PubMed XML Export Error

  • Application Version - e.g., OJS 3.1.2.4.

I am exporting xml using the PubMed plugin, as I need to legally deposit information regarding our publication with The British Library. All has exported well, with the exception of four outputs (one article, three poster records). In my limited xml understanding, it looks as though there is an issue with the export of the abstract information/details, as instead of it showing in the xml, it shows at text at the top of the error (shown in the screenshots). The third poster has some information in the abstract section of the xml, but it is spaced out and doesn’t look right.

Would someone be able to guide me with how I can overcome this error, please, so that I can export xml of these final four outputs?

Many thanks.

!

Hi @michellemayer,

Are you able to share your XML output (the same content that’s in these screenshots) as text, rather than images? That way I can run it through an XML validator to help pinpoint the issue.

-Roger
PKP staff

Hello Roger,

Many thanks for replying to my message and for looking into my export problem. I hope the following is what you need for the validator.

My best wishes,
Michelle

Article XML

<?xml version="1.0"?> European Association for the Teaching of Academic Writing (EATAW) Journal of Academic Writing 2225-8973 10 1 2020 12 18 Towards Nuanced Understandings of the Identities of EAL Doctoral Student Writers 75 86 10.18552/joaw.v10i1.598 eng Shem Macdonald School of Education, La Trobe University, Melbourne. s.macdonald@latrobe.edu.au Britta Schneider Monash University, Faculty of Medicine, Nursing and Health Sciences, Student Academic Support Unit. britta.schneider@monash.edu 2019 09 26 2020 12 01

Poster 1 XML

<?xml version="1.0"?> European Association for the Teaching of Academic Writing (EATAW) Journal of Academic Writing 2225-8973 10 1 2020 12 18 Supporting Academic Writing and Publication Practice: PhD Students in Engineering and their Supervisors 221 221 10.18552/joaw.v10i1.614 eng Alena Kasparkova VSB-TUO. alena.kasparkova@vsb.cz Kamila Etchegoyen Rosolová . etchegoyen@langdpt.cas.cz 2019 09 30 2020 11 02

Poster 2 XML

<?xml version="1.0"?> European Association for the Teaching of Academic Writing (EATAW) Journal of Academic Writing 2225-8973 10 1 2020 12 18 Evaluating Academic Literacies Course Types 222 222 10.18552/joaw.v10i1.624 eng Caroline Anne Dyche University of the West Indies Mona campus. caroline.dyche@uwimona.edu.jm Jessie Antwi-Cooper University of the West Indies, Mona campus. jessie.antwi@gmail.com 2019 10 01 2020 11 13

Poster 3 XML

<?xml version="1.0"?> European Association for the Teaching of Academic Writing (EATAW) Journal of Academic Writing 2225-8973 10 1 2020 12 18 Collaborating between Writing and STEM: Teaching Disciplinary Genres, Researching Disciplinary Interventions, and Engaging Science Audiences 223 223 10.18552/joaw.v10i1.581 eng Rachel C Riedner George Washington University. rach@gwu.edu Bill Briscoe George Washington University. briscoe@gwu.edu Alexander Van der Horst George Washington University. ajvanderhorst@gwu.edu Carol Hayes George Washington University. hayesc@gwu.edu Gary White George Washington University. gwhite@gwu.edu 2019 08 17 2020 10 28 Collaborating between Writing and STEM: Teaching Disciplinary Genres, Researching Disciplinary Interventions, and Engaging Science Audiences

This poster describes a multi-pronged effort to build a writing curriculum in Physics and other STEM fields at the George Washington University, USA. These efforts include curricular collaboration, a research study conducted by the Physicists and Writing Scholars, and external funding initiatives.

This project first began as a curricular collaboration through our Writing in the Disciplines (WID) curriculum, initiated by observations among Physics faculty that undergraduate students lack Physics specific writing skills. Writing faculty responded to this observation by introducing Physics faculty to the idea that writing can and must be taught, that the genres of Physics can be taught by Physics faculty, and that a focus on the writing process can improve student writing. Our curricular goal was to demonstrate to faculty who are unfamiliar with writing studies that writing is a means to learn in Physics (Anderson et al., 2017).

The first phase of our effort was to persuade Physics faculty that writing contributes to learning in Physics; we describe a collaboration between Physics and Writing faculty that developed assignments and made curricular interventions. This collaboration built upon scholarship in writing studies that argues genre instruction develops capacities and skills for student writing (Swales, 1990; Winsor, 1996). While genre is not a new concept in Writing Studies, for many Physics faculty the idea that they can teach – and have students learn – how to write in disciplinary genres is novel. Collaboration around curricular revisions enabled Writing and Physics faculty to teach students that learning how to write in a new genre is a skill that can be practiced (Ericsson, 2006; Kellogg & Whiteford, 2009). We developed a process for students to follow when faced with types of writing common to Physics, but potentially new to them, such as the abstract (written), lab research notebook (written), article summary (oral), letter to colleague (written), cover letter and resumé (written), elevator pitch (oral), proposal (written and oral), presentation on issues of ethics and equity in STEM (oral), research presentation (oral), poster (written), poster presentation (oral), final research report (written), and Symposium presentation (oral). The collaboration thus created pedagogical exchange between faculty as well as scholarly synergy between the disciplines of Physics and Writing Studies.

Physics faculty have observed that the curricular collaboration has had measurable results for students. Physics student participation in the campus research day has increased dramatically. We attribute this rise partly to the increased, explicit attention in classroom settings to how to engage with Physics genres of writing, especially abstracts and research posters.

While the collaboration successfully brought together a small but solid group of Writing and Physics faculty, it also raised questions about how to persuade a broader range of Physics faculty, and other science faculty, that teaching disciplinary genres can improve student writing, and that writing is a means of learning. Given that faculty in STEM disciplines find empirical research persuasive, our next step was to undertake a collaborative research project to measure the impact of the teaching of writing in Physics. The new curricular focus on genre asked students to conceptualize themselves as scientific writers in relation to specific Physics or STEM audiences. The collaborative research therefore investigates if teaching Physics genres improves writing and enables students to conceptualize themselves as emerging scientists engaged in professional communication (Poe et al., 2010;

Oh, my reply with the XML doesn’t look like the layout in which I inputted it.
Please say if I need to share the XML another way.

My best wishes,
Michelle

Hi @michellemayer,

Yes - I would need the full output of the XML (like what you shared in your initial screenshots). You could also try running the XML file through a validator like Best Online XML Validator Tool and letting me know what errors you see.

-Roger

Good morning Roger,

I’m not sure how I can share the XML in a non-picture format (I have them in .txt and .pdf on my device), so I have used the validator that you shared. The article and two of the posters have returned ‘valid XML’ notifications. However, the third poster XML gave this error.

Error : InvalidChar
Line : 71
Message : char ‘&’ is not expected.

I have been looking at the section where the abstract information should be, and I can only see in the XML. Shouldn’t I be seeing and somewhere in the coding?

Many thanks.
Michelle

My apologies; what I typed isn’t fully showing. My last sentence should say:

Michelle

Hi @michellemayer,

That’s fine re: sharing the text - now that I can see this error, that gives me a better sense of what the issue might be, and I think it may be tied to this other issue: Pubmed XML plugin not escaping special characters correctly in OJS3 - which would mean that you may wish to try updating the OJS PubMed export plugin that contains the bug fix for this issue, and then re-try your export. Also in this post they point out a validator specifically for PubMed, which you may wish to try as well (I wasn’t aware of this).

For the abstract piece - do your posters have formal abstracts in their metadata like the articles do? It looked like they didn’t from the screenshots you shared in the earlier post. It should be fine to have an empty <Abstract/> tag - it just serves as a placeholder for articles that don’t have abstracts in the article metadata (e.g. editorials).

-Roger

Hello again Roger,

Many thanks for your reply and the link to the other issue. We are due an upgrade to the platform, and I have requested the version upgrade with our university’s IT Services. Will a version upgrade overcome the bug fix, or will the plugin need its own upgrade? If a separate upgrade is required, I will need my contact in IT Services to do this on my behalf, as my admin rights will not be sufficient.

I see that there is an ampersand in the abstracts of the article, first and third posters; so is this possibly the issue? How interesting! If I were to remove these ampersands, this may let me overcome the problem whilst I wait for the version upgrade?
Issue

Looking at the posters, each of the records includes an abstract in the metadata, a .PDF of the poster plus an additional .PDF file containing the abstract document. Here is a link to the third poster: Collaborating between Writing and STEM: Teaching Disciplinary Genres, Researching Disciplinary Interventions, and Engaging Science Audiences | Journal of Academic Writing

Many thanks again for looking into my query.

Best wishes,
Michelle

Hi @michellemayer,

I believe that this particular issue is caused by the Pubmed export plugin - not the OJS core code, so updating just the plugin should hopefully address the issue. But you may want to consider updating OJS as well in order to take advantage of new features. You could try re-testing the export without the ampersands to be sure that it is in fact the issue.

-Roger
PKP staff

Hi Roger,

Many thanks again for your support. I raised a support call with my institution’s IT Services for the update of the plugin, and they have returned with this query:

“Regarding the update of PubMed XML Export Plugin, we need to be sure that the plugin used for the upgrade is compatible with Coventry University’s current OJS version - 3.1.2.4
Please can you get any pointers from the OJS technical team on how get the Pubmed xml plugin (i.e. compatible with OJS version 3.1.2.4 ) . If we can get the plugin, we will test it out on staging platform before going live with it.”

I’ve been looking through other threads on the forum, and some mention a plugin gallery. Is this something that a colleague with higher admin access than I will see or is the plugin gallery located in the PKP Community support?

Many thanks.
Michelle

Hi @michellemayer,

Your plugin gallery is located within your OJS installation (in OJS 3.1 is located under website settings: Chapter 6: Website Settings

However, there is a way to check plugin compatibility within OJS (and other PKP applications) is to check the current, web-based version of the plugin gallery: plugin-gallery/plugins.xml at main · pkp/plugin-gallery · GitHub (this is the version that gets updated on a regular basis and that you can refer your IT team to). If one searches in that file (using Ctrl+F), for the plugin that you are using you see a section that reads like this:

<compatibility application="ojs2"> <version>3.3.0.0</version> <version>3.3.0.1</version> <version>3.3.0.2</version> <version>3.3.0.3</version> </compatibility>

The <version> indicates which version of OJS that the plugin has been tested with, and should work with. So, in this case, this plugin has been tested with several different versions.

That said, for your particular case, the Pubmed plugin is a bit different. It lives in the Tools section of later versions of OJS and not the plugin gallery.
There are a number of plugins that are included in OJS by default, and those aren’t generally in the gallery (unless there’s a need to update them between OJS releases). So, what might be a good option for you, in this case, is to update your version of OJS, and as a part of that, the Pubmed plugin would be upgraded.

-Roger
PKP team