Set preferred order for metadata lookup when attaching new PDF

[DaveSwofford]

I'm finding that Crossref gives me the best data (author first names, abstracts) when using "Autocomplete Paper...". However, when I drag/drop a PDF icon to the library window and check "Attach to a new reference", the metadata seems to come from Pubmed by default. Is there a way to tell Bookends that if it finds a DOI in the PDF file, it should use Crossref rather than PubMed?

Ideally, the lookup would use a list similar to the one for OpenURL Servers in Preferences>Metadata but allow dragging the entries up or down to indicate the order in which these are queried.

[Jon]

In my experience PubMed provides better metadata than Crossref, and looking for DOIs on PubMed first is intentional. Having said that, Crossref is evolving (for example, it didn't provide abstracts until relatively recently, but PubMed has forever). And PubMed provides information such as full names as well -- the default filter can easily be configured to do that. These are the notes in the PubMed.fltr that explain how this is done:

To import PubMed keywords, enter MH in front of Keywords.

To import the full journal name, put JT instead of TA before Journal.

To import first names instead of initials, use FAU instead of AU before Authors (and FED in front of Ser Editors).

Please let me know if there is other information you'd like imported which Crossref provides but PubMed doesn't.

Jon
Sonny Software

[DaveSwofford]

Thanks! This info is extremely helpful, and I think modifying the PubMed filter is just what I need to solve my issue.

[Jon]

This has caused me to revisit the issue of author first names, and I see now that the FAU tag is available even for very old references (although the value may be the initials in these cases). This wasn't always true. I'll update the default PubMed.fltr in the next release so that it will import full names and not just initials. If you are using a modified filter it won't be affected. And if someone prefers initials, the filter can be edited in the "reverse direction" to fetch only those.

Jon
Sonny Software

[DaveSwofford]

Even though I (almost) never produce a document containing authors with first names, I find that having them helps me keep authors uniquely identifiable within Bookends (especially for common last names).

I have modified my own PubMed filter and it works great! I also want full *journal* names because I find it easier to keep them consistent internally. If you made that change as well, I wouldn't need to keep a separate version of the filter in ~/Library/Application Support/Bookends/Custom Import Filters but I can understand that other users might not want that.

Thanks again. I was having to resort to Google Scholar to get first names, which often worked but left me with poor metadata otherwise.

[Jon]

The reason I didn't default to full journal names in the filter is because PubMed doesn't capitalize them properly, which bothers me, at least. For example:

The Journal of biological chemistry
Lupus science & medicine
Frontiers in immunology

And also because we have a Medline glossary, which substitutes the proper full journal name (if you want) when formatting. So the name in the Journal field is really for personal use, and we are quite familiar with the abbreviated journal names. For publication Bookends will output the correct form for the intended publisher: the full or abbreviated journal name.

Jon
Sonny Software

[DaveSwofford]

Yeah, that case problem bugs me too. Every once in a while I have to clean them up using the Journal term list, which is a pain (but my OCD keeps me from just ignoring them).