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ENQUIRE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2023 Bash Publisher:bio.tools
Authors: Musella, Luca; Widmann, Max;
Musella, Luca; Widmann, Max;
ENQUIRE (Expanding Networks by Querying Unexpectedly Inter-Related Entities) offers an alternative to manual literature curation and database mining to study complex biomedical phenomena. ENQUIRE generates a co-occurrence network of genes and biomedical ontologies (MeSH) using a corpus of publications as input. The algorithm iteratively reconstructs and expands the network by generating PubMed queries from significant interrelations, until it obtains an interconnected network of genes and MeSH relevant to the input corpus.
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bio.tools
Software . 2023
License: GPL-3.0
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bio.tools
Software . 2023
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CoVEffect
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2023 Python Publisher:bio.tools
Authors: Bernasconi, Anna; Garcia, Giuseppe Serna; Invernici, Francesco;
Bernasconi, Anna; Garcia, Giuseppe Serna; Invernici, Francesco;
CoVEffect is an interactive web interface for deep learning-assisted scientific text annotation with effects of SARS-CoV-2 mutations and variants.
bio.toolsarrow_drop_down
bio.tools
Software . 2023
License: MIT
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bio.tools
Software . 2023
License: MIT
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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.
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bio.tools
Software . 2022
License: Apache-2.0
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bio.tools
Software . 2022
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BERT-Kcr
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022Publisher:bio.tools
Authors: Zhu, Xiaolei;
Zhu, Xiaolei;
BERT-Kcr is a tool for prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models.
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bio.tools
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bio.tools
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ProtTrans
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Python Publisher:bio.tools
Authors: Elnaggar, Ahmed; Heinzinger, Michael; Dallago, Christian; Wang, Yu;
Elnaggar, Ahmed; Heinzinger, Michael; Dallago, Christian; Wang, Yu;
ProtTrans is providing state of the art pre-trained models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using various Transformers Models.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: AFL-3.0
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ChemTables
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Python Publisher:bio.tools
Authors: Verspoor, Karin;
Verspoor, Karin;
ChemTables is a dataset for semantic classificationon tables in chemical patents.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: Apache-2.0
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bio.tools
Software . 2022
License: Apache-2.0
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text
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R Publisher:bio.tools
Authors: Kjell, Oscar; Giorgi, Salvatore; Schwartz, Andrew;
Kjell, Oscar; Giorgi, Salvatore; Schwartz, Andrew;
text id an R-package for analyzing and visualizing human language using natural language processing and deep learning. The language that individuals use contains a wealth of psychological information interesting for research.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: GPL-3.0
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
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ThermoScan
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 Python Publisher:bio.tools
Authors: Fariselli, Piero; Capriotti, Emidio;
Fariselli, Piero; Capriotti, Emidio;
ThermoScan is a tool for semi-automatic identification of protein stability data from PubMed.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
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bio.tools
Software . 2021
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RENET2
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 Python Publisher:bio.tools
Authors: Luo, Ruibang;
Luo, Ruibang;
RENET2 is a tool for high-performance full-text gene-disease relation extraction with iterative training data expansion.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: BSD-3-Clause
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: BSD-3-Clause
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PhenCards
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 Python Publisher:bio.tools
Authors: Wang, Kai;
Wang, Kai;
PhenCards is a web server for linking human phenotype information to biomedical knowledge.
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bio.tools
Software . 2021
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bio.tools
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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.

ENQUIRE
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2023 Bash Publisher:bio.tools
Authors: Musella, Luca; Widmann, Max;
Musella, Luca; Widmann, Max;
ENQUIRE (Expanding Networks by Querying Unexpectedly Inter-Related Entities) offers an alternative to manual literature curation and database mining to study complex biomedical phenomena. ENQUIRE generates a co-occurrence network of genes and biomedical ontologies (MeSH) using a corpus of publications as input. The algorithm iteratively reconstructs and expands the network by generating PubMed queries from significant interrelations, until it obtains an interconnected network of genes and MeSH relevant to the input corpus.
bio.toolsarrow_drop_down
bio.tools
Software . 2023
License: GPL-3.0
Data sources: bio.tools
linkLink to
shareshareShare
citeCite
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bio.toolsarrow_drop_down
bio.tools
Software . 2023
License: GPL-3.0
Data sources: bio.tools
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CoVEffect
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2023 Python Publisher:bio.tools
Authors: Bernasconi, Anna; Garcia, Giuseppe Serna; Invernici, Francesco;
Bernasconi, Anna; Garcia, Giuseppe Serna; Invernici, Francesco;
CoVEffect is an interactive web interface for deep learning-assisted scientific text annotation with effects of SARS-CoV-2 mutations and variants.
bio.toolsarrow_drop_down
bio.tools
Software . 2023
License: MIT
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2023
License: MIT
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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
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BERT-Kcr
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022Publisher:bio.tools
Authors: Zhu, Xiaolei;
Zhu, Xiaolei;
BERT-Kcr is a tool for prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
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bio.toolsarrow_drop_down
bio.tools
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ProtTrans
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Python Publisher:bio.tools
Authors: Elnaggar, Ahmed; Heinzinger, Michael; Dallago, Christian; Wang, Yu;
Elnaggar, Ahmed; Heinzinger, Michael; Dallago, Christian; Wang, Yu;
ProtTrans is providing state of the art pre-trained models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using various Transformers Models.
bio.toolsarrow_drop_down
bio.tools
Software . 2022
License: AFL-3.0
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bio.toolsarrow_drop_down
bio.tools
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ChemTables
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2022 Python Publisher:bio.tools
Authors: Verspoor, Karin;
Verspoor, Karin;
ChemTables is a dataset for semantic classificationon tables in chemical patents.
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
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text
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 R Publisher:bio.tools
Authors: Kjell, Oscar; Giorgi, Salvatore; Schwartz, Andrew;
Kjell, Oscar; Giorgi, Salvatore; Schwartz, Andrew;
text id an R-package for analyzing and visualizing human language using natural language processing and deep learning. The language that individuals use contains a wealth of psychological information interesting for research.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: GPL-3.0
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
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ThermoScan
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 Python Publisher:bio.tools
Authors: Fariselli, Piero; Capriotti, Emidio;
Fariselli, Piero; Capriotti, Emidio;
ThermoScan is a tool for semi-automatic identification of protein stability data from PubMed.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
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bio.tools
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RENET2
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 Python Publisher:bio.tools
Authors: Luo, Ruibang;
Luo, Ruibang;
RENET2 is a tool for high-performance full-text gene-disease relation extraction with iterative training data expansion.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: BSD-3-Clause
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: BSD-3-Clause
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PhenCards
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 Python Publisher:bio.tools
Authors: Wang, Kai;
Wang, Kai;
PhenCards is a web server for linking human phenotype information to biomedical knowledge.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
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Digital Humanities and Cultural Heritage
Research software
Other research products
Software
bio.tools