Finding common ground: integrating the eagle-i and VIVO ontologiesmhaendel
The document discusses integrating the eagle-i and VIVO ontologies into a single Integrated Semantic Framework (ISF) ontology to represent clinical and research expertise. It describes merging the ontologies by identifying overlapping entities and addressing representation issues like modeling people and their roles over time. The ontology merging process involved referencing existing entities from the source ontologies and incorporating external vocabularies while proposing new design patterns. The goal is to develop a standardized ontology and research profiling data exchange for connecting clinicians and researchers across institutions.
Enabling semantic search in a bio-specimen repository - ICBO 2013mhaendel
This document describes enabling semantic search of bio-specimen data from multiple repositories at OHSU. It discusses using entity recognition and mapping to SNOMED-CT to semantically annotate pathology reports. An OWL ontology was developed with subclass and part-of relationships to support description logic queries over the annotated concepts. This allows searching for anatomical sites associated with specific pathologies or diseases. Challenges include the structured-text format of reports and limitations of current natural language processing and ontology techniques.
This document provides information about Android 4.0 APIs and the CalendarContract content provider for accessing calendar data on Android devices. It outlines the key calendar tables and columns for querying events, calendars, and reminders, as well as details for creating calendar events that comply with iCalendar standards.
The Beatles were a popular rock band formed in 1960 in Liverpool, England, consisting of John Lennon, Paul McCartney, George Harrison, and Ringo Starr. They gained fame playing in small pubs in Liverpool before performing in larger venues internationally. Some of their most famous albums include Please Please Me, Sgt. Pepper's Lonely Hearts Club Band, and Abbey Road. They broke up in 1970 to pursue solo careers, and John Lennon and George Harrison later passed away in 1980 and 2001, respectively, while Ringo Starr and Paul McCartney continue their music careers.
Presented at Beyond the PDF2 in Amsterdam 2013 http://www.force11.org/beyondthepdf2. This talk describes preliminary data showing the lack of scientific reproducibility solely based on an inability to identify the material resources used in the research. Final work to be published soon!
Finding common ground: integrating the eagle-i and VIVO ontologiesmhaendel
The document discusses integrating the eagle-i and VIVO ontologies into a single Integrated Semantic Framework (ISF) ontology to represent clinical and research expertise. It describes merging the ontologies by identifying overlapping entities and addressing representation issues like modeling people and their roles over time. The ontology merging process involved referencing existing entities from the source ontologies and incorporating external vocabularies while proposing new design patterns. The goal is to develop a standardized ontology and research profiling data exchange for connecting clinicians and researchers across institutions.
Enabling semantic search in a bio-specimen repository - ICBO 2013mhaendel
This document describes enabling semantic search of bio-specimen data from multiple repositories at OHSU. It discusses using entity recognition and mapping to SNOMED-CT to semantically annotate pathology reports. An OWL ontology was developed with subclass and part-of relationships to support description logic queries over the annotated concepts. This allows searching for anatomical sites associated with specific pathologies or diseases. Challenges include the structured-text format of reports and limitations of current natural language processing and ontology techniques.
This document provides information about Android 4.0 APIs and the CalendarContract content provider for accessing calendar data on Android devices. It outlines the key calendar tables and columns for querying events, calendars, and reminders, as well as details for creating calendar events that comply with iCalendar standards.
The Beatles were a popular rock band formed in 1960 in Liverpool, England, consisting of John Lennon, Paul McCartney, George Harrison, and Ringo Starr. They gained fame playing in small pubs in Liverpool before performing in larger venues internationally. Some of their most famous albums include Please Please Me, Sgt. Pepper's Lonely Hearts Club Band, and Abbey Road. They broke up in 1970 to pursue solo careers, and John Lennon and George Harrison later passed away in 1980 and 2001, respectively, while Ringo Starr and Paul McCartney continue their music careers.
Presented at Beyond the PDF2 in Amsterdam 2013 http://www.force11.org/beyondthepdf2. This talk describes preliminary data showing the lack of scientific reproducibility solely based on an inability to identify the material resources used in the research. Final work to be published soon!
Getting (and giving) credit for all that we domhaendel
This document discusses the need to give proper attribution and credit to all contributions in the research process, not just authorship of publications. It notes that many roles and outputs are not adequately recognized currently. It introduces the open Research Information Framework (openRIF) which aims to develop ontologies and tools to connect people to their diverse research outputs and roles through interoperable systems in order to ensure proper attribution for all.
Quesa is a small village located in the mountains of Valencia, Spain, with around 743 inhabitants, mostly men. The village is surrounded by lakes and rivers and known for its scenic natural areas like Los Charcos. In August, the main festivities take place with firecrackers, music, and celebrations.
This talks gives some basic pointers on how to give power point presentations that are effective and get your point across. Great for young scientists, or really any academic field.
Envisioning a world where everyone helps solve diseasemhaendel
Keynote presented at the Semantic Web for Life Sciences conference in Cambridge, UK, December 9th, 2015
http://www.swat4ls.org/
The talk focuses on the use of ontologies for data integration to support rare disease diagnostics, and how so very many people unbeknownst to the patient or even to the researchers creating the data are involved in a diagnosis.
On the frontier of genotype-2-phenotype data integrationmhaendel
Presented at AMIA TBI 2016 BD2K Panel. A description of the Monarch Initiative's efforts to perform deep phenotyping data integration across species, facilitate exchange, and build computable G2P evidence modesl to aid variant interpretation.
Use of semantic phenotyping to aid disease diagnosismhaendel
This document discusses using semantic phenotyping to aid disease diagnosis. It outlines using ontologies to semantically annotate phenotypes seen in patients, animal models, and genes. This allows computation of semantic similarity between phenotypes to identify potential disease candidates. The document also discusses challenges such as uneven phenotype data distribution and differences in how phenotypes are described across species. It proposes building an integrated cross-species semantic framework called Uberpheno to address these challenges and better leverage animal models for diagnosing rare diseases.
Why the world needs phenopacketeers, and how to be onemhaendel
Keynote presented at the the Ninth International Biocuration Conference Geneva, Switzerland, April 10-14, 2016
The health of an individual organism results from complex interplay between its genes and environment. Although great strides have been made in standardizing the representation of genetic information for exchange, there are no comparable standards to represent phenotypes (e.g. patient disease features, variation across biodiversity) or environmental factors that may influence such phenotypic outcomes. Phenotypic features of individual organisms are currently described in diverse places and in diverse formats: publications, databases, health records, registries, clinical trials, museum collections, and even social media. In these contexts, biocuration has been pivotal to obtaining a computable representation, but is still deeply challenged by the lack of standardization, accessibility, persistence, and computability among these contexts. How can we help all phenotype data creators contribute to this biocuration effort when the data is so distributed across so many communities, sources, and scales? How can we track contributions and provide proper attribution? How can we leverage phenotypic data from the model organism or biodiversity communities to help diagnose disease or determine evolutionary relatedness? Biocurators unite in a new community effort to address these challenges.
A talk about the merger and refactoring of the eagle-i and VIVO ontologies presented by myself, Brian Lowe, Janos Hajagos, and Erich Bremer at the VIVO2013 conference in St. Louis
Getting (and giving) credit for all that we domhaendel
This document discusses the need to give proper attribution and credit to all contributions in the research process, not just authorship of publications. It notes that many roles and outputs are not adequately recognized currently. It introduces the open Research Information Framework (openRIF) which aims to develop ontologies and tools to connect people to their diverse research outputs and roles through interoperable systems in order to ensure proper attribution for all.
Quesa is a small village located in the mountains of Valencia, Spain, with around 743 inhabitants, mostly men. The village is surrounded by lakes and rivers and known for its scenic natural areas like Los Charcos. In August, the main festivities take place with firecrackers, music, and celebrations.
This talks gives some basic pointers on how to give power point presentations that are effective and get your point across. Great for young scientists, or really any academic field.
Envisioning a world where everyone helps solve diseasemhaendel
Keynote presented at the Semantic Web for Life Sciences conference in Cambridge, UK, December 9th, 2015
http://www.swat4ls.org/
The talk focuses on the use of ontologies for data integration to support rare disease diagnostics, and how so very many people unbeknownst to the patient or even to the researchers creating the data are involved in a diagnosis.
On the frontier of genotype-2-phenotype data integrationmhaendel
Presented at AMIA TBI 2016 BD2K Panel. A description of the Monarch Initiative's efforts to perform deep phenotyping data integration across species, facilitate exchange, and build computable G2P evidence modesl to aid variant interpretation.
Use of semantic phenotyping to aid disease diagnosismhaendel
This document discusses using semantic phenotyping to aid disease diagnosis. It outlines using ontologies to semantically annotate phenotypes seen in patients, animal models, and genes. This allows computation of semantic similarity between phenotypes to identify potential disease candidates. The document also discusses challenges such as uneven phenotype data distribution and differences in how phenotypes are described across species. It proposes building an integrated cross-species semantic framework called Uberpheno to address these challenges and better leverage animal models for diagnosing rare diseases.
Why the world needs phenopacketeers, and how to be onemhaendel
Keynote presented at the the Ninth International Biocuration Conference Geneva, Switzerland, April 10-14, 2016
The health of an individual organism results from complex interplay between its genes and environment. Although great strides have been made in standardizing the representation of genetic information for exchange, there are no comparable standards to represent phenotypes (e.g. patient disease features, variation across biodiversity) or environmental factors that may influence such phenotypic outcomes. Phenotypic features of individual organisms are currently described in diverse places and in diverse formats: publications, databases, health records, registries, clinical trials, museum collections, and even social media. In these contexts, biocuration has been pivotal to obtaining a computable representation, but is still deeply challenged by the lack of standardization, accessibility, persistence, and computability among these contexts. How can we help all phenotype data creators contribute to this biocuration effort when the data is so distributed across so many communities, sources, and scales? How can we track contributions and provide proper attribution? How can we leverage phenotypic data from the model organism or biodiversity communities to help diagnose disease or determine evolutionary relatedness? Biocurators unite in a new community effort to address these challenges.
A talk about the merger and refactoring of the eagle-i and VIVO ontologies presented by myself, Brian Lowe, Janos Hajagos, and Erich Bremer at the VIVO2013 conference in St. Louis
6. 参考URL
• Using OAuth with the Google Data APIs
- https://developers.google.com/gdata/articles/oauth
• OAuth 2.0 Playground
- https://code.google.com/oauthplayground/
• Google APIs Client Library for Java
- http://code.google.com/p/google-api-java-client
• Google Drive SDK
- https://developers.google.com/drive/