This document describes an embryo stage alignment tool that compares gene expression and morphological features across species to align embryonic development stages between vertebrates. The tool uses ontologies, databases, and user input to generate distance matrices and heat maps showing commonalities. It aims to standardize stage terminology and help comparative biology by identifying conserved developmental processes. Future improvements include using a more detailed anatomical ontology and clustering analyses.
Smart Approach for Real Time Gender Prediction of European School's Principal...Yatish Bathla
Supervised Machine learning is used to solve the binary classification problem on four datasets of European Survey of Schools: Information and Communication Technology (ICT) in Education (known as ESSIE) which is supported by Euro-pean Union (EU). To predict the gender of the principal based on their response for the ICT questionnaire, the authors applied four supervised machine learning algorithms (Sequential minimal optimization (SMO), Multilayer perception (ANN), Random Forest (RF) and Logistic Regression (LR) on ISCED-1, ISCED-2, ISCED-3A and ISCED-3B level of schools. The survey was conducted by the European Union in the academic year 2011-2012. The datasets have total 2933 instances & 164 attributes considered for the ISCED-1 level, 2914 in-stances & 164 attributes for the ISCED-2 level, 2203 instances & 164 attributes for the ISCED-3A level and 1820 instances & 164 attributes for the ISCED-3B level. One the one hand, SMO classifier outperformed others at ISCED-3A level and on the other hand, LR outperformed others at ISCED-1, ISCED-2 and ISCED-3B. Further, real time prediction and automatic process of the data sets are done by introducing the concepts of the web server. The server communicates with the European Union web server and displays the results in the form of web application. This smart approach saves the data process and interaction time of humans as well as represent the processed data of the Weka efficiently.
The talk explores following topics:
- What is the search relevance and why is it important?
- Relevance scoring in Elasticsearch
- Manipulating relevance with Query DSL structure
- Pros and cons in using Machine Learning for improving search relevance
- Using Learning to Rank (aka Machine Learning for better relevance) in Elasticsearch
Repeatable plant pathology bioinformatic analysis: Not everything is NGS dataLeighton Pritchard
Presentation on use of Galaxy for plant pathology bioinformatics, presented by Peter Cock, at the Genomics for Non-Model Organisms workshop, ISMB/ECCB, Vienna, Austria, 19 July 2011
Smart Approach for Real Time Gender Prediction of European School's Principal...Yatish Bathla
Supervised Machine learning is used to solve the binary classification problem on four datasets of European Survey of Schools: Information and Communication Technology (ICT) in Education (known as ESSIE) which is supported by Euro-pean Union (EU). To predict the gender of the principal based on their response for the ICT questionnaire, the authors applied four supervised machine learning algorithms (Sequential minimal optimization (SMO), Multilayer perception (ANN), Random Forest (RF) and Logistic Regression (LR) on ISCED-1, ISCED-2, ISCED-3A and ISCED-3B level of schools. The survey was conducted by the European Union in the academic year 2011-2012. The datasets have total 2933 instances & 164 attributes considered for the ISCED-1 level, 2914 in-stances & 164 attributes for the ISCED-2 level, 2203 instances & 164 attributes for the ISCED-3A level and 1820 instances & 164 attributes for the ISCED-3B level. One the one hand, SMO classifier outperformed others at ISCED-3A level and on the other hand, LR outperformed others at ISCED-1, ISCED-2 and ISCED-3B. Further, real time prediction and automatic process of the data sets are done by introducing the concepts of the web server. The server communicates with the European Union web server and displays the results in the form of web application. This smart approach saves the data process and interaction time of humans as well as represent the processed data of the Weka efficiently.
The talk explores following topics:
- What is the search relevance and why is it important?
- Relevance scoring in Elasticsearch
- Manipulating relevance with Query DSL structure
- Pros and cons in using Machine Learning for improving search relevance
- Using Learning to Rank (aka Machine Learning for better relevance) in Elasticsearch
Repeatable plant pathology bioinformatic analysis: Not everything is NGS dataLeighton Pritchard
Presentation on use of Galaxy for plant pathology bioinformatics, presented by Peter Cock, at the Genomics for Non-Model Organisms workshop, ISMB/ECCB, Vienna, Austria, 19 July 2011
Course: Bioinformatics for Biomedical Research (2014).
Session: 4.1- Introduction to RNA-seq and RNA-seq Data Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
DeepBlue epigenomic data server: programmatic data retrieval and analysis of ...Felipe Albrecht
Short description and updates about DeepBlue Epigenomic Data Server that I presented during the last Blueprint (http://www.blueprint-epigenome.eu/) Jamboree in Madrid (June 2016)
Because of the ubiquity of metaphors in language, metaphor processing is a very important task in the field of natural language processing. The first step towards metaphor processing, and probably the most difficult one, is metaphor detection. In the first part of this paper, we review the theoretical background for metaphors and the models and implementations that have been proposed for their detection. We then build corpora for detecting three types of metaphors: IS-A metaphors, metaphors formed with the preposition ‘of’ and metaphors formed with a verb. For the first two tasks, we train supervised classifiers using semantic features. For the third task, we use features commonly used in text categorization
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
An introduction on gene annotation & curation for the IAGC and BIPAA research communities.
Using VarSeq to Improve Variant Analysis Research WorkflowsDelaina Hawkins
Many questions must be answered when analyzing DNA sequence variants: How do I determine which variants are potentially deleterious? Is the sequencing quality sufficient? How do I prioritize the results? Which annotation sources may help answer my research question?
In this webinar presentation, we will review workflow strategies for quality control and analysis of DNA sequence variants using the VarSeq software package from Golden Helix. VarSeq is a powerful platform for analysis of DNA sequence variants in clinical and translational research settings. VarSeq provides researchers with easy access to curated public databases of variant annotation information, and also enables users to incorporate their own local databases or downloaded information about variants and genomic regions.
The presentation will include interactive demonstrations using VarSeq to analyze variants found by exome sequencing of an extended family with a complex disease. We will review strategies for assessing variant quality, applying genomic annotations, incorporating custom annotation sources, and creating variant filters in VarSeq. We will also demonstrate the PhoRank gene ranking algorithm and its application for prioritizing variants.
Using VarSeq to Improve Variant Analysis Research WorkflowsGolden Helix Inc
In this webinar presentation, we will review workflow strategies for quality control and analysis of DNA sequence variants using the VarSeq software package from Golden Helix. VarSeq is a powerful platform for analysis of DNA sequence variants in clinical and translational research settings. VarSeq provides researchers with easy access to curated public databases of variant annotation information, and also enables users to incorporate their own local databases or downloaded information about variants and genomic regions.
Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...Spark Summit
The detection and analysis of rare genomic events requires integrative analysis across large cohorts with terabytes to petabytes of genomic data. Contemporary genomic analysis tools have not been designed for this scale of data-intensive computing. This talk presents ADAM, an Apache 2 licensed library built on top of the popular Apache Spark distributed computing framework. ADAM is designed to allow genomic analyses to be seamlessly distributed across large clusters, and presents a clean API for writing parallel genomic analysis algorithms. In this talk, we’ll look at how we’ve used ADAM to achieve a 3.5× improvement in end-to-end variant calling latency and a 66% cost improvement over current toolkits, without sacrificing accuracy. We will talk about a recent recompute effort where we have used ADAM to recall the Simons Genome Diversity Dataset against GRCh38. We will also talk about using ADAM alongside Apache Hbase to interactively explore large variant datasets.
Uberon: opening up to community contributionsChris Mungall
Presentation from the 2nd Phenotypes Traversing All the Organisms (POTATO) Workshop https://www.biocuration2019.org/workshop-potato
Brief summary of Uberon and plan for opening up to community contributions
Course: Bioinformatics for Biomedical Research (2014).
Session: 4.1- Introduction to RNA-seq and RNA-seq Data Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
DeepBlue epigenomic data server: programmatic data retrieval and analysis of ...Felipe Albrecht
Short description and updates about DeepBlue Epigenomic Data Server that I presented during the last Blueprint (http://www.blueprint-epigenome.eu/) Jamboree in Madrid (June 2016)
Because of the ubiquity of metaphors in language, metaphor processing is a very important task in the field of natural language processing. The first step towards metaphor processing, and probably the most difficult one, is metaphor detection. In the first part of this paper, we review the theoretical background for metaphors and the models and implementations that have been proposed for their detection. We then build corpora for detecting three types of metaphors: IS-A metaphors, metaphors formed with the preposition ‘of’ and metaphors formed with a verb. For the first two tasks, we train supervised classifiers using semantic features. For the third task, we use features commonly used in text categorization
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
An introduction on gene annotation & curation for the IAGC and BIPAA research communities.
Using VarSeq to Improve Variant Analysis Research WorkflowsDelaina Hawkins
Many questions must be answered when analyzing DNA sequence variants: How do I determine which variants are potentially deleterious? Is the sequencing quality sufficient? How do I prioritize the results? Which annotation sources may help answer my research question?
In this webinar presentation, we will review workflow strategies for quality control and analysis of DNA sequence variants using the VarSeq software package from Golden Helix. VarSeq is a powerful platform for analysis of DNA sequence variants in clinical and translational research settings. VarSeq provides researchers with easy access to curated public databases of variant annotation information, and also enables users to incorporate their own local databases or downloaded information about variants and genomic regions.
The presentation will include interactive demonstrations using VarSeq to analyze variants found by exome sequencing of an extended family with a complex disease. We will review strategies for assessing variant quality, applying genomic annotations, incorporating custom annotation sources, and creating variant filters in VarSeq. We will also demonstrate the PhoRank gene ranking algorithm and its application for prioritizing variants.
Using VarSeq to Improve Variant Analysis Research WorkflowsGolden Helix Inc
In this webinar presentation, we will review workflow strategies for quality control and analysis of DNA sequence variants using the VarSeq software package from Golden Helix. VarSeq is a powerful platform for analysis of DNA sequence variants in clinical and translational research settings. VarSeq provides researchers with easy access to curated public databases of variant annotation information, and also enables users to incorporate their own local databases or downloaded information about variants and genomic regions.
Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...Spark Summit
The detection and analysis of rare genomic events requires integrative analysis across large cohorts with terabytes to petabytes of genomic data. Contemporary genomic analysis tools have not been designed for this scale of data-intensive computing. This talk presents ADAM, an Apache 2 licensed library built on top of the popular Apache Spark distributed computing framework. ADAM is designed to allow genomic analyses to be seamlessly distributed across large clusters, and presents a clean API for writing parallel genomic analysis algorithms. In this talk, we’ll look at how we’ve used ADAM to achieve a 3.5× improvement in end-to-end variant calling latency and a 66% cost improvement over current toolkits, without sacrificing accuracy. We will talk about a recent recompute effort where we have used ADAM to recall the Simons Genome Diversity Dataset against GRCh38. We will also talk about using ADAM alongside Apache Hbase to interactively explore large variant datasets.
Uberon: opening up to community contributionsChris Mungall
Presentation from the 2nd Phenotypes Traversing All the Organisms (POTATO) Workshop https://www.biocuration2019.org/workshop-potato
Brief summary of Uberon and plan for opening up to community contributions
Explore our comprehensive data analysis project presentation on predicting product ad campaign performance. Learn how data-driven insights can optimize your marketing strategies and enhance campaign effectiveness. Perfect for professionals and students looking to understand the power of data analysis in advertising. for more details visit: https://bostoninstituteofanalytics.org/data-science-and-artificial-intelligence/
Opendatabay - Open Data Marketplace.pptxOpendatabay
Opendatabay.com unlocks the power of data for everyone. Open Data Marketplace fosters a collaborative hub for data enthusiasts to explore, share, and contribute to a vast collection of datasets.
First ever open hub for data enthusiasts to collaborate and innovate. A platform to explore, share, and contribute to a vast collection of datasets. Through robust quality control and innovative technologies like blockchain verification, opendatabay ensures the authenticity and reliability of datasets, empowering users to make data-driven decisions with confidence. Leverage cutting-edge AI technologies to enhance the data exploration, analysis, and discovery experience.
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Leverage these privacy-preserving datasets for training and testing AI models without compromising sensitive information. Opendatabay prioritizes transparency by providing detailed metadata, provenance information, and usage guidelines for each dataset, ensuring users have a comprehensive understanding of the data they're working with. By leveraging a powerful combination of distributed ledger technology and rigorous third-party audits Opendatabay ensures the authenticity and reliability of every dataset. Security is at the core of Opendatabay. Marketplace implements stringent security measures, including encryption, access controls, and regular vulnerability assessments, to safeguard your data and protect your privacy.
2. Background
• Multiple stage alignment papers (Comparative
transcriptomics)
• Ontology (tracks the hierarchy and progression of
expression)
• XenoBase, Zfa, Mouse Atlas Project
• SES stages are supposed to be used to
standardize nomenclature across vertebrate
• Stage Alignment helps comparative biology
– In hourglass project will help determine clusters of
stages more defined than early, middle, late
3. Current
Tool
Pipeline
Distance matrix
Ontology
Databases
(Xenobase, Zfa)
Manual
Embryological
Stages Entry
Outside/User
Input
Secondary Gene
Expression Data
Stage Alignment Based on user inputted
aspects
Heat Maps
Ontological Analysis
Generates common features
list using interspecific
mappings , outputs absence
presence matrix
Distance
Algorithm
User Input
Filtering algorithm, filters
based on what user
wants to be included in
analysis
4. Using common OGGs (Euclidean correlation
across stages)
Using SES text mining matrices (Euclidean
correlation across stages)
Using common 144 features (Euclidean correlation
across stages)
5. Future Directions
• Uberon lacks a lot of mapping (for lower level
characters)
• Zfa: 345 listings
• Mmus: 415 listings
• Xenopus: 2245 listings
– Bugs and assumptions made
– Need to used anatomical reference ontology
• Uberon not ideal for matching anatomical parts
• K-means clustering
• Like-wise comparisons reveals a lack of specific
features
– The ends are disrupted.
