa
<span title="2021-05-25">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t7exsmmojvgjnhq3pflf7pk6zq" style="color: black;">Frontiers in Immunology</a> </i> &nbsp;

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Case-Control (CC) For case-control analyses, we used Bridging ImmunoGenomic Data-Analysis Workflow Gaps (BIGDAWG) (34) .  ...  We tested the same 11 HLA genes, and 19 haplotypes for CC analyses using BIGDAWG. Similar to gTDT and mTDT, we also performed various stratification CC analyses.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fimmu.2021.644838">doi:10.3389/fimmu.2021.644838</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34211458">pmid:34211458</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8240666/">pmcid:PMC8240666</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gqb5aqcnl5btlpudvxhtnikvvi">fatcat:gqb5aqcnl5btlpudvxhtnikvvi</a> </span>
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Kazutoyo Osoegawa, Lisa E. Creary, Gonzalo Montero-Martín, Kalyan C. Mallempati, Sridevi Gangavarapu, Stacy J. Caillier, Adam Santaniello, Noriko Isobe, Jill A. Hollenbach, Stephen L. Hauser, Jorge R. Oksenberg, Marcelo A. Fernández-Viňa. "High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility." Frontiers in Immunology (2021) 644838

Processing Analytical Queries over Polystore System for a Large Astronomy Data Repository

Manoj Poudel, Rashmi P. Sarode, Yutaka Watanobe, Maxim Mozgovoy, Subhash Bhalla
<span title="2022-03-04">2022</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/smrngspzhzce7dy6ofycrfxbim" style="color: black;">Applied Sciences</a> </i> &nbsp;

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In 2017, iPTF became the Zwicky Transient Factory, utilizing a rebuilt version of the same telescope that was used for iPTF.  ...  The proposed system does not employ wrappers and instead leverages native API calls such as BigDAWG or CloudMdsQL to achieve autonomy.  ... 
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Citation

Manoj Poudel, Rashmi P. Sarode, Yutaka Watanobe, Maxim Mozgovoy, Subhash Bhalla. "Processing Analytical Queries over Polystore System for a Large Astronomy Data Repository." Applied Sciences 12.5 (2022) 2663

Genome-wide association study of self-reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA-DR/DQ gene region

Seik-Soon Khor, Ryoko Morino, Kazuyuki Nakazono, Shigeo Kamitsuji, Masanori Akita, Maiko Kawajiri, Tatsuya Yamasaki, Azusa Kami, Yuria Hoshi, Asami Tada, Kenichi Ishikawa, Maaya Hine (+5 others)
<span title="2018-01-18">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;

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We analysed eQTL data for both the European ancestry sample based GTExPortal version 6p 41,108 and the Japanese ancestry sample based Human Genome Variation Database eQTL Release Version 8.1 43 .  ...  Basic immunogenetic analyses of HLA loci and alleles were performed using the R BIGDAWG package 111 .  ... 
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Seik-Soon Khor, Ryoko Morino, Kazuyuki Nakazono, Shigeo Kamitsuji, Masanori Akita, Maiko Kawajiri, Tatsuya Yamasaki, Azusa Kami, Yuria Hoshi, Asami Tada, Kenichi Ishikawa, Maaya Hine, Miki Kobayashi, Nami Kurume, Naoyuki Kamatani, Katsushi Tokunaga, Todd A. Johnson. "Genome-wide association study of self-reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA-DR/DQ gene region." Scientific Reports 8.1 (2018)

Semen quality is affected by HLA class I alleles together with sexually transmitted diseases

P. I. Marques, J. C. Gonçalves, C. Monteiro, B. Cavadas, L. Nagirnaja, N. Barros, A. Barros, F. Carvalho, A. M. Lopes, S. Seixas
<span title="2019-04-19">2019</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gx4uia7qvjhzjmxrch4xzfykzq" style="color: black;">Andrology</a> </i> &nbsp;

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This tool has the advantage of automatically detecting the genome version of inputted BAM files and using a population reference graph (PRG) framework to impute HLA alleles for 10 genes (HLA-A, HLA-B,  ...  Monteiro et al., the above association of HLA-DQA1*05:01 with Chlamydia alone seems improbable, given that its relative abundance compared to other bacterial taxa only reaches very low frequencies (f < 0.1%  ... 
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P. I. Marques, J. C. Gonçalves, C. Monteiro, B. Cavadas, L. Nagirnaja, N. Barros, A. Barros, F. Carvalho, A. M. Lopes, S. Seixas. "Semen quality is affected by HLA class I alleles together with sexually transmitted diseases." Andrology 7.6 (2019) 867-877

Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research

Venceslas Douillard, Erick C. Castelli, Steven J. Mack, Jill A. Hollenbach, Pierre-Antoine Gourraud, Nicolas Vince, Sophie Limou
<span title="2021-12-02">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;

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Individuals datasets may have been generated under any release version, which is why tools like the Allele Name Translation Tool (ANTT) have been developed to standardize datasets to a common release version  ...  The MHC region is the most gene-dense region of the human genome, with 1% of the human coding genes (>200) found in 0.1% of the genome length (Shiina et al., 2009) .  ... 
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Citation

Venceslas Douillard, Erick C. Castelli, Steven J. Mack, Jill A. Hollenbach, Pierre-Antoine Gourraud, Nicolas Vince, Sophie Limou. "Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research." Frontiers in Genetics (2021) 774916

Efficient Ontology-Based Data Integration with Canonical IRIs [chapter]

Guohui Xiao, Dag Hovland, Dimitris Bilidas, Martin Rezk, Martin Giese, Diego Calvanese
<span title="">2018</span> <i title="Springer International Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;

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In the following, we present our running example, which provides a simplified version of the experimental setting of Optique.  ...  The oracle databases are version 10g, and run on separate machines. 7 We realize that this setup does not comply with the normal clean setup of a database experiment.  ... 
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Guohui Xiao, Dag Hovland, Dimitris Bilidas, Martin Rezk, Martin Giese, Diego Calvanese. "Efficient Ontology-Based Data Integration with Canonical IRIs." Lecture Notes in Computer Science (2018) 697-713

HLA-C*04:01 Affects HLA Class I Heterozygosity and Predicted Affinity to SARS-CoV-2 Peptides, and in Combination With Age and Sex of Armenian Patients Contributes to COVID-19 Severity

Anahit Hovhannisyan, Vergine Madelian, Sevak Avagyan, Mihran Nazaretyan, Armine Hyussyan, Alina Sirunyan, Rubina Arakelyan, Zorayr Manukyan, Levon Yepiskoposyan, Karine R. Mayilyan, Frieda Jordan
<span title="2022-02-03">2022</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t7exsmmojvgjnhq3pflf7pk6zq" style="color: black;">Frontiers in Immunology</a> </i> &nbsp;

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HLA haplotype prediction and their association with the disease manifestation characteristics were performed using Bringing ImmunoGenomics Data Analysis Workflow Gaps (BIGDAWG) R package (30) .  ...  severe (P=0.15) symptoms composing the group of hospitalized inpatients The HLA alleles highlighted in bold and in italic fonts correspond to the association with COVID-19 severity at P <0.05 and 0.05< P<0.1  ...  All authors contributed to the final version of the manuscript.  ... 
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Anahit Hovhannisyan, Vergine Madelian, Sevak Avagyan, Mihran Nazaretyan, Armine Hyussyan, Alina Sirunyan, Rubina Arakelyan, Zorayr Manukyan, Levon Yepiskoposyan, Karine R. Mayilyan, Frieda Jordan. "HLA-C*04:01 Affects HLA Class I Heterozygosity and Predicted Affinity to SARS-CoV-2 Peptides, and in Combination With Age and Sex of Armenian Patients Contributes to COVID-19 Severity." Frontiers in Immunology (2022) 769900

PolicyCloud D2.5 STATE OF THE ART & REQUIREMENTS ANALYSIS M22

Boyan Kolev, Jose María Zaragoza, Patricio Martinez, Luis Miguel Garcia, Ofer Biran, Kostas Moutselos, Marios Koniaris, Christos Pavlatos, Aggelos Kolaitis, María Ángeles Sanguino, Jorge Montero, Ana Luiza Pontual (+22 others)
<span title="2021-11-08">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;

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As a result, this third and last version depicts the final technical requirements that have been identified after the delivery of the first two versions of the scientific reports, providing an extended  ...  version of the user scenarios, the definition of their datasets, along with an extensive survey regarding the regulatory constraints.  ...  A further improved presented by the polystore BigDAWG [31] , [32] which defines islands of information, where each island is related to a specific data model and language in order to provide access  ... 
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Boyan Kolev, Jose María Zaragoza, Patricio Martinez, Luis Miguel Garcia, Ofer Biran, Kostas Moutselos, Marios Koniaris, Christos Pavlatos, Aggelos Kolaitis, María Ángeles Sanguino, Jorge Montero, Ana Luiza Pontual, Miquel Milà, Ricard Munné, Giuseppe La Rocca, Dimosthenis Kyriazis, Athanasios Kiourtis, George Manias, Argyro Mavrogiorgou, Rafael Del Hoyo, Giannis Ledakis, Konstantinos Theodosiou, Konstantinos Oikonomou, Petya Nikolova, Christodoulos Maragkos, Stelios Betas, Konstantinos Nasias, Armend Duzha, Nikos Achilleopoulos, Iskra Yovkova, Ana Georgieva, Metodiyka Tarlyovska, Vega Rodrigálvarez, Javier Sancho. "PolicyCloud D2.5 STATE OF THE ART & REQUIREMENTS ANALYSIS M22." Zenodo (2021)

A Survey of State Management in Big Data Processing Systems [article]

Quoc-Cuong To, Juan Soto, Volker Markl
<span title="2018-08-01">2018</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>

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The effectiveness of BigDAWG in practical applications is discussed in Elmore et al. [30] .  ...  Experiments show that these two algorithms achieve very low imbalance (i.e., smaller than 0.1%) in large deployments. Katsipoulakis et al.  ... 
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Quoc-Cuong To, Juan Soto, Volker Markl. "A Survey of State Management in Big Data Processing Systems." arXiv (2018)

Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes

Alexander Immel, Felix M Key, András Szolek, Et Al, Verena J Schuenemann, Ella Reiter
<span title="2021-05-18">2021</span>

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Resulting vcf-files were further annotated by adding the ancestral allele and dbSNP IDs 679 version 147.  ...  Selection coefficients for the models with 1351 natural selection were -0.1 for HLA-B*51:01 and HLA-C*06:02 and 0.2 for DRB1*13:01 1352 (Supplementary Figure 5).  ... 
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Alexander Immel, Felix M Key, András Szolek, Et Al, Verena J Schuenemann, Ella Reiter. "Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes." (2021)