PUBMed Translator

hurschler

I call up a long list of entries (179 Entries). Click on the Zotero buttun:

- selecting one item works
- selecting multiple items works
- using the "Select All" button selects all in the list (e.g. 20) but the translator fails (An error occurred while saving this item. See Troubleshooting Translator Issues for more information)
- the "Deselect All" button does not work, items are not deselected

I often use large lists to generate collections, in the past it worked fine. Can anyone reproduce this?

Thanks,

Chris

adamsmith

Could you give us the exact search terms to try to replicate. I'm not aware of any problems with Pubmed. And is this using Zotero 4 or 5?

hurschler

Windows 7 (SP1)
Zotero 5.0.11
Firefox 55.0.1 64-bit
Zotero-Connector 5.0.17

PubMed Search: „radiostereometry“ (550 results)
Works for saving the maximum of 200 entries, “Deselect All” button does not work

PubMed Search: “hurschler” (176 results)
Does not work as described in my original post

I guess it just doesn’t like me ;-(

adamsmith

The import error is a problem with this entry: https://www.ncbi.nlm.nih.gov/pubmed/27752724
for some reason the pubmed XML data doesn't contain an article title, which makes the whole thing fail.

Looking at the XML a bit more this looks like it's on purpose. There is a field called "Vernacular Title" that does contain the title and we could fall back on that. @DWL-SDCA you deal with pubmed a lot. What's a good way to import the vernacular title? Just as is when there is no article title? Mark it somehow, e.g. with square brackets like library catalogs do?

adamsmith

(I'll check and see if I can replicate the deselect issue later when I'm on Zotero 5)

adamsmith

@adomasven I can replicate "Deselect All" not working at all on multiple sites on Firefox 55/Zotero Connector 5.0.17 on Windows 10.

DWL-SDCA

Vernacular title: The short answer is, not yet. This became a problem 6 to 8 weeks ago with several nonEnglish PubMed journals. The English language title and/or abstract is either omitted or is included but placed within the wrong tags. If I could find a pattern to the errors we could either change our parser to allow for it or I could work with the NLM tech folks to make changes on their end. This is almost certainly an issue from the content of the metadata files as submitted by the journal publishers. A problem with one article record from a journal issue seems to mean there will be a problem with all of its articles but not necessarily articles from other issues of the journal. I've noticed that this problem has become increasingly common with articles originally in Cyrillic or Chinese characters.

I'm actively perusing this problem but I've been making only slow, if any, progress. The SafetyLit PubMed XML parser captures all language versions. With the problem records the English and nonEnglish titles and abstracts are not brought into the appropriate fields. Sometimes, the PubMed record omits English language titles (but includes an English abstract). Edit: I haven't tried this with Juris-m. Are the Juris-m translators different from the Zotero translators?

On another issue, 6 weeks ago a different problem arose. Until recently a new record would be assigned an EDAT and the date wouldn't change. Now it seems that the EDAT Is assigned simultaneously with the CRDT. EDAT=date the record published to the database (aka Entrez). CRDT=date the record was created (and before the final automatic edits have been processed). Now, the EDAT can change. This means that my automatic daily searches that were based upon the EDAT suddenly began identifying records that were first included in a previous day's search -- 1/2 to 2/3 of the new day's results were duplicates of the previous day's search results. So, the effort on their part to "have records available to searchers as quickly as possible" means that I had to change my search to be based on the CRDT. (Records assigned a CRDT were not yet available to searchers and only available after the EDAT assigned. Now, for the first few days, the EDAT doesn't have the original meaning.)

As these tag-label problems appeared at about the same time, I suspect that they both may be related to some other change in policy concerning the PubMed system.

DWL-SDCA

Notice the ArticleTitle close tag at about line 25. There is no opening tag. Sometimes there will be ArticleTitle opening and closing tags with no title contained.

For example, a French language article:

<PubmedArticle>
<MedlineCitation Status="Publisher" Owner="NLM">
<PMID Version="1">28805501</PMID>
<DateCreated>
<Year>2017</Year>
<Month>08</Month>
<Day>14</Day>
</DateCreated>
<DateRevised>
<Year>2017</Year>
<Month>08</Month>
<Day>14</Day>
</DateRevised>
<Article PubModel="Print-Electronic">
<Journal>
<ISSN IssnType="Electronic">1757-9767</ISSN>
<JournalIssue CitedMedium="Internet">
<PubDate>
<Year>2017</Year>
<Month>Aug</Month>
<Day>01</Day>
</PubDate>
</JournalIssue>
<Title>Global health promotion</Title>
<ISOAbbreviation>Glob Health Promot</ISOAbbreviation>
</Journal>
<ArticleTitle/>
<Pagination>
<MedlinePgn>1757975917701689</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1177/1757975917701689</ELocationID>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Le Vigouroux</LastName>
<ForeName>Alain</ForeName>
<Initials>A</Initials>
<AffiliationInfo>
<Affiliation>1. Agence régionale de santé Nouvelle Aquitaine, Délégation départementale de la Charente-Maritime, La Rochelle, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Marcheix</LastName>
<ForeName>Cécile</ForeName>
<Initials>C</Initials>
<AffiliationInfo>
<Affiliation>2. Agence régionale de santé Nouvelle Aquitaine, Délégation départementale de la Vienne, Poitiers, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Autès</LastName>
<ForeName>Erwan</ForeName>
<Initials>E</Initials>
<AffiliationInfo>
<Affiliation>3. Agence régionale de santé Nouvelle Aquitaine, Direction de la santé publique, Bordeaux, France. Ecole normale supérieure de Lyon, laboratoire IHRIM (doctorant), Lyon, France.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>fre</Language>
<PublicationTypeList>
<PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<VernacularTitle>Gouvernance des politiques publiques favorables à la santé : l’expérience menée en Poitou-Charentes, France.</VernacularTitle>
<ArticleDate DateType="Electronic">
<Year>2017</Year>
<Month>08</Month>
<Day>01</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>England</Country>
<MedlineTA>Glob Health Promot</MedlineTA>
<NlmUniqueID>101497462</NlmUniqueID>
<ISSNLinking>1757-9759</ISSNLinking>
</MedlineJournalInfo>
<KeywordList Owner="NOTNLM">
<Keyword MajorTopicYN="N">Agence régionale de santé</Keyword>
<Keyword MajorTopicYN="N">changement organisationnel</Keyword>
<Keyword MajorTopicYN="N">efficacité</Keyword>
<Keyword MajorTopicYN="N">gouvernance</Keyword>
<Keyword MajorTopicYN="N">partenariat</Keyword>
<Keyword MajorTopicYN="N">politique</Keyword>
<Keyword MajorTopicYN="N">priorisation</Keyword>
<Keyword MajorTopicYN="N">promotion de la santé</Keyword>
<Keyword MajorTopicYN="N">prévention</Keyword>
<Keyword MajorTopicYN="N">santé publique</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="entrez">
<Year>2017</Year>
<Month>8</Month>
<Day>15</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed">
<Year>2017</Year>
<Month>8</Month>
<Day>15</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2017</Year>
<Month>8</Month>
<Day>15</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>aheadofprint</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">28805501</ArticleId>
<ArticleId IdType="doi">10.1177/1757975917701689</ArticleId>
</ArticleIdList>
</PubmedData>
</PubmedArticle>



adomasven

Deselect All issue fixed in 5.0.18 version of the Connector