Workshop Papers‎ > ‎


Analogical publishing: Using shared referent structure to connect potential collaborators

R. K. Belew


Presentation prepared for BeyondPDF11

Topics: 1.3 Document management tools; 2.5 Systems for combining and rendering annotated documents; 3. Use cases and examples; 5 Attribution

Science (and hence the publishing of science, the entire industry of STM publishing, ...) is special, within the range of other cultural activities. This meeting brings us together as both producers and consumers of Science. A few observations, before giving brief descriptions of two projects in progress:

  • Our job as Scientists is to observe new things, give them names, and relate them to other True things people have said in the past. If we can use extant language of our colleagues to describe what we’ve seen, it is so much simpler! But one way or another, we need to convey to others an account that they -- and then our shared audiences -- can integrate (build upon, critcize, refine, ...) into what they each believe to be True.
  • ’Social networking’ seems to be big these days:). But of course Scientists (along with every other member of society) have long been been socializing, in networks. The tacit social systems (PhD advising, postdocs, summer conferences, the system of peer review, journal publishing, editting, ...) Scientists tend to take for granted need to be made explicit and studied closely.
  • Inter-disciplinary collaborations are one place that Science’s tacit features may be exposed. Among our intra-disciplinary colleagues (e.g., at a summer conference), our specialized technical language (jargon, lingo, argot, patois, vernacular, ... ) can be used naturally. Yet the same terms can easily becomes confused as we try to negotiate meanings with others from different backgrounds [AINEPGlossary]. Publishing conventions (what counts as the minimal-publishable-unit, the role of students and postdocs, even author ordering) need to be similarly negotiated as disciplary boundries are crossed.
  • If there are two things that should make the specific instance STM worthy of general interest (to Adobe, but also Google, Microsoft, IBM, Oracle, ...) they might be:
    • the processes that integrate the new language, new media (including but not starting with diagrams like that in WatsonCrick53, to visualizations generally, data sets, executable models, audio and video, entirely new modes of communication) that Scientists generate for their peers often become useful across wider audiences;
    • the record of prior Scientific ’progress’ that this group has generated represents an especially an well-documented precident for analysis and prediction of other groups’ dynamics.

Our pain is their pain!


HIVortal describes a ’vertical portal,’ drilling down through a wide range of an information resources but exclusively related to the subject matter of HIV and AIDS, towards a common purpose of facillitating research by an active group of investigators and their subsequent audiences. The collaborators’ interest ranges from combinatorial search to visualization, computational chemistry, wet-lab experimentation, through clinical application. The long-term (12 year) nature of the interaction has allowed both a common language, and a system of mutual trust to develop among investigators across these disciplines. In the words of one participant, HIVortal is “Facebook for us”!

We describe a software protype supporting collaborative research among this highly inter-disciplinary group of PIs. We focus on NCBI resources as primary, but also consider PDB, GenomeOntology,, and PharmGKB. Traditional keyword and citation analyses are supplemented by references made to data objects (sequences, genes, proteins, taxonomic entries) common to all biological scientists, as well as other data specific to HIV drug resistance (viral mutations, inhibitor properties). Shared data references help to reconcile the semantics of otherwise disjoint vocabularies. The key insight is that when shared resources are made analogical to features of the virus, everyone naturally knows “where” to look.

Peer review

Peer review is frequently mentioned as the linchpin of many academic activities, from publishing, to funding, career advancement and entire program review. Reviewing is currently viewed as an important act of academic citizenship, done over and above participants’ other responsibilities, and so done with whatever attention they can muster. We propose PR2, a system that increases the incentive for the reviewer by providing an explicit reward. Once all of STM has adopted PR2, we predict the quality of peer reviewing, and so the content being published, will improve because reviewers know their efforts will really matter to their career.

Richard Belew,
Jan 22, 2011, 6:09 PM