Anthony Gitter

That error message is new to me. Hopefully the warning status and your successful conversion indicate it may be safe to ignore. A few quick Google and GitHub issue searches...

I can't open your linked docx file in Word on Windows either. I could open a [recent docx](https://github.com/greenelab/covid19-review/blob/260d4e4bd61fef9c4f3dc72487196809c309535f/pharmaceuticals-manuscript.docx) from the COVID-19 review though. The error from Word points to this...

Is this equation numbering problem blocking your resubmission? In https://github.com/manubot/rootstock/issues/435#issuecomment-1072870077 I describe initial attempts to use pandoc-crossref for numbering. It has some peculiarities and breaks some of Manubot's interactive HTML...

> So we're aware that it's not supported and adding a PubmedBookArticle parser would be a bit of work. I agree that adding a new parser isn't going to be...

Manubot recently added support for citation aliases defined using Markdown's link reference syntax. [This section](https://github.com/manubot/rootstock/blob/main/USAGE.md#citation-aliases) of the documentation shows examples. The behavior is slightly different from your desired behavior shown...

Now I better understand what you are trying to achieve. However, Manubot and the pandoc-manubot-cite Pandoc filter are not designed to do that. The Pandoc filter is designed to identify...

Does using templating open up any better options for the markdown syntax? I haven't thought of any specific syntax proposals that I like. Something like `{{CHEBI:53438}}` or `{{CHEBI:53438.expanded}}` could be...

Good feature suggestion @epogrebnyak I would also be interested in a `manubot cite --from-file` (or similar) for https://github.com/manubot/rootstock/issues/223. In that use case, it would be used with the `--render` option.

This makes the most sense to me as an optional ID in addition to free text affiliations but not as the primary way to specify affiliations. Specifying one or more...

Nice suggestion @cthoyt. You comment also prompted me to check on the ROR status of the Morgridge Institute. I noted in 2019 it did not have a ROR ID, but...