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BioVAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Shell 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
Data sources: bio.tools
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ODAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools NIH | Ontology-based Informatio...
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.
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bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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bio.tools
Software . 2019
License: Unlicense
Data sources: bio.tools
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ImmunoCluster
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R bio.tools
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.
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bio.tools
Software . 2021
License: MIT
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
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Calchas
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 JavaScript bio.tools EC | iManageCancer, EC | P-MEDICINE
Authors: Koumakis, Lefteris; Koumakis, Lefteris;
Koumakis, Lefteris; Koumakis, Lefteris;
A web based framework that takes advantage of domain specific ontologies, and Natural Language Processing, aiming to empower exploration of biomedical resources via semantic-based querying and search. The NLP engine analyzes the input free-text query and translates it into targeted queries with terms from the underlying ontology. Each query is passed to the semantically-annotated tools repository, and based on similarity matches, it ranks the available resources.
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bio.tools
Software . 2017
Data sources: bio.tools
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bio.tools
Software . 2017
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InterVar
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018 Python 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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TISSUES
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018bio.tools 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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BO-LSTM
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Python bio.tools FCT | UID/CEC/00408/2013, FCT | PTDC/CCI-BIO/28685/2017, FCT | PD/BD/106083/2015
Authors: BioTM;
BioTM;
Model to detect and classify relations in text, representing each entity of domain-specific ontologies as the sequence of its ancestors in the ontology. BO-LSTM is implemented as a recurrent neural network with long short-term memory units and using open biomedical ontologies.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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DigChem
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools
Authors: Lee, Hyunju;
Lee, Hyunju;
Identification of disease-gene-chemical relationships from Medline abstracts.
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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
Data sources: bio.tools
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Logol
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2015bio.tools
Authors: GenOuest;
GenOuest;
Pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic).
bio.toolsarrow_drop_down
bio.tools
Software . 2015
License: CECILL-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2015
License: CECILL-2.0
Data sources: bio.tools
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rREST
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools
Authors: Yao, Dezhong; ValdÃ©s Sosa, Pedro A.;
Yao, Dezhong; ValdÃ©s Sosa, Pedro A.;
Regularized reference electrode standardization technique.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-3.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-3.0
Data sources: bio.tools
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16 Research products

BioVAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Shell 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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ODAE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools NIH | Ontology-based Informatio...
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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ImmunoCluster
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R bio.tools
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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Calchas
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 JavaScript bio.tools EC | iManageCancer, EC | P-MEDICINE
Authors: Koumakis, Lefteris; Koumakis, Lefteris;
Koumakis, Lefteris; Koumakis, Lefteris;
A web based framework that takes advantage of domain specific ontologies, and Natural Language Processing, aiming to empower exploration of biomedical resources via semantic-based querying and search. The NLP engine analyzes the input free-text query and translates it into targeted queries with terms from the underlying ontology. Each query is passed to the semantically-annotated tools repository, and based on similarity matches, it ranks the available resources.
bio.toolsarrow_drop_down
bio.tools
Software . 2017
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2017
Data sources: bio.tools
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InterVar
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018 Python 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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TISSUES
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018bio.tools 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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BO-LSTM
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Python bio.tools FCT | UID/CEC/00408/2013, FCT | PTDC/CCI-BIO/28685/2017, FCT | PD/BD/106083/2015
Authors: BioTM;
BioTM;
Model to detect and classify relations in text, representing each entity of domain-specific ontologies as the sequence of its ancestors in the ontology. BO-LSTM is implemented as a recurrent neural network with long short-term memory units and using open biomedical ontologies.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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DigChem
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools
Authors: Lee, Hyunju;
Lee, Hyunju;
Identification of disease-gene-chemical relationships from Medline abstracts.
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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Logol
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2015bio.tools
Authors: GenOuest;
GenOuest;
Pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic).
bio.toolsarrow_drop_down
bio.tools
Software . 2015
License: CECILL-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2015
License: CECILL-2.0
Data sources: bio.tools
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rREST
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools
Authors: Yao, Dezhong; ValdÃ©s Sosa, Pedro A.;
Yao, Dezhong; ValdÃ©s Sosa, Pedro A.;
Regularized reference electrode standardization technique.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-3.0
Data sources: bio.tools
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bio.tools
Software . 2019
License: GPL-3.0
Data sources: bio.tools
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