define section types (subSubSection types in GG)

[myrmoteras]

@gsautter @tcatapano Following is a list of section types to be included in taxpub, especially for EJT and then implmented in GoldenGateImagine

keywords to include all the keywords listed in this section. Ideally they are parsed out and also submitted to BLR

materials_methods Materials and methods is a standard section in scientific papers describing the methods, standards, abbreviations, materials used in the article. This is already introduced, but hardly ever used (at least by me)

results this section describes the results obtained in the study. In taxonomic studies it also includes the treatments.

discussion This section explains the results, puts them in context and draws conclusion (sometimes its own subSubSection. In EJT it has subSubSubSections which are not generic put specific to the article

conservation This section discusses the conservation status of the respective taxon, including often references to RedLists and management plans.

Sections specific to EJT

backmatter includes all the description of the history of the manuscript, distribution of the article

document-head includes all the headers, title, authors, affiliations of the authors, emails, Zoobank numbers. this seems to be the same as frontatter

citation includes the suggested way to cite the article

[myrmoteras]

subSubsection type =materials_methods

this section often has subSubSubsections. I don't know what to do with it?

[myrmoteras]

subSubSection type = results

[myrmoteras]

subSubSection type = discussion

[myrmoteras]

subSubSection type = backmatter

[myrmoteras]

subSubSection type = frontmatter, citation

[tcatapano]

To be consistent with the JATS model, we should consider Abstract, Keywords, and Citation as components of Front Matter.

[myrmoteras]

but are those named parts in the Front Matter, thus subSubSecton of subsection type=frontMatter? Or how do we have to mark up this section?
Can you let @gsautter know?

[gsautter]

@tcatapano no need to ... following anyway.

[gsautter]

Just need some idea about how to identify these individual types ...

• "Abstract" and "Keywords" should be straightforward (I tend to think we already have "abstract" anyway, so only the keywords to add)
• "Citation" might be a bit more of a challenge
• "FrontMatter" appears to be pretty much equivalent to what is now "document_head"

[tcatapano]

This is a little vague to me. Not sure what to check on. I'll deal with it when I get samples with the new sec-types.

…

On Fri, Dec 29, 2017 at 12:05 PM, Donat Agosti ***@***.***> wrote: but are those named parts in the Front Matter, thus subSubSecton of subsection type=frontMatter? Or how do we have to mark up this section? Can you let @gsautter <https://github.com/gsautter> know? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA7A8lvU9GWUaCgRxv-fW3A4ubwkKvEZks5tFUYQgaJpZM4RL2GU> .

[myrmoteras]

@tcatapano
You can use all the EJT- > EJT-380, where I started to add the section types mentioned above. See FF8C361F1A148106227F5719FFEEB51A EJT_article sheet

Citation (see image at the top of this issue) is essentially a bibRef in the front matter. When you do the mark up of the bibRef in EJT, this is always the first bibRef that is discovered by the tagger and neeed then be removed.

[gsautter]

Add "phylogeny" (see https://github.com/plazi/Plazi-Communications/issues/750 for example).

[tcatapano]

I think should be recommended values, which can be enforced via schematron.

[tcatapano]

Removing from 1.0 milestone

[tcatapano]

See #73 . Closing