HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20180411

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Hi,

I didn't send this to the group, thinking it too much too late, but if you get/want to bring these up...

Jodi's presentation was really thoughtful and very useful. Seems like we all had offline conversations since hearing it. I put a summary of some of my offline discussions, essentially to reframe the context of Alex's points, at http://ask2cy.com/poststructuralist.txt

In answer to Jodi's last question in her final slide: What are we modeling?

This seems to depend on the role of a scientific article in scientific discourse. If we consider "scientific discourse" itself to be a process in nature, then we can treat the physical publication as yet another artifact of the natural process. Then we can use Barry Smith and Werner Cuester "ontological realism" as the answer: We are modeling reality!

Elements of the articles may be useful in helping us understand the process of discovery of knowledge, but the final test is in our ability to apply the knowledge in nature. That documents come with "rhetorical blocks" is only to be tested by taking the discussion beyond the article to the process in the lab and in the science meetings and review panels.

To connect a "document" to a process of knowledge discovery that happens in nature is really difficult. The conversion of static paper publications to living, annotatable electronic publications offers new opportunity to understand the rhetorical process of science, but I continue to think we can capture this discourse best in a form that never passes through the rhetorical blocks of paper documents.

I'm thinking that when they invented the automobile engine, they didn't just unharness the horse, put the engine in its place, and control it with reins.

Howard


Original Message-----

From: public-semweb-lifesci-request@w3.org [1] On Behalf Of Waard, Anita de A (ELS-AMS) Sent: Sunday, April 17, 2011 4:57 PM To: Alexander Garcia Castro; Jodi Schneider Cc: barend mons; M. Scott Marshall; Tim Clark; HCLS IG; Alberto Accomazzi; Sophia Ananiadou; Philip Bourne; Gully Burns; Daniel, Ronald (ELS-SDG); Rahul Dave; Alf Eaton; Matthew Gamble; Yolanda Gil; Alyssa Goodman; Paul Groth; Tudor Groza; Hays, Ellen (ELS-BUR); Maryann Martone; David R Newman; Scerri, Antony (ELS-CAM); Jack Park; Silvio Peroni; Steve Pettifer; Philippe Rocca-Serra; Cartic Ramakrishnan; RebholzSchuhmann; David Shotton; Kaitlin Thaney; Karin Verspoor; Lynette Hirschman; Susanna-Assunta Sansone; Kees van Bochove; Katy Wolstencroft; Jun Zhao; Paul Groth Subject: RE: HCLS Scientific Discourse Call Monday, 11 April 2011 10 am EST, 3 PM BST: talk by Jodi Schneider

Dear all,

Jodi's talk last week seemed to spur on a great amount of discussion, and this week, as we don't have a speaker, I would like to spend our time about the issues Jodi's talk brought up. These include: - Alex's points below - links between the paper and workflow and experimental ontologies; - The connection (and if there is one) between nanopublications/triples/research highlights (will explain on the call) and medium-grained structure - Uses for medium-grained structure mark up: what would be a good set of use cases? Can we find some concrete projects to work on? - An issue that has been discussed on a few calls now which we can also discuss is the difference between data, author's intent, persuasive structure and nanopublication-type summaries. - A point that Joanne raised: can we plan a meeting to discuss this stuff in person?

I am sure much more will come up, once we start talking. Feel free to send around more questions before the call, so we have a list of them to consider before we start.

Thanks, and look forward to talking to you tomorrow,

Best,

- Anita.

Anita de Waard Disruptive Technologies Director, Elsevier Labs http://elsatglabs.com/labs/anita/ a.dewaard@elsevier.com



Original Message-----

From: Jodi Schneider Date: 12 April 2011 17:37:22 GMT+01:00 To: Alexander Garcia Castro Cc: ...

Hi Alex,

Thanks for the discussion! I talked about fine-grained ontologies not because we're making one, but to get a better understanding of what a "middle-grained ontology" should be, and how we can provide a bridge between the coarse-grained document structure and the fine-grained structures.

ORB itself doesn't have a fine grained structure -- it's focused on the head, body, and tail, and refines the body with IMRAD: http://www.w3.org/2001/sw/hcls/notes/orb/ Rather, there are a *lot* of existing fine-grained ontologies (such as the domain ontologies you mention, as well as document-focused and rhetoric-focused ontologies), and my goal is to figure out how to bridge between ORB's coarse structure and those fine-grained ontologies with a middle-grained ontology. Those "fine-grained ontologies" are not all the same kind of thing: they differ (ontologically!) because some are focused on the document, others on the process of science, and some on the reasoning ("why") behind the science.


At other times, the group has discussed *why* we need papers and not just better open data with the sort of e-science and workflow/provenance recording you discuss. Anita calls the paper "a story that persuades with data", and I think the main challenge is not about replacing the description of experiments (you're right--that's best served by domain-specific ontologies!). Rather, the challenge is in understanding and explaining how the experiment is *used* as part of the rhetoric: **why** should this particular data persuade a domain scientist?

I'm not exactly sure what you mean by "Once the structure of the document is solved". For instance, if we want to create a claims network (which many of us would find exciting and useful), we need to extract the claims out of the document. Yet those claims appear throughout the document -- they're not limited to the introduction, or discussion, or conclusion -- and can (Anita assures us) be repeated throughout the document. And it's not just claims but also evidence that will need to be extracted. I'd like to hear more about your thoughts on document structure -- because your understanding of what's needed could help focus efforts.

Thanks again, and let me know what you think! -Jodi


Original Message-----

From: public-semweb-lifesci-request@w3.org on behalf of Alexander Garcia Castro Sent: Mon 4/11/2011 11:25 To: Jodi Schneider Cc:...

Hi Jodi, nice talk.

As a general question, shouldn't the description of experiments be something to be described by domain specific ontologies? Also, there are repositories for experiments, e.g Array express for microarrays; there are also minimal standards for reporting several experimental procedures, shouldn't the sections in the document make use of, pointing to, these resources? if ORB and other document related ontologies go into describing experimental information I am afraid it may be difficult to maintain and not very practical to implement.

fine-graining ORB should, in my opinion, make use of other ontologies for addressing domain specific issues. for instance, if a researcher wants to go deeper into materials and methods most likely the information that will allow him/her to "replicate" the experiment will be living somewhere else in the web; also, most likely there will be an ontology for specific experimental procedures, measures, etc involved.

Once the structure of the document is solved it is easy to use resources such as bio2rdf to resolve it against existing resources in the web. if not, then authors can easily point to these external resources -AO can easily deal with such a use case. my point is, experimental information is highly domain specific and there are now ontologies (OBI) and repositories for experimental information as well as efforts for standardizing minimal amounts of information (http://www.mibbi.org/index.php/Main_Page) for reporting specific experimental procedures, shouldn't the fine grained structure of ORB seek to make use of these resources?