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Session 15

Title: Structuring research and publications
Moderator: Roman Gurinovich
Participants: .......Johanna, Lambert, Guido
- The problem (as outlined by Roman): People trying to gather content from research papers have a hard time today. Opportunities of releasing results in a structured way are hardly used, even though there are plenty in todays web. 
- Participant from the workshop brings up the positive example of the Taverna workbench. (Though no well known use of this tool at least in Germany.) There are in fact several examples of scholarly workflow software, which sometimes seems to be too hard to learn (?). URI: -> there are a lot more of these scientific workflow management tools, but it is mentioned that they all lack a common standard (under discussion: WSDL, BPL or even UML?)
- Apparently, publishing becomes more often ruled by e.g. formatting constraints, which is basically a good thing. Still missing tools sustaining workflow which fits to these requierements.
- Example from Roman: One of his own lab workflows (fromthe area of life sciences) creating a Google Docs extension for usage within google docs.
- Implicit usage of IMRAD-Format ( is common (but the term is not). IMRAD refers to the typical research paper structure, which is the base of analysis of documents in the presented project.
- Articles are processed into two target formats, a Word document and an enhanced XML document, where e.g. the person name is attributed to its ORCID iD
- semantic description (of e.g. laboratory inventory used) is attributed to a text paragraph, on XML level
- as you type, the tool gives you recommendations on how to annotate your text, which you can follow with only a few clicks
- This Google Docs app is about to be released in a few weeks, as a proprietary but mostly free to used tool
- Roman and his group is aware of the Open Science Framework

- Discussion
- Roman points out that the tool will not definitely be constrained to Google Docs in the future. Collaborative writing today mostly takes part in Google Docs. In order to tackle the adoption problem, they choose this as start
- Participant recommends pandoc for conversion to MarkDown (*.md) and from there to "anything" else
- also, (cf. ), and JATS (journal article taggings suite)