Add and update metadata in PubMed export based on NLM feedback

[jmacgreg]

A client using OJS 3.1 received the following feedback from NLM support about the content produced by our PubMed plugin. Most of this looks relatively straightforward to include.

• Use the current Document Type Definition:

• Use the journal’s NLM Title Abbreviation in the JournalTitle element.

• Include the PublicationType element and select the most appropriate value from the list here [https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.PublicationType_O].

• Include keywords, following the tagging instructions here [https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.Can_I_submit_author_keywor].

• Include Copyright information [https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.CopyrightInformation_O].

• Include conflict of interest statements [https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.CoiStatement_O].

• Include funding information [https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.Can_I_submit_grant_informa].

• Tag structured abstracts using one of these options [https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.How_should_structured_abst] and remove from the end of each abstract section.

• Information about tagging affiliations, including multiple affiliations per author, is here [https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.Affiliation_O].

[mgscano]

A Client using 3.1 here.
The PubMed team just issued new guidelines to all providers.

0. The updated PubMed Publisher DTD is available here: https://dtd.nlm.nih.gov/ncbi/pubmed/in/PubMed.dtd

1. Please update your XML file submissions to use the new DOCTYPE header:

<!DOCTYPE ArticleSet PUBLIC "-//NLM//DTD PubMed 2.8//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/in/PubMed.dtd">

2. Reference Lists
   We encourage you to supply reference lists in your XML submissions.
   Use the
   <ReferenceList>, <Title>, <Reference>, <Citation>, <PMID> and <ArticleIdList>
   elements to supply references.
   The reference lists will not display in current production PubMed, but they will be available in the PubMed XML and they will display in PubMed Labs (see: https://www.ncbi.nlm.nih.gov/labs/pubmed/23728647). Because the reference lists are not going to display in production PubMed, the current citation validator will not display these lists. An enhancement to PMDM to allow editing of reference lists is underway and we will send an email when this work is complete.
   For sample XML, please see "How do I submit reference lists?" at https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.How_do_I_submit_reference

3. Plain Language Summaries
   The <OtherAbstract> element can now contain an article's plain language summary, when a summary was published in the article version of record. Use the Type attribute "plain-language-summary" to properly identify the plain language summary:
   <OtherAbstract Language="eng" Type="plain-language-summary">In patients with type 2 diabetes, blood sugar levels are higher and vary more than in healthy people. In the past, some drugs that were used to treat diabetes by controlling blood sugar levels increased the risk of certain complications... </OtherAbstract>

Plain language summaries will display in PubMed below the abstract.
Please see "OtherAbstract" at "https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.OtherAbstract_O"

4. Grant Country and Acronym
   We have expanded the grant structure to allow publishers to supply the agency's acronym and country. >Use the <Param> element with the Name attributes "acronym" and "country" as shown below:

<Object Type="grant">
<Param Name="id">12345</Param>
<Param Name="grantor">National Health and Medical Research Council</Param>
<Param Name="acronym">NHMRC</Param>
<Param Name="country">Australia</Param>
</Object>
</ObjectList>

At this time, the new allowed values are only accepted in new XML submissions. We are planning a future enhancement to PMDM to allow editing and updating of these fields.
We will continue to add the country and acronym for the granting agencies listed on this web page: https://www.nlm.nih.gov/bsd/grant_acronym.html
If you are supplying only grant agencies from the list above, you do not have to change your submissions. The new Name values allow you to assign the acronym and country where we do not programmatically add them.
Please see "Can I provide grant information?" at https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.Can_I_submit_grant_informa

5. New Publication Type "Systematic Review"
   You can now supply the publication type "Systematic Review" in your XML file submissions:
   <PublicationType>Systematic Review</PublicationType>
   This publication type may also be applied by NLM during MEDLINE indexing. Please restrict the use of this publication type to those articles that align with the NLM definition of Systematic Review.
   Please see https://www.ncbi.nlm.nih.gov/mesh/2028176.

[pmangahis]

+1 from a hosted client (2 journals) that would be interested in this updated plugin.

[pmangahis]

+1 from a potential hosted client

[pmangahis]

+from 2 additional hosted clients