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How Will FDA’s new precision FDA Science 2.0 Collaboration Platform Protect Data? Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)

How Will FDA’s new precisionFDA Science 2.0 Collaboration Platform Protect Data?

Reporter: Stephen J. Williams, Ph.D.

As reported in MassDevice.com

FDA launches precisionFDA to harness the power of scientific collaboration

FDA VoiceBy: Taha A. Kass-Hout, M.D., M.S. and Elaine Johanson

Imagine a world where doctors have at their fingertips the information that allows them to individualize a diagnosis, treatment or even a cure for a person based on their genes. That’s what President Obama envisioned when he announced his Precision Medicine Initiative earlier this year. Today, with the launch of FDA’s precisionFDA web platform, we’re a step closer to achieving that vision.

PrecisionFDA is an online, cloud-based, portal that will allow scientists from industry, academia, government and other partners to come together to foster innovation and develop the science behind a method of “reading” DNA known as next-generation sequencing (or NGS). Next Generation Sequencing allows scientists to compile a vast amount of data on a person’s exact order or sequence of DNA. Recognizing that each person’s DNA is slightly different, scientists can look for meaningful differences in DNA that can be used to suggest a person’s risk of disease, possible response to treatment and assess their current state of health. Ultimately, what we learn about these differences could be used to design a treatment tailored to a specific individual.

The precisionFDA platform is a part of this larger effort and through its use we want to help scientists work toward the most accurate and meaningful discoveries. precisionFDA users will have access to a number of important tools to help them do this. These tools include reference genomes, such as “Genome in the Bottle,” a reference sample of DNA for validating human genome sequences developed by the National Institute of Standards and Technology. Users will also be able to compare their results to previously validated reference results as well as share their results with other users, track changes and obtain feedback.

Over the coming months we will engage users in improving the usability, openness and transparency of precisionFDA. One way we’ll achieve that is by placing the code for the precisionFDA portal on the world’s largest open source software repository, GitHub, so the community can further enhance precisionFDA’s features.Through such collaboration we hope to improve the quality and accuracy of genomic tests – work that will ultimately benefit patients.

precisionFDA leverages our experience establishing openFDA, an online community that provides easy access to our public datasets. Since its launch in 2014, openFDA has already resulted in many novel ways to use, integrate and analyze FDA safety information. We’re confident that employing such a collaborative approach to DNA data will yield important advances in our understanding of this fast-growing scientific field, information that will ultimately be used to develop new diagnostics, treatments and even cures for patients.

fda-voice-taha-kass-1x1Taha A. Kass-Hout, M.D., M.S., is FDA’s Chief Health Informatics Officer and Director of FDA’s Office of Health Informatics. Elaine Johanson is the precisionFDA Project Manager.

 

The opinions expressed in this blog post are the author’s only and do not necessarily reflect those of MassDevice.com or its employees.

So What Are the Other Successes With Such Open Science 2.0 Collaborative Networks?

In the following post there are highlighted examples of these Open Scientific Networks and, as long as

  • transparancy
  • equal contributions (lack of heirarchy)

exists these networks can flourish and add interesting discourse.  Scientists are already relying on these networks to collaborate and share however resistance by certain members of an “elite” can still exist.  Social media platforms are now democratizing this new science2.0 effort.  In addition the efforts of multiple biocurators (who mainly work for love of science) have organized the plethora of data (both genomic, proteomic, and literature) in order to provide ease of access and analysis.

Science and Curation: The New Practice of Web 2.0

Curation: an Essential Practice to Manage “Open Science”

The web 2.0 gave birth to new practices motivated by the will to have broader and faster cooperation in a more free and transparent environment. We have entered the era of an “open” movement: “open data”, “open software”, etc. In science, expressions like “open access” (to scientific publications and research results) and “open science” are used more and more often.

Curation and Scientific and Technical Culture: Creating Hybrid Networks

Another area, where there are most likely fewer barriers, is scientific and technical culture. This broad term involves different actors such as associations, companies, universities’ communication departments, CCSTI (French centers for scientific, technical and industrial culture), journalists, etc. A number of these actors do not limit their work to popularizing the scientific data; they also consider they have an authentic mission of “culturing” science. The curation practice thus offers a better organization and visibility to the information. The sought-after benefits will be different from one actor to the next.

Scientific Curation Fostering Expert Networks and Open Innovation: Lessons from Clive Thompson and others

  • Using Curation and Science 2.0 to build Trusted, Expert Networks of Scientists and Clinicians

Given the aforementioned problems of:

        I.            the complex and rapid deluge of scientific information

      II.            the need for a collaborative, open environment to produce transformative innovation

    III.            need for alternative ways to disseminate scientific findings

CURATION MAY OFFER SOLUTIONS

        I.            Curation exists beyond the review: curation decreases time for assessment of current trends adding multiple insights, analyses WITH an underlying METHODOLOGY (discussed below) while NOT acting as mere reiteration, regurgitation

 

      II.            Curation providing insights from WHOLE scientific community on multiple WEB 2.0 platforms

 

    III.            Curation makes use of new computational and Web-based tools to provide interoperability of data, reporting of findings (shown in Examples below)

 

Therefore a discussion is given on methodologies, definitions of best practices, and tools developed to assist the content curation community in this endeavor

which has created a need for more context-driven scientific search and discourse.

However another issue would be Individual Bias if these networks are closed and protocols need to be devised to reduce bias from individual investigators, clinicians.  This is where CONSENSUS built from OPEN ACCESS DISCOURSE would be beneficial as discussed in the following post:

Risk of Bias in Translational Science

As per the article

Risk of bias in translational medicine may take one of three forms:

  1. a systematic error of methodology as it pertains to measurement or sampling (e.g., selection bias),
  2. a systematic defect of design that leads to estimates of experimental and control groups, and of effect sizes that substantially deviate from true values (e.g., information bias), and
  3. a systematic distortion of the analytical process, which results in a misrepresentation of the data with consequential errors of inference (e.g., inferential bias).

This post highlights many important points related to bias but in summarry there can be methodologies and protocols devised to eliminate such bias.  Risk of bias can seriously adulterate the internal and the external validity of a clinical study, and, unless it is identified and systematically evaluated, can seriously hamper the process of comparative effectiveness and efficacy research and analysis for practice. The Cochrane Group and the Agency for Healthcare Research and Quality have independently developed instruments for assessing the meta-construct of risk of bias. The present article begins to discuss this dialectic.

  • Information dissemination to all stakeholders is key to increase their health literacy in order to ensure their full participation
  • threats to internal and external validity  represent specific aspects of systematic errors (i.e., bias)in design, methodology and analysis

So what about the safety and privacy of Data?

A while back I did a post and some interviews on how doctors in developing countries are using social networks to communicate with patients, either over established networks like Facebook or more private in-house networks.  In addition, these doctor-patient relationships in developing countries are remote, using the smartphone to communicate with rural patients who don’t have ready access to their physicians.

Located in the post Can Mobile Health Apps Improve Oral-Chemotherapy Adherence? The Benefit of Gamification.

I discuss some of these problems in the following paragraph and associated posts below:

Mobile Health Applications on Rise in Developing World: Worldwide Opportunity

According to International Telecommunication Union (ITU) statistics, world-wide mobile phone use has expanded tremendously in the past 5 years, reaching almost 6 billion subscriptions. By the end of this year it is estimated that over 95% of the world’s population will have access to mobile phones/devices, including smartphones.

This presents a tremendous and cost-effective opportunity in developing countries, and especially rural areas, for physicians to reach patients using mHealth platforms.

How Social Media, Mobile Are Playing a Bigger Part in Healthcare

E-Medical Records Get A Mobile, Open-Sourced Overhaul By White House Health Design Challenge Winners

In Summary, although there are restrictions here in the US governing what information can be disseminated over social media networks, developing countries appear to have either defined the regulations as they are more dependent on these types of social networks given the difficulties in patient-physician access.

Therefore the question will be Who Will Protect The Data?

For some interesting discourse please see the following post

Atul Butte Talks on Big Data, Open Data and Clinical Trials

 

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Mozilla Science Lab Promotes Data Reproduction Through Open Access: Report from 9/10/2015 Online Meeting

Reporter: Stephen J. Williams, Ph.D.

Mozilla Inc. is developing a platform for scientists to discuss the issues related to developing a framework to share scientific data as well as tackle the problems of scientific reproducibility in an Open Access manner. According to their blog

https://blog.mozilla.org/blog/2013/06/14/5992/

We’re excited to announce the launch of the Mozilla Science Lab, a new initiative that will help researchers around the world use the open web to shape science’s future.

Scientists created the web — but the open web still hasn’t transformed scientific practice to the same extent we’ve seen in other areas like media, education and business. For all of the incredible discoveries of the last century, science is still largely rooted in the “analog” age. Credit systems in science are still largely based around “papers,” for example, and as a result researchers are often discouraged from sharing, learning, reusing, and adopting the type of open and collaborative learning that the web makes possible.

The Science Lab will foster dialog between the open web community and researchers to tackle this challenge. Together they’ll share ideas, tools, and best practices for using next-generation web solutions to solve real problems in science, and explore ways to make research more agile and collaborative.

On their blog they highlight various projects related to promoting Open Access for scientific data

On September 10, 2015 Mozilla Science Lab had their scheduled meeting on scientific data reproduce ability.  The meeting was free and covered by ethernet and on social media. The Twitter hashtag for updates and meeting discussion is #mozscience (https://twitter.com/search?q=%23mozscience )

Open Access Meeting Announcement on Twitter

https://twitter.com/MozillaScience/status/641642491532283904

//platform.twitter.com/widgets.js

mozilla science lab

Mozilla Science Lab @MozillaScience

Join @khinsen @abbycabs + @EvoMRI tmrw (11AM ET) to hear about replication, publishing + #openscience. Details: https://etherpad.mozilla.org/sciencelab-calls-sep10-2015 …

AGENDA:

  • Mozilla Science Lab Updates
  • Staff welcomes and thank yous:
  • Welcoming Zannah Marsh, our first Instructional Designer
  • Workshopping the “Working Open” guide:
    • Discussion of Future foundation and GitHub projects
    • Discussion of submission for open science project funding
  • Contributorship Badges Pilot – an update! – Abby Cabunoc Mayes – @abbycabs
  • Will be live on GigaScience September 17th!
  • Where you can jump in: https://github.com/mozillascience/paperbadger/issues/17
  • Questions regarding coding projects – Abby will coordinate efforts on coding into their codebase
  • The journal will publish and authors and reviewers get a badge and their efforts and comments will appear on GigaScience: Giga Science will give credit for your reviews – supports an Open Science Discussion

Roadmap for

  • Fellows review is in full swing!
  • MozFest update:
  • Miss the submission deadline? You can still apply to join our Open Research Accelerator and join us for the event (PLUS get a DOI for your submission and 1:1 help)

A discussion by Konrad Hinsen (@khinsen) on ReScience, a journal focused on scientific replication will be presented:

  • ReScience – a new journal for replications – Konrad Hinsen @khinsen
  • ReScience is dedicated to publishing replications of previously published computational studies, along with all the code required to replicate the results.
  • ReScience lives entirely on GitHub. Submissions take the form of a Git repository, and review takes place in the open through GitHub issues. This also means that ReScience is free for everyone (authors, readers, reviewers, editors… well, I said everyone, right?), as long as GitHub is willing to host it.
  • ReScience was launched just a few days ago and is evolving quickly. To stay up to date, follow @ReScienceEds on Twitter. If you want to volunteer as a reviewer, please contact the editorial board.

The ReScience Journal Reproducible Science is Good. Replicated Science is better.

ReScience is a peer-reviewed journal that targets computational research and encourages the explicit reproduction of already published research promoting new and open-source implementations in order to ensure the original research is reproducible. To achieve such a goal, the whole editing chain is radically different from any other traditional scientific journal. ReScience lives on github where each new implementation is made available together with the comments, explanations and tests. Each submission takes the form of a pull request that is publicly reviewed and tested in order to guarantee any researcher can re-use it. If you ever reproduced computational result from the literature, ReScience is the perfect place to publish this new implementation. The Editorial Board

Notes from his talk:

– must be able to replicate paper’s results as written according to experimental methods

– All authors on ReScience need to be on GitHub

– not accepting MatLab replication; replication can involve computational replication;

  • Research Ideas and Outcomes Journal – Daniel Mietchen @EvoMRI
    • Postdoc at Natural Museum of London doing data mining; huge waste that 90% research proposals don’t get used so this journal allows for publishing proposals
    • Learned how to write proposals by finding a proposal online open access
    • Reviewing system based on online reviews like GoogleDocs where people view, comment
    • Growing editorial and advisory board; venturing into new subject areas like humanities, economics, biological research so they are trying to link diverse areas under SOCIAL IMPACT labeling
    • BIG question how to get scientists to publish their proposals especially to improve efficiency of collaboration and reduce too many duplicated efforts as well as reagent sharing
    • Crowdfunding platform used as post publication funding mechanism; still in works
    • They need a lot of help on the editorial board so if have a PhD PLEASE JOIN
  • Website:
  • Background:
  • Science article:
  • Some key features:
  • for publishing all steps of the research cycle, from proposals (funded and not yet funded) onwards
  • maps submissions to societal challenges
  • focus on post-publication peer review; pre-submission endorsement; all reviews public
  • lets authors choose which publishing services they want, e.g. whether they’d like journal-mediated peer review
  • collaborative WYSIWYG authoring and publishing platform based on JATS XML

A brief discussion of upcoming events on @MozillaScience

Meetings are held 2nd Thursdays of each month

Additional plugins, coding, and new publishing formats are available at https://www.mozillascience.org/

Other related articles on OPEN ACCESS Publishing were published in this Open Access Online Scientific Journal, include the following:

Archives of Medicine (AOM) to Publish from “Leaders in Pharmaceutical Business Intelligence (LPBI)” Open Access On-Line Scientific Journal http://pharmaceuticalintelligence.com

Annual Growth in NIH Clicks: 32% Open Access Online Scientific Journal http://pharmaceuticalintelligence.com

Collaborations and Open Access Innovations – CHI, BioIT World, 4/29 – 5/1/2014, Seaport World Trade Center, Boston

Elsevier’s Mendeley and Academia.edu – How We Distribute Scientific Research: A Case in Advocacy for Open Access Journals

Reconstructed Science Communication for Open Access Online Scientific Curation

The Fatal Self Distraction of the Academic Publishing Industry: The Solution of the Open Access Online Scientific Journals

 

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Scientific Curation Fostering Expert Networks and Open Innovation: Lessons from Clive Thompson

Life-cycle of Science 2

 

 

 

 

 

 

 

 

 

 

 

Curators and Writer: Stephen J. Williams, Ph.D. with input from Curators Larry H. Bernstein, MD, FCAP, Dr. Justin D. Pearlman, MD, PhD, FACC and Dr. Aviva Lev-Ari, PhD, RN

(this discussion is in a three part series including:

Using Scientific Content Curation as a Method for Validation and Biocuration

Using Scientific Content Curation as a Method for Open Innovation)

 

Every month I get my Wired Magazine (yes in hard print, I still like to turn pages manually plus I don’t mind if I get grease or wing sauce on my magazine rather than on my e-reader) but I always love reading articles written by Clive Thompson. He has a certain flair for understanding the techno world we live in and the human/technology interaction, writing about interesting ways in which we almost inadvertently integrate new technologies into our day-to-day living, generating new entrepreneurship, new value.   He also writes extensively about tech and entrepreneurship.

October 2013 Wired article by Clive Thompson, entitled “How Successful Networks Nurture Good Ideas: Thinking Out Loud”, describes how the voluminous writings, postings, tweets, and sharing on social media is fostering connections between people and ideas which, previously, had not existed. The article was generated from Clive Thompson’s book Smarter Than you Think: How Technology is Changing Our Minds for the Better.Tom Peters also commented about the article in his blog (see here).

Clive gives a wonderful example of Ory Okolloh, a young Kenyan-born law student who, after becoming frustrated with the lack of coverage of problems back home, started a blog about Kenyan politics. Her blog not only got interest from movie producers who were documenting female bloggers but also gained the interest of fellow Kenyans who, during the upheaval after the 2007 Kenyan elections, helped Ory to develop a Google map for reporting of violence (http://www.ushahidi.com/, which eventually became a global organization using open-source technology to affect crises-management. There are a multitude of examples how networks and the conversations within these circles are fostering new ideas. As Clive states in the article:

 

Our ideas are PRODUCTS OF OUR ENVIRONMENT.

They are influenced by the conversations around us.

However the article got me thinking of how Science 2.0 and the internet is changing how scientists contribute, share, and make connections to produce new and transformative ideas.

But HOW MUCH Knowledge is OUT THERE?

 

Clive’s article listed some amazing facts about the mountains of posts, tweets, words etc. out on the internet EVERY DAY, all of which exemplifies the problem:

  • 154.6 billion EMAILS per DAY
  • 400 million TWEETS per DAY
  • 1 million BLOG POSTS (including this one) per DAY
  • 2 million COMMENTS on WordPress per DAY
  • 16 million WORDS on Facebook per DAY
  • TOTAL 52 TRILLION WORDS per DAY

As he estimates this would be 520 million books per DAY (book with average 100,000 words).

A LOT of INFO. But as he suggests it is not the volume but how we create and share this information which is critical as the science fiction writer Theodore Sturgeon noted “Ninety percent of everything is crap” AKA Sturgeon’s Law.

 

Internet live stats show how congested the internet is each day (http://www.internetlivestats.com/). Needless to say Clive’s numbers are a bit off. As of the writing of this article:

 

  • 2.9 billion internet users
  • 981 million websites (only 25,000 hacked today)
  • 128 billion emails
  • 385 million Tweets
  • > 2.7 million BLOG posts today (including this one)

 

The Good, The Bad, and the Ugly of the Scientific Internet (The Wild West?)

 

So how many science blogs are out there? Well back in 2008 “grrlscientistasked this question and turned up a total of 19,881 blogs however most were “pseudoscience” blogs, not written by Ph.D or MD level scientists. A deeper search on Technorati using the search term “scientist PhD” turned up about 2,000 written by trained scientists.

So granted, there is a lot of

goodbadugly

 

              ….. when it comes to scientific information on the internet!

 

 

 

 

 

I had recently re-posted, on this site, a great example of how bad science and medicine can get propagated throughout the internet:

http://pharmaceuticalintelligence.com/2014/06/17/the-gonzalez-protocol-worse-than-useless-for-pancreatic-cancer/

 

and in a Nature Report:Stem cells: Taking a stand against pseudoscience

http://www.nature.com/news/stem-cells-taking-a-stand-against-pseudoscience-1.15408

Drs.Elena Cattaneo and Gilberto Corbellini document their long, hard fight against false and invalidated medical claims made by some “clinicians” about the utility and medical benefits of certain stem-cell therapies, sacrificing their time to debunk medical pseudoscience.

 

Using Curation and Science 2.0 to build Trusted, Expert Networks of Scientists and Clinicians

 

Establishing networks of trusted colleagues has been a cornerstone of the scientific discourse for centuries. For example, in the mid-1640s, the Royal Society began as:

 

“a meeting of natural philosophers to discuss promoting knowledge of the

natural world through observation and experiment”, i.e. science.

The Society met weekly to witness experiments and discuss what we

would now call scientific topics. The first Curator of Experiments

was Robert Hooke.”

 

from The History of the Royal Society

 

Royal Society CoatofArms

 

 

 

 

 

 

The Royal Society of London for Improving Natural Knowledge.

(photo credit: Royal Society)

(Although one wonders why they met “in-cognito”)

Indeed as discussed in “Science 2.0/Brainstorming” by the originators of OpenWetWare, an open-source science-notebook software designed to foster open-innovation, the new search and aggregation tools are making it easier to find, contribute, and share information to interested individuals. This paradigm is the basis for the shift from Science 1.0 to Science 2.0. Science 2.0 is attempting to remedy current drawbacks which are hindering rapid and open scientific collaboration and discourse including:

  • Slow time frame of current publishing methods: reviews can take years to fashion leading to outdated material
  • Level of information dissemination is currently one dimensional: peer-review, highly polished work, conferences
  • Current publishing does not encourage open feedback and review
  • Published articles edited for print do not take advantage of new web-based features including tagging, search-engine features, interactive multimedia, no hyperlinks
  • Published data and methodology incomplete
  • Published data not available in formats which can be readably accessible across platforms: gene lists are now mandated to be supplied as files however other data does not have to be supplied in file format

(put in here a brief blurb of summary of problems and why curation could help)

 

Curation in the Sciences: View from Scientific Content Curators Larry H. Bernstein, MD, FCAP, Dr. Justin D. Pearlman, MD, PhD, FACC and Dr. Aviva Lev-Ari, PhD, RN

Curation is an active filtering of the web’s  and peer reviewed literature found by such means – immense amount of relevant and irrelevant content. As a result content may be disruptive. However, in doing good curation, one does more than simply assign value by presentation of creative work in any category. Great curators comment and share experience across content, authors and themes. Great curators may see patterns others don’t, or may challenge or debate complex and apparently conflicting points of view.  Answers to specifically focused questions comes from the hard work of many in laboratory settings creatively establishing answers to definitive questions, each a part of the larger knowledge-base of reference. There are those rare “Einstein’s” who imagine a whole universe, unlike the three blind men of the Sufi tale.  One held the tail, the other the trunk, the other the ear, and they all said this is an elephant!
In my reading, I learn that the optimal ratio of curation to creation may be as high as 90% curation to 10% creation. Creating content is expensive. Curation, by comparison, is much less expensive.

– Larry H. Bernstein, MD, FCAP

Curation is Uniquely Distinguished by the Historical Exploratory Ties that Bind –Larry H. Bernstein, MD, FCAP

The explosion of information by numerous media, hardcopy and electronic, written and video, has created difficulties tracking topics and tying together relevant but separated discoveries, ideas, and potential applications. Some methods to help assimilate diverse sources of knowledge include a content expert preparing a textbook summary, a panel of experts leading a discussion or think tank, and conventions moderating presentations by researchers. Each of those methods has value and an audience, but they also have limitations, particularly with respect to timeliness and pushing the edge. In the electronic data age, there is a need for further innovation, to make synthesis, stimulating associations, synergy and contrasts available to audiences in a more timely and less formal manner. Hence the birth of curation. Key components of curation include expert identification of data, ideas and innovations of interest, expert interpretation of the original research results, integration with context, digesting, highlighting, correlating and presenting in novel light.

Justin D Pearlman, MD, PhD, FACC from The Voice of Content Consultant on The  Methodology of Curation in Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation The Art of Scientific & Medical Curation

 

In Power of Analogy: Curation in Music, Music Critique as a Curation and Curation of Medical Research Findings – A Comparison, Drs. Larry Bernstein and Aviva Lev-Ari likens the medical and scientific curation process to curation of musical works into a thematic program:

 

Work of Original Music Curation and Performance:

 

Music Review and Critique as a Curation

Work of Original Expression what is the methodology of Curation in the context of Medical Research Findings Exposition of Synthesis and Interpretation of the significance of the results to Clinical Care

… leading to new, curated, and collaborative works by networks of experts to generate (in this case) ebooks on most significant trends and interpretations of scientific knowledge as relates to medical practice.

 

In Summary: How Scientific Content Curation Can Help

 

Given the aforementioned problems of:

        I.            the complex and rapid deluge of scientific information

      II.            the need for a collaborative, open environment to produce transformative innovation

    III.            need for alternative ways to disseminate scientific findings

CURATION MAY OFFER SOLUTIONS

        I.            Curation exists beyond the review: curation decreases time for assessment of current trends adding multiple insights, analyses WITH an underlying METHODOLOGY (discussed below) while NOT acting as mere reiteration, regurgitation

 

      II.            Curation providing insights from WHOLE scientific community on multiple WEB 2.0 platforms

 

    III.            Curation makes use of new computational and Web-based tools to provide interoperability of data, reporting of findings (shown in Examples below)

 

Therefore a discussion is given on methodologies, definitions of best practices, and tools developed to assist the content curation community in this endeavor.

Methodology in Scientific Content Curation as Envisioned by Aviva lev-Ari, PhD, RN

 

At Leaders in Pharmaceutical Business Intelligence, site owner and chief editor Aviva lev-Ari, PhD, RN has been developing a strategy “for the facilitation of Global access to Biomedical knowledge rather than the access to sheer search results on Scientific subject matters in the Life Sciences and Medicine”. According to Aviva, “for the methodology to attain this complex goal it is to be dealing with popularization of ORIGINAL Scientific Research via Content Curation of Scientific Research Results by Experts, Authors, Writers using the critical thinking process of expert interpretation of the original research results.” The following post:

Cardiovascular Original Research: Cases in Methodology Design for Content Curation and Co-Curation

 

http://pharmaceuticalintelligence.com/2013/07/29/cardiovascular-original-research-cases-in-methodology-design-for-content-curation-and-co-curation/

demonstrate two examples how content co-curation attempts to achieve this aim and develop networks of scientist and clinician curators to aid in the active discussion of scientific and medical findings, and use scientific content curation as a means for critique offering a “new architecture for knowledge”. Indeed, popular search engines such as Google, Yahoo, or even scientific search engines such as NCBI’s PubMed and the OVID search engine rely on keywords and Boolean algorithms …

which has created a need for more context-driven scientific search and discourse.

In Science and Curation: the New Practice of Web 2.0, Célya Gruson-Daniel (@HackYourPhd) states:

To address this need, human intermediaries, empowered by the participatory wave of web 2.0, naturally started narrowing down the information and providing an angle of analysis and some context. They are bloggers, regular Internet users or community managers – a new type of profession dedicated to the web 2.0. A new use of the web has emerged, through which the information, once produced, is collectively spread and filtered by Internet users who create hierarchies of information.

.. where Célya considers curation an essential practice to manage open science and this new style of research.

As mentioned above in her article, Dr. Lev-Ari represents two examples of how content curation expanded thought, discussion, and eventually new ideas.

  1. Curator edifies content through analytic process = NEW form of writing and organizations leading to new interconnections of ideas = NEW INSIGHTS

i)        Evidence: curation methodology leading to new insights for biomarkers

 

  1. Same as #1 but multiple players (experts) each bringing unique insights, perspectives, skills yielding new research = NEW LINE of CRITICAL THINKING

ii)      Evidence: co-curation methodology among cardiovascular experts leading to cardiovascular series ebooks

Life-cycle of Science 2

The Life Cycle of Science 2.0. Due to Web 2.0, new paradigms of scientific collaboration are rapidly emerging.  Originally, scientific discovery were performed by individual laboratories or “scientific silos” where the main method of communication was peer-reviewed publication, meeting presentation, and ultimately news outlets and multimedia. In this digital era, data was organized for literature search and biocurated databases. In an era of social media, Web 2.0, a group of scientifically and medically trained “curators” organize the piles of data of digitally generated data and fit data into an organizational structure which can be shared, communicated, and analyzed in a holistic approach, launching new ideas due to changes in organization structure of data and data analytics.

 

The result, in this case, is a collaborative written work above the scope of the review. Currently review articles are written by experts in the field and summarize the state of a research are. However, using collaborative, trusted networks of experts, the result is a real-time synopsis and analysis of the field with the goal in mind to

INCREASE THE SCIENTIFIC CURRENCY.

For detailed description of methodology please see Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation The Art of Scientific & Medical Curation

 

In her paper, Curating e-Science Data, Maureen Pennock, from The British Library, emphasized the importance of using a diligent, validated, and reproducible, and cost-effective methodology for curation by e-science communities over the ‘Grid:

“The digital data deluge will have profound repercussions for the infrastructure of research and beyond. Data from a wide variety of new and existing sources will need to be annotated with metadata, then archived and curated so that both the data and the programmes used to transform the data can be reproduced for use in the future. The data represent a new foundation for new research, science, knowledge and discovery”

— JISC Senior Management Briefing Paper, The Data Deluge (2004)

 

As she states proper data and content curation is important for:

  • Post-analysis
  • Data and research result reuse for new research
  • Validation
  • Preservation of data in newer formats to prolong life-cycle of research results

However she laments the lack of

  • Funding for such efforts
  • Training
  • Organizational support
  • Monitoring
  • Established procedures

 

Tatiana Aders wrote a nice article based on an interview with Microsoft’s Robert Scoble, where he emphasized the need for curation in a world where “Twitter is the replacement of the Associated Press Wire Machine” and new technologic platforms are knocking out old platforms at a rapid pace. In addition he notes that curation is also a social art form where primary concerns are to understand an audience and a niche.

Indeed, part of the reason the need for curation is unmet, as writes Mark Carrigan, is the lack of appreciation by academics of the utility of tools such as Pinterest, Storify, and Pearl Trees to effectively communicate and build collaborative networks.

And teacher Nancy White, in her article Understanding Content Curation on her blog Innovations in Education, shows examples of how curation in an educational tool for students and teachers by demonstrating students need to CONTEXTUALIZE what the collect to add enhanced value, using higher mental processes such as:

  • Knowledge
  • Comprehension
  • Application
  • Analysis
  • Synthesis
  • Evaluation

curating-tableA GREAT table about the differences between Collecting and Curating by Nancy White at http://d20innovation.d20blogs.org/2012/07/07/understanding-content-curation/

 

 

 

 

 

 

 

 

 

 

 

University of Massachusetts Medical School has aggregated some useful curation tools at http://esciencelibrary.umassmed.edu/data_curation

Although many tools are related to biocuration and building databases but the common idea is curating data with indexing, analyses, and contextual value to provide for an audience to generate NETWORKS OF NEW IDEAS.

See here for a curation of how networks fosters knowledge, by Erika Harrison on ScoopIt

(http://www.scoop.it/t/mobilizing-knowledge-through-complex-networks)

 

“Nowadays, any organization should employ network scientists/analysts who are able to map and analyze complex systems that are of importance to the organization (e.g. the organization itself, its activities, a country’s economic activities, transportation networks, research networks).”

Andrea Carafa insight from World Economic Forum New Champions 2012 “Power of Networks

 

Creating Content Curation Communities: Breaking Down the Silos!

 

An article by Dr. Dana Rotman “Facilitating Scientific Collaborations Through Content Curation Communities” highlights how scientific information resources, traditionally created and maintained by paid professionals, are being crowdsourced to professionals and nonprofessionals in which she termed “content curation communities”, consisting of professionals and nonprofessional volunteers who create, curate, and maintain the various scientific database tools we use such as Encyclopedia of Life, ChemSpider (for Slideshare see here), biowikipedia etc. Although very useful and openly available, these projects create their own challenges such as

  • information integration (various types of data and formats)
  • social integration (marginalized by scientific communities, no funding, no recognition)

The authors set forth some ways to overcome these challenges of the content curation community including:

  1. standardization in practices
  2. visualization to document contributions
  3. emphasizing role of information professionals in content curation communities
  4. maintaining quality control to increase respectability
  5. recognizing participation to professional communities
  6. proposing funding/national meeting – Data Intensive Collaboration in Science and Engineering Workshop

A few great presentations and papers from the 2012 DICOSE meeting are found below

Judith M. Brown, Robert Biddle, Stevenson Gossage, Jeff Wilson & Steven Greenspan. Collaboratively Analyzing Large Data Sets using Multitouch Surfaces. (PDF) NotesForBrown

 

Bill Howe, Cecilia Aragon, David Beck, Jeffrey P. Gardner, Ed Lazowska, Tanya McEwen. Supporting Data-Intensive Collaboration via Campus eScience Centers. (PDF) NotesForHowe

 

Kerk F. Kee & Larry D. Browning. Challenges of Scientist-Developers and Adopters of Existing Cyberinfrastructure Tools for Data-Intensive Collaboration, Computational Simulation, and Interdisciplinary Projects in Early e-Science in the U.S.. (PDF) NotesForKee

 

Ben Li. The mirages of big data. (PDF) NotesForLiReflectionsByBen

 

Betsy Rolland & Charlotte P. Lee. Post-Doctoral Researchers’ Use of Preexisting Data in Cancer Epidemiology Research. (PDF) NoteForRolland

 

Dana Rotman, Jennifer Preece, Derek Hansen & Kezia Procita. Facilitating scientific collaboration through content curation communities. (PDF) NotesForRotman

 

Nicholas M. Weber & Karen S. Baker. System Slack in Cyberinfrastructure Development: Mind the Gaps. (PDF) NotesForWeber

Indeed, the movement of Science 2.0 from Science 1.0 had originated because these “silos” had frustrated many scientists, resulting in changes in the area of publishing (Open Access) but also communication of protocols (online protocol sites and notebooks like OpenWetWare and BioProtocols Online) and data and material registries (CGAP and tumor banks). Some examples are given below.

Open Science Case Studies in Curation

1. Open Science Project from Digital Curation Center

This project looked at what motivates researchers to work in an open manner with regard to their data, results and protocols, and whether advantages are delivered by working in this way.

The case studies consider the benefits and barriers to using ‘open science’ methods, and were carried out between November 2009 and April 2010 and published in the report Open to All? Case studies of openness in research. The Appendices to the main report (pdf) include a literature review, a framework for characterizing openness, a list of examples, and the interview schedule and topics. Some of the case study participants kindly agreed to us publishing the transcripts. This zip archive contains transcripts of interviews with researchers in astronomy, bioinformatics, chemistry, and language technology.

 

see: Pennock, M. (2006). “Curating e-Science Data”. DCC Briefing Papers: Introduction to Curation. Edinburgh: Digital Curation Centre. Handle: 1842/3330. Available online: http://www.dcc.ac.uk/resources/briefing-papers/introduction-curation– See more at: http://www.dcc.ac.uk/resources/briefing-papers/introduction-curation/curating-e-science-data#sthash.RdkPNi9F.dpuf

 

2.      cBIO -cBio’s biological data curation group developed and operates using a methodology called CIMS, the Curation Information Management System. CIMS is a comprehensive curation and quality control process that efficiently extracts information from publications.

 

3. NIH Topic Maps – This website provides a database and web-based interface for searching and discovering the types of research awarded by the NIH. The database uses automated, computer generated categories from a statistical analysis known as topic modeling.

 

4. SciKnowMine (USC)- We propose to create a framework to support biocuration called SciKnowMine (after ‘Scientific Knowledge Mine’), cyberinfrastructure that supports biocuration through the automated mining of text, images, and other amenable media at the scale of the entire literature.

 

  1. OpenWetWareOpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. Learn more about us.   If you would like edit access, would be interested in helping out, or want your lab website hosted on OpenWetWare, pleasejoin us. OpenWetWare is managed by the BioBricks Foundation. They also have a wiki about Science 2.0.

6. LabTrove: a lightweight, web based, laboratory “blog” as a route towards a marked up record of work in a bioscience research laboratory. Authors in PLOS One article, from University of Southampton, report the development of an open, scientific lab notebook using a blogging strategy to share information.

7. OpenScience ProjectThe OpenScience project is dedicated to writing and releasing free and Open Source scientific software. We are a group of scientists, mathematicians and engineers who want to encourage a collaborative environment in which science can be pursued by anyone who is inspired to discover something new about the natural world.

8. Open Science Grid is a multi-disciplinary partnership to federate local, regional, community and national cyberinfrastructures to meet the needs of research and academic communities at all scales.

 

9. Some ongoing biomedical knowledge (curation) projects at ISI

IICurate
This project is concerned with developing a curation and documentation system for information integration in collaboration with the II Group at ISI as part of the BIRN.

BioScholar
It’s primary purpose is to provide software for experimental biomedical scientists that would permit a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. This project is funded by NIGMS from 2008-2012 ( RO1-GM083871).

10. Tools useful for scientific content curation

 

Research Analytic and Curation Tools from University of Queensland

 

Thomson Reuters information curation services for pharma industry

 

Microblogs as a way to communicate information about HPV infection among clinicians and patients; use of Chinese microblog SinaWeibo as a communication tool

 

VIVO for scientific communities– In order to connect this information about research activities across institutions and make it available to others, taking into account smaller players in the research landscape and addressing their need for specific information (for example, by proving non-conventional research objects), the open source software VIVO that provides research information as linked open data (LOD) is used in many countries.  So-called VIVO harvesters collect research information that is freely available on the web, and convert the data collected in conformity with LOD standards. The VIVO ontology builds on prevalent LOD namespaces and, depending on the needs of the specialist community concerned, can be expanded.

 

 

11. Examples of scientific curation in different areas of Science/Pharma/Biotech/Education

 

From Science 2.0 to Pharma 3.0 Q&A with Hervé Basset

http://digimind.com/blog/experts/pharma-3-0/

Hervé Basset, specialist librarian in the pharmaceutical industry and owner of the blog “Science Intelligence“, to talk about the inspiration behind his recent book  entitled “From Science 2.0 to Pharma 3.0″, published by Chandos Publishing and available on Amazon and how health care companies need a social media strategy to communicate and convince the health-care consumer, not just the practicioner.

 

Thomson Reuters and NuMedii Launch Ground-Breaking Initiative to Identify Drugs for Repurposing. Companies leverage content, Big Data analytics and expertise to improve success of drug discovery

 

Content Curation as a Context for Teaching and Learning in Science

 

#OZeLIVE Feb2014

http://www.youtube.com/watch?v=Ty-ugUA4az0

Creative Commons license

 

DigCCur: A graduate level program initiated by University of North Carolina to instruct the future digital curators in science and other subjects

 

Syracuse University offering a program in eScience and digital curation

 

Curation Tips from TED talks and tech experts

Steven Rosenbaum from Curation Nation

http://www.youtube.com/watch?v=HpncJd1v1k4

 

Pawan Deshpande form Curata on how content curation communities evolve and what makes a good content curation:

http://www.youtube.com/watch?v=QENhIU9YZyA

 

How the Internet of Things is Promoting the Curation Effort

Update by Stephen J. Williams, PhD 3/01/19

Up till now, curation efforts like wikis (Wikipedia, Wikimedicine, Wormbase, GenBank, etc.) have been supported by a largely voluntary army of citizens, scientists, and data enthusiasts.  I am sure all have seen the requests for donations to help keep Wikipedia and its other related projects up and running.  One of the obscure sister projects of Wikipedia, Wikidata, wants to curate and represent all information in such a way in which both machines, computers, and humans can converse in.  About an army of 4 million have Wiki entries and maintain these databases.

Enter the Age of the Personal Digital Assistants (Hellooo Alexa!)

In a March 2019 WIRED article “Encyclopedia Automata: Where Alexa Gets Its Information”  senior WIRED writer Tom Simonite reports on the need for new types of data structure as well as how curated databases are so important for the new fields of AI as well as enabling personal digital assistants like Alexa or Google Assistant decipher meaning of the user.

As Mr. Simonite noted, many of our libraries of knowledge are encoded in an “ancient technology largely opaque to machines-prose.”   Search engines like Google do not have a problem with a question asked in prose as they just have to find relevant links to pages. Yet this is a problem for Google Assistant, for instance, as machines can’t quickly extract meaning from the internet’s mess of “predicates, complements, sentences, and paragraphs. It requires a guide.”

Enter Wikidata.  According to founder Denny Vrandecic,

Language depends on knowing a lot of common sense, which computers don’t have access to

A wikidata entry (of which there are about 60 million) codes every concept and item with a numeric code, the QID code number. These codes are integrated with tags (like tags you use on Twitter as handles or tags in WordPress used for Search Engine Optimization) so computers can identify patterns of recognition between these codes.

Now human entry into these databases are critical as we add new facts and in particular meaning to each of these items.  Else, machines have problems deciphering our meaning like Apple’s Siri, where they had complained of dumb algorithms to interpret requests.

The knowledge of future machines could be shaped by you and me, not just tech companies and PhDs.

But this effort needs money

Wikimedia’s executive director, Katherine Maher, had prodded and cajoled these megacorporations for tapping the free resources of Wiki’s.  In response, Amazon and Facebook had donated millions for the Wikimedia projects.  Google recently gave 3.1 million USD$ in donations.

 

Future postings on the relevance and application of scientific curation will include:

Using Scientific Content Curation as a Method for Validation and Biocuration

 

Using Scientific Content Curation as a Method for Open Innovation

 

Other posts on this site related to Content Curation and Methodology include:

The growing importance of content curation

Data Curation is for Big Data what Data Integration is for Small Data

6 Steps to More Effective Content Curation

Stem Cells and Cardiac Repair: Content Curation & Scientific Reporting

Cancer Research: Curations and Reporting

Cardiovascular Diseases and Pharmacological Therapy: Curations

Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation The Art of Scientific & Medical Curation

Exploring the Impact of Content Curation on Business Goals in 2013

Power of Analogy: Curation in Music, Music Critique as a Curation and Curation of Medical Research Findings – A Comparison

conceived: NEW Definition for Co-Curation in Medical Research

The Young Surgeon and The Retired Pathologist: On Science, Medicine and HealthCare Policy – The Best Writers Among the WRITERS

Reconstructed Science Communication for Open Access Online Scientific Curation

 

 

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