Upgrade StoragePubmed ID
Is there a way for Zotero to import the Pubmed ID (from NCBI Pubmed) into a separate field. Right now it is located in the "Extras" field.
This is an old discussion that has not been active in a long time. Before commenting here, you should strongly consider starting a new discussion instead. If you think the content of this discussion is still relevant, you can link to it from your new discussion.
On a smaller note, in the "Extras" field, Zotero puts in the text "PMID:". Not a major problem, but this may an issue in some situations.
I'm new to Zotero and I really like it but I find the way PMID are stored very inconvenient. As an 'Extra', it doesn't even export the field in a RIS format. It really needs its own 'accession number' field.
I'd love to add that to the translator but I am new to the system and I'm not sure how to proceed.
Is anyone working on it? Or could anyone one help me get started?
It involves changing more than the translator, doesn't it?
I know the whole thing is open-source but how does one actually contribute?
1. The PMID and PMCID identifiers definitely need to have separate fields, rather than being lumped into the 'Extras" field. If this can be implemented in the way Tjowens suggests, that would be ideal.
In my research field, the vast majority of the references will have a PMID associated with it. My preference is to rename all of my pdf attachments by PMID and to use the PMID for citations while writing a manuscript. Other research fields would prefer a different ID - the ability to select and add more identifiers would be brilliant.
2. It would also be really handy to have these ID fields available in the middle column (ie the middle pane of zotero that lists the articles found within a specific folder, you can customize what columns appear by the button at the top right of the panel). This would allow the articles to be sorted by these ID numbers, as well as quickly identifying articles that are missing ID numbers in the 'My Library' folder.
3. Perhaps in the future it would be possible to search automatically search the various databases (repositories) to pull down the unique IDs? (ie press the PMID search button to search the specific reference for an ID at NCBI or the PMC button to pull down the PMCID). I suppose this would mean expanding the 'repositories' field in the same way as Tjowens is suggesting for the ID field? Because of the relationship between the repositories and ID fields, should these be combined in some way?
Keep up the great work!
For journal articles, would it be worth having a separate tab for ID (along with the tabs for Info, Notes, Attachments, Tags and Related) where the multiple identifiers could be stored?
The Info tab would focus more on information about the journal article (authors, date, citation etc) while the ID tab would display information about the ID links to external repositories, such as PMID, PMC, Ovid, ISI, Arxiv etc.
One difficulty is that if you create an item from one of the publisher websites like ScienceDirect, PMID does not get filled in. So there's currently no way that to get both the full text AND the PMID in one item in an automated fashion. If I understand the foregoing discussion here, someone has proposed a "fetch PMID function" for existing items, which would be useful.
I'd also like to suggest a (slightly OT) feature (I will put it in feature requests thread as well) that the DOI field and whatever becomes of the PMID field are "clickable" from the right pane info tab in the same way that the URL field is.
NCBI has some useful tools for scripting:
1. esearch: get PMID using a general query, returned in XML
example, to translate doi into PMID (doi is stored in an 'AID' field):
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=%2210.1016/j.ccr.2009.02.016%22[AID]
2. efetch: get a complete record using PMID; various report formats available
example:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=19345332&report=medline
3. conversion of PMID to PMCID
http://www.ncbi.nlm.nih.gov/sites/pmctopmid
General info can be found at:
http://www.ncbi.nlm.nih.gov/entrez/query/static/advancedentrez.html
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed
In principal, these can be used to get the PMCID, when it exists, even when the paper originates from a publisher's site and only the doi is known.
Finally, just a reminder that PMCID != PMID.
Thanks to the Zotero team and congrats on the progress so far!
I'd like to see the MR number and arXiv ID on equal footing with the DOI field, and be exported to BibTeX as mrnumber and eprint fields. (I don't use anything other than BibTeX, so I don't know how those fields should be exported to RIS or whatever.) I don't know the best way to do that, in terms of UI or programming, but it's essential for mathematical references. Without it, Zotero is probably of limited use to me.
BTW, here's an example: if you know the article has MR number 2394455, you just append that to the canonical URL (just like you use dx.doi.org) and get http://www.ams.org/mathscinet-getitem?mr=2394455. Many articles have a list of references and also a link to forward references.
source ID/acronym = PMID/MR
source record ID =000000000
If the cross reference field mentioned by Pankaj above is a single instance, then it wouldn't suit - populating PMID, PMC and DOI should be possible.
Similarly Zotero users may find it useful to have the identifier as a clickable link (as in dsquared's examples or expanded wikipedia cite journal templates).
The following is the list from the current Template:Cite_journal
# pmid: The document's PubMed Unique Identifier, such as 15128012
# pmc: The document's PubMed Central article number (PMCID) for full-text free repository of an article, such as 246835
# doi: A digital object identifier for the document, such as 10.1130/0091-7613(1990)018<1153:TAFSIA>2.3.CO;2.
# bibcode: The document's bibcode in the Astrophysics Data System, e.g., 1924MNRAS..84..308E
# id: A unique identifier, used if none of the above are applicable. In this case, you need to specify the kind of identifier you are using, preferably with a template like {{US patent}}, {{MR}} / {{MathSciNet}}, {{Zbl}}, {{arXiv}}, {{JSTOR}} or {{JFM}}. (Use one of the more specialized parameters if possible; they are linked automatically. In other words, don't use id = PMID 15128012 anymore. Use pmid = 15128012.)
Also a number of the BioMed journals provide good citation metadata for their online abstracts or articles. Zotero doesn't seem to be mining this to populate the citation fields.
A number of journals use the citation_ form, with additional Dublin Core dc. elements
and Nature adds prism elements, but standardization is limited. arXiv doesn't provide more than the title as metadata and PLoS XHTML is different again.
#meta_field_name value
citation_volume 7
dc.title SOMAP: a novel interactive approach to multiple protein sequences alignment
citation_authors Parry-Smith, D.J.; Attwood, T.K.
citation_id 7/2/233
citation_issue 2
citation_date 04/01/1991
citation_firstpage 233
citation_title SOMAP: a novel interactive approach to multiple protein sequences alignment
citation_mjid bioinfo;7/2/233
citation_journal_title Bioinformatics
dc.contributor Parry-Smith, D.J.
dc.contributor Attwood, T.K.
dc.identifier 10.1093/bioinformatics/7.2.233
citation_publisher Oxford Univ Press
citation_doi 10.1093/bioinformatics/7.2.233
citation_abstract_html_url http://bioinformatics.oxfordjournals.org/cgi/content/abstract/7/2/233
citation_issn 1367-4803
citation_issn 1460-2059
citation_pdf_url http://bioinformatics.oxfordjournals.org/cgi/reprint/7/2/233.pdf
dc.date 04/01/1991
robots NOARCHIVE
Hacky perl for dumping this available on request
Agree that a solution to this is needed. It looks like there need to be simultaneous commitments in two projects to get things moving: BIBO and Zotero, with CSL following suit afterward with processor support. There has been a suggestion, at least, of an extensible namespace for identifiers in BIBO. Would be great to hear whether team Zotero is willing to take a look at this post-2.0. It certainly is an important item.
When importing directly from a PMID, Zotero stores the PMID [MEDLINE:pmid] in the Extra field [ZOTERO:Extra]. This wouldn't be as big an issue if ZOTERO:Extra were included in the default RIS export from Zotero, but it's not.
Please include PMID in a ZOTERO:AccessionNumber or ZOTERO:PMID field and map it to RIS:AN as ########[pmid]
We could speculate on the progression of standards and where it fits best for another 2 years, or do something that *just works* for the majority of users now without them having to write custom translators. The current state is broken.
I don't think there's great enthusiasm to hack the RIS translator/export. The problem with RIS is that it's a bad standard, if you want a better solution find one that involves a decent standard (MODS or Bibliontology RDF, e.g.). At this point my position (which is in no way Zotero's official position) is that it's not Zotero's problem that crappy proprietary citation managers don't support modern bibliographic standards (or in the case of Endnote any standard).
Also, I will point out that, for life sciences, there are 2 identifiers that are needed:
- PMID (PubMed ID)
- PMCID (PubMed Central ID)
The PMCID should be imported from a PMCID record, of course, but it should also be imported automatically from any Pubmed record that has an associated entry in PubMed Central (and thus a PMCID).
Finally, PMCID needs to be available for inclusion in bilbliographic styles, to satisfy NIH reporting requirements.
Thanks to all.
there is broad agreement on this, it's just a question of having the field changes implemented in Zotero, on that see the thread pinned at the top of the forum.
edit: and yes, CSL has both PMID and PMCID variables now.
You'll have to manually go to the pubmed entry and look up the PMCID and add it as PMCID: PMC123456
to the extra field. Zotero does extract that information and it is used in the National Library of Medicine Grant style.
PMID: 12345 PMCID: PMC12345
When using the Library of Medicine Grant style, I got output that looked like this:
PMID: 12345
I am not good at XML, but I looked at the macro "pmcid" and changed the line:
<text variable="PMCID" prefix=" PMCID: "/>
to read:
<text variable="note"/>
which then gave me:
PMID: 12345 PMCID: PMC12345 PMID: 12345
so I deleted the line:
<text variable="PMID" prefix=" PMID: "/>
and got:
PMID: 12345 PMCID: PMC12345
Having the PMID in there too doesn't hurt, so I think I'm happy. I'm sure, however, that this is quite clumsy, but now it works for my situation. Do you have a suggestion for a better fix?
Also, I noticed that for articles that were internet citations, I was missing a space between the Availabe from and the PMID entry, thus:
Available from: http://www.ncbi.nlm.nih.gov/pubmed/12345PMID: 12345 PMCID: PMC12345
[Sorry, but the comment editor interprets the above line as an actual link. It is not. Same caution applies below.]
I changed the macro call near the end of the file from:
<text macro="access"/>
to
<text macro="access" suffix=" "/>
and I got:
Available from: http://www.ncbi.nlm.nih.gov/pubmed/12345 PMID: 12345 PMCID: PMC12345
Again, I hope that this is helpful, but I am clumsy with XML.