The following results are related to Digital Humanities and Cultural Heritage. Are you interested to view more results? Visit OpenAIRE - Explore.

Digital Humanities and Cultural Heritage
2018-2022
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ReGEO
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019Publisher:bio.toolsFunded by:NIH | Estimation Methods for No...
NIH| Estimation Methods for Nonlinear ODE Models in AIDS Research
Authors: Wu, Canglin;
Wu, Canglin;
Restructured version of Gene Expression Omnibus (GEO) that provides a user friendly interface for curating GEO database
bio.toolsarrow_drop_down
bio.tools
Software . 2019
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
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PubTator Central
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019Publisher:bio.tools
Authors: Lu, Zhiyong;
Lu, Zhiyong;
Web-based application that provides computer-annotated biomedical concepts, such as genes and mutations, in PubMed citations and PMC full-text articles.
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bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
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ODAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019Publisher:bio.toolsFunded by:NIH | Ontology-based Informatio...
NIH| Ontology-based Information Network to Support Vaccine Research
Authors: He, Oliver;
He, Oliver;
Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.tools
Software . 2019
License: Unlicense
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BioVAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Shell Publisher:bio.tools
Authors: Trieu, Hai-Long;
Trieu, Hai-Long;
BioVAE is a pre-trained latent variable language model for biomedical text mining. Large scale pre-trained language models (PLMs) have advanced state-of-the-art (SOTA) performance on various biomedical text mining tasks. The power of such PLMs can be combined with the advantages of deep generative models. These are examples of these combinations. However, they are trained only on general domain text, and biomedical models are still missing. In this work, we describe BioVAE, the first large scale pre-trained latent variable language model for the biomedical domain, which uses the OPTIMUS framework to train on large volumes of biomedical text. The model shows SOTA performance on several biomedical text mining tasks when compared to existing publicly available biomedical PLMs.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: Apache-2.0
Data sources: bio.tools
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bio.tools
Software . 2022
License: Apache-2.0
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InterVar
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018 Python Publisher:bio.tools
Authors: Wang, Kai;
Wang, Kai;
Helps human reviewers interpret the clinical significance of variants. InterVar can take a pre-annotated or VCF file as input and generate automated interpretation on 18 criteria.
bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Other
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Other
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3Dscript
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Java Publisher:bio.tools
Authors: Schmid, Benjamin;
Schmid, Benjamin;
Creates high-quality 3D/4D animations using a natural-language based syntax.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: BSD-2-Clause
Data sources: bio.tools
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bio.tools
Software . 2019
License: BSD-2-Clause
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ImmunoCluster
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R Publisher:bio.toolsFunded by:UKRI | DTP Bid Led by King's Col...
UKRI| DTP Bid Led by King's College London
Authors: Arnold, James N.; Kordasti, Shahram;
Arnold, James N.; Kordasti, Shahram;
A computational framework for the non-specialist to profile cellular heterogeneity in cytometry datasets. The immunoCluster package uses the scDataViz bioconductor package’s vizualization tools and adaptation of the SingleCellExperiment data structure to build simple and flexible cytometry analysis workflows like those outlined in Nowicka et al. (2017) CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
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TISSUES
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018Publisher:bio.toolsFunded by:NIH | Admin Core
NIH| Admin Core
Authors: Jensen, Lars Juhl; Gorodkin, Jan;
Jensen, Lars Juhl; Gorodkin, Jan;
TISSUES is a weekly updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. We map all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. We finally visualize these scores on a schematic human body to provide a convenient overview.
bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: CC-BY-4.0
Data sources: bio.tools
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bio.tools
Software . 2018
License: CC-BY-4.0
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Doc2Hpo
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 JavaScript Publisher:bio.toolsFunded by:NIH | Deep phenotyping in Elect...
NIH| Deep phenotyping in Electronic Health Records for Genomic Medicine
Authors: Wang, Kai; Weng, Chunhua;
Wang, Kai; Weng, Chunhua;
Web application for efficient and accurate Human Phenotype Ontology (HPO) concept curation.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
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AmtDB
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Python Publisher:bio.tools
Authors: Pačes, Jan; Ehler, Edvard; Novotný, Jiří;
Pačes, Jan; Ehler, Edvard; Novotný, Jiří;
This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Paleolithic to roughly Iron Age times, focusing on an Euroasian geographical area. We provide both the mtDNA sequences (in FASTA format), and the metadata for the samples (IDs, dates, geolocation, site, culture, mtDNA haplogroup etc., available to download in a tab-delimited text file).
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: CC-BY-4.0
Data sources: bio.tools
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bio.tools
Software . 2019
License: CC-BY-4.0
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The following results are related to Digital Humanities and Cultural Heritage. Are you interested to view more results? Visit OpenAIRE - Explore.

ReGEO
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019Publisher:bio.toolsFunded by:NIH | Estimation Methods for No...
NIH| Estimation Methods for Nonlinear ODE Models in AIDS Research
Authors: Wu, Canglin;
Wu, Canglin;
Restructured version of Gene Expression Omnibus (GEO) that provides a user friendly interface for curating GEO database
bio.toolsarrow_drop_down
bio.tools
Software . 2019
Data sources: bio.tools
linkLink to
shareshareShare
citeCite
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
Data sources: bio.tools
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PubTator Central
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019Publisher:bio.tools
Authors: Lu, Zhiyong;
Lu, Zhiyong;
Web-based application that provides computer-annotated biomedical concepts, such as genes and mutations, in PubMed citations and PMC full-text articles.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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citeCite
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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ODAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019Publisher:bio.toolsFunded by:NIH | Ontology-based Informatio...
NIH| Ontology-based Information Network to Support Vaccine Research
Authors: He, Oliver;
He, Oliver;
Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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BioVAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Shell Publisher:bio.tools
Authors: Trieu, Hai-Long;
Trieu, Hai-Long;
BioVAE is a pre-trained latent variable language model for biomedical text mining. Large scale pre-trained language models (PLMs) have advanced state-of-the-art (SOTA) performance on various biomedical text mining tasks. The power of such PLMs can be combined with the advantages of deep generative models. These are examples of these combinations. However, they are trained only on general domain text, and biomedical models are still missing. In this work, we describe BioVAE, the first large scale pre-trained latent variable language model for the biomedical domain, which uses the OPTIMUS framework to train on large volumes of biomedical text. The model shows SOTA performance on several biomedical text mining tasks when compared to existing publicly available biomedical PLMs.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: Apache-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: Apache-2.0
Data sources: bio.tools
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InterVar
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018 Python Publisher:bio.tools
Authors: Wang, Kai;
Wang, Kai;
Helps human reviewers interpret the clinical significance of variants. InterVar can take a pre-annotated or VCF file as input and generate automated interpretation on 18 criteria.
bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Other
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Other
Data sources: bio.tools
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3Dscript
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Java Publisher:bio.tools
Authors: Schmid, Benjamin;
Schmid, Benjamin;
Creates high-quality 3D/4D animations using a natural-language based syntax.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: BSD-2-Clause
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: BSD-2-Clause
Data sources: bio.tools
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ImmunoCluster
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R Publisher:bio.toolsFunded by:UKRI | DTP Bid Led by King's Col...
UKRI| DTP Bid Led by King's College London
Authors: Arnold, James N.; Kordasti, Shahram;
Arnold, James N.; Kordasti, Shahram;
A computational framework for the non-specialist to profile cellular heterogeneity in cytometry datasets. The immunoCluster package uses the scDataViz bioconductor package’s vizualization tools and adaptation of the SingleCellExperiment data structure to build simple and flexible cytometry analysis workflows like those outlined in Nowicka et al. (2017) CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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TISSUES
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018Publisher:bio.toolsFunded by:NIH | Admin Core
NIH| Admin Core
Authors: Jensen, Lars Juhl; Gorodkin, Jan;
Jensen, Lars Juhl; Gorodkin, Jan;
TISSUES is a weekly updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. We map all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. We finally visualize these scores on a schematic human body to provide a convenient overview.
bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: CC-BY-4.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: CC-BY-4.0
Data sources: bio.tools
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Doc2Hpo
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 JavaScript Publisher:bio.toolsFunded by:NIH | Deep phenotyping in Elect...
NIH| Deep phenotyping in Electronic Health Records for Genomic Medicine
Authors: Wang, Kai; Weng, Chunhua;
Wang, Kai; Weng, Chunhua;
Web application for efficient and accurate Human Phenotype Ontology (HPO) concept curation.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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AmtDB
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Python Publisher:bio.tools
Authors: Pačes, Jan; Ehler, Edvard; Novotný, Jiří;
Pačes, Jan; Ehler, Edvard; Novotný, Jiří;
This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Paleolithic to roughly Iron Age times, focusing on an Euroasian geographical area. We provide both the mtDNA sequences (in FASTA format), and the metadata for the samples (IDs, dates, geolocation, site, culture, mtDNA haplogroup etc., available to download in a tab-delimited text file).
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bio.tools
Software . 2019
License: CC-BY-4.0
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: CC-BY-4.0
Data sources: bio.tools
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