note that replacing the file-paths should no longer be necessary - see here for more:
www.zotero.org/support/kb/importing_records_from_endnote
If you want to go with your version, though, the filepath shouldn't be in quotation marks.
I.e. you want to have
L1 - file://C:/Users/myname/Documents/EndNote/savanna_UVM.Data/PDF/AgnewADQ_etal_1993_JVegScience_vegswitch-2620602995/AgnewADQ_etal_1993_JVegScience_vegswitch.pdf
Are those actually in the file? Where do they come from?
I tried importing an Endnote library as above and while most of the pdf's successfully imported, roughly 20% did not. I can go ahead and import the pdfs for each entry manually from the endnote directory folder holding the pdfs but this is time consuming. Any idea why some pdfs would not import but most would? Endnote sometimes assigns unusual names to the pdf files with hashes and spaces etc. in the filenames and I'm wondering if this could be the problem?
TY - JOUR
AB - To determine why herbaceous productivity in tropical and subtropical savanas is often significantly higher under crowns of isolated trees than in adjacent grasslands, experimental plots were established in three concentric zones, crown, tree-root, and grassland, surrounding isolated trees of Acacia tortilis in low-rainfall and high-rainfall savannas in Tsavo National Park, Kenya. Plots were fetilized (to determine the importance of nutrient enrichment by trees), sahded (to determine the importance of crown shade), fertilized and shaded (to identify fertilizer x shade interactions), or trench (tree roots entering plots were severed to determine the importance of belowground competition between overstory trees and understory herbaceous plants). In addition, vertical root distributions of trees and herbaceous species were determined, and root systems of A. tortilis saplings were excavated.
At both sites fertilization significantly increased herbaceous productivity in tree-root and grassland zones, but not in canopy zones; artificial shade had no effect on productivity at the low-rainfall site but increased productivity in the tree-root zone at high-rainfall zite; and severing tree roots had no effect on herbaceous productivity at the low-rainfall site, but increased productivity in the crown and tree-root zones at the high-rainfall site. Roots of herbaceous and woody species co-occurred within the same soil horizons, but tree roots extended farther into grasslands at the low-rainfall site than at the high-rainfall site.
These studies suggest that savanna trees competed more intensely with understory plants at wetter sites, where their roots terminated in or near crown zones, than at drier sites, where their roots extended farther into open grassland. Nutrients added by trees to crown zones in the form of tree litter and animal droppings increased understory productivity by fertilizing nutrient-limited soils. Shade contributed more to regrowth after severe defoliation than to growth under more normal conditions.
AU - Belsky, A. Joy
DA - June 1994
KW - Acacia tortilis, fertilization, grassland productivity, root architecture, shade, tree-grass competition, trenching, tropical savannas
L1 - internal-pdf://3071889152eGrassCompe#FD764-1677916928/3071889152eGrassCompe#FD764.pdf
M1 - 4
PY - 1994
SP - 922-932
ST - Influences of Trees on Savanna Productivity: Tests of Shade, Nutrients, and Tree-Grass Competition
T2 - Ecology
TI - Influences of Trees on Savanna Productivity: Tests of Shade, Nutrients, and Tree-Grass Competition
VL - 75
ID - 122
ER -
yes, that's exactly what we need.
Are you sure there is a slash (/) in the filename? That would most certainly break import - specifically, Zotero (and any other program) would treat the part before the slash as a folder.
If there really is a slash that'd be a serious bug in Endnote and I wouldn't know how we could work around that easily.
Yes, that is really a slash but it is also really a pdf within a folder with a really weird name. This is how endnote seems to store pdfs. But the following RIS entry and pdf imported just fine with the same structure, i.e., a pdf within a strangely named folder.
that seems like 39942855681312205.pdf is the filename and 39942855681312205-1761803008 the folder (and along the same lines above). That would be OK.
(You can check that in the PDF folder in Endnote)
If that's the case I don't see an obvious problem. This is on Windows?
Yes, you are correct about the file and pdf. But second RIS file above (filename 39942855681312205.pdf) imported just fine, but the first RIS file and pdf from above (i.e., 3071889152eGrassCompe#FD764.pdf) did not. I was wondering if the '#' in the second pdf name might cause a problem.
the pound sigh (#) certainly looks like the most likely culprit, though I can't see any reason it wouldn't work - I'll take a closer look as soon as I can, but might take a little.
Thank you for your response. I didn't see where the patch was posted when following the link above. Could you point out where it is in more detail? Thanks.
you probably don't want to patch Zotero yourself. Either wait two weeks until 4.0 comes out, wait a couple of days until the beta comes out, or install a branch xpi
http://www.zotero.org/support/dev_builds#zotero_40_branch which should be reasonably stable at the moment.
I am importing EndNote X6 library using RefMan RIS style. My problem is that only one PDF file is imported for each library entry when there are multiple attachments (it is not uncommon to have multiple supplements). This is not a series problem because I can use Word to open the RIS text file and do a global search- and-replace to add “L1 - “ before each “internal-pdf:” (without the quotation marks). I was just wondering if this is the only (or better) way to cope with, or I have been missing something.
The other thing is that once I have imported the library from EndNote with multiple attachments, every one of them would be marked as “Full Text (PDF)”, while they are actually in various formats (text, doc, xls, etc). Is there any way that I can edit the tag “Full Text (PDF)” to something more meaningful such as “Supplement 1”, or to the actual file name, which usually contains some hint about the sequence of supplement, like “1471-2229-9-137-s4.doc”?
adamsmith, thanks for your swift reply. Here is one typical record as you requested.
TY - JOUR
AB - Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions can be asked. .... The random sequencing-based approach to identify microsatellites was rapid, cost-effective and identified thousands of useful microsatellite loci in a previously unstudied species.
AD - Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA; Department of Biology & Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA
AU - CASTOE, TODD A.
AU - POOLE, ALEXANDER W.
AU - GU, WANJUN
AU - KONING, A. P. JASON de
AU - DAZA, JUAN M.
AU - SMITH, ERIC N.
AU - POLLOCK, DAVID D.
L1 - internal-pdf://2009 Castoe Mol Eco Resources-1114744832/2009 Castoe Mol Eco Resources.pdf
internal-pdf://sm001-1634838528/sm001.pdf
internal-pdf://sm002-2305927424/sm002.txt
internal-pdf://sm003-2624695040/sm003.xls
M1 - 9999
N1 - 10.1111/j.1755-0998.2009.02750.x
PY - 2009
SN - 1755-0998
ST - Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence
T2 - Molecular Ecology Resources
TI - Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence
UR - http://dx.doi.org/10.1111/j.1755-0998.2009.02750.x
VL - 9999
ID - 3
ER -
Hi, I had exactly the same problem as kaekang.hwu (Mar 24th 2013) regarding the associated file labelling - everything I import is labelled in the middle pane as 'Full Text PDF', whether it's a .doc, .pdf, .xls, and with no regard to the file name - I would love to have this fixed, our company are looking to transfer its whole library to Zotero but I don't think we will until this is fixed, because it really impedes finding things effectively via browsing. Just to let you know am having the same issue!
Useless. EndNote clearly has major difficulties with later versions of Word. So I thought I would try Zotero, but it seems completely ill-equipped to deal with the EndNote user who is trying to move to Zotero. Trying to import my EndNote database is impossible. I get the database but none of the attached pdf files. And when I try to edit the EndNote export file and import it into Zotero I get nothing but "format not supported" errors. So I'm stuck between EndNote's inability to support the latest versions of Word and Zotero's inability to actually handle EndNote databases. Flip this!
It's not the content of the RIS that appears to be the problem, but the format of the file that Zotero can't seem to read if it's been edited. The bottom line is that this is an impossibly complicated process for bringing an EndNote library into Zotero. For now I'll be sticking to an older version of Word that does work with EndNote. I really don't have time to jump through all the hoops that Zotero seems to need to get an EndNote library with pdfs imported.
we don't know what exactly you're doing, but the instructions above work out of the box -including pdfs - when followed. They don't require any editing of files (and if you're using anything but RIS you're not following the instructions). But if you're not interested in troubleshooting this we can't help you, obviously.
Whether it's a problem with the RIS format or Zotero import will only be clear if you post a sample RIS entry.
The only "hoop" Zotero requires you to jump through for importing the RIS file with PDF attachments is placing the RIS file in the correct location. All the other hoops are fixing EndNote's export issues, which will be the same issues for any other software that tries to import EndNote's RIS format.
Upgrade Storage
www.zotero.org/support/kb/importing_records_from_endnote
If you want to go with your version, though, the filepath shouldn't be in quotation marks.
I.e. you want to have
L1 - file://C:/Users/myname/Documents/EndNote/savanna_UVM.Data/PDF/AgnewADQ_etal_1993_JVegScience_vegswitch-2620602995/AgnewADQ_etal_1993_JVegScience_vegswitch.pdf
Are those actually in the file? Where do they come from?
Both ways worked, indeed.
The last version of Zotero doesn't need any change as you say.
This is great!
TY - JOUR
AB - To determine why herbaceous productivity in tropical and subtropical savanas is often significantly higher under crowns of isolated trees than in adjacent grasslands, experimental plots were established in three concentric zones, crown, tree-root, and grassland, surrounding isolated trees of Acacia tortilis in low-rainfall and high-rainfall savannas in Tsavo National Park, Kenya. Plots were fetilized (to determine the importance of nutrient enrichment by trees), sahded (to determine the importance of crown shade), fertilized and shaded (to identify fertilizer x shade interactions), or trench (tree roots entering plots were severed to determine the importance of belowground competition between overstory trees and understory herbaceous plants). In addition, vertical root distributions of trees and herbaceous species were determined, and root systems of A. tortilis saplings were excavated.
At both sites fertilization significantly increased herbaceous productivity in tree-root and grassland zones, but not in canopy zones; artificial shade had no effect on productivity at the low-rainfall site but increased productivity in the tree-root zone at high-rainfall zite; and severing tree roots had no effect on herbaceous productivity at the low-rainfall site, but increased productivity in the crown and tree-root zones at the high-rainfall site. Roots of herbaceous and woody species co-occurred within the same soil horizons, but tree roots extended farther into grasslands at the low-rainfall site than at the high-rainfall site.
These studies suggest that savanna trees competed more intensely with understory plants at wetter sites, where their roots terminated in or near crown zones, than at drier sites, where their roots extended farther into open grassland. Nutrients added by trees to crown zones in the form of tree litter and animal droppings increased understory productivity by fertilizing nutrient-limited soils. Shade contributed more to regrowth after severe defoliation than to growth under more normal conditions.
AU - Belsky, A. Joy
DA - June 1994
KW - Acacia tortilis, fertilization, grassland productivity, root architecture, shade, tree-grass competition, trenching, tropical savannas
L1 - internal-pdf://3071889152eGrassCompe#FD764-1677916928/3071889152eGrassCompe#FD764.pdf
M1 - 4
PY - 1994
SP - 922-932
ST - Influences of Trees on Savanna Productivity: Tests of Shade, Nutrients, and Tree-Grass Competition
T2 - Ecology
TI - Influences of Trees on Savanna Productivity: Tests of Shade, Nutrients, and Tree-Grass Competition
VL - 75
ID - 122
ER -
and the pdf is
3071889152eGrassCompe#FD764-1677916928/3071889152eGrassCompe#FD764.pdf
Is this the information that you needed?
Are you sure there is a slash (/) in the filename? That would most certainly break import - specifically, Zotero (and any other program) would treat the part before the slash as a folder.
If there really is a slash that'd be a serious bug in Endnote and I wouldn't know how we could work around that easily.
TY - JOUR
AU - Belsky, A. Joy
AU - Canham, Charles D.
KW - savanna, forest, gap, patch
L1 - internal-pdf://39942855681312205-1761803008/39942855681312205.pdf
M1 - 2
N1 - 00063568
ArticleType: primary_article / Full publication date: Feb., 1994 / Copyright © 1994 American Institute of Biological Sciences and University of California Press
PY - 1994
SP - 77-84
ST - Forest Gaps and Isolated Savanna Trees
T2 - BioScience
TI - Forest Gaps and Isolated Savanna Trees
UR - http://www.jstor.org/stable/1312205
VL - 44
ID - 2502
ER -
and pdf 39942855681312205-1761803008/39942855681312205.pdf
(You can check that in the PDF folder in Endnote)
If that's the case I don't see an obvious problem. This is on Windows?
This is on a Apple machine.
http://www.zotero.org/support/dev_builds#zotero_40_branch which should be reasonably stable at the moment.
The other thing is that once I have imported the library from EndNote with multiple attachments, every one of them would be marked as “Full Text (PDF)”, while they are actually in various formats (text, doc, xls, etc). Is there any way that I can edit the tag “Full Text (PDF)” to something more meaningful such as “Supplement 1”, or to the actual file name, which usually contains some hint about the sequence of supplement, like “1471-2229-9-137-s4.doc”?
Not sure about the label - obviously having non-PDFs labelled as PDFs isn't good, though.
TY - JOUR
AB - Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions can be asked. .... The random sequencing-based approach to identify microsatellites was rapid, cost-effective and identified thousands of useful microsatellite loci in a previously unstudied species.
AD - Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA; Department of Biology & Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA
AU - CASTOE, TODD A.
AU - POOLE, ALEXANDER W.
AU - GU, WANJUN
AU - KONING, A. P. JASON de
AU - DAZA, JUAN M.
AU - SMITH, ERIC N.
AU - POLLOCK, DAVID D.
L1 - internal-pdf://2009 Castoe Mol Eco Resources-1114744832/2009 Castoe Mol Eco Resources.pdf
internal-pdf://sm001-1634838528/sm001.pdf
internal-pdf://sm002-2305927424/sm002.txt
internal-pdf://sm003-2624695040/sm003.xls
M1 - 9999
N1 - 10.1111/j.1755-0998.2009.02750.x
PY - 2009
SN - 1755-0998
ST - Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence
T2 - Molecular Ecology Resources
TI - Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence
UR - http://dx.doi.org/10.1111/j.1755-0998.2009.02750.x
VL - 9999
ID - 3
ER -
The only "hoop" Zotero requires you to jump through for importing the RIS file with PDF attachments is placing the RIS file in the correct location. All the other hoops are fixing EndNote's export issues, which will be the same issues for any other software that tries to import EndNote's RIS format.