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.”
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.
From pages 459-460 of “Alzheimer Research Forum: a knowledge base and e-community for AD research”
Tags: 1996, AlzForum, copyright, PubMed
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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.
Tags: argumentation, decision-making, evidence, evidence informatics, informatics, reasoning, sense-making
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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.
Tags: communication theory, discourse communities, genre
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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:
- the new, best-in-class argumentation ontology for scientific publishing, the Micropublication Ontology,described in Tim, Paolo, and Carole Goble‘s Journal of Biomedical Semantics article in July 2014 (doi:10.1186/2041-1480-5-28); or see the ontology itself)
- the Open Annotation Data Model for linking quotes (in our case to link claims, data, methods, and materials in Micropublications directly to the source text in biomedical papers and drug labels)
- the Drug Interaction Knowledge Base (DIKB) an existing, hand-constructed knowledge base of evidence about drug-drug interactions, including its evidence taxonomy
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.
Tags: argumentation ontologies, evidence informatics, LISC2014 at ISWC2014, micropublications, ontologies, Open Annotation Data Model
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Publishers from HighWire Press are experimenting with a plugin called SocialCite. This is intended to rate the evidence, citation by citation. Like this:
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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Jason Priem has a wonderful slidedeck on how to smoothly transition from today’s practices in scientific communication to the future. Here is my reading of the argument given in Jason’s slides:
Communicating science is a central and essential part of doing science, and we have always used the best technology available.
Yet currently, there are several problems with journals, the primary form of scholarly communication.
Journal publication is
- Hard to innovate
- Restrictive format: function follows form
- Inconsistent quality control
These problems are fixable, if we realize that journals serve four traditional functions:
By decoupling these functions, into an a la carte publishing menu, we can fix the scholarly communication system. Decoupled scholarly outlets already exist. Jason mentions some outlets (I would say these mainly serve registration functions, maybe also dissemination ones):
- Math Overflow
- Faculty of 1000 Research
- the blag-o-sphere
Jason doesn’t mention here — but we could add to this list — systems for data publishing, e-science workflow, and open notebook science; these may fulfil registration and archiving functions. Also, among existing archiving systems, we could add the journal archiving functions of LOCKSS is the main player I’m familiar with.
To help with the certification functions, we have altmetrics tools like Impact Story (Jason’s Sloan Founded project with Heather Piwowar).
Jason’s argument well worth reading in full; it’s a well-articulated argument for decoupling journal functions, with some detailed descriptions of altmetrics. The core argument is very solid, and of wide interest: Unlike previous articulations for “pre-publication peer review”, this argument will make sense to everyone who believes in big data, I think. There are other formats: video of the talk and a draft article called “Decoupling the scholarly journal”.
Briefly noted in some of my earlier tweets.
Tags: altmetrics, decoupled journal, journal publishing, prepublication peer review
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Increasingly, I’m using Google Docs with collaborators. Yesterday, one of them pointed out the new “Research” search tab within Google Docs. (Tools->Research). I’m a bit surprised that your searches don’t show up on your collaborators’ screen. I’m particularly surprised that sharing searches doesn’t seem possible.
Google Docs' new 'Research' tab promotes search within Google Docs.
Apparently, it is pretty new. More at the Google Docs blog.
Tags: Google Docs, search
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One thing I can say about Kindle: error reporting is easier.
You report problems in context, by selecting the offending text. No need to explain where - just what the problem is.
Feedback receipt is confirmed, along with the next steps for how it will be used.
By contrast, to report problems to academic publishers, you often must fill out an elaborate form (e.g. Springer or Elsevier). Digging up contact information often requires going to another page (e.g. ACM.). Some make you *both* go to another page to leave feedback and then fill out a form (e.g. EBSCO). Do any academic publishers keep the context of what journal article or book chapter you’re reporting a problem with? (If so, I’ve never noticed!)
Tags: crowdsourcing, error reporting, kindle, publishing, typos
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