Send Digests to PubMed

[Melissa37]

Problem / Motivation

• WHO wants this? eLife journal (production)
• WHEN and WHERE do they want it? Send Digests to PubMed so they appear on the site for readers along with normal abstracts
• WHAT do they want?
• WHY do they want this? If we can send them and get more exposure, we might as well do it!

Proposed solution

These are the instructions from PubMed: OtherAbstract (O) ... OtherAbstract can also contain a plain language summary if the Type attribute is 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>

It would be a case of pulling in Digests to the PubMed conversion pipeline

Clarification needed and assumptions

@gnott

---

Tasks

• [x] Check digest content is available from parsed XML for inclusion in the PubMed deposit
• [x] Strip <p> and <p> tags from the digest
• [x] Set the <OtherAbstract> tag if a digest is present
• [x] Strip out <italic> tags, or convert them to <i> tags - will this field at PubMed ever support inline tagging? @Melissa37 Answer: Yes, inline tagging is allowed
• [x] Commit code change
• [x] Merge and deploy into production workflows
• [x] Question for @Melissa37: Do we want to resubmit any previous eLife articles, using the replaces tag these can have their plain-language-summary shown on PubMed? Answer: Not at this time.

Technical notes

• We could use this technology
• More notes or suggestions

User interface / Wireframes

[gnott]

Some initial progress so far: I see this field does not seem to support any tagging like <i> tags, and if so they are shown as <i>...</i> on the PubMed citation file validator result.

Fortunately the elife-aritcle library is currently already placing eLife-style digest content into the article object as the Article.digest property.

I think we can safely assume for now if an article has a digest, we'll assume it is in English (eng) and it is a plain language summary.

Here is how a sample looks as a result on the PubMed citation file validator, with a very no-nonsense label for the summary:

[gnott]

It looks like this field only supports one block of text with no paragraphs, so all the paragraphs from a digest will be joined together to form the plain language summary.

[Melissa37]

Thanks for this @gnott I think it's fine for it to be one block of text, but I am confused about italics - are you sying no italics are allowed in Digests or that you ahve to change the tagging to make them appear as italics in PubMed?

Cheers!

[gnott]

It looks like I was incorrect about the inline tagging support in my first tests. I have a working example now. It turns out the <i> tag was being converted to <i> in the XML output and is why the PubMed validator page was displaying the tags. The plain language summary does allow inline tagging that I can see. I will update the code to produce the best output.

[gnott]

@Melissa37 we have some code that is looking good and is ready to deploy. Perhaps to check next week on call discussion?

[Melissa37]

Sounds good - and I'll add it to the planning team agenda to make sure everyone is in agreement.

Cheers M

Melissa Harrison Head of Production Operations

Tel: +44 1223 855340

http://elifesciences.org

On Fri, Jan 31, 2020 at 5:22 PM Graham Nott notifications@github.com wrote:

@Melissa37 https://github.com/Melissa37 we have some code that is looking good and is ready to deploy. Perhaps to check next week on call discussion?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/elifesciences/elife-pubmed-feed/issues/77?email_source=notifications&email_token=ABOFQJEAHJKF6K7WJYX2GLLRARM5TA5CNFSM4KKD3VQ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKPLUDA#issuecomment-580827660, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABOFQJCREA4RZD2KUQFPEHDRARM5TANCNFSM4KKD3VQQ .

-- eLife Sciences Publications, Ltd is a limited liability non-profit non-stock corporation incorporated in the State of Delaware, USA, with company number 5030732, and is registered in the UK with company number FC030576 and branch number BR015634 at the address Westbrook Centre, Milton Road, Cambridge, CB4 1YG.

[Melissa37]

Only do this going forward and for normal resupplies and approved to deploy whenever ready!

[gnott]

Deploying the code now.

[gnott]

I will close the issue because all is done, but please feel welcome to add comments if something is wrong after reviewing the results.

[gnott]

Here is a first example from today https://pubmed.ncbi.nlm.nih.gov/31939735/

[gnott]

I see there is no space character between paragraphs, I will do a little fix for that.