Updates to chapter 1

[gsrohde]

Updated some links and a contact address. Added a note about variant database schemas in use and changed wording in places to clarify some points.

[gsrohde]

@dlebauer Please note that a few other updates may be in order:

1. The “Please cite” section probably needs updating.
2. Section 1.3 may need updating to reflect other sources of data and other species of specific interest (e.g. Sorghum bicolor).

The page as it stands is very "EBI-centric".

[gsrohde]

@dlebauer I think this is about ready to be merged. But first look at the comment I just made on the citation example.

[gsrohde]

I updated the citation information in the citation example and merged it in. But I realized this is essentially the same as the reference to the paper given at the start of the Citation section of this document except for being in CMOS style as opposed to APA style.

So I'm a little confused: The instructions for citing use of data from an instance of BETYdb say to "Refer to the footer of the instance of BETYdb that you are using for citation information." But all the instances I checked (the ones that have URLs listed in the machines table) refer to the GCB paper (doi:10.1111/gcbb.12420) with two exceptions:

• The Purdue site just has "David LeBauer, Dan Wang, and Michael Dietze, 2010. Biofuel Ecophysiological Traits and Yields Database Version 1.0. Energy Biosciences Institute, Urbana, IL." (Is this site even active? I wasn't able to sign up).
• The TERRA-REF site has no citation information at all but just says "The TERRA Reference phenotyping data will be public no later than November 2018. At that point, data will be available within two days of collection. Until then, data access may be granted by request, but with embargo terms described in our data release policy".

Are you simply providing for some future state in which different BETYdb instances will eventually have different citation information? Otherwise, if all BETYdb instances should (and when corrected will) refer to the GCB paper, then this paragraph of the documentation isn't needed and should be omitted.

[dlebauer]

• The purdue site is inactive to my knowledge and likely is on a very old version.

Are you simply providing for some future state in which different BETYdb instances will eventually have different citation information?

Yes, first, this is a messy problem. The GCBB paper should really reference the contents of BETYdb.org. But almost all of the data is synced to BU, Brookhaven, Wisconsin, and UA so it is reasonable for these sites to use the same citation. TERRA REF is an exception - the data is independent of the pecan network and once we get a doi for the public data I will put that in the footer.

But the larger answer is that my expectation is that each site would create their own configuration files and not use defaults.yml. I think that we could encourage this by using dummy placeholder values everywhere - including the name, text, citation, icons and pictures - that are equivalent to the (000) 000-0000 phone number - that make it clear these values need to be filled in, and to gently encourage maintainers to do this.

[gsrohde]

@dlebauer I'm not sure why this PR is still saying Changes requested. Can it be merged?

[dlebauer]

That is odd. Would be nice if @github provided a link to the outstanding changes, but it looks like everything has been addressed.

[dlebauer]

I guess it was waiting on me to review and approve all of the changes. I'll merge