Ability to add more than one publication for Phylogenetic Justification desired.

[Ksepka]

Currently, only one can be added. We have been specifying the first by publication date. It would be preferable to have an "add another phylogenetic publication" paper since often there are more than one relevant citations.

[jimallman]

@Ksepka, I've added support for multiple phylogeny publications for each linked fossil of a calibration. (Note that these don't currently appear anywhere on the site, other than the calibration editor. I assume they'll be exposed in the API that @dleehr is building.)

I've also upgraded the Manage Publications page to protect against deleting any publication that is linked to one or more calibrations, whether as its main publication, a linked fossil's "fossil publication", or one of its phylogeny publications. There's now a detailed display of all linked calibrations for each publication.

[Ksepka]

Looks like the feature is in place, but I don't see the phylogenetic publication(s) displayed anywhere on the results pages.

Note the interace in editing looks good, but I have not tried to modify any calibrations since we are (I assume) still in a no new data entry interval. If that is lifted, let me know and I will start updating.

[jimallman]

Looks like the feature is in place, but I don't see the phylogenetic publication(s) displayed anywhere on the results pages.

Yes, I mentioned this above. To date, we've never shown the phylogenetic publication in the clalibration display page. Lots of little questions here:

1. Should these appear under the phylogenetic justification heading? Before or after the justification text?
2. Do they need more explanation, or is it enough just to list them? Show the compact reference, or the full reference text?
3. Does the order matter? (I believe these will appear in the order shown in the edit page, but this might not be guaranteed.)

Note the interace in editing looks good, but I have not tried to modify any calibrations since we are (I assume) still in a no new data entry interval. If that is lifted, let me know and I will start updating.

We're still in a hands-off period, but that only applies to data you want to keep. I have dumped (saved) the database as of midnight last night, so you can't do much damage. As always, you can experiment with my [test calibration] to see how the data-entry UI behaves, and we can use this to test the display choices outlined above. @dleehr will let us know when the new server is ready for testing and for working with "real" (production) data.

[Ksepka]

OK - getting back to this one here are my thoughts:

1. The citations should appear with their own heading "Phylogenetic References" under the Phylogenetic Justification headings.
2. Just listing is fine. They should show the full reference.
3. Order should be the same as ordered by the data enterer.

[jimallman]

@Ksepka , this brings us back to the multiple-fossils scenario as discussed at length in #40. There we decided to show only the justification for the fossil marked as "primary" (or the only fossil, if there's just one).

If we want to show all phylo-publications, I propose we feature the primary publication at the head of the list, with a special marker [Primary fossil] or [See justification above] or similar. (Suggestions welcome.)

Should I also include the justification text (if any) for other supporting fossils, possibly hidden behind a link to be expanded on demand?

[jparham]

As it happens a single calibration, even those based on a single fossil, may require more than one phylogenetic reference. I think it would be best just to keep it simple and not worry about designating "primary publications" and instead just list them as Dan suggested. The explanation for how these references are will be in the papers themselves.

[jimallman]

@jparham , the notion of a primary fossil is already in the code. Its purpose is to determine which justification text (which is per-fossil) appears under phylogenetic justification heading on a calibration's display page. This appears in the UI if more than one fossil is added for a calibration:

As described in the help text above, only this "primary" fossil appears in the calibration display page, while all related fossils (and their justifications) would appear in API results for this calibration. It sounds like we're reconsidering this..?

If we want to show multiple related fossils, and/or the phylogenetic publication for each (please clarify), don't we need to match the phylo justification text (in a separate section) with its fossil?

[jparham]

There is a disconnect here. I am not supporting the listing of multiple fossils, just multiple references. I tried to explain that a primary fossil may require more than one citation for phylogenetic justification. In this case there is no "primary publication" just a publication OR list of publications (if necessary) associated with each fossil.

[jimallman]

Thanks for clarification! I had forgotten that we only show a single (only or "primary") fossil on the calibration display page. This renders my concerns above moot! With this understanding, @Ksepka's directions above should be straightforward to implement. Apologies for the multi-fossil derail!

[jimallman]

This is working now on the old dev server:

Note that if a DOI is found for any reference, the link will appear.

@dleehr: Looping you into this conversation. Once this issue is closed, please pull the latest master to fossilcalibrations.org.

[dleehr]

thanks for the heads up, will do!

[jimallman]

@dleehr, I'm adding the API label to this issue, since I assume these publications would be included in the API response for a calibration.

[Ksepka]

Just wanted to check in on this one - are we going to "turn on" the Phylogenetic Reference(s) feature on the real site? I assume it is already in place based on the way things look on the old development site.

[dleehr]

I updated the fossilcalibrations.org site with the latest master code today, so this is now enabled