PKP Support

by **luis.pugnaloni** » Fri Mar 12, 2010 5:35 am

We started our journal last year (2009), and from the beginning we deposit DOIs in CrossRef using the XML files generated by the OJS Export plugin. However, we have realized now that the Simple Text Query at CrossRef is unable to locate our successfully deposited items.

I far as I can see, the Export pluging do not generate <pages> <first_page> <last_page> <other_pages>. It does generate <item_number>, where the pages are inserted. I presume this is why CrossRef cannot find our DOIs.

Any hint as to whether this is indeed a bug? Any possible prompt solution? If this is a bug, all deposited items in CrossRef which XML files where created with OJS will need to be corrected. This has a $2.0 cost per item for the journal. Are there others affected?

Kind regards,
Luis

by **jmacgreg** » Tue Mar 16, 2010 4:55 pm

Hi Luis,

I asked our developers about this issue. They said that the Crossref plugin was up to date when we developed it, and this is the first issue that we've heard about it. Would you be able to provide us with a link to your journal and a sample crossref XML file or two to take a look at? You can email me directly at jmacgreg at gmail dot com if you don't want to make the information public.

Cheers,
James

by **luis.pugnaloni** » Tue Mar 16, 2010 8:51 pm

Dear James,

Thanks for your reply. I copy here two XML files generated for two articles in our journal www.papersinphysics.org

The first corresponds to volume 1 (2009) and was generated with the OJS 2.2.3 that had implemented CrossRef Schema 3.0.3 (stable release)
The second corresponds to volume 2 (2010) and was generated with the OJS 2.2.4 that had implemented CrossRef Schema 4.0.3 (stable release)

<?xml version="1.0" encoding="UTF-8"?>
<doi_batch xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.crossref.org/schema/3.0.3" version="3.0.3" xsi:schemaLocation="http://www.crossref.org/schema/3.0.3 http://www.crossref.org/schema/3.0.3/crossref3.0.3.xsd"><head><doi_batch_id>PIP_1252687117</doi_batch_id><timestamp>1252687117</timestamp><depositor><name>Luis A. Pugnaloni</name><email_address>editorialoffice@papersinphysics.org</email_address></depositor><registrant>Papers in Physics</registrant></head><body><journal><journal_metadata><full_title>Papers in Physics</full_title><abbrev_title>Pap. Phys.</abbrev_title><issn media_type="electronic">1852-4249</issn></journal_metadata><journal_issue><publication_date media_type="online"><month>09</month><day>10</day><year>2009</year></publication_date><journal_volume><volume>1</volume></journal_volume><issue>0</issue></journal_issue><journal_article publication_type="full_text"><titles><title>A note on the consensus time of mean-field majority-rule dynamics</title></titles><contributors><person_name contributor_role="author" sequence="first"><given_name>Damián H.</given_name><surname>Zanette</surname></person_name></contributors><publication_date media_type="online"><month>09</month><day>10</day><year>2009</year></publication_date>
<publisher_item><item_number>010002</item_number></publisher_item><doi_data><doi>10.4279/pip.010002</doi>
<resource>http://www.papersinphysics.org/index.php/papersinphysics/article/view/8</resource></doi_data></journal_article></journal></body>
</doi_batch>

<?xml version="1.0" encoding="UTF-8"?>
<doi_batch xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.crossref.org/schema/4.3.0" version="4.3.0" xsi:schemaLocation="http://www.crossref.org/schema/4.3.0 http://www.crossref.org/schema/4.3.0/crossref4.3.0.xsd"><head><doi_batch_id>PIP_1268757498</doi_batch_id><timestamp>1268757498</timestamp><depositor><name>Luis A. Pugnaloni</name><email_address>editorialoffice@papersinphysics.org</email_address></depositor><registrant>Papers in Physics</registrant></head><body><journal><journal_metadata><full_title>Papers in Physics</full_title><abbrev_title>Pap. Phys.</abbrev_title><issn media_type="electronic">1852-4249</issn></journal_metadata><journal_issue><publication_date media_type="online"><month>02</month><day>18</day><year>2010</year></publication_date><journal_volume><volume>2</volume></journal_volume><issue>0</issue></journal_issue><journal_article publication_type="full_text"><titles><title>Multilayer approximation for a confined fluid in a slit pore</title></titles><contributors><person_name contributor_role="author" sequence="first"><given_name>G. J.</given_name><surname>Zarragoicoechea</surname></person_name><person_name contributor_role="author" sequence="additional"><given_name>A. G.</given_name><surname>Meyra</surname></person_name><person_name contributor_role="author" sequence="additional"><given_name>V. A.</given_name><surname>Kuz</surname></person_name></contributors><publication_date media_type="online"><month>03</month><day>16</day><year>2010</year></publication_date>
<publisher_item><item_number>020002</item_number></publisher_item><doi_data><doi>10.4279/pip.020002</doi>
<resource>http://www.papersinphysics.org/index.php/papersinphysics/article/view/23</resource></doi_data></journal_article></journal></body>
</doi_batch>

The tags <publisher_item><item_number>020002</item_number></publisher_item> do enclose the page number we have assigned to this second article, for example. However, I had a look at the CrossRef schema and I guess that something like <pages> <first_page> <last_page> <other_pages> should appear in the XML file rather than <publisher_item><item_number>.

I feel this might be a serious bug as many articles published under OJS may be not linked by other journals if they cannot find the corresponding DOI directly by querying CrossRef.

Regards,
Luis

by **jmacgreg** » Mon Mar 22, 2010 11:28 am

Hi Luis,

I took a look at the 4.3.0 schema, and I can't see any significant change that would make the <pages> elements useful or necessary to be listed. If I'm missing the significance here, please explain more fully if possible. I'm wondering if perhaps there's a processing time before items appear? If you could also post the queries you are using with the Simple Text Query interface, I'd appreciate it.

FYI, the move from 3.0.3 to 4.3.0 is detailed in the following report: http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=4803. I'll also ask Alec to take a quick look at this thread.

Cheers,
James

by **asmecher** » Mon Mar 22, 2010 12:50 pm

Hi Luis,

Regarding the change in CrossRef versions, I read through their published changelogs between the two versions and didn't see anything relevant to OJS. The version number has been incremented to indicate the new level of support, but the generated extracts themselves are otherwise the same.

Regards,
Alec Smecher
Public Knowledge Project Team

by **luis.pugnaloni** » Tue Mar 23, 2010 10:24 am

Hi Alec and James,

I do not think there is a problem since change from 3.0.3 to 4.3.0 CrossRef schema. I feel there is something wrong already in the XML generated by OJS for the 3.0.3 schema.

If I go to the Simple text query http://www.crossref.org/SimpleTextQuery/
and I put this info for one of our items deposited in September 2009

S. A. Sartarelli, L. Szybisz, Correlation between asymmetric profiles in slits and standard prewetting lines, Pap. Phys. 1, 010001 (2009)

I do not obtain the corresponding DOI, which is http://dx.doi.org/10.4279/PIP.010001

I have tried some other ways of writing the reference in the Simple text query but was unsuccessful.

The XML corresponding to this item, which I have deposited in September 2009 (generated by OJS under schema 3.0.3) is the following

<?xml version="1.0" encoding="UTF-8"?>
<doi_batch xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.crossref.org/schema/3.0.3" version="3.0.3" xsi:schemaLocation="http://www.crossref.org/schema/3.0.3 http://www.crossref.org/schema/3.0.3/crossref3.0.3.xsd"><head><doi_batch_id>PIP_1252663219</doi_batch_id><timestamp>1252663219</timestamp><depositor><name>Luis A. Pugnaloni</name><email_address>editorialoffice@papersinphysics.org</email_address></depositor><registrant>Papers in Physics</registrant></head><body><journal><journal_metadata><full_title>Papers in Physics</full_title><abbrev_title>Pap. Phys.</abbrev_title><issn media_type="electronic">1852-4249</issn></journal_metadata><journal_issue><publication_date media_type="online"><month>09</month><day>10</day><year>2009</year></publication_date><journal_volume><volume>1</volume></journal_volume><issue>0</issue></journal_issue><journal_article publication_type="full_text"><titles><title>Correlation between asymmetric profiles in slits and standard prewetting lines</title></titles><contributors><person_name contributor_role="author" sequence="additional"><given_name>Salvador A.</given_name><surname>Sartarelli</surname></person_name><person_name contributor_role="author" sequence="first"><given_name>Leszek</given_name><surname>Szybisz</surname></person_name></contributors><publication_date media_type="online"><month>09</month><day>10</day><year>2009</year></publication_date><publisher_item><item_number>010001</item_number></publisher_item><doi_data><doi>10.4279/pip.010001</doi><resource>http://www.papersinphysics.org/index.php/papersinphysics/article/view/7</resource></doi_data></journal_article></journal></body></doi_batch>

I had a look at one other journal that use OJS and deposits DOIs in CrossRef. I did not manage to get the corresponding DOI for an item I saw in their page. However, non-OJS journals do not present this problem. I think many, if not all OJS journals depositing DOIs may be missing crosslinking from other journals in CrossRef because of this. Each time they query the system the DOI does not come back and the item misses a link.

BTW, in OJS, each time one accesses an Abstract page for an article, the page title includes the journal name, journal volume, and year. But not page numbers for that article are included. This prevent the reader from an easy way of knowing the full reference.

More IT knowledgeable chaps will use the reading tools and so look into the "how to cite" section. Unfortunately, the full correct reference is not created at least for the BibTex format where the article pages are not included.

I might be missing something in how to setup OJS to do all this right and so the article page numbers do not appear in all places one should expect them to appear (i.e. XML for CrossRef, page title in the abstract of articles, and "how to cite" reading tools). However, when I look fellow OJS journals the same seems to happens to all of them.

I am truly worried about this issue. Please, do consider this with some priority.

Kind regards,
Luis

by **jmacgreg** » Tue Mar 30, 2010 11:11 pm

Hi Luis,

I tried using the Schematron-based metadata quality check from http://crossref.org/02publishers/parser.html on your 4.3.0 XML file, and it came up with no errors. Both files also validate. From what I can tell from the Crossref help documentation, so long as the XML file includes the <item_number> information, you should be ok -- that said, I've submitted the missing page number issue as a bug here; please feel free to CC yourself for future updates. In the meantime, I've also emailed the Crossref support folks about this, and will write an update when I hear back.

Cheers,
James

by **jmacgreg** » Wed Mar 31, 2010 10:56 am

Hi Luis,

I've heard back from the Crossref support folks. They found an issue in the last XML file you posted that results in it not being seen as expected using the Simple Text Query -- you've written the query to look for Sartarelli as the first author, but you have given Szybisz the "first" value in the XML deposit file. Switching the author order around in the Query and searching for "L. Szybisz, S. A. Sartarelli, Correlation between asymmetric profiles in slits and standard prewetting lines, Pap. Phys. 1, 010001 (2009)" will return the correct result. Apparently, their system gives a lot of weight to author order in returning results, especially for first authors; first pages (when available) also improve the the query match.

They say that the metadata associated for this DOI should be updated; and furthermore that there isn't a cost associated with updating metadata associated with a DOI, just for the original deposit. You may want to try manually changing your deposit XML to include the relevant first page information rather than the item_number information and reupload; and of course, keep an eye on the bug report I linked to previously for further updates.

I'll also note that if you think that the plugin is somehow incorrectly attributing a "first" designation to the incorrect author, please let us know. If I compare to your articles online though, it looks like your other examples do get the "first" designation correct.

Cheers,
James

by **luis.pugnaloni** » Mon Apr 05, 2010 11:17 am

Dear James,

Many thanks for this. I can see the problem with author order. However, I don't quite understand why the OJS has put the wrong order in some items.

Some items in Pap. Phys. do still present problems, even though the the XML has the right author order. This is the list of items not recognized by the simple text query.

Damián H. Zanette, A note on the consensus time of mean-field majority-rule dynamics, Pap. Phys. 1, 010002 (2009)

Damián H. Zanette, Answer to the Commentary on "A note on the consensus time of mean-field majority-rule dynamics", Pap. Phys. 1, 010004 (2009)

Alejandro David Mariotti, Elena Brandaleze, Gustavo C. Buscaglia, Parametric study of the interface behavior between two immiscible liquids flowing through a porous medium, Pap. Phys. 1, 010007 (2009)

D. Kunik, L. I. Pietrasanta, O. E. Martínez, Surface Percolation and Growth. An alternative scheme for breaking the diffraction limit in optical patterning, Pap. Phys. 1, 010008 (2009)

I'll ask CrossRef about this.

Shall I post a new topic regarding the page number of articles not being displayed in the abstract page? Also teh page number is missing in "How to cite item" in the reading tools.

Cheers,
Luis

by **jmacgreg** » Wed Apr 07, 2010 2:29 pm

Hi Luis,

Thanks for offering to follow up with Crossref -- please, if/when you do, please feel free to CC me: jmacgreg at gmail dot com. I am also happy to investigate when/whether OJS is mis-ordering the authors in the export file, and will get back to you on that.

Regarding the other issues:

1. Page numbers don't appear on the Abstract page. This is expected behaviour, but you can add this functionality easily enough. To add page numbers to your abstract, you can add something like:

Code: Select all: <p>{translate key="article.pageNumbers"} {$article->getPages()|escape}</p>

... to templates/article/article.tpl (that's the template file that controls the abstract and HTML galley display), wherever you think suits, probably under the <div id="authorString">.... block. You'll also want to add the translation key to your locale files -- something like:

Code: Select all: <message key="article.pageNumbers">Page numbers in print version: </message>

in locale/en_US/locale.xml, and any other locale files for the locales you support.

2. Page numbers not appearing in citations. I believe this will be rectified in OJS 2.3.2 (and OCS 2.3.1) -- see http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=5003. Citation support will be receiving a lot more careful attention overall as time goes forward and we implement citation management tools from Lemon8.

Cheers,
James

by **luis.pugnaloni** » Mon Apr 12, 2010 10:27 am

Dear James,

Thanks for the advise on how to put page numbers in the abstract page of the article.

Back to the CrossRef XML, I have found that the Export plugin is setting as the first author the one that the OJS takes as the principal contact for correspondence. This corresponding author not always is the first author. as a consequence, CrossRef do not locate items correctly in the on-line Simple text query.

Any chance that this be corrected soon? In the meantime one can fiddle the XML files.

One other problem I have found is that articles signed by authors whose names carry a tilde (e.g. Spanish names) cannot be found by the CrossRef Simple text query. See this XML I have deposited in CrossRef that should be found by using the reference "D. Kunik, L. I. Pietrasanta, O. E. Martínez, Surface Percolation and Growth. An alternative scheme for breaking the diffraction limit in optical patterning, Pap. Phys. 1, 010008 (2009)"

<?xml version="1.0" encoding="UTF-8"?>
<doi_batch xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.crossref.org/schema/3.0.3" version="3.0.3" xsi:schemaLocation="http://www.crossref.org/schema/3.0.3 http://www.crossref.org/schema/3.0.3/crossref3.0.3.xsd"><head><doi_batch_id>PIP_1263247293</doi_batch_id><timestamp>1263247293</timestamp><depositor><name>Luis A. Pugnaloni</name><email_address>editorialoffice@papersinphysics.org</email_address></depositor><registrant>Papers in Physics</registrant></head><body><journal><journal_metadata><full_title>Papers in Physics</full_title><abbrev_title>Pap. Phys.</abbrev_title><issn media_type="electronic">1852-4249</issn></journal_metadata><journal_issue><publication_date media_type="online"><month>09</month><day>10</day><year>2009</year></publication_date><journal_volume><volume>1</volume></journal_volume><issue>0</issue></journal_issue><journal_article publication_type="full_text"><titles><title>Surface Percolation and Growth. An alternative scheme for breaking the diffraction limit in optical patterning</title></titles><contributors><person_name contributor_role="author" sequence="first"><given_name>D.</given_name><surname>Kunik</surname></person_name><person_name contributor_role="author" sequence="additional"><given_name>L. I.</given_name><surname>Pietrasanta</surname></person_name><person_name contributor_role="author" sequence="additional"><given_name>O. E.</given_name><surname>Martínez</surname></person_name></contributors><publication_date media_type="online"><month>01</month><day>11</day><year>2010</year></publication_date><publisher_item><item_number>010008</item_number></publisher_item><doi_data><doi>10.4279/pip.010008</doi><resource>http://www.papersinphysics.org/index.php/papersinphysics/article/view/21</resource></doi_data></journal_article></journal></body></doi_batch>

BTW, I haven't hear from CrossRef yet. If I insist I'll cc to you.

Many thanks,
Luis

by **jmacgreg** » Thu Apr 15, 2010 10:30 am

Hi Luis,

Back to the CrossRef XML, I have found that the Export plugin is setting as the first author the one that the OJS takes as the principal contact for correspondence. This corresponding author not always is the first author. as a consequence, CrossRef do not locate items correctly in the on-line Simple text query.

Any chance that this be corrected soon? In the meantime one can fiddle the XML files.

That's another good catch. I've posted a bug report for this: http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=5316. Please feel free to CC yourself for future updates.

One other problem I have found is that articles signed by authors whose names carry a tilde (e.g. Spanish names) cannot be found by the CrossRef Simple text query. See this XML I have deposited in CrossRef that should be found by using the reference "D. Kunik, L. I. Pietrasanta, O. E. Martínez, Surface Percolation and Growth. An alternative scheme for breaking the diffraction limit in optical patterning, Pap. Phys. 1, 010008 (2009)"

This sounds like a problem on the Crossref side to me -- their parser should definitely be able to take special characters into account. It might be worth following up with them about this as well, if/when you hear back.

Cheers,
James

PKP Support

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