In the PMC database from NCBI, I can find about 70 articles by H. S. Burr from 1938-1950. Attached is
a screengrab of the sort of thing I see. But in Pubmed connection in Endnote (X3), I can’t find those papers. What connection do I need to choose in Endnote so that I can see these old Yale Journal of Biology and Medicine
papers from PubMed Central? I’ve downloaded the latest list of connection files and I don’t see anything there for PubMed Central. Anyone know?
Thank you,
Mike
It appears the PubMed and PubMed Central are two distinct databases. According to the PubMed Central FAQ: “PubMed Central (PMC) is an electronic archive of full-text journal articles, offering free access to its contents. PMC contains nearly 2 million articles, most of which have a corresponding entry in PubMed.” So it seems in order to conduct a comprehensive search, one will have to check both PubMed Central and PubMed.
There doesn’t appear to be any EndNote connection file for PubMed Central nor does PubMed Central allow for direct exporting of search results into EndNote. It’s possible, however, to create a filter (with some manipulation of the search results text file) for EndNote that will capture basic information (e.g., author, title, journal title, date, volume, issue, start page, and PMCID number - see image taken of the resulting text file).
If you wish to submit requests for a connection file or filter go to:
http://www.endnote.com/support/enconnreq.asp (to request a connection file)
http://www.endnote.com/support/enfilterreq.asp (to request an import filter)
> It’s possible, however, to create a filter (with some manipulation of the search results text file) for EndNote that
> will capture basic information (e.g., author, title, journal title, date, volume, issue, start page, and PMCID number
is there any information out there on how to create such a filter? I saw the attachment you posted but I’m not sure how to create the filter. Any help would be greatly appreciated.
thanks,
Mike
Although EndNote’s “Help” feature has information about filters and until a training video is available on the subject, the manual is probably the most informative resource. You might check for upcoming live EndNote webinars as they also are a good source of information: http://www.endnote.com/training/
Creating a filter is one issue but, as mentioned in a prior posting, examination of a sample PubMedCentral search result (saved as a .txt file) suggests some modification is needed - insertion of “tags” for the title and author name fields to help the filter identify and import the information into EndNote correctly.
**Refer to Image1 for steps 1-2:
The PubMedCentral text file shows potential problems for importing the title and author name into the EndNote library (i.e., title does not have a unique and consistent tag; author name has no preceding tag.)
To circumvent this problem and enable importing, tags for the title (TI) and author name (AU) may be inserted by creating and running a macro in MS Word. (The macro can be linked to a button on the toolbar for easy access.) Once the tags have been added, re-save the text file.
**Refer to Image 2 for step 3:
Obviously other packages have similar problems with PMC. I found this cludge at the U of Ark on a way to retrieve results one by one for refworks. I a similar workflow would suffice here. Perhaps someone should approach Pubmed Central and ask them to engineer a more direct way to produce a tagged file.
http://libinfo.uark.edu/eresources/refworksfilters.asp?TitleCode=PUBMEDCENTRAL
Oh wait. If there aren’t any pubmed links, then it won’t work, so I went to www.endnote.com and found a filter which I am currently testing and editing the workflow slightly. Watch this space!
I downloaded the Endnote pubmed central filter, but it didn’t work. So I edited the tags that appeared in the data set the Burr HS results file contained. There were numerous fields tags with the wrong spacing. I didn’t change those that didn’t appear in the dataset, because I didn’t know what they should be.
Instructions on downloading from PMC are in the file.
Pubmed-Central-NLM.enf (3.06 KB)
thank you!! This is great - it did properly import the text file I was able to save (attached). One thing though: the original PMC website gives free full-text PDFs for each one (attached is the screengrab). Is there any way to have the “get full text” functionality of Endnote be able to chase these down and automatically attach them to each selected reference (imported using your filter), the way it can do for PubMed?
thanks again!
Mike
Burr refs to import.txt (25.4 KB)
That is a full text retrieval question for the suggestions/tech support people and pubmed central. If they (pubmed central) would incorporate a URL into their medline tagged output, it would make it easier at least for you to get the link, if not the PDF automatically.
Pubmed should really have a few more fields as I look at this. As many of these are book reviews, it seems that these “look” like he wrote the books rather than reviewed the books. Do these appear in other databases, formated more completely?
Pubmed should really have a few more fields as I look at this. As many of these are book reviews, it seems that these “look” like he wrote the books rather than reviewed the books. Do these appear in other database formated more completely?
> As many of these are book reviews, it seems that these “look” like he wrote the books rather than reviewed the books.
> Do these appear in other databases, formated more completely?
some of these are book reviews but others are regular journal articles. I haven’t found them in any other databases.
Thank you for your help!
Mike Levin
Please note that it is against PubMed Central policy to systematically retrieve data.
CrazyGeko is correct, PubMed and PubMed Central are spearate databases. PubMed is a citation database and allows bulk retrieval. PubMed Central is a full-text database and much of the content in the database is copyrighted and the agreements between PubMed Central and the publishers of the content prohibit bulk downloading.
From PMC’s website:
http://www.ncbi.nlm.nih.gov/pmc/about/copyright.html
Restrictions on Systematic Downloading of Articles
Crawlers and other automated processes may NOT be used to systematically retrieve batches of articles from the PMC web site. Bulk downloading of articles from the main PMC web site, in any way, is prohibited because of copyright restrictions.
I’m not trying to scrape large amounts of data - I have a dozen or so specific papers that I want (from the 1930’s!). I think this is well within the purpose of PMC. Indeed, the whole point as I understand is to make content freely available. A condition of NIH funding for example is that some (6?) months after my papers appear in regular scientific journals, I have to submit the full-tect content to PMC to be freely downloadable by anyone.
Your intent is certainly within the purpose, but there’s no way for computers to dinstinguish your actions from those of a group whose intent is to take full text data and use it in another database (it has been tried).
All of the content in PMC is in the database because the publisher has agreed to allow PMC to archive and display it. Even the NIH-funded content that is required to be in PMC is subject to those agreements.
PMC has no choice but to honor those agreements and restrict all automatic retrieval, regardless of the user’s intent.
You can use EndNote’s Find Full Text feature to attempt to get full text articles from PubMed Central. You just need to be sure that the “PubMed LinkOut” option in checked in Preferences.
You can select multiple records but EndNote then uses a semi-automated process to go and get them one at a time. This is not a systematic or bulk downloading process.
Jason Rollins, the EndNote team
@jasonr wrote:
You can use EndNote’s Find Full Text feature to attempt to get full text articles from PubMed Central.
um, what connection file do I use to connect to PubMed Central? Connecting to PubMed regular doesn’t see some papers that are in PMC, so I can’t use the Find Full Text feature. How do I get the actual import to work from PMC?
Mike
There is no EndNote connection file for PubMed Central - only for the main PubMed database. You would need to import the records into EndNote first [PubMed Central does offer export options] and then use the Find Full Text feature.
Although, this might really be a question for the NLM - why are there full text items listed in PubMed Central that are not listed in the main PubMed database. I imagine that others [and not just EndNote customers] might be interested in an answer to this?
Jason Rollins, the EndNote team
PubMed, PubMed Central, and LinkOut are all separate resources, though heavily connected (I know it’s confusing).
PubMed: Citations only, no restriction on automatic retrieval.
LinkOut: Connected to PubMed citations, provided by publisher; may or may not include link to PMC full text, usually includes link to publisher’s full text
PubMed Central: Full-text, no automatic retrieval allowed.
@jasonr wrote:
…why are there full text items listed in PubMed Central that are not listed in the main PubMed database
Because PubMed and PubMed Central are different databases, they have different data. Yes, much of it overlaps, but there are full-text articles in PubMed Central’s archive that PubMed considers “non-indexable” material (http://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.How_do_I_determine_i)..)
PubMed is a citation and abstract service of the NLM. PubMed Central is a digital archive of biomedical and life science journal literature. PMC does not have the same indexing restrictions as PubMed because PMC is an archive, not an citation and abstracting service.
