Resource Identification Initiative_RDA_March2014
•
1 like•378 views
Poster presentation about the Resource Identification Initiative (http://www.force11.org/Resource_identification_initiative) at the Research Data Alliance meeting in Dublin, Ireland in March 2014 (https://rd-alliance.org/rda-third-plenary-meeting.html).
Report
Share
Report
Share
Download to read offline
Recommended
On the Reproducibility of Science: Unique Identification of Research Resourc...
Poster presentation at the Data Information Literacy Symposium at Purdue University in Indiana, Sept. 2013. This study is published here: https://peerj.com/articles/148/
Model Organism Linked Data
Model organisms such as budding yeast provide a common platform to interrogate and understand cellular and physiological processes. Knowledge about model organisms, whether generated during the course of scientific investigation, or extracted from published articles, are made available by model organism databases (MODs) such as the Saccharomyces Genome Database (SGD) for powerful, data-driven bioinformatic analyses. Integrative platforms such as InterMine offer a standard platform for MOD data exploration and data mining. Yet, today’s bioinformatic analyses also requires access to a significantly broader set of structured biomedical data, such as what can be found in the emerging network of Linked Open Data (LOD). If MOD data could be provisioned as FAIR (Findable, Accessible, Interoperable, and Reusable), then scientists could leverage a greater amount of interoperable data in knowledge discovery.
The goal of this proposal is to increase the utility of MOD data by implementing standards-compliant data access interfaces that interoperate with Linked Data. We will focus our efforts on developing interfaces for data access, data retrieval, and query answering for SGD. Our software will publish InterMine data as LOD that are semantically annotated with ontologies and be retrieved using standardized formats (e.g. JSON-LD, Turtle). We will facilitate the exploration of MOD data for hypothesis testing, by implementing efficient query answering using Linked Data Fragments, and by developing a set of graphical user interfaces to search for data of interest, explore connections, and answer questions that leverage the wider LOD network. Finally, we will develop a locally and cloud-deployable image to enable the rapid deployment of the proposed infrastructure. Our efforts to increase interoperability and ease of deployment for biomedical data repositories will increase research productivity and reduce costs associated with data integration and warehouse maintenance.
CoBRA guideline : a tool to facilitate sharing, reuse, and reproducibility of...
CoBRA guideline : a tool to facilitate sharing, reuse, and reproducibility of...Research Data Alliance
CoBRA is a reporting guideline that provides a standardized way to cite bioresources in scientific publications. It aims to improve transparency, openness, and reproducibility of research. The guideline recommends citing each bioresource used in the methods section with its name, ID, organization, number of access, and date of last access. Adding a [BIORESOURCE] tag helps track bioresource use. CoBRA endorsement by organizations like EQUATOR and BBMRI-ERIC aims to facilitate its wider adoption.How many medline platforms on the web?
The document discusses various biomedical literature search platforms and alternatives to PubMed/Medline. It summarizes PubMed/Medline's history and features. It then evaluates PubMed as both a success and tragedy due to its poor interface but large userbase. Several alternative search platforms like GoPubMed, Quertle and BibliMed are introduced as having better search experiences and interfaces than PubMed/Medline. The document recommends using alternative platforms for more efficient searching, accessing full texts and identifying experts.
Making it Easier, Possibly Even Pleasant, to Author Rich Experimental Metadata
Biomedical researchers will remain stymied in their ability to take full advantage of the Big Data revolution if they can never find the datasets that they need to analyze, if there is lack of clarity about what particular datasets contain, and if data are insufficiently described.
CEDAR, an NIH BD2K Center of Excellence, aims to develop methods and tools to vastly ease the burden of authoring good experimental metadata, and to maximally use this information to zero in on datasets of interest.
creation of DNA barcoding database with website
The document describes the creation of a DNA barcode reference library for identifying ayurvedic herb species. A website and database were developed to house the reference library. The website includes information on DNA barcoding and molecular markers. The database stores taxonomic and barcode sequence data. A species identification engine was also created using Python modules to analyze query sequences against the reference library and output identification results. The reference library and identification tools can help authenticate ayurvedic herbs and improve safety and reliability. However, the library is still incomplete and standardization is needed for full integration of DNA barcoding into herbal identification.
Identifying and tracking research resources using RRIDs: a practical approach
At this presentation, you will learn (1) Why you need to use Research Resource identifier (RRID) (2) What is Resource Identification Initiative (3) How dkNET.org supports RRID (4) What can you do with RRID
A Few Simple Things Authors Can Do to Make Their Data More Discoverable and R...
A Few Simple Things Authors Can Do to Make Their Data More Discoverable and R...Phoenix Bioinformatics
This document discusses simple steps authors can take to make their research data more discoverable and reusable, including identifying the research organisms in the abstract, title and metadata, using unique identifiers for genes/gene products, making tables in publications available as text files, submitting data to appropriate repositories, and following FAIR data principles. Applying these practices will help researchers more easily find and utilize relevant data.Recommended
On the Reproducibility of Science: Unique Identification of Research Resourc...
Poster presentation at the Data Information Literacy Symposium at Purdue University in Indiana, Sept. 2013. This study is published here: https://peerj.com/articles/148/
Model Organism Linked Data
Model organisms such as budding yeast provide a common platform to interrogate and understand cellular and physiological processes. Knowledge about model organisms, whether generated during the course of scientific investigation, or extracted from published articles, are made available by model organism databases (MODs) such as the Saccharomyces Genome Database (SGD) for powerful, data-driven bioinformatic analyses. Integrative platforms such as InterMine offer a standard platform for MOD data exploration and data mining. Yet, today’s bioinformatic analyses also requires access to a significantly broader set of structured biomedical data, such as what can be found in the emerging network of Linked Open Data (LOD). If MOD data could be provisioned as FAIR (Findable, Accessible, Interoperable, and Reusable), then scientists could leverage a greater amount of interoperable data in knowledge discovery.
The goal of this proposal is to increase the utility of MOD data by implementing standards-compliant data access interfaces that interoperate with Linked Data. We will focus our efforts on developing interfaces for data access, data retrieval, and query answering for SGD. Our software will publish InterMine data as LOD that are semantically annotated with ontologies and be retrieved using standardized formats (e.g. JSON-LD, Turtle). We will facilitate the exploration of MOD data for hypothesis testing, by implementing efficient query answering using Linked Data Fragments, and by developing a set of graphical user interfaces to search for data of interest, explore connections, and answer questions that leverage the wider LOD network. Finally, we will develop a locally and cloud-deployable image to enable the rapid deployment of the proposed infrastructure. Our efforts to increase interoperability and ease of deployment for biomedical data repositories will increase research productivity and reduce costs associated with data integration and warehouse maintenance.
CoBRA guideline : a tool to facilitate sharing, reuse, and reproducibility of...
CoBRA guideline : a tool to facilitate sharing, reuse, and reproducibility of...Research Data Alliance
CoBRA is a reporting guideline that provides a standardized way to cite bioresources in scientific publications. It aims to improve transparency, openness, and reproducibility of research. The guideline recommends citing each bioresource used in the methods section with its name, ID, organization, number of access, and date of last access. Adding a [BIORESOURCE] tag helps track bioresource use. CoBRA endorsement by organizations like EQUATOR and BBMRI-ERIC aims to facilitate its wider adoption.How many medline platforms on the web?
The document discusses various biomedical literature search platforms and alternatives to PubMed/Medline. It summarizes PubMed/Medline's history and features. It then evaluates PubMed as both a success and tragedy due to its poor interface but large userbase. Several alternative search platforms like GoPubMed, Quertle and BibliMed are introduced as having better search experiences and interfaces than PubMed/Medline. The document recommends using alternative platforms for more efficient searching, accessing full texts and identifying experts.
Making it Easier, Possibly Even Pleasant, to Author Rich Experimental Metadata
Biomedical researchers will remain stymied in their ability to take full advantage of the Big Data revolution if they can never find the datasets that they need to analyze, if there is lack of clarity about what particular datasets contain, and if data are insufficiently described.
CEDAR, an NIH BD2K Center of Excellence, aims to develop methods and tools to vastly ease the burden of authoring good experimental metadata, and to maximally use this information to zero in on datasets of interest.
creation of DNA barcoding database with website
The document describes the creation of a DNA barcode reference library for identifying ayurvedic herb species. A website and database were developed to house the reference library. The website includes information on DNA barcoding and molecular markers. The database stores taxonomic and barcode sequence data. A species identification engine was also created using Python modules to analyze query sequences against the reference library and output identification results. The reference library and identification tools can help authenticate ayurvedic herbs and improve safety and reliability. However, the library is still incomplete and standardization is needed for full integration of DNA barcoding into herbal identification.
Identifying and tracking research resources using RRIDs: a practical approach
At this presentation, you will learn (1) Why you need to use Research Resource identifier (RRID) (2) What is Resource Identification Initiative (3) How dkNET.org supports RRID (4) What can you do with RRID
A Few Simple Things Authors Can Do to Make Their Data More Discoverable and R...
A Few Simple Things Authors Can Do to Make Their Data More Discoverable and R...Phoenix Bioinformatics
This document discusses simple steps authors can take to make their research data more discoverable and reusable, including identifying the research organisms in the abstract, title and metadata, using unique identifiers for genes/gene products, making tables in publications available as text files, submitting data to appropriate repositories, and following FAIR data principles. Applying these practices will help researchers more easily find and utilize relevant data.2016 ACS Semantic Approaches for Biochemical Knowledge Discovery
A presentation to the American Chemical Society in the asession for Chemistry, Data, & the Semantic Web: An Important Triple to Advance Science:
Pub med
PubMed is a free database of over 23 million citations and abstracts for biomedical literature from Medline, life sciences journals, and online books. It is maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM). PubMed provides bibliographic information and links to full-text content from publishers and libraries. Users can search PubMed using keywords, controlled vocabularies like MeSH, or advanced search techniques and filters to find relevant journal articles and resources.
Resource Identification Initiative
Presentation on the Resource Identification Pilot Project, an initiative to develop a machine-processable citation system for key research resources used in scientific studies
Introduction to PubMed for LIS students
PubMed is a database of biomedical citations and abstracts maintained by the US National Library of Medicine. It contains over 20 million citations dating back to the 1950s. PubMed indexes MEDLINE citations and includes citations supplied by publishers as well as those in process. MeSH, or Medical Subject Headings, is a controlled vocabulary used for indexing articles in PubMed. Searching PubMed involves identifying key concepts in a search question and searching each concept separately before combining results. MyNCBI allows users to customize PubMed displays, save searches and collections. Alternative interfaces to PubMed include Pubget, LigerCat, and GoPubMed.
Diagnostic criteria and clinical guidelines standardization to automate case ...
This document discusses standardizing clinical guidelines for adverse event classification using the Adverse Event Reporting Ontology (AERO). It describes how AERO encodes guidelines like Brighton Collaboration for diagnosing conditions like anaphylaxis from vaccine reports. It also discusses how AERO can integrate data like classifying reports in the Vaccine Adverse Event Reporting System according to encoded guidelines and linking to other datasets like DrugBank. The goal is automated adverse event diagnosis and integration of reporting data.
Phenotypes and models portal at the rat genome database
The Phenotypes and Models Portal at the Rat Genome Database provides access to physiological data and information about disease models in rats. The portal combines existing rat data with new physiological data and has four branches: 1) phenotype data from multiple organ system studies, 2) information on rat strains and disease models, 3) a PhenoMiner tool to query data integrated across ontologies, and 4) new strain medical records providing overviews of commonly used disease models with their characteristics, phenotypes, and omics data. The portal aims to help researchers choose appropriate rat strains for studying physiology and disease.
TAIR Presentation ASPB 2016
How to use The Arabidopsis Information Resource (TAIR) and biological ontologies for translational plant biology.
CDD poster
The document discusses a collaboration between researchers from Drexel University, UCSF, and Indiana University aimed at accelerating drug discovery for malaria. The collaboration uses an open science and collaborative drug discovery approach, sharing research over blogs, wikis, and other online platforms. Specifically, the collaboration links synthetic chemistry from Drexel, malaria biology and screening from UCSF, and computational docking from Indiana University to filter a library of compounds for testing against malaria. The researchers have shared screening data and characterized compounds in online databases to make their findings openly accessible.
W3C HCLS Dataset Description Guidelines
Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. This document describes a consensus among participating stakeholders in the Health Care and the Life Sciences domain on the description of datasets using the Resource Description Framework (RDF). This specification meets key functional requirements, reuses existing vocabularies to the extent that it is possible, and addresses elements of data description, versioning, provenance, discovery, exchange, query, and retrieval.
2016 bmdid-mappings
Bio2RDF is an open-source project that offers a large and
connected knowledge graph of Life Science Linked Data. Each dataset is expressed using its own vocabulary, thereby hindering integration, search, query, and browse data across similar or identical types of data. With growth and content changes in source data, a manual approach to maintain mappings has proven untenable. The aim of this work is to develop a (semi)automated procedure to generate high quality mappings
between Bio2RDF and SIO using BioPortal ontologies. Our preliminary results demonstrate that our approach is promising in that it can find new mappings using a transitive closure between ontology mappings. Further development of the methodology coupled with improvements in
the ontology will offer a better-integrated view of the Life Science Linked Data
Semantic approaches for biomedical knowledge discovery - Discovery Science 20...
With its focus on investigating the basis for the sustained existence
of living systems, modern biology has always been a fertile, if not
challenging, domain for formal knowledge representation and automated
reasoning. With thousands of databases and hundreds of ontologies now
available, there is a salient opportunity to integrate these for
discovery. In this talk, I will discuss our efforts to build a rich
foundational network of ontology-annotated linked data, develop
methods to intelligently retrieve content of interest, uncover
significant biological associations, and pursue new avenues for drug
discovery. As the portfolio of Semantic Web technologies continue to
mature in terms of functionality, scalability, and an understanding of
how to maximize their value, researchers will be strategically poised
to pursue increasingly sophisticated KR projects aimed at improving
our overall understanding of human health and disease.
bio: Dr. Michel Dumontier is an Associate Professor of Medicine
(Biomedical Informatics) at Stanford University. His research aims to
find new treatments for rare and complex diseases. His research
interest lie in the publication, integration, and discovery of
scientific knowledge. Dr. Dumontier serves as a co-chair for the World
Wide Web Consortium Semantic Web in Health Care and Life Sciences
Interest Group (W3C HCLSIG) and is the Scientific Director for
Bio2RDF, a widely used open-source project to create and provide
linked data for life sciences.
iBioSearch: The Integrated Biological Database Search
The document proposes a solution called iBioSearch that aims to provide a unified search interface for biologists to search over 1000 biological databases. It does this by first collecting interfaces from various biological databases and then reverse engineering them to generate a global schema (metamodel) that represents common search capabilities across interfaces. It maps each interface as an instance of this metamodel to extract search entities and criteria. It then clusters entities and consolidates criteria to generate a non-redundant global biological search interface (GBWS) for biologists. Future work involves testing this approach with biologists and expanding the methodology.
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalie...
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalie...CEDAR: Center for Expanded Data Annotation and Retrieval
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.NCBO Tools and Web services
The document describes tools and web services from the National Center for Biomedical Ontology (NCBO) including the Ontology Web Services, Ontology Widgets, NCBO Annotator, NCBO Resource Index, and Ontology Recommender. The NCBO Annotator is an open access web service that annotates text with terms from ontologies in BioPortal and includes a variety of customization parameters. The NCBO Resource Index provides an ontology-based search across publicly available biomedical resources.
ReVeaLD: A user-driven domain-specific interactive search platform for biomed...
1) ReVeaLD is an interactive search platform that allows biomedical researchers to query linked open data sources using natural language queries or a visual interface.
2) It addresses challenges of accessing heterogeneous biomedical data sources by providing a domain-specific language and query templates to form SPARQL queries for multiple data sources.
3) The system was evaluated on tasks involving formulating queries using the domain-specific language concepts and linked open data catalog, and it was found that familiarity with the domain-specific language concepts and a smaller set of concepts improved query formulation times.
COVID-19 Research in India and Changing Scholarly Publishing Paradigm
Indian researchers have published over 89 papers on COVID-19 research. Most papers come from ICMR and AIIMS in New Delhi. States like Uttar Pradesh and Bihar have published few papers despite large populations. The National Institute of Virology in Pune has collaborated widely. Top journals include the Indian Journal of Medical Research. Research focuses on epidemiology, diabetes/COVID interactions, and environmental impacts. More clinical and virology research is needed. The pandemic is shifting publishing norms as preprint servers rapidly share new findings.
CEDAR: Web-Based Tools for Accelerating the Creation of Standardized Metadata
Mark A. Musen, John Graybeal, Martin J. O'Connor, Marcos Martínez-Romero, Attila L. Egyedi, Debra Willrett, S. Ahmad Chan Bukhari, Steven H. Kleinstein, Kei-Hoi Cheung, Elizabeth Thomson, Alejandra Gonzalez-Beltran, Phillipe Rocca-Serra, and Susanna-Assunta Sansone
Citation collaboration Open Access Week 2015 SF
#OAW15SF Event "Let's Collaborate: Boost your citations and visibility": Citations expose the global collaborations that underlie scholarly research. ScienceOpen is a new platform to track citations and collaborate with researchers.
PubChem Database
An introduction to searching this NCBI chemistry database in support of research into drug properties.
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...CEDAR: Center for Expanded Data Annotation and Retrieval
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.Fall 2012 Simply Delicious brochure
This document is an order form and catalog for Simply Delicious cookie dough and baked goods. It lists over 50 products including different flavors of cookie dough, rolls, pies, breads, and gift cards. The prices range from $13 to $30 per item. Additional information provided includes that each box of cookie dough contains 48 preportioned cookies and indicates if items are kosher.
Human: Thank you, that's a great high-level summary that captures the key details while being concise.
More Related Content
What's hot
2016 ACS Semantic Approaches for Biochemical Knowledge Discovery
A presentation to the American Chemical Society in the asession for Chemistry, Data, & the Semantic Web: An Important Triple to Advance Science:
Pub med
PubMed is a free database of over 23 million citations and abstracts for biomedical literature from Medline, life sciences journals, and online books. It is maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM). PubMed provides bibliographic information and links to full-text content from publishers and libraries. Users can search PubMed using keywords, controlled vocabularies like MeSH, or advanced search techniques and filters to find relevant journal articles and resources.
Resource Identification Initiative
Presentation on the Resource Identification Pilot Project, an initiative to develop a machine-processable citation system for key research resources used in scientific studies
Introduction to PubMed for LIS students
PubMed is a database of biomedical citations and abstracts maintained by the US National Library of Medicine. It contains over 20 million citations dating back to the 1950s. PubMed indexes MEDLINE citations and includes citations supplied by publishers as well as those in process. MeSH, or Medical Subject Headings, is a controlled vocabulary used for indexing articles in PubMed. Searching PubMed involves identifying key concepts in a search question and searching each concept separately before combining results. MyNCBI allows users to customize PubMed displays, save searches and collections. Alternative interfaces to PubMed include Pubget, LigerCat, and GoPubMed.
Diagnostic criteria and clinical guidelines standardization to automate case ...
This document discusses standardizing clinical guidelines for adverse event classification using the Adverse Event Reporting Ontology (AERO). It describes how AERO encodes guidelines like Brighton Collaboration for diagnosing conditions like anaphylaxis from vaccine reports. It also discusses how AERO can integrate data like classifying reports in the Vaccine Adverse Event Reporting System according to encoded guidelines and linking to other datasets like DrugBank. The goal is automated adverse event diagnosis and integration of reporting data.
Phenotypes and models portal at the rat genome database
The Phenotypes and Models Portal at the Rat Genome Database provides access to physiological data and information about disease models in rats. The portal combines existing rat data with new physiological data and has four branches: 1) phenotype data from multiple organ system studies, 2) information on rat strains and disease models, 3) a PhenoMiner tool to query data integrated across ontologies, and 4) new strain medical records providing overviews of commonly used disease models with their characteristics, phenotypes, and omics data. The portal aims to help researchers choose appropriate rat strains for studying physiology and disease.
TAIR Presentation ASPB 2016
How to use The Arabidopsis Information Resource (TAIR) and biological ontologies for translational plant biology.
CDD poster
The document discusses a collaboration between researchers from Drexel University, UCSF, and Indiana University aimed at accelerating drug discovery for malaria. The collaboration uses an open science and collaborative drug discovery approach, sharing research over blogs, wikis, and other online platforms. Specifically, the collaboration links synthetic chemistry from Drexel, malaria biology and screening from UCSF, and computational docking from Indiana University to filter a library of compounds for testing against malaria. The researchers have shared screening data and characterized compounds in online databases to make their findings openly accessible.
W3C HCLS Dataset Description Guidelines
Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. This document describes a consensus among participating stakeholders in the Health Care and the Life Sciences domain on the description of datasets using the Resource Description Framework (RDF). This specification meets key functional requirements, reuses existing vocabularies to the extent that it is possible, and addresses elements of data description, versioning, provenance, discovery, exchange, query, and retrieval.
2016 bmdid-mappings
Bio2RDF is an open-source project that offers a large and
connected knowledge graph of Life Science Linked Data. Each dataset is expressed using its own vocabulary, thereby hindering integration, search, query, and browse data across similar or identical types of data. With growth and content changes in source data, a manual approach to maintain mappings has proven untenable. The aim of this work is to develop a (semi)automated procedure to generate high quality mappings
between Bio2RDF and SIO using BioPortal ontologies. Our preliminary results demonstrate that our approach is promising in that it can find new mappings using a transitive closure between ontology mappings. Further development of the methodology coupled with improvements in
the ontology will offer a better-integrated view of the Life Science Linked Data
Semantic approaches for biomedical knowledge discovery - Discovery Science 20...
With its focus on investigating the basis for the sustained existence
of living systems, modern biology has always been a fertile, if not
challenging, domain for formal knowledge representation and automated
reasoning. With thousands of databases and hundreds of ontologies now
available, there is a salient opportunity to integrate these for
discovery. In this talk, I will discuss our efforts to build a rich
foundational network of ontology-annotated linked data, develop
methods to intelligently retrieve content of interest, uncover
significant biological associations, and pursue new avenues for drug
discovery. As the portfolio of Semantic Web technologies continue to
mature in terms of functionality, scalability, and an understanding of
how to maximize their value, researchers will be strategically poised
to pursue increasingly sophisticated KR projects aimed at improving
our overall understanding of human health and disease.
bio: Dr. Michel Dumontier is an Associate Professor of Medicine
(Biomedical Informatics) at Stanford University. His research aims to
find new treatments for rare and complex diseases. His research
interest lie in the publication, integration, and discovery of
scientific knowledge. Dr. Dumontier serves as a co-chair for the World
Wide Web Consortium Semantic Web in Health Care and Life Sciences
Interest Group (W3C HCLSIG) and is the Scientific Director for
Bio2RDF, a widely used open-source project to create and provide
linked data for life sciences.
iBioSearch: The Integrated Biological Database Search
The document proposes a solution called iBioSearch that aims to provide a unified search interface for biologists to search over 1000 biological databases. It does this by first collecting interfaces from various biological databases and then reverse engineering them to generate a global schema (metamodel) that represents common search capabilities across interfaces. It maps each interface as an instance of this metamodel to extract search entities and criteria. It then clusters entities and consolidates criteria to generate a non-redundant global biological search interface (GBWS) for biologists. Future work involves testing this approach with biologists and expanding the methodology.
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalie...
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalie...CEDAR: Center for Expanded Data Annotation and Retrieval
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.NCBO Tools and Web services
The document describes tools and web services from the National Center for Biomedical Ontology (NCBO) including the Ontology Web Services, Ontology Widgets, NCBO Annotator, NCBO Resource Index, and Ontology Recommender. The NCBO Annotator is an open access web service that annotates text with terms from ontologies in BioPortal and includes a variety of customization parameters. The NCBO Resource Index provides an ontology-based search across publicly available biomedical resources.
ReVeaLD: A user-driven domain-specific interactive search platform for biomed...
1) ReVeaLD is an interactive search platform that allows biomedical researchers to query linked open data sources using natural language queries or a visual interface.
2) It addresses challenges of accessing heterogeneous biomedical data sources by providing a domain-specific language and query templates to form SPARQL queries for multiple data sources.
3) The system was evaluated on tasks involving formulating queries using the domain-specific language concepts and linked open data catalog, and it was found that familiarity with the domain-specific language concepts and a smaller set of concepts improved query formulation times.
COVID-19 Research in India and Changing Scholarly Publishing Paradigm
Indian researchers have published over 89 papers on COVID-19 research. Most papers come from ICMR and AIIMS in New Delhi. States like Uttar Pradesh and Bihar have published few papers despite large populations. The National Institute of Virology in Pune has collaborated widely. Top journals include the Indian Journal of Medical Research. Research focuses on epidemiology, diabetes/COVID interactions, and environmental impacts. More clinical and virology research is needed. The pandemic is shifting publishing norms as preprint servers rapidly share new findings.
CEDAR: Web-Based Tools for Accelerating the Creation of Standardized Metadata
Mark A. Musen, John Graybeal, Martin J. O'Connor, Marcos Martínez-Romero, Attila L. Egyedi, Debra Willrett, S. Ahmad Chan Bukhari, Steven H. Kleinstein, Kei-Hoi Cheung, Elizabeth Thomson, Alejandra Gonzalez-Beltran, Phillipe Rocca-Serra, and Susanna-Assunta Sansone
Citation collaboration Open Access Week 2015 SF
#OAW15SF Event "Let's Collaborate: Boost your citations and visibility": Citations expose the global collaborations that underlie scholarly research. ScienceOpen is a new platform to track citations and collaborate with researchers.
PubChem Database
An introduction to searching this NCBI chemistry database in support of research into drug properties.
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...CEDAR: Center for Expanded Data Annotation and Retrieval
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.What's hot (20)
2016 ACS Semantic Approaches for Biochemical Knowledge Discovery
2016 ACS Semantic Approaches for Biochemical Knowledge Discovery
Diagnostic criteria and clinical guidelines standardization to automate case ...
Diagnostic criteria and clinical guidelines standardization to automate case ...
Phenotypes and models portal at the rat genome database
Phenotypes and models portal at the rat genome database
Semantic approaches for biomedical knowledge discovery - Discovery Science 20...
Semantic approaches for biomedical knowledge discovery - Discovery Science 20...
iBioSearch: The Integrated Biological Database Search
iBioSearch: The Integrated Biological Database Search
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalie...
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalie...
ReVeaLD: A user-driven domain-specific interactive search platform for biomed...
ReVeaLD: A user-driven domain-specific interactive search platform for biomed...
COVID-19 Research in India and Changing Scholarly Publishing Paradigm
COVID-19 Research in India and Changing Scholarly Publishing Paradigm
CEDAR: Web-Based Tools for Accelerating the Creation of Standardized Metadata
CEDAR: Web-Based Tools for Accelerating the Creation of Standardized Metadata
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...
Viewers also liked
Fall 2012 Simply Delicious brochure
This document is an order form and catalog for Simply Delicious cookie dough and baked goods. It lists over 50 products including different flavors of cookie dough, rolls, pies, breads, and gift cards. The prices range from $13 to $30 per item. Additional information provided includes that each box of cookie dough contains 48 preportioned cookies and indicates if items are kosher.
Human: Thank you, that's a great high-level summary that captures the key details while being concise.
Amigos 1809
Este documento habla sobre la amistad y el rol de un amigo. Un amigo no puede resolver todos los problemas ni tener todas las respuestas, pero puede escuchar y buscar soluciones juntos. Aunque no puede cambiar el pasado ni el futuro, estará presente cuando se le necesite. Un amigo ofrece su mano para levantarse, pero no puede evitar que tropiecen. Apoya las decisiones de los demás y les ofrece espacio para crecer.
Dentist in Richmond Virginia 4 Advantages of Professional Teeth Whitening Tre...
Dentist in Richmond Virginia 4 Advantages of Professional Teeth Whitening Tre...freddiehornedoconsulting
Professional teeth whitening treatments have several advantages over at-home whitening kits. They provide immediate results, often whitening teeth in under an hour. Professional treatments use stronger bleaching agents that can whiten teeth several shades brighter. They are also better able to remove deep stains. Additionally, dentists are able to properly apply the bleaching gel to whiten teeth effectively while avoiding sensitivity issues.Salesforce Administration Training In Noida Delhi NCR
This course is for experienced Salesforce administrators who want to increase their skills in using Salesforce to solve business needs. It covers topics like customizing Salesforce with objects and apps, building complex reports and dashboards, and automating business processes. Administrators will learn through real-world scenarios to work more efficiently and get the most out of Salesforce.
Apg academy of entrepreneurship.presentation
The document discusses entrepreneurial needs such as leadership training, business model development, networking, and overcoming adversity. It contrasts traditional education programs which focus on passive classroom learning and incidental services, with an approach that emphasizes active experiential learning, stakeholder engagement, environmental scanning, and thinking outside the box. The conclusion warns entrepreneurs not to "swim with the sharks" and give their business away, but rather to build a sustainable business.
Anne Meininger Usa
The document summarizes procedures for information exchange regarding regulations in the United States. It outlines the notice and comment process where federal agencies issue notices of proposed regulations, accept public comments, and publish final rules addressing the comments. It also describes the U.S. Federal Register as the main source for finding these notices and rules, and an electronic tool called RegAlert that tracks regulations in U.S. states.
Ananda Nagar II Bhubaneswar
http://bit.ly/ananda-nagar-ii-bhubaneswar
You will probably agree that a “house” reflects the personality, the aesthetic sense and taste of the owner, who builds it brick-by-brick. A “Duplex Core House” gives you all these benefits, without the maddening confusion, toil & strain. It is immensely suitable for very busy but uncompromising people who have distinct taste and dream for their own “home”.
Android Training in Delhi NCR by Ducat
Android is an open-source, Linux-based operating system designed primarily for touchscreen mobile devices such as smartphones and tablet computers. It is developed by Google and the Open Handset Alliance. Initially created by Android Inc., which was acquired by Google in 2005, Android was unveiled in 2007 along with the founding of the Open Handset Alliance, a consortium of technology companies devoted to advancing open standards for mobile devices. Google releases Android code as open source under the Apache License. The Android Open Source Project, led by Google, maintains and develops Android. Since 2008, Android has seen numerous updates that have incrementally improved the operating system, adding new features and fixing bugs. The latest release is Android 4.4.4 KitKat
Griegos2
Este documento presenta un resumen de los principales poetas líricos de la antigua Grecia como Alcmán de Esparta, Safo de Lesbos y Anacreonte, incluyendo fragmentos de sus obras. También define la lírica como un género literario que busca expresar emociones y sentimientos y que se cantaba acompañado de la lira en la antigua Grecia. Finalmente, proporciona algunas fuentes bibliográficas sobre este tema.
Touchpad Monitored Car
In the present study, innovative idea of touchpad controlled vehicle and its real life implication is
described. Generally in such system touchpad is interfaced with ADC [0808/MCP 3208] which gives the coordinates
of the points touch by the user on touchpad. But in this research work Programmable
Intercombination Circuit (PIC) [18F4550/18C4550] is used purposefully instead of ADC as input signal were
in analog which required converting into digital signal. PIC can be used to interface touchpad and also perform
serial port programming far better than ADC. PIC gives output to 8051 microcontroller which uses keil
software program in C for input and output programming. Test drive was done to crosscheck the performance
of touchpad as well as vehicle and it was observed that car was running at corresponding given location
directed by touchpad at al instants.
2Bytesprog2 course_2014_c8_units
The document discusses programming units in Pascal. It explains that a unit divides code into an interface section and implementation section. The interface section defines constants, types, variables and function/procedure headers that are visible to other units/programs. The implementation section contains the private code and is not visible outside the unit. An example unit is provided that contains functions for exponentiation and reversing numbers, and a procedure for printing a linked list backwards. The document also demonstrates using the example unit in a sample program.
edson francisco bonfim
Não foi possível resumir o documento, pois ele não continha nenhum conteúdo. O documento não pôde ser encontrado.
Verdad neurolinguistica (con sonido)
El documento habla sobre cómo los pensamientos, palabras y acciones de una persona pueden afectar su destino. Indica que si una persona continúa pensando y hablando negativamente sobre su trabajo, cuerpo, vehículo o situación financiera, es probable que esas cosas empeoren. También dice que los pensamientos positivos y las conversaciones optimistas con fe, esperanza y amor pueden atraer mejores resultados. Finalmente, resume que los pensamientos se convierten en palabras, las palabras en acciones, las acciones en hábitos, los hábitos en el carácter de una
Viewers also liked (18)
Dentist in Richmond Virginia 4 Advantages of Professional Teeth Whitening Tre...
Dentist in Richmond Virginia 4 Advantages of Professional Teeth Whitening Tre...
Salesforce Administration Training In Noida Delhi NCR
Salesforce Administration Training In Noida Delhi NCR
Similar to Resource Identification Initiative_RDA_March2014
Biocuration 2014 - The Resource Identification Initiative
The document discusses the Resource Identification Initiative (RII) which aims to improve reproducibility in scientific research by promoting the use of Research Resource Identifiers (RRIDs) in published literature. An experiment analyzing over 800 biological resources across multiple journals found that only about 50% were identifiable. The RII is developing standards and tools to integrate RRIDs into the publishing workflow so that resources are consistently and uniquely identified in a machine-readable way. This could help credit data contributions, enable data reanalysis, and improve reproducibility overall. A pilot project is underway to test the inclusion of RRIDs in publications.
Why should my institution support RRIDs?
Reproducibility woes touch all aspects of the research enterprise. RRIDs are a thoughtful and arguably necessary tool for combating the issue.
Research resources: curating the new eagle-i discovery system
Poster presentation at the International Society for Biocuration Conference in Washington, DC in 2012.
dkNET Poster ENDO 2016
The NIDDK Information Network (dkNET) portal facilitates access to research resources relevant to metabolic, digestive, and kidney diseases. dkNET functions as a search engine to discover resources across millions of records in hundreds of biomedical databases. It provides the ability to search across data sources, a resource registry, and the literature. dkNET aims to make it easy to find relevant research resources through its concept-based search interface.
Rii stock centerdir_aug9_2016
Given at the NIH stock center directors meeting, August 8, 2016. Author: Anita Bandrowski
Project: Resource Identification Initiative http://scicrunch.org/resources
Topic: How is model organism data being used in literature
The Role of Libraries in Data Management and Curation
The Role of Libraries in Data Management and Curation, presented at the American Library Association conference in Las Vegas, NV, 07/29/14.
Abstract:
As increasing amounts of data are being generated, applying best practices in handling data is important, and librarians are well poised to assist users. During this session, we will discuss the role of libraries in assisting with data management, application of metadata, ontologies, data standards, and the publication of data in repositories and on the Semantic Web. This talk will describe best data practices and engage the attendees in interactive activities to demonstrate these principles.
Biositemaps: A Framework for Biomedical Resource Discovery
Poster from the American Medical Informatics Association Translational Bioinformatics Summit (AMIA TBI), 2011
Role of wikipedia in academic research
This study surveyed 151 Indian research scholars to understand their use of Wikipedia during doctoral research. It found that most respondents used Wikipedia more than other information sources like reference books and search engines, especially for collecting initial research materials. Computer Science, Commerce, and Management scholars relied on Wikipedia more heavily than those in other fields. While Wikipedia was a frequently used starting point, researchers also consulted other sources of information.
Information seeking
This document provides an overview of how to effectively search for information to answer a research question. It discusses developing a focused question using PICO elements, identifies appropriate biomedical databases like Medline and Embase, explains peer review of sources, and demonstrates using MeSH terms and Boolean operators to search Medline through Ovid. It also discusses evaluating websites, citation management software, and when to consult a librarian for help.
Martone acs presentation
Presentation at the American Chemical Society, San Diego, March 13, 2016: Global Initiatives in Research Data Management & Discovery Symposium
dkNET Poster Experimental Biology 2019
dkNET is a portal that provides researchers access to diverse research resources and tools to improve rigor and reproducibility. It supports the use of Research Resource Identifiers (RRIDs) to properly identify research tools in publications. dkNET also provides Resource Reports that give detailed information on tools, their usage metrics, ratings, and alerts about potential issues. Additionally, it offers services like Reproducibility Reports and a Hypothesis Center to facilitate rigorous research.
How to Get Indexed in International Citation Databases
Citations—often termed as intellectual transactions, acknowledgment of intellectual debts, and conceptual association—are a link between the author’s current study and already published work. It not only provides credibility to the author’s work but also helps funders evaluate the impact of the research study. Citation indexes are maintained for information retrieval of both cited and citing work, facilitating the literature search process. It also helps authors in identifying the number of citations that their papers have received. Citation data is considered as a legitimate measure to rank authors, journals, and publishers. Through this webinar, we aim to provide information about citation indexing and how authors and publishers can get indexed in established citation databases.
Questions Activity Scientific Foundati.docx
1. The document outlines steps for critically analyzing scientific claims, including evaluating a study's research design, data analysis and conclusions, and subjecting claims to peer review.
2. Key aspects of research design that should be assessed include the use of control and experimental groups, identification of dependent and independent variables, and controlling for confounding factors.
3. A critical evaluation of whether conclusions follow from the presented data, including through statistical analysis, allows for determining the validity of claims. Subjecting research to peer review is important for establishing the validity of findings through independent scrutiny.
Gaining credit for sharing research data
This document summarizes a presentation about publishing research data with Scientific Data. It discusses the benefits of sharing research data, including generating more analyses and reuse. It outlines Scientific Data's process for publishing Data Descriptors, which include both human-readable articles and machine-readable metadata. Data Descriptors can be published at any point in the research process. The presentation notes that Data Descriptors provide credit for data generators, enable discovery and reuse of data, and have resulted in data being cited and reused in different fields and by the public.
NER Public Health Digital Library Project
The New England Region's Public Health Digital Library Project was presented by Elaine Martin, DA, and Karen Dahlen. The project aims to build a digital public health library that will help make information resources, such as full-text journal articles, evidence-based guidelines, and systematic reviews available to public health professionals in all 50 U.S. states.
Annotation And Curation Of Human Genomic Variations An ELIXIR Implementation...
This document summarizes the results of an international survey conducted by ELIXIR, an intergovernmental organization that hosts life science resources. The survey aimed to understand how researchers use databases and tools for annotating and curating human genomic variations. It found that over 90 respondents from 18 countries considered several ELIXIR-supported resources as crucial or very important. Respondents acknowledged features promoted by ELIXIR like quality and maintenance of resources. The survey helps ELIXIR identify how to improve its resources and services for genomic research.
Funders and RRIDs
RRIDs were created jointly by NIH, Journal Editors, UCSD and other researchers; RRIDs function in support of NIH guidelines for Rigor and Transparency
Martone grethe
The document discusses methodologies for sharing long-tail data and what has been learned. It notes that unique identifiers (PIDs) are important for identifying entities across contexts. Standards like MINI and common data elements (CDEs) help ensure data is findable, accessible, and reusable. The Neuroscience Information Framework (NIF) aggregates ontologies and searches over 200 data sources to organize information. What we have learned is that data should be in repositories, not personal servers; people are key to these efforts; and resources should be comprehensive and support each other to advance open data sharing.
Review of literature
The document discusses the importance and process of reviewing literature for research. It states that a literature review identifies what is already known about the topic, potential gaps, and helps develop hypotheses and research questions. The review examines primary sources like research reports and secondary sources like summaries. It provides examples of electronic databases and online journals that can be searched, as well as printed sources such as nursing journals, research reports, dissertations, and books. The purpose is to convey previous knowledge on the topic and help improve research methodologies.
Thesis defense, Heather Piwowar, Sharing biomedical research data
Presentation by Heather Piwowar as PhD dissertation defense on March 24, 2010 at the Dept of Biomedical Informatics, U of Pittsburgh. "Foundational studies for
measuring the impact, prevalence, and patterns of publicly sharing biomedical research data." I passed :)
Similar to Resource Identification Initiative_RDA_March2014 (20)
Biocuration 2014 - The Resource Identification Initiative
Biocuration 2014 - The Resource Identification Initiative
Research resources: curating the new eagle-i discovery system
Research resources: curating the new eagle-i discovery system
The Role of Libraries in Data Management and Curation
The Role of Libraries in Data Management and Curation
Biositemaps: A Framework for Biomedical Resource Discovery
Biositemaps: A Framework for Biomedical Resource Discovery
How to Get Indexed in International Citation Databases
How to Get Indexed in International Citation Databases
Annotation And Curation Of Human Genomic Variations An ELIXIR Implementation...
Annotation And Curation Of Human Genomic Variations An ELIXIR Implementation...
Thesis defense, Heather Piwowar, Sharing biomedical research data
Thesis defense, Heather Piwowar, Sharing biomedical research data
More from Nicole Vasilevsky
CRDC-H Draft Model Presentation to Nodes
The document discusses the Community Cancer Data Harmonization (CCDH) project which aims to harmonize data across different cancer research data commons (CRDCs). It provides an overview of the multi-step process used to develop a harmonized data model called CRDC-H. This includes:
1. Standardizing documentation of source node models
2. Generating an Aggregated Data Model (ADM) representing all source model elements
3. Mapping the ADM to standard models like BRIDG and FHIR
4. Refactoring the ADM into a more normalized Conceptual Domain Model (CDM) prototype
The presentation describes the first phase of work focusing on harmonizing administrative and biospecimen
An Introduction to CCDH
Overview of the Center for Cancer Data Harmonization (CCDH) at the Joint meeting of the CRDC & the CCDH.
Teaching Data Science to Undergraduate Students
This document summarizes Nicole Vasilevsky's presentation on teaching data science to undergraduate students. It discusses the need for data science training, the open educational resources (OERs) developed by OHSU Library to address this need, and workshops offered including "Data and Donuts". The OERs cover the entire research process, from finding data to analysis to sharing results. Workshops are hands-on and interactive. Future plans include continuing "Data and Donuts" and potentially a larger OHSU Library Data Science Institute. The overall goal is to provide accessible data science training to address the growing demand.
Improving Knowledge Discovery Through Development of Big Data to Knowledge S...
Poster presentation at the Oregon Health & Science University (OHSU) BICC 25 year anniversary celebration.
Empowering patients by increasing accessibility to clinical terminology
Flash talk at Medical Library Association Pacific Northwest Chapter meeting in Portland, OR on October 18, 2016.
http://pnc-mla.cloverpad.org/annual2016
Authors: Erin Foster, Mark Engelstad, Chris Mungall, Peter Robinson, Sebastian Kohler, Melissa Haendel and Nicole Vasilevsky
Data science education resources for everyone
The document summarizes data science education resources developed by researchers at Oregon Health & Science University. It describes the challenges of managing vast amounts of biomedical data and the goal of providing training to address this issue. The team developed skills courses and open educational resources (OERs) on topics across the data science life cycle. Courses included introductory, advanced, and targeted workshops. OER modules covered a range of data science topics and mapped to competencies for health sciences librarians. The team seeks to disseminate the resources broadly while addressing challenges around customization for different users and protection of intellectual property.
Enhancing the Human Phenotype Ontology for Use by the Layperson
Presentation at the International Conference on Biological Ontology & BioCreative, August 1-4, 2016, Corvallis, Oregon, USA.
Abstract
In rare or undiagnosed diseases, physicians rely upon genotype and phenotype information in order to compare abnormalities to other known cases and to inform diagnoses. Patients are often the best sources of information about their symptoms and phenotypes. The Human Phenotype Ontology (HPO) contains over 12,000 terms describing abnormal human phenotypes. However, the labels and synonyms in the HPO primarily use medical terminology, which can be difficult for patients and their families to understand. In order to make the HPO more accessible to non-medical experts, we systematically added new synonyms using non-expert terminology (i.e., layperson terms) to the existing HPO classes or tagged existing synonyms as layperson. As a result, the HPO contains over 6,000 classes with layperson synonyms.
Enhancing the Human Phenotype Ontology for Use by the Layperson
The document describes efforts to enhance the Human Phenotype Ontology (HPO) by adding layperson synonyms to make it more useful and accessible for patients. The workflow involved systematically reviewing over 12,000 HPO classes, searching external sources to identify potential layperson synonyms, assigning the synonyms and validating their use, and integrating the new synonyms into the HPO ontology. As a result, 44% of existing HPO synonyms are now classified as layperson terms, increasing the usability and interoperability of HPO for patients, clinicians and researchers.
Couture Curricula - BD2K Data Science Tailored to Your Needs
Poster presentation at Force2016 (https://www.force11.org/meetings/force2016) describing Big Data to Science (BD2K) efforts at Oregon Health & Science University.
Monarch Initiative Poster - Rare Disease Symposium 2015
Poster presentation at the Rare Disease Symposium at Oregon Health & Science University in Portland, Oregon, 2015.
http://openwetware.org/wiki/OHSU_Rare_Disease_Research_Consortium_Symposium_2015
Acrl march2015 final
This document summarizes roles for libraries in providing research data management services. It describes data services at the University of Oregon Library including consultations, education workshops, and developing data management web pages. It discusses support for documentation provided by the University of Idaho Library through instruction sessions, research consultations, and emphasizing good documentation practices. It outlines data management trainings provided by Oregon Health & Science University Library including workshops with researchers, individual consultations, and developing new data services.
More from Nicole Vasilevsky (11)
Improving Knowledge Discovery Through Development of Big Data to Knowledge S...
Improving Knowledge Discovery Through Development of Big Data to Knowledge S...
Empowering patients by increasing accessibility to clinical terminology
Empowering patients by increasing accessibility to clinical terminology
Enhancing the Human Phenotype Ontology for Use by the Layperson
Enhancing the Human Phenotype Ontology for Use by the Layperson
Enhancing the Human Phenotype Ontology for Use by the Layperson
Enhancing the Human Phenotype Ontology for Use by the Layperson
Couture Curricula - BD2K Data Science Tailored to Your Needs
Couture Curricula - BD2K Data Science Tailored to Your Needs
Monarch Initiative Poster - Rare Disease Symposium 2015
Monarch Initiative Poster - Rare Disease Symposium 2015
Recently uploaded
bordetella pertussis.................................ppt
Bordettela is a gram negative cocobacilli spread by air born drop let
BREEDING METHODS FOR DISEASE RESISTANCE.pptx
Plant breeding for disease resistance is a strategy to reduce crop losses caused by disease. Plants have an innate immune system that allows them to recognize pathogens and provide resistance. However, breeding for long-lasting resistance often involves combining multiple resistance genes
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Bob Reedy - Nitrate in Texas Groundwater.pdf
Presented at June 6-7 Texas Alliance of Groundwater Districts Business Meeting
Shallowest Oil Discovery of Turkiye.pptx
The Petroleum System of the Çukurova Field - the Shallowest Oil Discovery of Türkiye, Adana
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero WaterTexas Alliance of Groundwater Districts
Presented at June 6-7 Texas Alliance of Groundwater Districts Business MeetingMicronuclei test.M.sc.zoology.fisheries.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
The binding of cosmological structures by massless topological defects
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Cytokines and their role in immune regulation.pptx
This presentation covers the content and information on "Cytokines " and their role in immune regulation .
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
The debris of the ‘last major merger’ is dynamically young
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...Abdul Wali Khan University Mardan,kP,Pakistan
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skillsUnlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
Phenomics assisted breeding in crop improvement
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
Recently uploaded (20)
bordetella pertussis.................................ppt
bordetella pertussis.................................ppt
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
The binding of cosmological structures by massless topological defects
The binding of cosmological structures by massless topological defects
Cytokines and their role in immune regulation.pptx
Cytokines and their role in immune regulation.pptx
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Resource Identification Initiative_RDA_March2014
- 1. Fiona Murphy1, The Resource Identification Initiative Consortium, Maryann Martone2 1Wiley Publishing, Chichester, United Kingdom, 2Center for Research in Biological Systems, University of California, San Diego, CA The Resource Identification Initiative is designed to help researchers sufficiently cite the key resources used to produce the scientific findings reported in the biomedical literature. A diverse group of collaborators are leading the project, including the Neuroscience Information Framework and the Oregon Health & Science University Library, with the support of the National Institutes of H e a l t h a n d t h e I n t e r n a t i o n a l Neuroinformatics Coordinating Facility. Introduction The Problem: Research Resources are Unidentifiable in the Published Literature Sponsored by: The Resource Identification Initiative: Making science more reproducible #RII Research resources reported in the biomedical literature often lack sufficient detail to enable reproducibility or reuse. In this study, 5 resource types were evaluated in the published literature (248 papers from 84 journals) and it was determined if the resources were identifiable identified based on specific criteria for each type. Almost 50% of the resources were unidentifiable overall. Vasilevsky et al (2013) PeerJ 1:e148 The Resource Iden4fica4on Ini4a4ve aims to enable resource iden4fica4on within the biomedical literature through a pilot study promo4ng the use of unique Research Resource Iden.fiers (RRIDs). In addi4on to being unique, RRID’s meet three key criteria, they are: The Pilot Study: February-April 2014 An4bodies SoFware & Tools Model Organisms Research Resource Identifiers should be: Machine Readable Consistent across publishers and journals Free to generate and access RRIDs are available in the Resource Iden.fica.on Portal: scicrunch.org/resources ç How to Participate in the Pilot Study: More info: Force11.org/Resource_Iden4fica4on_Ini4a4ve | rii-‐help@scicrunch.org | Beta Testers Needed! Free gi>s are offered to all beta testers! 3.Author goes to Research Identification Portal to locate RRID 2. Editor or Publisher asks for inclusion of RRID 1. Researcher submits a manuscript for publication Sample citation: Polyclonal rabbit anti-MAPK3 antibody,Abgent, Cat# AP7251E, RRID:AB_2140114 4. RRID is included in Methods section and as Keyword Resource Iden4fica4on Portal