Presented at the Feb 2015, NISO Virtual Conference
Scientific Data Management: Caring for Your Institution and its Intellectual Wealth
http://www.niso.org/news/events/2015/virtual_conferences/sci_data_management/
This is a presentation I gave at the Library of Congress as part of a NFAIS/FLICC/CENDI meeting as outlined here: http://www.chemspider.com/blog/making-the-web-work-for-science-presentation-at-the-library-of-congress.html
The presentation provides an overview of some of the challenges the publishers face moving forward, how they are responding to it, how InChI is an enabling technology, how quality is important.
The Path to Open Science with Illustrations from Computational Biology - A presentation made at the Microsoft 2011 Latin America Faculty Summit Cartagena, Columbia, May 18, 2011.
Altmetrics attempts to provide timely measures of an impact through the use of metrics from HTML views and downloads of scholarly articles, blog posts, tweets, bookmarks, etc. Publishers of scientific research have enabled altmetrics on their articles, open source applications are available for platforms to display altmetrics on scientific research and subscription models have been created to measure the use that research articles receive online. This presentation reviews some of the current models for providing altmetrics along with information on a selection the providers that have made altmetrics available for general use.
Recomendations for infrastructure and incentives for open science, presented to the Research Data Alliance 6th Plenary. Presenter: William Gunn, Director of Scholarly Communications for Mendeley.
Link resolver failures, erroneous URLs, EZproxy
configuration errors and inaccurate metadata in e-resource
records are commonplace problems reported by users in
pursuit of e-resource access. This presentation describes
the categorisation and analysis of data generated from the
troubleshooting process over the period of an academic
year. The process is designed to be pre-emptive, seeking to
anticipate e-resource problems that users may encounter,
and productive, providing insight to inform user instruction
and trigger mechanisms to create enhanced electronic
access for users.
Geraldine O Beirn, Queen’s University Belfast
This is a presentation I gave at the Library of Congress as part of a NFAIS/FLICC/CENDI meeting as outlined here: http://www.chemspider.com/blog/making-the-web-work-for-science-presentation-at-the-library-of-congress.html
The presentation provides an overview of some of the challenges the publishers face moving forward, how they are responding to it, how InChI is an enabling technology, how quality is important.
The Path to Open Science with Illustrations from Computational Biology - A presentation made at the Microsoft 2011 Latin America Faculty Summit Cartagena, Columbia, May 18, 2011.
Altmetrics attempts to provide timely measures of an impact through the use of metrics from HTML views and downloads of scholarly articles, blog posts, tweets, bookmarks, etc. Publishers of scientific research have enabled altmetrics on their articles, open source applications are available for platforms to display altmetrics on scientific research and subscription models have been created to measure the use that research articles receive online. This presentation reviews some of the current models for providing altmetrics along with information on a selection the providers that have made altmetrics available for general use.
Recomendations for infrastructure and incentives for open science, presented to the Research Data Alliance 6th Plenary. Presenter: William Gunn, Director of Scholarly Communications for Mendeley.
Link resolver failures, erroneous URLs, EZproxy
configuration errors and inaccurate metadata in e-resource
records are commonplace problems reported by users in
pursuit of e-resource access. This presentation describes
the categorisation and analysis of data generated from the
troubleshooting process over the period of an academic
year. The process is designed to be pre-emptive, seeking to
anticipate e-resource problems that users may encounter,
and productive, providing insight to inform user instruction
and trigger mechanisms to create enhanced electronic
access for users.
Geraldine O Beirn, Queen’s University Belfast
Brace for Impact: New Means for Measuring Research MetricsMary Ellen Sloane
As open access journals and repositories gain a foothold in scholarly communication, researchers are finding that the traditional impact factor and citation count metrics only reflect a portion of the dissemination of scholarly works.
New technology, research, and citation tools aid our ability to measure the influence of research. A matrix of tools and initiatives, like PLoS Article-Level Metrics, BePress’ Author Dashboard, Mendeley, Altmetrics, and ImpactStory are providing a more robust picture of scholarly communication today.
This presentation provides an overview of the impact factor system and new tools for gathering metrics and their relevance for librarians and researchers.
Presentation given at the Library Information Technology Association (LITA) Forum in Louisville, KY, in November 2013.
Presentation about OHSL's new initiative, Mycroft Cognitive Assistant®, which is intended to streamline the operational aspects of research using IBM Watson cognitive computing capabilities.
This concept can be applied to the wisdom of clinicians inside healthcare institutions. By gathering and sharing course content and tools between care facilities, hospitals can be connected to more than just the technical cloud. They can be connected to the wisdom of the cloud.
Linked Data: Opportunities for Entrepreneurs3 Round Stones
Multidisciplinary engineer and entrepreneur David Wood discusses the reasons, approaches and success stories for structured data on the World Wide Web. Linked Data is placed in context with the rest of the Web and that context is used to suggest some areas ripe for entrepreneurial innovation.
Globlal Perspective on Open Research: A Bird's Eye ViewLeslie Chan
Presentation at the University of Cape Town, Aug. 5, 2011. This talk was part of the OpenUCT initiative and the Scholarly Communication in Africa Programme. It provides an overview of the changing research landscape and the particular importance of open access and other forms of open collaboration for solving some of the pressing problems of development research. The presentation argues for the importance of policy development in support of research collaboration and the development of enriched metrics for evaluating the development impact of research.
Altmetrics Day Workshop - Internet Librarian International 2014Andy Tattersall
Altmetrics in the Academy - Implementing strategies in the library for better academic engagement, dissemination and measurement
Workshop abstract:
Altmetrics are increasingly gaining support and interest as an alternative way of disseminating and measuring scholarly output. Championed by early career researchers, librarians and information professionals, Altmetrics are to research as MOOCs are to learning. Like MOOCs most still do not understand their potential or how they could fit with or replace existing modes of delivery and assessment.
The first half of the workshop will help delegates gain an understanding of what Altmetrics are and how they can fit within academic library services. The second half of the session will deliver case studies, tools and techniques to help LIS professionals encourage better usage of Altmetrics.
10:00: What do you want from the day? What are your experiences of Altmetrics
10.40am: Altmetrics: an overview or Altmetrics and the day/where are we now?
A history, roadmap, how it fits in
11 am: Altmetrics within institutions: data, IR integration/other tools/library catalogue integration
what data is there? coverage of articles/datasets/other research outputs, mendeley demographic data
case studies of uses
examples of IR integration/motivations
primo/summon/other ones..
altmetric for institutions - integration with existing platforms
free explorer (and we’ll explore the data using this later)
11.30 Break
12.00pm Altmetrics in the Academy - getting academics and librarians on board
12.40 Brainstorming session: Value in Altmetrics: what questions do people have around this? what are their biggest concerns?
13.00 Lunch
2 pm: Getting familiar with the tools - practical session experimenting with the Altmetric explorer - half an hour (set tasks - eg create a list, pull out the most interesting mentions)
Good practice, guidelines, tips
2:45pm: At the coal face - experiences of a researcher using Altmetrics in practice
3.30pm: Break
3.45 pm: Getting mobile, how using mobile apps can help you engage more with Altmetrics
4.05 pm What’s on the horizon? What does the future for scholarly dissemination and impact.
4.40 wrap up and questions
Altmetrics: the movement, the tools, and the implicationsKR_Barker
The October 2015 iteration of the class created and taught by Andrea Denton and Kimberley R. Barker, both of the UVA Claude Moore Health Sciences Library.
The Right Metrics for Generation Open [Open Access Week 2014]Impactstory Team
The traditional way to understand and demonstrate your impact–through citation counts–doesn’t meet the needs of today’s researchers. What Generation Open needs is altmetrics.
In this presentation, we cover:
- what altmetrics are and the types of altmetrics today’s researchers can expect to receive,
- how you can track and share those metrics to get all the credit you deserve, and
- real life examples of scientists who used altmetrics to get grants and tenure
Big Data in Biomedicine – An NIH PerspectivePhilip Bourne
Keynote at the IEEE International Conference on Bioinformatics and Biomedicine, Washington DC, November 10, 2015.
https://cci.drexel.edu/ieeebibm/bibm2015/
Brace for Impact: New Means for Measuring Research MetricsMary Ellen Sloane
As open access journals and repositories gain a foothold in scholarly communication, researchers are finding that the traditional impact factor and citation count metrics only reflect a portion of the dissemination of scholarly works.
New technology, research, and citation tools aid our ability to measure the influence of research. A matrix of tools and initiatives, like PLoS Article-Level Metrics, BePress’ Author Dashboard, Mendeley, Altmetrics, and ImpactStory are providing a more robust picture of scholarly communication today.
This presentation provides an overview of the impact factor system and new tools for gathering metrics and their relevance for librarians and researchers.
Presentation given at the Library Information Technology Association (LITA) Forum in Louisville, KY, in November 2013.
Presentation about OHSL's new initiative, Mycroft Cognitive Assistant®, which is intended to streamline the operational aspects of research using IBM Watson cognitive computing capabilities.
This concept can be applied to the wisdom of clinicians inside healthcare institutions. By gathering and sharing course content and tools between care facilities, hospitals can be connected to more than just the technical cloud. They can be connected to the wisdom of the cloud.
Linked Data: Opportunities for Entrepreneurs3 Round Stones
Multidisciplinary engineer and entrepreneur David Wood discusses the reasons, approaches and success stories for structured data on the World Wide Web. Linked Data is placed in context with the rest of the Web and that context is used to suggest some areas ripe for entrepreneurial innovation.
Globlal Perspective on Open Research: A Bird's Eye ViewLeslie Chan
Presentation at the University of Cape Town, Aug. 5, 2011. This talk was part of the OpenUCT initiative and the Scholarly Communication in Africa Programme. It provides an overview of the changing research landscape and the particular importance of open access and other forms of open collaboration for solving some of the pressing problems of development research. The presentation argues for the importance of policy development in support of research collaboration and the development of enriched metrics for evaluating the development impact of research.
Altmetrics Day Workshop - Internet Librarian International 2014Andy Tattersall
Altmetrics in the Academy - Implementing strategies in the library for better academic engagement, dissemination and measurement
Workshop abstract:
Altmetrics are increasingly gaining support and interest as an alternative way of disseminating and measuring scholarly output. Championed by early career researchers, librarians and information professionals, Altmetrics are to research as MOOCs are to learning. Like MOOCs most still do not understand their potential or how they could fit with or replace existing modes of delivery and assessment.
The first half of the workshop will help delegates gain an understanding of what Altmetrics are and how they can fit within academic library services. The second half of the session will deliver case studies, tools and techniques to help LIS professionals encourage better usage of Altmetrics.
10:00: What do you want from the day? What are your experiences of Altmetrics
10.40am: Altmetrics: an overview or Altmetrics and the day/where are we now?
A history, roadmap, how it fits in
11 am: Altmetrics within institutions: data, IR integration/other tools/library catalogue integration
what data is there? coverage of articles/datasets/other research outputs, mendeley demographic data
case studies of uses
examples of IR integration/motivations
primo/summon/other ones..
altmetric for institutions - integration with existing platforms
free explorer (and we’ll explore the data using this later)
11.30 Break
12.00pm Altmetrics in the Academy - getting academics and librarians on board
12.40 Brainstorming session: Value in Altmetrics: what questions do people have around this? what are their biggest concerns?
13.00 Lunch
2 pm: Getting familiar with the tools - practical session experimenting with the Altmetric explorer - half an hour (set tasks - eg create a list, pull out the most interesting mentions)
Good practice, guidelines, tips
2:45pm: At the coal face - experiences of a researcher using Altmetrics in practice
3.30pm: Break
3.45 pm: Getting mobile, how using mobile apps can help you engage more with Altmetrics
4.05 pm What’s on the horizon? What does the future for scholarly dissemination and impact.
4.40 wrap up and questions
Altmetrics: the movement, the tools, and the implicationsKR_Barker
The October 2015 iteration of the class created and taught by Andrea Denton and Kimberley R. Barker, both of the UVA Claude Moore Health Sciences Library.
The Right Metrics for Generation Open [Open Access Week 2014]Impactstory Team
The traditional way to understand and demonstrate your impact–through citation counts–doesn’t meet the needs of today’s researchers. What Generation Open needs is altmetrics.
In this presentation, we cover:
- what altmetrics are and the types of altmetrics today’s researchers can expect to receive,
- how you can track and share those metrics to get all the credit you deserve, and
- real life examples of scientists who used altmetrics to get grants and tenure
Big Data in Biomedicine – An NIH PerspectivePhilip Bourne
Keynote at the IEEE International Conference on Bioinformatics and Biomedicine, Washington DC, November 10, 2015.
https://cci.drexel.edu/ieeebibm/bibm2015/
Open Access and Research Communication: The Perspective of Force11Maryann Martone
Presentation at the National Federation of Advanced Information Services Workshop: Open Access to Published Research: Current Status and Future Directions, Philadelphia, PA USA November 22, 2013
Creating Sustainable Communities in Open Data Resources: The eagle-i and VIVO...Robert H. McDonald
This is the slidedeck for my ACRL 2015 TechConnect Presentation with Nicole Vasilevsky (OHSU). For more on the program see - <a>http://bit.ly/1xcQbCr</a>.
A discussion of the role of taxonomies in developing tools to organize and discover information about people. Presented by Bert Carelli as part of the Special Libraries Association’s “Leveraging Your Taxonomy” series.
Scott Edmunds slides for class 8 from the HKU Data Curation (module MLIM7350 from the Faculty of Education) course covering science data, medical data and ethics, and the FAIR data principles.
Presentation to the J. Craig Venter Institute, Dec. 2014Mark Wilkinson
This is largely a compilation of various other talks that I have posted here - a summary of the past 3+ years of work on SADI/SHARE. It includes the (now well-worn!!) slides about SHARE, as well as some of the more contemporary stuff about how we extended GALEN clinical classes with richer semantic descriptions, and then used them to do automated clinical phenotype analysis. Also includes the slide-deck related to automated Measurement Unit conversion (related to our work on semantically representing Framingham clinical risk assessment rules)
So... for anyone who regularly follows my uploads, there isn't much "new" in here, but at least it's all in one place now! :-)
"Linked Data, an opportunity to mitigate complexity pharmaceutical research and development" A poster accapted for first international workshop on linked web data management in Uppsala, 25 March, 2011
Open science curriculum for students, June 2019Dag Endresen
Living Norway seminar on Open Science in Trondheim 12th June 2019.
https://livingnorway.no/2019/04/26/living-norway-seminar-2019/
https://www.gbif.no/events/2019/living-norway-seminar.html
Research process and research data management. Many universities are looking at how they can better serve the needs of researchers. Ken Chad Consulting worked with the University of Westminster to look the needs and attitudes of researchers and admin staff in terms of research data management (RDM). The result led the University to look first at the whole lifecycle and workflows of research administration. This in turn led to the innovative, rapid development of a system to support researchers and admin staff. Presented by Suzanne Enright (University of Westminster) and Ken Chad at the annual UKSG conference in April 2014
Similar to Force11: Enabling transparency and efficiency in the research landscape (20)
Patient-led deep phenotyping using a lay-friendly version of the Human Phenot...mhaendel
Presented at AMIA TBI CRI 2018.
Rare disease patients are expert in their medical history and these patients not only are some of the most engaged, but also they can themselves provision data for use in clinical evaluation. We therefore created a lay-person version of our clinical deep phenotyping instrument, the Human Phenotype Ontology. Here, we evaluate the diagnostic utility of this lay-HPO, and debut a new software tool for patient-led deep phenotyping.
The Software and Data Licensing Solution: Not Your Dad’s UBMTA mhaendel
Presented at the Association of University Technology Managers (AUTM) Annual Conference 2018
Moderator: Arvin Paranjpe, Oregon Health & Science University
Speakers: Frank Curci, Ater Wynne LLP
Melissa Haendel, Oregon Health & Science University
Charles Williams, University of Oregon
Big data is an open frontier, and it’s quickly expanding. However, transaction costs and legal barriers stand squarely in the way of meaningful, far-reaching data integration. We’ll grapple with the issues regarding a large-scale data integration project across humans, model and non-model organisms. Without pointing fingers, we’ll also share a few highlights from the (Re)usable Data Project, which outlined a five-part rubric to evaluate data licenses with respect to clarity and the reuse and redistribution of data. In addition, the topic raises the question: How well-suited are off-the-shelf software and data licenses for universities? Data scientists and software programmers are all too quick to pick one when they release their technology on GitHub. What should technology transfer professionals
recommend? We’ll discuss the usefulness and attributes of a uniform software and data license for university researchers and software programmers.
Equivalence is in the (ID) of the beholdermhaendel
Presented at PIDapalooza 2018. https://pidapalooza.org/
Determining identifier equivalency is key to data integration and to realizing the scientific discoveries that can only be made by collating our vast disconnected data stores.
There are two key problems in determining equivalency - conceptual and syntactic alignment. Conceptual alignment often relies on Xrefs and string-matching against synonyms. There is indeed a better way! Algorithmic determination of identifier equivalency across different sources can use a combination of Xrefs, priors rules, existing semantic relations, and synonyms to create equivalency cliques than can highlight the discrepancies in conceptual definitions for manual review. This is especially useful for data sources annotated with concept drift and differences, such as diseases. Syntactic issues are that there are so many variations of the same identifier, making data joins difficult. We present a framework to reconcile and provide authoritative and integration-ready prefixed identifiers (CURIES), to capture and consolidate prefixes and to build links across key resource registries. The combination of JSON-LD context technology with a prefix metadata repository provides the basis for the infrastructure to handle identifiers in a consistent fashion. Finally, this architecture also allows resources to be self describing "beacons" with respect to their identifiers.
Building (and traveling) the data-brick road: A report from the front lines ...mhaendel
The NIH Data Commons must treat the data it will contain not unlike the mortar and stones of a road. To help our fellow scientists travelers use the road, we must engineer for heavy traffic and diverse destinations. There are many steps to architecting a robust and persistent road. First, the data must be sourced and manipulated into common data models. This requires versioned access to the data, equivalency determination of identifiers within the data or minting of new ones for the data and/or within it, manipulating the data according to common data models (e.g. a genotype-to-pehnotype association in one source may relate a variant to a disease, where in another it may be a set of alleles associated with a set of phenotypes, each source models the data differently). Inclusion of the data in the Commons must meet all licensing restrictions, which are varied and usually poorly declared, as well as security, HIPAA, and ethics requirements. Software tools are needed to perform the Enhance-Transform-Load (ETL) process on a regular cycle to keep the data current, and to assess changes and quality assurance over time. For records that disappear, there needs to be a way to keep an archive of them. Once in the Commons, the data requires a map to navigate the roads: where do you want to go? Indexing and search across the data requires having the data be self-reporting - loading ontologies used in the data for indexing and providing faceted query over these and other attributes, sophisticated text mining tools, relevance ranking, and equivalency and similarity determination from amongst different providers. Once found, the users need vehicles to drive upon the road. These are their workspaces, the place where they design and implement the operations they need in order to get where they want to go. Unimaginable scientific emeralds are to be found at the end of the road, as the sum of all the data, if well integrated and made computationally reusable, has proven to be well beyond the sum of its parts in getting us where we want to go.
Reusable data for biomedicine: A data licensing odysseymhaendel
Biomedical data integrators grapple with a fundamental blocker in research today: licensing for data use and redistribution. Complex licensing and data reuse restrictions hinder most publicly-funded, seemingly “open” biomedical data from being put to its full potential. Such issues include missing licenses, non-standard licenses, and restrictive provisions. The sheer diversity of licenses are particularly thorny for those that aim to redistribute data. Redistributors are often required to contact each sub-source to obtain permissions, and this is complicated by the fact that on each side of the agreement there may be multiple legal entities involved and some sub-sources may themselves already be aggregating data from other sub-sources. Furthermore, interpreting legal compliance with source data licensing and use agreements is complicated, as data is often manipulated, shared, and redistributed by many types of research groups and users in various and subtle ways. Here, we debut a new effort, the (Re)usable Data Project, where we have created a five-part rubric to evaluate biomedical data sources and their licensing information to determine the degree to which unnegotiated and unrestricted reuse and redistribution are provided. We have tested the (Re)usable Data rubric against various biomedical data sources, ranking each source on a scale of zero to five stars, and have found that approximately half of the resources rank poorly, getting 2.5 stars or less. Our goal is to help biomedical informaticians and other users navigate the plethora of issues in reusing and redistributing biomedical data. The (Re)usable Data project aims to promote standardization and ease of reuse licensing practices by data providers.
Data Translator: an Open Science Data Platform for Mechanistic Disease Discoverymhaendel
Architecture of language and data translation that underlays the NCATS Biomedical Data Translator. Presented at the Fanconi Anemia Annual Meeting. http://fanconi.org/index.php/research/annual_symposium
How open is open? An evaluation rubric for public knowledgebasesmhaendel
Presented at the 2017 International Biocuration Conference.
Data relevant to any given scientific investigation is highly decentralized across thousands of specialized databases. Within the Biocuration community, we recognize that the value of open scientific knowledge bases is that they make scientific knowledge easier to find and compute, thereby maximizing impact and minimizing waste. The ever-increasing number of databases makes us necessarily question what are our priorities with respect to maintaining them, developing new ones, or senescing/subsuming ones that have completed in their mission. Therefore, open biomedical data repositories should be carefully evaluated according to quality, accessibility, and value of the database resources over time and across the translational divide.
Traditional citation count and publication impact factors as a measure of success or value are known to be inadequate to assess the usefulness of a resource. This is especially true for integrative resources. For example, almost everyone in biomedicine relies on PubMed, but almost no one ever cites or mentions it in their publications. While the Nucleic Acids Research Database issues have increased citation of some databases, many still go unpublished or uncited; even novel derivations of methodology, applications, and workflows from biomedical knowledge bases are often “adapted” but never cited. There is a lack of citation best practices for widely used biomedical database resources (e.g. should a paper be cited? A URL? Is mention of the name and access date sufficient?).
We have developed a draft evaluation rubric for evaluating open science databases according to the commonly cited FAIR principles -- Findable, Accessible, Interoperable, and Reusable, but with three additional principles: Traceable, Licensed, and Connected. These additions are largely overlooked and underappreciated, yet are critical to reuse of the knowledge contained within any given database. It is worth noting that FAIR principles apply not only to the resource as a whole, but also to their key components; this “fractal FAIRness” means that even the license, identifiers, vocabularies, APIs themselves must be Findable, Accessible, Interoperable, Reusable, etc. Here we report on initial testing of our evaluation rubric on the recent NIH/Wellcome Trust Open Science projects and seek community input for how to further advance this rubric as a Biocuration community resource.
Deep phenotyping to aid identification of coding & non-coding rare disease v...mhaendel
Whole-exome sequencing has revolutionized disease research, but many cases remain unsolved because ~100-1000 candidates remain after removing common or non-pathogenic variants. We present Genomiser to prioritize coding and non-coding variants by leveraging phenotype data encoded with the Human Phenotype Ontology and a curated database of non-coding Mendelian variants. Genomiser is able to identify causal regulatory variants as the top candidate in 77% of simulated whole genomes.
Global Phenotypic Data Sharing Standards to Maximize Diagnostics and Mechanis...mhaendel
Presented at the IRDiRC 2017 conference in Paris, Feb 9th, 2017 (http://irdirc-conference.org/). This talk reviews use of the Human Phenotype Ontology for phenotype comparisons against other patients, known diseases, and animal models for diagnostic discovery. It also discusses the new Phenopackets Exchange mechanism for open phenotypic data sharing.
www.monarchinitiative.org
www.phenopackets.org
www.human-phenotype-ontology.org
Credit where credit is due: acknowledging all types of contributionsmhaendel
This is an update for COASP (http://oaspa.org/conference/) on the representation of attribution beyond authorship of a publication. Publications are proxies for the projects and people that area actually engaged in the work, and represent the dissemination aspect. How can we better understand the individual contributions and their impact? The openRIF, openVIVO and FORCE11 Attribution WG efforts aim to represent scholarship in a computationally tractable manner so as to enable credit and evaluation of all types of scholarly contributions.
The Human Phenotype Ontology (HPO) was developed to describe phenotypic abnormalities, aka, “deep phenotyping”, whereby symptoms and characteristic phenotypic findings (a phenotypic profile) are captured. The HPO has been utilized to great success for assisting computational phenotype comparison against known diseases, other patients, and model organisms to support diagnosis of rare disease patients. Clinicians and geneticists create phenotypic profiles based on clinical evaluation, but this is time consuming and can miss important phenotypic features. Patients are sometimes the best source of information about their symptoms that might otherwise be missed in a clinical encounter. However, HPO primarily use medical terminology, which can be difficult for patients and their families to understand. To make the HPO accessible to patients, we systematically added non-expert terminology (i.e., layperson terms) synonyms. Using semantic similarity, patient-recorded phenotypic profiles can be evaluated against those created clinically for undiagnosed patients to determine the improvement gained from the patient-driven phenotyping, as well as how much the patient phenotyping narrows the diagnosis. This patient-centric HPO can be utilized by all: in patient-centered rare disease websites, in patient community platforms and registries, or even to post one’s hard-to-diagnosed phenotypic profile on the Web.
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.
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.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Force11: Enabling transparency and efficiency in the research landscape
1. Melissa Haendel, PhD
Oregon Health & Science University
Future of Research Communications and E-Scholarship
Enabling transparency and efficiency
in the research landscape
@force11rescomm@ontowonka
3. The Research Life Cycle
TECHNIQUE
COLLABORATION
PUBLICATIONDATASET
GRANT
4. Impetus for change: Is our
current method serving science?
47/50 major preclinical
published cancer studies
could not be replicated
“The scientific community assumes
that the claims in a preclinical
study can be taken at face value-
that although there might be some
errors in detail, the main message
of the paper can be relied on and
the data will, for the most part,
stand the test of time.
Unfortunately, this is not always
the case.”
Begley and Ellis, 29 MARCH 2012 | VOL 483 |
NATURE | 531
5. Not all content is available for
synthesis and discovery
Search PubMed: Spinal
Muscular Atrophy
6. The scientific corpus is
fragmented
~25 million articles
total, each covering
a fragment of the
biomedical space
Each publisher owns
a fragment of a
particular field
The current process
is inefficient and
slow
Wiley
Elsevier
MacMillian
Oxford
Spinal Muscular Atrophy
7. Committee on Academic
Promotions
What Counts
Money
Grants
Papers
Teaching
Service
What Does Not
Sharing data
Sharing software
Open access
Collaboration
Patents
Startups
Getting Ahead as a Computational Biologist in Academia PLOS Comp Biol
doi:10.1371/journal.pcbi.1002001
8. Beyond the PDF
Conference/unconference
where all stakeholders come
together as equals to
discuss issues
– Publishers
– Technologists
– Scholars
– Library scientists
– Humanists
– Policy makers
– Funders
Incubator for change
What would you do to
change scholarly
communication?
San Diego, Jan 2011 ...... Amsterdam, March 2013........Oxford, 2015
http://www.force11.org/beyondthepdf2
9. FORCE11
Future of Research Communications and E-
Scholarship:
A grass roots effort to accelerate the pace and nature
of scholarly communications and e-scholarship through
technology, education and community
Why 11? We were born in 2011 in Dagstuhl,
Germany
Principles laid out in the FORCE11 Manifesto
FORCE11 launched in July 2012
www.force11.org @
10. Promote community, cross-
fertilization and interoperability
FORCE11 helps facilitate
communications across
disciplines and communities
Issues are not identical but we
can learn from each other
Community platform
– Meetings
– Discussions
– Tools and resources
– Blogs
– Event calendar
– Community projects
Working groups
– Data Citation
– Resource identification
initiative
– Attribution
– Data
standards/Biosharing
11. Data Citation Working Group
FORCE11 provides a neutral
space for bringing groups
together
35 individuals
representing > 20
organizations concerned
with data citation
Conducted a review of
current data citation
recommendations from
4 different organizations
Arrived at consensus
principles
http://www.force11.org/datacitation
12. Data Citation Principles
Consensus Data
Citation
principles ready
for comment
Designed to be
high level and
easy to
understand
1. Importance
2. Credit and
Attribution
3. Evidence
4. Unique
identifiers
5. Access
6. Persistence
7. Versioning
8. Interoperability
and flexibility
15. Challenge: Working with Web Data
Often have inadequate descriptions so we don’t know what they
are about or how they were constructed
Datasets change over time, but often don’t come with versioning
information
May have been constructed using other data, but it’s not clear
which version of data was used or whether these were modified
Data may be available in a variety of formats
There may be multiple copies of data from different providers,
but it’s unclear if they are exact copies or derivatives
Version of standard or vocabulary used not indicated
Data registries are not synchronized and can contain conflicting
information
16. W3C HCLS Dataset Description
Develop a guidance note for reusing existing
vocabularies to describe datasets with RDF
– Mandatory, recommended, optional descriptors
– Identifiers
– Versioning
– Attribution
– Provenance
– Content summarization
Recommend vocabulary-linked attributes and
value sets
Provide reference editor and validation
19. Journal guidelines for methods are often poor and
space is limited
“All companies from which materials were obtained should
be listed.” - A well-known journal
Reproducibility is dependent at a minimum, on
using the same resources. But…
24. Sample citation:
Polyclonal rabbit anti-
MAPK3
antibody, Abgent, Cat#
AP7251E,
RRID:AB_2140114
1.
Research
er
submits a
manuscri
pt for
publicatio
n
2. Editor or
Publisher
asks for
inclusion of
RRID
3. Author goes to
Research
Identification
Portal to locate
RRID
4. RRID is
included
in
Methods
section
and
as
Keyword
Publishing Workflow
25. What is the relationship of a
person to a publication?
26. Example Scenario
Melissa creates mouse1
David creates mouse2
Layne uses performs RNAseq analysis on
mouse1 and mouse2 to generate
dataset3, which he subsequently
curates and analyzes
Layne writes publication pmid:12345
about the results of his analysis
Layne explicitly credits Melissa as an
author but not David.
27. Credit is connected
=> Credit to Melissa is asserted, but credit to David can be inferred
28. Attribution Working Group
https://www.force11.org/group/attributionwg
Project CredIT
VIVO-ISF ontology
PROV
the Becker model
Transitive credit
The Scholarly Contributions and Roles ontology
Goal is catalyze rapid convergence on requirements, approaches, and
practical implementation of a system for tracking contributions to any
scholarly product.
29. The 1K Challenge
What would you do with £1k today to make
research communication better, anticipating
the increasing scale of people and
machines?
30. Starting at Ground Zero
CONSULTATIONS
Researcher + 2-3 from
Data Stewardship Team
31. Researchers DO need
assistance:
Finding and choosing data
standards
File versioning
Applying metadata to
facilitate data sharing
“Gummi Bear” themed
data management
exercise resonated well
with students
Lack of awareness of
services and expertise
offered by the Library
OHSU Library is
developing data
services for researchers
http://laughingsquid.com/the-anatomy-of-a-
gummy-bear-by-jason-freeny/
Conclusions and new
directions
DOI:10.6083/M4QC0273
33. FORCE11 Vision
• Modern technologies enable vastly improve knowledge transfer and far wider
impact; freed from the restrictions of paper, numerous advantages appear
• We see a future in which scientific information and scholarly communication more
generally become part of a global, universal and explicit network of knowledge
• To enable this vision, we need to create and use new forms of scholarly
publication that work with reusable scholarly artifacts
• To obtain the benefits that networked knowledge promises, we have to put in
place reward systems that encourage scholars and researchers to participate and
contribute
• To ensure that this exciting future can develop and be sustained, we have to
support the rich, variegated, integrated and disparate knowledge offerings
that new technologies enable
What is the 21st century equivalent of the library?
Science used to be pretty linear, and slow.
Clone by phone.
Now science is a web of interconnected resources and activities, only a portion of which is the scientific literature.
Should science be reproducible? Can it be? How would we make it so? How will we evaluate reproducibility? What does the scholarly article need to be or connect to to make it a venue for reproducibility?
First 6 results in Pub Med for SMA: Can’t access, 3 different publishers. Only one is freely available.
This WG came out of the first one. Example here are recommendations having to do with allowing metadata identifier systems.
Paper is in preprint and will be out soon.
NIH funded BD2K initiative to develop recommendations for a data discovery index.
RRID Working group, has numerous publishers and journals that have implemented.
We are working on determining how to deal with this longer term- is this a new data citation that goes alongside the paper. Needs to be in the keywords do it is mineable.
Not all contributions to a work end up in an authorship
A graph representing this scenario. Note also that we intentionally attributed melissa on the publication, but not david. David’s attribution could be inferred from the graph.
There are many contributors to the work presented.
Some of the slides in this deck are directly adapted or borrowed from the above people, thank you very much.
Maryann is currently the president of Force11.
Phil was instrumental in helping start Force11.
Michel is co-leading the HCLS data set description
Nicole did the research resource identification project
Stephanie keeps the Force in Force11