RDAP13 Amy Nurnberger: Publishers Like Open Science (too)ASIS&T
Amy Nurnberger, Center for Digital Research and Scholarship (CDRS), Columbia University Libraries/Information Services
Publishers Like Open Science (too): the perks of institutional repository / publisher partnerships
Panel: Partnerships between institutional repositories, domain repositories, and publishers
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
Progeny Clinical is the ideal pedigree and clinical data management software solution for family-based studies. Since 1996, we’ve been providing research institutions and clinical genetic services worldwide the ability to draw pedigrees and track patient history data. You can configure the database to include unlimited fields, design data entry screens, enable security features to restrict access for specific users, run queries over the data, and more. All of this functionality integrates with Progeny Lab or Progeny LIMS so all users work off of the same database if you desire.
ICBO2017 - Supporting Ontology-Based Standardization of Biomedical Metadata i...marcosmartinezromero
In this talk I describe the main features CEDAR developed
to make it possible to easily construct Web-based
metadata-acquisition forms, enrich those forms with ontology
concepts, and then fill out the forms to create ontology-annotated
descriptions of scientific experiments
The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developedthe CEDAR Workbenchis a suite of Web-based tools and REST APIs that allows users to construct metadata templates, to fill in templates to generate high-quality metadata, and to share and manage these resources. The CEDAR Workbench provides a versatile, REST-based environment for authoring metadata that are enriched with terms from ontologies. The metadata are available as JSON, JSON-LD, or RDF for easy integration in scientific applications and reusability on the Web. Users can leverage our APIs for validating and submitting metadata to external repositories. The CEDAR Workbench is freely available and open-source.
The availability of high-quality metadata is key to facilitating discovery in the large variety of scientific datasets that are increasingly becoming publicly available. However, despite the recent focus on metadata, the diversity of metadata representation formats and the poor support for semantic markup typically result in metadata that are of poor quality. There is a pressing need for a metadata representation format that provides strong interoperation capabilities together with robust semantic underpinnings. In this talk, we describe such a format, together with open-source Web-based tools that support the acquisition, search, and management of metadata. We outline an initial evaluation using metadata from a variety of biomedical repositories.
RDAP13 Amy Nurnberger: Publishers Like Open Science (too)ASIS&T
Amy Nurnberger, Center for Digital Research and Scholarship (CDRS), Columbia University Libraries/Information Services
Publishers Like Open Science (too): the perks of institutional repository / publisher partnerships
Panel: Partnerships between institutional repositories, domain repositories, and publishers
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
Progeny Clinical is the ideal pedigree and clinical data management software solution for family-based studies. Since 1996, we’ve been providing research institutions and clinical genetic services worldwide the ability to draw pedigrees and track patient history data. You can configure the database to include unlimited fields, design data entry screens, enable security features to restrict access for specific users, run queries over the data, and more. All of this functionality integrates with Progeny Lab or Progeny LIMS so all users work off of the same database if you desire.
ICBO2017 - Supporting Ontology-Based Standardization of Biomedical Metadata i...marcosmartinezromero
In this talk I describe the main features CEDAR developed
to make it possible to easily construct Web-based
metadata-acquisition forms, enrich those forms with ontology
concepts, and then fill out the forms to create ontology-annotated
descriptions of scientific experiments
The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developedthe CEDAR Workbenchis a suite of Web-based tools and REST APIs that allows users to construct metadata templates, to fill in templates to generate high-quality metadata, and to share and manage these resources. The CEDAR Workbench provides a versatile, REST-based environment for authoring metadata that are enriched with terms from ontologies. The metadata are available as JSON, JSON-LD, or RDF for easy integration in scientific applications and reusability on the Web. Users can leverage our APIs for validating and submitting metadata to external repositories. The CEDAR Workbench is freely available and open-source.
The availability of high-quality metadata is key to facilitating discovery in the large variety of scientific datasets that are increasingly becoming publicly available. However, despite the recent focus on metadata, the diversity of metadata representation formats and the poor support for semantic markup typically result in metadata that are of poor quality. There is a pressing need for a metadata representation format that provides strong interoperation capabilities together with robust semantic underpinnings. In this talk, we describe such a format, together with open-source Web-based tools that support the acquisition, search, and management of metadata. We outline an initial evaluation using metadata from a variety of biomedical repositories.
The metadata about scientific experiments are crucial for finding, reproducing, and reusing the data that the metadata describe. We present a study of the quality of the metadata stored in BioSample—a repository of metadata about samples used in biomedical experiments managed by the U.S. National Center for Biomedical Technology Information (NCBI). We tested whether 6.6 million BioSample metadata records are populated with values that fulfill the stated requirements for such values. Our study revealed multiple anomalies in the analyzed metadata. The BioSample metadata field names and their values are not standardized or controlled—15% of the metadata fields use field names not specified in the BioSample data dictionary. Only 9 out of 452 BioSample-specified fields ordinarily require ontology terms as values, and the quality of these controlled fields is better than that of uncontrolled ones, as even simple binary or numeric fields are often populated with inadequate values of different data types (e.g., only 27% of Boolean values are valid). Overall, the metadata in BioSample reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements. The aberrancies in the metadata are likely to impede search and secondary use of the associated datasets.
A Lined Data Approach to Interoperability between Biomedical Resource Invento...Trish Whetzel
Overview of Resource Representation Coordination efforts to coordinate the representation of resources from Biositemaps, eagle-i, and the Neuroscience Information Framework.
The Center for Expanded Data Annotation and Retrieval (CEDAR) has developed a suite of tools and services that allow scientists to create and publish metadata describing scientific experiments. Using these tools and services—referred to collectively as the CEDAR Workbench—scientists can collaboratively author metadata and submit them to public repositories. A key focus of our software is semantically enriching metadata with ontology terms. The system combines emerging technologies, such as JSON-LD and graph databases, with modern software development technologies, such as microservices and container platforms. The result is a suite of user-friendly, Web-based tools and REST APIs that provide a versatile end-to-end solution to the problems of metadata authoring and management. This talk presents the architecture of the CEDAR Workbench and focuses on the technology choices made to construct an easily usable, open system that allows users to create and publish semantically enriched metadata in standard Web formats.
Presentation for the San Francisco #IDCC14 conference (http://www.dcc.ac.uk/events/idcc14/day-two-papers). The presentation covers publishing zooarchaeology data with Open Context (http://opencontext.org) to study the spread of farming from the Near East to Europe through Anatolia. It looks at editorial processes, linked data annotation, and other workflow concerns relating to making raw data more usable for comparative analysis.
Analysis of Evergreen Software: Brittany N. EmgeBrittany N. Emge
A short analysis of Evergreen software. A final project for Valdosta State University's MLIS 7505: Applied Technologies in Libraries by Brittany N. Emge.
Brown, Christopher C. “The Front Face of the ERM: How we Left Our Home-Grown
Database Management System and Enbraced a More Innovative One.” Presentation
given at the Innovative Users Group 2013, 25 April 2013, San Francisco, CA.
The metadata about scientific experiments are crucial for finding, reproducing, and reusing the data that the metadata describe. We present a study of the quality of the metadata stored in BioSample—a repository of metadata about samples used in biomedical experiments managed by the U.S. National Center for Biomedical Technology Information (NCBI). We tested whether 6.6 million BioSample metadata records are populated with values that fulfill the stated requirements for such values. Our study revealed multiple anomalies in the analyzed metadata. The BioSample metadata field names and their values are not standardized or controlled—15% of the metadata fields use field names not specified in the BioSample data dictionary. Only 9 out of 452 BioSample-specified fields ordinarily require ontology terms as values, and the quality of these controlled fields is better than that of uncontrolled ones, as even simple binary or numeric fields are often populated with inadequate values of different data types (e.g., only 27% of Boolean values are valid). Overall, the metadata in BioSample reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements. The aberrancies in the metadata are likely to impede search and secondary use of the associated datasets.
A Lined Data Approach to Interoperability between Biomedical Resource Invento...Trish Whetzel
Overview of Resource Representation Coordination efforts to coordinate the representation of resources from Biositemaps, eagle-i, and the Neuroscience Information Framework.
The Center for Expanded Data Annotation and Retrieval (CEDAR) has developed a suite of tools and services that allow scientists to create and publish metadata describing scientific experiments. Using these tools and services—referred to collectively as the CEDAR Workbench—scientists can collaboratively author metadata and submit them to public repositories. A key focus of our software is semantically enriching metadata with ontology terms. The system combines emerging technologies, such as JSON-LD and graph databases, with modern software development technologies, such as microservices and container platforms. The result is a suite of user-friendly, Web-based tools and REST APIs that provide a versatile end-to-end solution to the problems of metadata authoring and management. This talk presents the architecture of the CEDAR Workbench and focuses on the technology choices made to construct an easily usable, open system that allows users to create and publish semantically enriched metadata in standard Web formats.
Presentation for the San Francisco #IDCC14 conference (http://www.dcc.ac.uk/events/idcc14/day-two-papers). The presentation covers publishing zooarchaeology data with Open Context (http://opencontext.org) to study the spread of farming from the Near East to Europe through Anatolia. It looks at editorial processes, linked data annotation, and other workflow concerns relating to making raw data more usable for comparative analysis.
Analysis of Evergreen Software: Brittany N. EmgeBrittany N. Emge
A short analysis of Evergreen software. A final project for Valdosta State University's MLIS 7505: Applied Technologies in Libraries by Brittany N. Emge.
Brown, Christopher C. “The Front Face of the ERM: How we Left Our Home-Grown
Database Management System and Enbraced a More Innovative One.” Presentation
given at the Innovative Users Group 2013, 25 April 2013, San Francisco, CA.
Get Satisfaction Customer Success Summit Morning KeynoteGet Satisfaction
http://bit.ly/1clmLDG, Best Practices of Community Management: The day started off geared towards our heroes, community managers and the techies. These will be collaborative sessions that are all about sharing best practices, learned knowledge, and tapping into the wealth of experience that you all bring to the table. Sessions were broken up into two tracks: Business Value and Best Practices of Community Management
Deep Dives on Special Topics (Product Training & Developers)
Anita Bandrowski explains how the uniform resource layer of the Neuroscience Information Framework allows several interesting questions about the state of scientific research to be answered.
9,548 to 19,463 sq ft of Showroom/Warehouse For Lease in EdmontonChad Griffiths
95 Street and 12 Avenue SW
Edmonton, Alberta
• New building with Fall 2015 occupancy
• 9,548 to 19,463 sq ft of showroom/warehouse space available
• 28’ clear ceiling heights with grade level loading
• National autobody and national tire/repair companies already secured
• Car dealerships in the vicinity include Lexus, Audi, Volvo, Volkswagen, Chrysler and soon Mercedes-Benz and Toyota
• Detailed renderings/drawings available
Zoning: EIB (Ellerslie Industrial Business)
Loading: Grade, Note: Dock may be possible
Ceiling: 28’ clear
Occupancy: Fall 2015
Net Rental Rate: Starting at $12.50/sq.ft./annum
Additional Rent: $3.50/sq.ft. (2015 estimate) includes proportionate share of property taxes, building insurance, common area maintenance and management fees
An introduction to the Joint Information Systems Committee Resource Discovery iKit. Includes a look at controlled vocabularies declared in the Resource Discovery Framework (RDF)/Simple Knowledge Organisation System (SKOS) and wikipedia entries. Presented by Tony Ross at the CILIPS Centenary Conference Branch and Group Day which took place 5 Jun 2008.
De-centralized but global: Redesigning biodiversity data aggregation for impr...taxonbytes
Biodiversity data pose fundamental challenges for unification-based paradigms of data science. In particular, a hierarchical, backbone-driven approach to aggregating global biodiversity data tends to limit community engagement. Data quality, trust, fitness for use, and impact are similarly reduced. This presentation will outline an alternative, de-centralized design for aggregating biodiversity data globally. The design requires a coordinative approach to representing and reconciling evolving systematic perspectives, and further social but technologically mediated coordination between regionally and taxonomically constrained "communities of practice" (sensu Wenger, 2000, https://doi.org/10.1177/135050840072002). Important next steps in this direction include the development of use cases that quantify the benefits of a de-centralized biodiversity data aggregation - in terms of lowering costs to expert engagement, raising efficiency of curation, validating novel integration services, and improving reproducibility and provenance tracking across heterogenous data structures and portals.
Creating Sustainable Communities in Open Data Resources: The eagle-i and VIVO...Robert H. McDonald
This is the slidedeck for my ACRL 2015 TechConnect Presentation with Nicole Vasilevsky (OHSU). For more on the program see - <a>http://bit.ly/1xcQbCr</a>.
RDAP14: Maryann Martone, Keynote, The Neuroscience Information FrameworkASIS&T
Research Data Access and Preservation Summit, 2014
San Diego, CA
March 26-28, 2014
Maryann Martone, Principal Investigator, Neuroscience Information Framework, University of California, San Diego
the Neuroscience Information Framework has over 100 big data databases indexed, allowing us to ask big data landscape questions. Anita Bandrowski presents an overview of the NIF system and provides insights into the addiction data landscape to JAX laboratories.
Maryann Martone
Making Sense of Biological Systems: Using Knowledge Mining to Improve and Validate Models of Living Systems; NIH COBRE Center for the Analysis of Cellular Mechanisms and Systems Biology, Montana State University, Bozeman, MT
August 24, 2012
JMeter webinar - integration with InfluxDB and GrafanaRTTS
Watch this recorded webinar about real-time monitoring of application performance. See how to integrate Apache JMeter, the open-source leader in performance testing, with InfluxDB, the open-source time-series database, and Grafana, the open-source analytics and visualization application.
In this webinar, we will review the benefits of leveraging InfluxDB and Grafana when executing load tests and demonstrate how these tools are used to visualize performance metrics.
Length: 30 minutes
Session Overview
-------------------------------------------
During this webinar, we will cover the following topics while demonstrating the integrations of JMeter, InfluxDB and Grafana:
- What out-of-the-box solutions are available for real-time monitoring JMeter tests?
- What are the benefits of integrating InfluxDB and Grafana into the load testing stack?
- Which features are provided by Grafana?
- Demonstration of InfluxDB and Grafana using a practice web application
To view the webinar recording, go to:
https://www.rttsweb.com/jmeter-integration-webinar
Accelerate your Kubernetes clusters with Varnish CachingThijs Feryn
A presentation about the usage and availability of Varnish on Kubernetes. This talk explores the capabilities of Varnish caching and shows how to use the Varnish Helm chart to deploy it to Kubernetes.
This presentation was delivered at K8SUG Singapore. See https://feryn.eu/presentations/accelerate-your-kubernetes-clusters-with-varnish-caching-k8sug-singapore-28-2024 for more details.
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
As AI technology is pushing into IT I was wondering myself, as an “infrastructure container kubernetes guy”, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefit’s both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
Neuro-symbolic is not enough, we need neuro-*semantic*Frank van Harmelen
Neuro-symbolic (NeSy) AI is on the rise. However, simply machine learning on just any symbolic structure is not sufficient to really harvest the gains of NeSy. These will only be gained when the symbolic structures have an actual semantics. I give an operational definition of semantics as “predictable inference”.
All of this illustrated with link prediction over knowledge graphs, but the argument is general.
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
2. Resource?
http://neuinfo.org
…websites that have significant value to the greater neuroscience
community, including biomedical resources. For the most part, these are
limited to not-for-profit. It shall be considered an individual resource if it is
maintained by a single entity, and has the properties of one or more
individual web pages that are related by a theme and HTML links. Most
often the individual pages share portions of the URL, however, unrelated
URLs may be incorporated into a single web resource. In the event that a
subgroup of pages represents a sufficient shift in theme, it should be
classified as an independent resource. For example, the department of
neuroscience of a university (resource 1) may have a lab led by a
researcher (resource 2).
Website/web tool produced by or useful to, a
biomedical researcher
3. How Can We Find Resources?
“I would like funding to create
an RNAi database because
one does not exist.” –
biomedical researcher
But…
http://neuinfo.org
There must be a
place where
researchers can go
to find resources
before they create
them again!
4. How Can We Find Resources?
http://neuinfo.org
Database (2200)
Software tool (900)
Biobanks (550)
Services (100)
6. Each resource implements
a different, though related
model; systems are
complex and difficult to
learn, in many cases
Access to Biomedical Resources
Must Be Uniform!
http://neuinfo.org
7. Need a Common Platform for
Access to Biological Data
http://neuinfo.org
8. Need a Common Platform for
Access to Biological Data
Not just RDF!
Not just XML!
Nosql! –no
Data, to a biologist is something that can be
understood.
“…according to Bonda (2000) the Amygdaloid
nucleus is connected to Field CA1 in the young adult
monkey, subjected to the following conditions...”
http://neuinfo.org
9. Are We There Yet?
Of 2200 databases that NIF has in the Registry, we
have only deeply registered 200
Of the 800 software tools, <100 have deep metadata
and user communities
Not yet, but some things can help
If you have a tool / data please register at
http://neuinfo.org/cindy.php
If you have a choice, use open formats
If you have a choice, use common vocabularies
If you can, in papers and databases, use identifiers
http://neuinfo.org
10. Diseases of nervous system
Neurodegenerative
Seizuredisorders
Neoplasticdiseaseofnervous
system
NIH
Reporter
NIFdatafederatedsources
http://neuinfo.org