Re: [Bibdesk-users] What is your workflow?
On 9 May 2008, at 10:17 AM, James Owen wrote: However, for some reason, BibDesk is no longer putting the contents of the doi: field into the Doi: field in my bibtex archive. It used to, before 1.3.15. is there some problem with case sensitivity? If I added a doi field as well as a Doi field, would that work? It seems to know that it is a DOI, as when I paste in the DOI, a link appears in the sidebar to dx.doi.org/DOI. I am still getting used to BD's new behavior myself, but it sounds like you intend to copy the doi to a doi field, rather than (or in addition to) using it as a linked file. I am not sure it with 1.3.15 when the change occurred, but BD, as you probably know, now handles links and attached files independently of the url and doi fields. Yes, I realise that, but what I hadn't realised was that BibDesk actually deletes the URL and DOI fields if they are present in imported bibtex. In general, the behavior seems to be that if you drop a link or doi onto a record, it will be handled as an attached file, and put into the attached files pane. If you want the doi or url to get into the doi or url field, you have to copy it there yourself. Actually, if the doi is present as a field in the bibtex you are importing, BibDesk will put it in the DOI field for you. I am sure that Christiaan will not know whether to laugh or cry if I haven't got this right, as I have asked many similar questions here as well, which have received excellent answers. Having written a long email explaining the problem, I have found the solution, which as far I as can tell from the archives, has not been given previously. When you run the Convert script, there are options to Keep the legacy fields. Now if you go to Default Fields Preferences in the Preferences, there are buttons to set the global behaviour, which seems to set as Default to Remove the legacy fields. (I guess this is Default as I have never set it.) This definitely has been discussed. In fact this option in the prefs was added as a result of such a discussion, and I've mentioned that I added these options in that discussion. The setting sin the prefs allow you to choose either one of these behaviors: - keep only the fields - keep only the linked files/URLs - keep both I wonder if there should be an option to keep standard fields (required/optional fields) and remove others. I would ask strongly that if it is currently default to remove the legacy fields from the raw bibtex, that this be changed to keep them, for the reasons I gave in my previous email, notably interoperability with other people not using BibDesk, which sadly in my institute is nearly everybody, as there are few Macs. The default behavior is *not* to remove the legacy fields. You can check this by launching BibDesk after removing the preferences at ~/ Library/Preferences/edu.ucsd.cs.mmccrack.bibdesk.plist (I just did). So you must have changed that setting at some point, perhaps without knowing what it was doing. Christiaan The DOI field is very important to me, as I use it in html templates, and also it is a quick thing to drop into Spotlight to find a paper, which quite often it turns out I do. I have about 630 papers in my main database, and I am gradually throwing away all other PDFs. Often I find I have 3-4 duplicates, in different places. So the file linking is as crucial to BibDesk as it is to iTunes. Imagine having to go track down an MP3 file that iTunes said you had somewhere. The import Service, and/or the drag-and-drop import from Websites, the use of an aux file to select items, which can then be exported to make a subsidiary bibtex file, and especially the new URL handling and file linking in the sidebar, are all things that totally amazes people. My old boss took one look at me doing this, and asked how to get the program for his research group, and recently a colleague, who has just inherited a MacBook having come from Linux, put it this way : Oooh, that's very, very, very nice. Nifty. tee hee. You don't even have to drop the PDF onto the window - just select the line in the library window Oh this is going to make things *so* much easier Now I need a Mac desktop for work. Sigh... So BibDesk is definitely selling Macs to people in the science community. ;-) James - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] What is your workflow?
On 6 May 2008, at 20:41, [EMAIL PROTECTED] wrote: Hi There, I am sorry to bother you, but I found myself rather lost when using Bibdesk. I truly love it, and I am physicist/chemist using BibTeX for quite some time, but I am fairly new to mac and to Bibdesk. I would like to ask, if you can somehow search Web of science. Or, if you can't, how you at least import stuff you already found? What is (or should be) the typical workflow? In my case, it's so: I find my papers, using safari/camino browser, download them to a folder, give them some stupid name, which doesn't follow well-thought pattern, then close browser and open them in Preview and copy and paste author,title and other fields to Bibdesk, where I end up filing new local url for corresponding pdf file. It's rather slow and frankly annoying. I bet it can do better. Can you please kick me in the right direction? My workflow is: go to journal e.g. Phys. Rev. B, find article. Download pdf. Meanwhile, at the button marked article options, select view bibtex. (Other journals do this differently, but get yourself to the same state.) This goes to a new browser page with the bibtex entry for the paper. Shade the bibtex. Go to apple menu, top left, scroll down to Services. First entry is BibDesk, across to add to Bibliography. Selected bibtex from webpage is parsed, and added to currently open Bibdesk archive. Drag and drop pdf from downloads folder to sidebar of Bibdesk item window, which has automatically opened on import, which then autofiles the pdf to your preferred pdfs folder. This is then searchable in Spotlight, and a link to the journal webpage is then available, via the URL or the DOI from the bibtex. However, for some reason, BibDesk is no longer putting the contents of the doi: field into the Doi: field in my bibtex archive. It used to, before 1.3.15. is there some problem with case sensitivity? If I added a doi field as well as a Doi field, would that work? It seems to know that it is a DOI, as when I paste in the DOI, a link appears in the sidebar to dx.doi.org/DOI. James - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] What is your workflow?
On 8 May 2008, at 4:44 PM, James Owen wrote: On 6 May 2008, at 20:41, [EMAIL PROTECTED] wrote: Hi There, I am sorry to bother you, but I found myself rather lost when using Bibdesk. I truly love it, and I am physicist/chemist using BibTeX for quite some time, but I am fairly new to mac and to Bibdesk. I would like to ask, if you can somehow search Web of science. Or, if you can't, how you at least import stuff you already found? What is (or should be) the typical workflow? In my case, it's so: I find my papers, using safari/camino browser, download them to a folder, give them some stupid name, which doesn't follow well-thought pattern, then close browser and open them in Preview and copy and paste author,title and other fields to Bibdesk, where I end up filing new local url for corresponding pdf file. It's rather slow and frankly annoying. I bet it can do better. Can you please kick me in the right direction? My workflow is: go to journal e.g. Phys. Rev. B, find article. Download pdf. Meanwhile, at the button marked article options, select view bibtex. (Other journals do this differently, but get yourself to the same state.) This goes to a new browser page with the bibtex entry for the paper. Shade the bibtex. Go to apple menu, top left, scroll down to Services. First entry is BibDesk, across to add to Bibliography. Selected bibtex from webpage is parsed, and added to currently open Bibdesk archive. Drag and drop pdf from downloads folder to sidebar of Bibdesk item window, which has automatically opened on import, which then autofiles the pdf to your preferred pdfs folder. This is then searchable in Spotlight, and a link to the journal webpage is then available, via the URL or the DOI from the bibtex. However, for some reason, BibDesk is no longer putting the contents of the doi: field into the Doi: field in my bibtex archive. It used to, before 1.3.15. is there some problem with case sensitivity? If I added a doi field as well as a Doi field, would that work? It seems to know that it is a DOI, as when I paste in the DOI, a link appears in the sidebar to dx.doi.org/DOI. James That question has been answered several times on this list, including very recently. Christiaan - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] What is your workflow?
On 9 May 2008, at 12:14 AM, Robin wrote: On Tue, May 6, 2008 at 7:41 PM, [EMAIL PROTECTED] wrote: Hi There, I am sorry to bother you, but I found myself rather lost when using Bibdesk. I truly love it, and I am physicist/chemist using BibTeX for quite some time, but I am fairly new to mac and to Bibdesk. I would like to ask, if you can somehow search Web of science. Or, if you can't, how you at least import stuff you already found? What is (or should be) the typical workflow? In my case, it's so: I find my papers, using safari/camino browser, download them to a folder, give them some stupid name, which doesn't follow well-thought pattern, then close browser and open them in Preview and copy and paste author,title and other fields to Bibdesk, where I end up filing new local url for corresponding pdf file. It's rather slow and frankly annoying. I bet it can do better. Can you please kick me in the right direction? Yours, Jirka C. I just thought I'd add, since I haven't seen it mentioned yet, that Google Scholar has an option to display BibTex for results. Go to Scholar Preferences and select Show links to import citations in Bibtex. So my workflow is usually to search the title and or author: field in google scholar (where I often find the paper anyway), click on the appropriate citation, copy it and paste it into Bibdesk (although I will check out the Services menu after the tip in this thread). The entries from Google can be of mixed quality - but it's certainly enough for maintaining your own archive. I've found some inconsistencies in journal abbreviations, author names etc. that need to be cleaned up before publication (ie proof read the typeset bibliography carefully) but overall I find it a major time saver. After downloading I add the file (easy to find whatever name the archive gives it since it's most the most recently downloaded) to the new entry in bibdesk and let it autofile. Most of the papers I read aren't in pubmed and I find login's/proxies for web of science and other university paid for services more inconvenient so I find this the easiest way. Cheers Robin Be aware that support for Google Scholar is already build right into BibDesk. If you search Google Scholar in the web group, importing a match is just a single click away. Christiaan - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] What is your workflow?
In article [EMAIL PROTECTED], [EMAIL PROTECTED] wrote: nbsp;Hi There, I am sorry to bother you, but I found myself rather lost when using Bibdesk. I truly love it, and I am physicist/chemist using BibTeX for quite some time, but I am fairly new to mac and to Bibdesk. I would like to ask, if you can somehow search Web of science. See the Searches menu. You can search Web of Science directly if your IP address is allowed. BibDesk also reads .isi files if you download those manually from Web of Science. -- adam - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
