QOTD: Working out scientific insights on paper, Lavoisier case study

July 12th, 2017
by jodi

…language does do much of our thinking for us, even in the sciences, and rather than being an unfortunate contamination, its influence has been productive historically, helping individual thinkers generate concepts and theories that can then be put to the test. The case made here for the constitutive power of figures [of speech] per se supports the general point made by F.L. Holmes in a lecture addressed to the History of Science Society in 1987. A distinguished historian of medicine and chemistry, Holmes based his study of Antoine Lavoisier on the French chemist’s laboratory notebooks. He later examined drafts of Lavoisier’s published papers and discovered that Lavoisier wrote many versions of his papers and in the course of careful revisions gradually worked out the positions he eventually made public (Holmes, 221). Holmes, whose goal as a historian is to reconstruct the careful pathways and fine structure of scientific insights, concluded from his study of Lavoisier’s drafts

We cannot always tell whether a thought that led him to modify a passage, recast an argument, or develop an alternative interpretation occurred while he was still engaged in writing what he subsequently altered, or immediately afterward, or after some interval during which he occupied himself with something else; but the timing is, I believe, less significant than the fact that the new developments were consequences of the effort to express ideas and marshall supporting information on paper (225).

– page xi of Rhetorical Figures in Science by Jeanne Fahnestock, Oxford University Press, 1999.

She is quoting Frederich L. Holmes. 1987. Scientific writing and scientific discovery. Isis 78:220-235. DOI:10.1086/354391

As Moore summarizes,

Lavoisier wrote at least six drafts of the paper over a period of at least six months. However, his theory of respiration did not appear until the fifth draft. Clearly, Lavoisier’s writing helped him refine and understand his ideas.

Moore, Randy. Language—A Force that Shapes Science. Journal of College Science Teaching 28.6 (1999): 366. http://www.jstor.org/stable/42990615
(which I quoted in
a review I wrote recently)

Fahnestock adds:
“…Holmes’s general point [is that] there are subtle interactions ‘between writing, thought, and operations in creative scientific activity’ (226).”

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David Liebovitz: Achieving Care transformation by Infusing Electronic Health Records with Wisdom

May 1st, 2017
by jodi

Today I am at the Health Data Analytics summit. The title of the keynote talk is Achieving Care transformation by Infusing Electronic Health Records with Wisdom. It’s a delight to hear from a medical informaticist: David M. Liebovitz (publications in Google Scholar), MD, FACP, Chief Medical Information Officer, The University of Chicago. He graduated from University of Illinois in electrical engineering, making this a timely talk as the engineering-focused Carle Illinois College of Medicine gets going.

David Liebovitz started with a discussion of the data problems — problem lists, medication lists, family history, rules, results, notes — which will be familiar to anyone using EHRs or working with EHR data. He draws attention also to the human problems — both in terms of provider “readiness” (e.g. their vision for population-level health) as well as about “current expectations”. (An example of such an expectation is a “main clinician satisfier” he closed with: U Chicago is about to turn on outbound faxing from the EHR!) He mentioned also the importance of resilience.

He mentioned customizing systems as a risk when the vendor makes upstream changes (this is not unique to healthcare but a threat to innovation and experimentation with information systems in other industries.) Still, in managing the EHR, there is continual optimization, scored based on a number of factors. He mentioned:

  • Safety
  • Quality/patient experience
  • Regulatory/legal
  • Financial
  • Usability/productivity
  • Availability of alternative solutions

As well as weighting for old requests.

He emphasized the complexity of healthcare in several ways:

complexity of drug purchasing

An image from “Prices That Are Too High”, Chapter 5, The Healthcare Imperative: Lowering Costs and Improving Outcomes: Workshop Series Summary (2010)

  • Icosystem’s diagram of the complexity of the healthcare system
Complexity of the healthcare system

Icosystem – complexity of the healthcare system

  • Another complexity is the modest impact of medical care compared to other factors
    • such as the impact of socioeconomic and political context on equity in health and well-being (see the WHO image below).
    • For instance, there is a large impact of health behaviors, which “happen in larger social contexts.” (See the Relative Contribution of Multiple Determinants to Health, August 21, 2014, Health Policy Briefs)

Given this complexity, David Liebovitz stresses that we need to start with the right model, “simultaneously improving population health, improving the patient experience of care, and reducing per capita cost”. (See Stiefel M, Nolan K. A Guide to Measuring the Triple Aim: Population Health, Experience of Care, and Per Capita Cost. IHI Innovation Series white paper. Cambridge, Massachusetts: Institute for Healthcare Improvement; 2012).

triple aims to measure healthcare improvement

Table 1 from Stiefel M, Nolan K. A Guide to Measuring the Triple Aim: Population Health, Experience of Care, and Per Capita Cost. IHI Innovation Series white paper. Cambridge, Massachusetts: Institute for Healthcare Improvement; 2012.

Given the modest impact of medical care, and of data, he suggests that we should choose the right outcomes.

David Liebovitz says that “not enough attention has been paid to usability”; I completely agree and suggest that information scientists, human factors engineeers, and cognitive ergonomists help mainstream medical informaticists fill this gap. He put up Jakob Nielsen’s 10 usability heuristics for user interface design A vivid example is whether a patient’s resuscitation preferences are shown (which seems to depend on the particular EHR screen): the system doesn’t highlight where we are in the system. For providers, he says user control and freedom are very important. He suggests that there are only a few key tasks. A provider should be able to do ANY of these things wherever they are in the chart:

  • put a note
  • order something
  • send a message

Similarly, EHR should support recognition (“how do I admit a patient again?”) rather than requiring recall.

Meanwhile, on the decision support side he highlights the (well-known) problems around interruptions by saying that speed is everything and changing direction is much easier than stopping. Here he draws on some of his own work, describing what he calls a “diagnostic process aware workflow”

David Liebovitz. Next steps for electronic health records to improve the diagnostic process. Diagnosis 2015 2(2) 111-116. doi:10.1515/dx-2014-0070

Can we predict X better? Yes, he says (for instance pointing to Table 3 of “Can machine-learning improve cardiovascular risk prediction using routine clinical data?” and its machine learning analysis of over 300,000 patients, based on variables chosen from previous guidelines and expert-informed selection–generating further support for aspects such as aloneness, access to resources, socio-economic status). But what’s really needed, he says, is to:

  • Predict the best next medical step, iteratively
  • Predict the best next lifestyle step, iteratively
  • (And what to do about genes and epigenetic measures?)

He shows an image of “All of our planes in the air” from flightaware, drawing the analogy that we want to work on “optimal patient trajectories” — predicting what are the “turbulent events” to avoid”. This is not without challenges. He points to three:

He closes suggesting that we:

  • Finish the basics
  • Address key slices of the spectrum
  • Descriptive/prescriptive
  • Begin the prescriptive journey: impact one trajectory at a time.

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QOTD: Scholarly communication online, circa 1996

December 2nd, 2015
by jodi

Here is a glimpse into scholarly communication 20 years ago, from a paper about Alzforum, the Alzheimer Research Forum website. “In July of 1996, the website made its debut at the International Conference on Alzheimer’s Disease and Related Disorders in Osaka, Japan.”1

Having established a foothold in cyberspace, the challenge for Alzforum was and continues to be to define new types of scientific publishing that take advantage of the speed and wide distribution of the Web and to curate and add value to information available from other public sources. This is a perennial challenge, thanks to the rapid advances in biomedical resources on the Web.

This uphill struggle, however, seems less strenuous when we compare the current situation with the “old days.” Recall that in 1996, PubMed did not exist! (PubMed was launched in June of 1997.) Medical institutions had access to Medline, but in order for Alzforum to produce its Papers of the Week listings, the editor had to ask the Countway Medical Library at Harvard Medical School to provide weekly text files listing newly indexed AD papers. The Alzforum hired a curator to paraphrase each abstract so that this information could be posted without violating journal copyrights. These documents were manually edited, sent out in a weekly email to the advisors for comments, and compiled into a static HTML page. Looking back, we can see that the entire process seems as antiquated as the hand-copying of manuscripts in the Middle Ages.

(emphasis mine)

From pages 459-460 of “Alzheimer Research Forum: a knowledge base and e-community for AD research”2

  1. page 458, Kinoshita, June, and Gabrielle Strobel. “Alzheimer Research Forum: a knowledge base and e-community for AD research.” in Alzheimer: 100 Years and Beyond, Mathias Jucker, Konrad Beyreuther, Christian Haass, Roger M. Nitsch, Yves Christen, eds. Berlin Heidelberg:Springer-Verlag, 2006: 457-463. []
  2. Kinoshita, June, and Gabrielle Strobel. “Alzheimer Research Forum: a knowledge base and e-community for AD research.” in Alzheimer: 100 Years and Beyond, Mathias Jucker, Konrad Beyreuther, Christian Haass, Roger M. Nitsch, Yves Christen, eds. Berlin Heidelberg:Springer-Verlag, 2006: 457-463. []

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Evidence Informatics

January 20th, 2015
by jodi

I sent off my revised abstract to ECA Lisbon 2015, the European Conference on Argumentation. Evidence informatics, in 75 words:

Reasoning and decision-making are common throughout human activity. Increasingly, human reasoning is mediated by information technology, either to support collective action at a distance, or to support individual decision-making and sense-making.

We will describe the nascent field of “evidence informatics”, which considers how to structure reasoning and evidence. Comparing and contrasting evidence support tools in different disciplines will help determine reusable underlying principles, shared between fields such as legal informatics, evidence-based policy, and cognitive ergonomics.

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Genre defined, a quote from John Swales

October 21st, 2014
by jodi

A genre comprises a class of communicative events, the members of which share some set of communicative purposes. These purposes are recognized by the expert members of the parent discourse community and thereby constitute the rationale for the genre. This rationale shapes the schematic structure of the discourse and influences and constrains choice of content and style. Communicative purpose is both a privileged criterion and one that operates to keep the scope of a genre as here conceived narrowly focused on comparable rhetorical action. In addition to purpose, exemplars of a genre exhibit various patterns of similarity in terms of structure, style, content and intended audience. If all high probability expectations are realized, the exemplar will be viewed as prototypical by the parent discourse community. The genre names inherited and produced by discourse communities and imported by others constitute valuable ethnographic communication, but typically need further validation.1

  1. Genre defined, from John M. Swales, page 58, Chapter 3 “The concept of genre” in Genre Analysis: English in academic and research settings. Cambridge University Press 1990. Reprinted with other selections in
    The Discourse Studies Reader: Main currents in theory and analysis (see pages 305-316). []

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Linked Science 2014 paper: Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base

October 19th, 2014
by jodi

Today I’m presenting a talk in the ISWC 2014 Workshop on Linked Science 2014—Making Sense Out of Data (LISC2014). The LISC2014 paper is joint work with Paolo Ciccarese, Tim Clark and Richard D. Boyce. Our goal is to make the evidence in a scientific knowledge base easier to access and audit — to make the knowledge base easier to maintain as scientific knowledge and drug safety regulations change. We are modeling evidence (data, methods, materials) from biomedical communications in the medication safety domain (drug-drug interactions).

The new architecture for the drug-drug interaction knowledge base is based on:

This is part of a 4-year National Library of Medicine project, “Addressing gaps in clinically useful evidence on drug-drug interactions” (1R01LM011838-01)

Abstract of our paper, “Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base.”:

Semantic web technologies can support the rapid and transparent validation of scientific claims by interconnecting the assumptions and evidence used to support or challenge assertions. One important application domain is medication safety, where more efficient acquisition, representation, and synthesis of evidence about potential drug-drug interactions is needed. Exposure to potential drug-drug interactions (PDDIs), defined as two or more drugs for which an interaction is known to be possible, is a significant source of preventable drug-related harm. The combination of poor quality evidence on PDDIs, and a general lack of PDDI knowledge by prescribers, results in many thousands of preventable medication errors each year. While many sources of PDDI evidence exist to help improve prescriber knowledge, they are not concordant in their coverage, accuracy, and agreement. The goal of this project is to research and develop core components of a new model that supports more efficient acquisition, representation, and synthesis of evidence about potential drug-drug interactions. Two Semantic Web models—the Micropublications Ontology and the Open Annotation Data Model—have great potential to provide linkages from PDDI assertions to their supporting evidence: statements in source documents that mention data, materials, and methods. In this paper, we describe the context and goals of our work, propose competency questions for a dynamic PDDI evidence base, outline our new knowledge representation model for PDDIs, and discuss the challenges and potential of our approach.

Citation: Schneider, Jodi, Paolo Ciccarese, Tim Clark, and Richard D. Boyce. “Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base.” Linked Science 2014 at ISWC 2014.

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Rating the evidence, citation by citation?

September 4th, 2014
by jodi

Publishers from HighWire Press are experimenting with a plugin called SocialCite. This is intended to rate the evidence, citation by citation. Like this:

SocialCite at PNAS, HighWire Press from  http://www.pnas.org/content/108/14/5488.full#ref-list-1

SocialCite at PNAS, HighWire Press from http://www.pnas.org/content/108/14/5488.full#ref-list-1:

So far a few publishers (including PNAS) have implemented it as a pilot. Apparently the Journal of Bone and Joint Surgery is apparently leading this effort, I’d be really interested in speaking with them further:

Find out more about SocialCite from their website or the slidedeck from their debut at the HighwirePress meeting.

I’m *very* curious to hear what peopel think of this — it really surprised me.

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Library Linked Data at ALA 2014

June 6th, 2014
by jodi

Linked Data is big at the 2014 American Library Association meeting! All day Friday & Saturday, plus Sunday morning, you can get your recommended dose of Library Linked Data. See you in Las Vegas?

Friday June 27
I’ll be speaking and moderating a question session in this full-day preconference.
Practical Linked Data with Open Source (separate ticket needed)
Friday, June 27, 2014 – 8:30am to 4:00pm
N258, Las Vegas Convention Center
This pre-conference combines theory and practice by giving participants a working knowledge of the creation and use of linked data and linked data applications. This session will ground participants in linked data models and patterns through hands-on exercises. Participants will go home with a working knowledge of the state of the art of linked data in open source library systems and the use of linked data to solve metadata problems across libraries, archives, and museums

Saturday June 28
I will be speaking about international developments in LLD in Part I:
International Developments in Library Linked Data: Think Globally, Act Globally (Part One)
Saturday, June 28, 2014 – 8:30am to 10:00am
N264, Las Vegas Convention Center

International Developments in Library Linked Data: Think Globally, Act Globally – Part Two
Saturday, June 28, 2014 – 10:30am to 11:30am
S230, Las Vegas Convention Center
Libraries have the potential to make major contributions to the Semantic Web, but are still emerging as global participants. RDA implementation and the BibFrame initiative have drawn fresh attention to the promise and potential of linked data. What are the international developments in linked data, emerging from libraries and other memory institutions? Come hear our speakers address current projects, opportunities and challenges.

Taking action: Linked data for digital collection managers
Saturday, June 28, 2014 – 1:00pm to 2:30pm
S222, Las Vegas Convention Center

The linked data movement has gained momentum. But how does paradigm shift affect digital collection workflows? This workshop will provide key theoretical concepts of linked data and engaging hands-on activities demonstrating how CONTENTdm metadata can be transformed into linked data. The workshop will also provide a forum to discuss how linked data might alter our current practices and workflows. This workshop is geared toward beginners and is designed for curious exploration and active learning.

OCLC The Power of Shared Data: What’s New and What’s Next?
Saturday, June 28, 2014 – 3:00pm to 4:00pm
N116, Las Vegas Convention Center
Join OCLC’s Ted Fons and Richard Wallis to understand how OCLC is leveraging your WorldCat holdings to give your institution broader visibility on the Web. In this session, we will detail current features, planned enhancements and new developments related to linked data.

Sunday June 29
Linked Library Data Interest Group
Sunday, June 29, 2014 – 8:30am to 10:00am
N237, Las Vegas Convention Center
Talk by Jon Phipps & discussion to follow. (Sunday, sadly, I’m on a plane to another meeting.)

Jon Phipps, of Metadata Management, will present a talk on:

RDA and LOD — FTW or WTF? : A Fair and Balanced Point of View.

Is RDA just “the rules” or is it a robust bibliographic metadata model designed specifically to support rich, FRBRized, distributed LOD that just happens to come with several thousand “pages” of rules? What’s this “unconstrained” stuff? Why does RDA RDF have URIs I can’t “read” and will never remember (and what are lexical aliases)? Why are there so many definitions for “Work” anyway? How is RDA handling versioning and releases? How is RDA using Git and GitHub? Why does any of this matter to my data and, more importantly, me?

You’ve got questions? Maybe Jon Phipps has some answers (except for that last one). Jon is a partner in Metadata Management Associates, a consultancy specializing in, wait for it … metadata management, and has been collaborating with various groups of well-intentioned folks trying to define RDA as a data model for what seems like centuries, and thinks that quite recently the JSC has pretty much nailed it.

A question and answer period and a lively managed discussion will follow the presentation. More info & speaker biography.

Understanding Schema.org
Sunday, June 29, 2014 – 10:30am to 11:30am
S230, Las Vegas Convention Center
Jason Clark and Dan Scott

Schema.org is an effort among major search engines to promote better linking of Web content through the use of metadata attributes in HTML markup, allowing for improved access to digital objects. The ALCTS/LITA Metadata Standards Committee invites you to hear speakers who are active in schema.org development in libraries, and who will discuss initiatives in this area within the GLAM community which promote a broader understanding of the development of bibliographic information among these communities.

Kudos to the LITA / ALCTS Linked Library Data Interest Group and ALCTS/LITA Metadata Standards Committee for facilitating a great program!

Above information from the American Library Association and its Linked Library Data Interest Group (updated June 17): double-check room numbers at the conference website, and add sessions to your conference scheduler.

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QOTD – physical computing

October 13th, 2013
by jodi

Personal computers have evolved in an office environment in which you sit on your butt, moving only your fingers, entering and receiving information censored by your conscious mind. That is not your whole life, and probably not even the best part. We need to think about computers that sense more of your body, serve you in more places, and convey the physical expression in addition to information.

Dan O’Sullivan and Tom Igoe, Physical Computing: Sensing and Controlling the Physical World with Computers

via Jon Froehlich at DSST 2013 in his talk about the UMd HCIL hackerspace.

Slides for Jon’s talk, “If You Build It, They Will Come: Reflecting on the Successes (and Failures) of Building a Collaborative Workspace to Support Creativity, Experimentation, and Making”, are available via his talks page, as a huge PPTX here). Highly recommended if you’re interested in makerspaces/hackerspaces in academic institutions.

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Ph.D. viva – public talk

October 1st, 2013
by jodi

Here are the slides from the public part of my Ph.D. viva (thesis defense), on “Enabling reuse of arguments and opinions in open collaboration systems”. There is also a downloadable PDF version of the slides. Or see the thesis/dissertation itself and its data (index page) (note added 2016-04-22).

Video to follow: thanks to Hugo Hromic for streaming & recording that!

Title: “Enabling reuse of arguments and opinions in open collaboration systems”

Abstract: The World Wide Web enables large-scale collaboration, even between groups of individuals previously unknown to one another. These collaborations produce tangible outputs, such as encyclopedias (Wikipedia), electronic books (Distributed Proofreaders), maps (OpenStreetMap) and open source software packages (Firefox). In such open collaboration systems, decisions are made through open online discussions in which anyone can participate, and those decisions are based on the written arguments and opinions that individuals contribute, sometimes in large volumes.

Sense-making and coordination is an important component of collaboration, but it is particularly challenging when individuals disagree. When large volumes of opinions and arguments are expressed, popular or emotive choices can be identified through coarse approaches such as sampling, sentiment, or voting. But these do not identify the reasons for disagreement, which may be needed in order to reach decisions. For example, about 500 discussions each week in Wikipedia concern whether a particular topic should be covered in the encyclopedia. Discussions may involve comments from 2-200 people, and some topics are contentious.

This thesis addresses the problem of analyzing, integrating, and reconciling arguments and opinions in goal-oriented online discussions. We emphasize the structure of arguments by providing a new, reconfigurable Web interface. Our interface improves the perceived usefulness, perceived ease of use, and information completeness, thus providing meaningful support for the discussion.

The thesis addresses the following three research questions:
– What are the opportunities and requirements for providing argumentation support?
– Which arguments are used in open collaboration systems?
– How can we structure and display opinions and arguments to support their use and reuse?

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