Just discovered today, while looking for the name of the researcher that I had a number of citations in Jabref . . . couldn’t find his name . . . and then tried the name of the paper in which his team all worked and that citation is gone??? Is there a number of citations that suddenly Jabref will remove older citations to be able to add new ones???
This one article is kind of a key item in my research . . . seemingly misplaced?? How would that happen??? Did not have any system crashes on the machine . . . . I probably have the full text in the XML_database that I could check to see if it is still there, but just the line item is gone . . . but there were a number of articles I have from this team of researchers . . . they all seem to now be gone or misplaced?? Wha happen, mon?
Correction . . . I did find the attached paper in the XML database and then by searching that I did find the citation . . . but then it was in the sub-group it was assigned to, and searching the exact name of the article did not retrieve it to less than 3K citations to scroll through . . . .
So possibly this is a “search” problem??? Or a “sub-group” listing problem???
Thanks for the reply . . . took a fast look . . . I’ll have to check out the suggestions more thoroughly later . . . . But, I would have to say, “mea culpa” . . . like we have in the US a lot of so-called “low information voters” . . . I have not gotten under the hood of Jabref very well . . . other than to transfer my data over from Bookends a few years back, once I got it set up . . . I’m mostly using it as a data dump, just keeping my hand in data acquisition with it. But, yesterday I wanted to show a student that citation and looking into the sub-group, which only has 120 citations . . . it wasn’t “there” . . . . So, egg on my face once again.
I’ll check through using your suggestions and see if that improves the situation. I’ll post back on it when I have executed your commands. : - )
You are not supposed to have to go under the hood of JabRef in order to use it ^^
And as I mentioned, there has been somewhat recent changes to search that might be throwing you off.
But, yesterday I wanted to show a student that citation and looking into the sub-group, which only has 120 citations . . . it wasn’t “there” . . . . So, egg on my face once again.
Which group type is the main group and the sub group?
Appreciate the follow up . . . by “under the hood” I just meant getting into the GUI preferences, and/or actually learning about how to do stuff . . . . I didn’t mean rifle into the code or such type behaviors . . .
As far as the sub group type . . . I’m away from my Jabref installed machine until tomorrow evening or so . . . can’t check that out. But the left side panel where “groups” can be added into the database . . . and then right-clicking on the selected group allows the line item citation to be added into the group . . . . That also might be a problem area, as I have had issues with not being able to add citations into the groups, a few times, since I have started playing with JabRef. The solution in the past has been to move up to the latest dev version . . . which I did recently.
A lot of other “stuff” going on in my life, so I couldn’t know if I double checked to make sure each item is in the proper group . . . . I just said “sub-group” to mean a “group” within the 6.8K total citations in the database.
I did just last year write an article using the errant citation, so at that time I was able to search the PMID number and find it, but yesterday or whatever, even searching the PMID was not bringing the citation up as “found” . . . it was all “not found.”
Searching is considerably different in the latest development versions that use Lucene syntax and there is work going on to make the transition less disruptive. The Lucene syntax also affects search-groups, so you may find entries missing from search-groups that previously worked. The groups are converted during upgrade but some groups may need manual adjustment due to some fundamental differences in the search functionality.
All your groups are defined at the bottom of the .bib file, so if you are not sure which groups contain search syntax, you can find them easily in the .bib file, rather than checking one by one in the GUI.
To search for an author using the latest syntax use the form author:Esteelpaz
Also note that until recently JabRef imported PMIDs from XML data (references collected via the browser extension or online searches in JabRef) but did not import PMIDs from PubMed text files. Missing PMIDs baffled me for a long time until I finally realised this and at my request the maintainers promptly changed the importer.
Replying here, in answer to your questions in both of your posts . . . . Seems like maybe this is a “search” problem . . . . I ran “neuroendocrine mechanism of electroacupuncture in the treatment of hypertension” which is the title of the article, and it found “no results” . . . . One of the authors is Dr Longhurst, I ran author=longhurst and that also showed “no results” . . . .
OK . . . after I posted the previous data, I then read your post . . . and running author:longhurst did bring 21 hits, including the one I was looking for . . . .
But, then, question is why does it bring 0 results running almost the exact title??
PS: So, further investigation . . . when I copy/pasted the exact title into the searchbar, without the quotes I get the 3698 hits . . . when I use the quotes front and back then it finds the exact article, 1 hit. So that part is now more clear . . . .
Searching without quotes defaults to a union expression (Boolean “OR”), which is why you are getting so many results. Lucene syntax is a lot like, or possibly the same as, some literature databases that let you search using proximity operators, wildcards, ranges, boosting, Boolean operators and so on. Note that the results are probabilistic and not merely “yes” or “no” matches. See examples here: Apache Lucene - Query Parser Syntax
There do seem to be some things to watch out for regarding searching the beginning/middle/whole field, case-sensitivity, and regular expressions and JabRef (or any app that uses Lucene) may behave a little differently than the Lucene documentation would suggest.
I haven’t entirely demystified these things yet. For example, searching for title:"systematic review" matches everything I would expect, but searching for title:": systematic review" only matches entries that have a space before the colon (succeeds for “Something : a systematic review” and not “Something: a systematic review”) while adding a word before the colon (e.g., title:"something: a systematic review") finds titles that contain “Something: a systematic review”.
Remember too that you can use a portable JabRef installation to use released and development versions at the same time if you need to restore your old workflow for a while.
Thanks for the detailed follow up . . . does seem like a bit more effort will be needed to learn the new updates . . . .
So the quote above is interesting, to use both released and dev at the same time?? Do you mean there is a download of such a dual hybrid, or both are installed and pointed to the various databases . . . and depending on one’s mood, “stable” or “unstable” the choice to boot one or the other would be made??
For the most part now, higher education process is done, just keeping my hand in the research gathering to see if I can get some enthusiasm to write a new article . . . . : - 0
Yes, but in the present scenario your mood would need to include wanting two copies of your library, since the latest release has “breaking changes”, or using different versions of JabRef to work on different libraries. I suggested this mainly as an option to allow uninterrupted work in the old version while experimenting with a copy of your library in the new version. For instance, the replay of your student scenario would have gone “Hmm, that’s weird. Where’s my paper? Let me get out of this experimental dev software and open my regular library … Ah here it is”. No egg on face.
You might want to just keep going with the version you have installed now that you are past the initial surprise of the Lucene search. You have a large library, and the latest JabRef has given me much better performance with respect to searching and navigating my groups. Otherwise, the portable version is good for running JabRef on a USB or a computer where you don’t have admin permission.
When you mentioned the “XML database”, I think you meant the .bib file that is your library. Unlike EndNote, Zotero, and most other reference managers, JabRef (if installed the typical way) stores your data in a plain text file rather than a SQL database. You can access the file directly, as I think you did. You can also do this under normal circumstances such as if you wanted to perform a find-and-replace throughout the library while visually confirming each change, or perhaps overhaul your group naming scheme without the burden of right-clicking and modifying each one.
Thanks for the follow up on it . . . Might be able to check it later today, or in a few days . . . ?? I’ll post back on it when I have a chance to test it out.
Alrighty, upgraded to 6.0 and just put the basic – endocrine – in the searchbar and it pulled 85 citations out of the 5.8K and in there was the “Neuroendocrine mechanisms” article that I had originally been trying to find . . . . So, considering that often times my memory of the exact title disappears after a few weeks, this upgraded search engine got me in the ballpark with a basic search. So far so good. I’ll keep testing it out, see what else pops up in the use of it.
