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Missing affiliation data #4

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jure opened this Issue Sep 29, 2014 · 11 comments

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@jure

jure commented Sep 29, 2014

Not sure if this is an actual issue, i.e., is this data available somewhere and is not exposed the API, or does CrossRef not collect it at all?

E.g. affiliations on a PLOS paper (http://api.plos.org/search?wt=json&start=0&rows=10&fl=id,title_display,subject,counter_total_month,affiliate,author_display,abstract,journal,article_type,publication_date&fq=!article_type_facet:%22Issue%20Image%22%20AND%20doc_type:full&sort=counter_total_month%20desc&api_key=7Jne3TIPu6DqFCK&q=title:%22hello%22):

"affiliate": [
"School of Psychology, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom",
"Department of Psychology, Princeton University, Princeton, New Jersey, United States of America",
"Voice Neurocognition Laboratory, Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom",
"Département de Psychologie, Université de Montréal, Montréal, Quebec, Canada",
"Institut des Neurosciences de La Timone, Université Aix-Marseille, Marseille, France",
"Northwestern University, United States of America"
]

And CrossRef doesn't have it: http://api.crossref.org/works/10.1371/journal.pone.0090779

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ckoscher Sep 29, 2014

CrossRef's deposit schema allows for the inclusion of author
affiliation. However, PLOS is not sending that data into us.

Chuck

On 9/29/14 6:06 AM, Jure Triglav wrote:

Not sure if this is an actual issue, i.e., is this data available somewhere and is not exposed the API, or does CrossRef not collect it at all?

E.g. affiliations on a PLOS paper (http://api.plos.org/search?wt=json&start=0&rows=10&fl=id,title_display,subject,counter_total_month,affiliate,author_display,abstract,journal,article_type,publication_date&fq=!article_type_facet:%22Issue%20Image%22%20AND%20doc_type:full&sort=counter_total_month%20desc&api_key=7Jne3TIPu6DqFCK&q=title:%22hello%22):

"affiliate": [
"School of Psychology, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom",
"Department of Psychology, Princeton University, Princeton, New Jersey, United States of America",
"Voice Neurocognition Laboratory, Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom",
"Département de Psychologie, Université de Montréal, Montréal, Quebec, Canada",
"Institut des Neurosciences de La Timone, Université Aix-Marseille, Marseille, France",
"Northwestern University, United States of America"
]

And CrossRef doesn't have it: http://api.crossref.org/works/10.1371/journal.pone.0090779


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#4

ckoscher commented Sep 29, 2014

CrossRef's deposit schema allows for the inclusion of author
affiliation. However, PLOS is not sending that data into us.

Chuck

On 9/29/14 6:06 AM, Jure Triglav wrote:

Not sure if this is an actual issue, i.e., is this data available somewhere and is not exposed the API, or does CrossRef not collect it at all?

E.g. affiliations on a PLOS paper (http://api.plos.org/search?wt=json&start=0&rows=10&fl=id,title_display,subject,counter_total_month,affiliate,author_display,abstract,journal,article_type,publication_date&fq=!article_type_facet:%22Issue%20Image%22%20AND%20doc_type:full&sort=counter_total_month%20desc&api_key=7Jne3TIPu6DqFCK&q=title:%22hello%22):

"affiliate": [
"School of Psychology, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom",
"Department of Psychology, Princeton University, Princeton, New Jersey, United States of America",
"Voice Neurocognition Laboratory, Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom",
"Département de Psychologie, Université de Montréal, Montréal, Quebec, Canada",
"Institut des Neurosciences de La Timone, Université Aix-Marseille, Marseille, France",
"Northwestern University, United States of America"
]

And CrossRef doesn't have it: http://api.crossref.org/works/10.1371/journal.pone.0090779


Reply to this email directly or view it on GitHub:
#4

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kjw Sep 29, 2014

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Right, as Chuck says, contributor affiliation is something CrossRef accepts in metadata deposits, but it is optional and in practice not many publishers include them. Because of that I haven't included them in the REST API - but I can certainly put them in.

I'll leave this open to track inclusion of affiliation in the REST API responses.

Beyond that, we're into ideas about how to encourage publishers to deposit data with CrossRef. This goes from - do they understand that metadata they deposit to CrossRef is used within the wider scholarly communication community, to do they have readers and authors telling them this is something they want, to do they have the ability to change their systems easily to deposit CrossRef metadata in full, regardless if they want to or not?

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kjw commented Sep 29, 2014

Right, as Chuck says, contributor affiliation is something CrossRef accepts in metadata deposits, but it is optional and in practice not many publishers include them. Because of that I haven't included them in the REST API - but I can certainly put them in.

I'll leave this open to track inclusion of affiliation in the REST API responses.

Beyond that, we're into ideas about how to encourage publishers to deposit data with CrossRef. This goes from - do they understand that metadata they deposit to CrossRef is used within the wider scholarly communication community, to do they have readers and authors telling them this is something they want, to do they have the ability to change their systems easily to deposit CrossRef metadata in full, regardless if they want to or not?

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jure Sep 29, 2014

Thanks for the explanation, @ckoscher and @kjw, that makes things quite clear. Just as an observation, working with a small publisher, we send CrossRef NLM XMLs using the web deposit feature and while the XMLs include affiliation information, CrossRef's submission processor is discarding that information, i.e. you get:

<contributors>
<person_name sequence="first" contributor_role="author">
<given_name>Matej</given_name>
<surname>Štuhec</surname>
</person_name>
</contributors>

from something like:

        <contrib contrib-type="author">
          <name>
            <surname>Štuhec</surname>
            <given-names>Matej</given-names>
          </name>
          <xref ref-type="aff" rid="aff1">1</xref>
          <xref ref-type="corresp" rid="cor1">*</xref>
        </contrib>
        <aff id="aff1">
          <label>1</label><addr-line><named-content content-type="department">Department of Clinical Pharmacy</named-content></addr-line>, <institution>Ormož Hospital</institution>, <addr-line><named-content content-type="city">Ormož</named-content></addr-line>, <country>Slovenia</country>
        </aff>

I don't know what the volume of submissions through this endpoint is, but it seems like something that could be improved. Any idea what the percentage of documents with non-nil affiliations is?

In any case, I would love it if you included this information in the API, even though it's rarely available. We can make good use of it, when it is.

jure commented Sep 29, 2014

Thanks for the explanation, @ckoscher and @kjw, that makes things quite clear. Just as an observation, working with a small publisher, we send CrossRef NLM XMLs using the web deposit feature and while the XMLs include affiliation information, CrossRef's submission processor is discarding that information, i.e. you get:

<contributors>
<person_name sequence="first" contributor_role="author">
<given_name>Matej</given_name>
<surname>Štuhec</surname>
</person_name>
</contributors>

from something like:

        <contrib contrib-type="author">
          <name>
            <surname>Štuhec</surname>
            <given-names>Matej</given-names>
          </name>
          <xref ref-type="aff" rid="aff1">1</xref>
          <xref ref-type="corresp" rid="cor1">*</xref>
        </contrib>
        <aff id="aff1">
          <label>1</label><addr-line><named-content content-type="department">Department of Clinical Pharmacy</named-content></addr-line>, <institution>Ormož Hospital</institution>, <addr-line><named-content content-type="city">Ormož</named-content></addr-line>, <country>Slovenia</country>
        </aff>

I don't know what the volume of submissions through this endpoint is, but it seems like something that could be improved. Any idea what the percentage of documents with non-nil affiliations is?

In any case, I would love it if you included this information in the API, even though it's rarely available. We can make good use of it, when it is.

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kjw Sep 29, 2014

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Thanks for the feedback, @jure. So I take it you are using (by way of the web deposit forms) CrossRef's XSLT for JATS to CrossRef deposit XML transformation. @ckoscher - can we get Patricia to look at including translation of affiliation data in that XSLT?

In fact, I wonder if we can include the XSLT in its own github repository to allow people external to CrossRef to contribute changes to it. I know that we are missing translation of some other important information, such as funding and full-text links.

Contributor

kjw commented Sep 29, 2014

Thanks for the feedback, @jure. So I take it you are using (by way of the web deposit forms) CrossRef's XSLT for JATS to CrossRef deposit XML transformation. @ckoscher - can we get Patricia to look at including translation of affiliation data in that XSLT?

In fact, I wonder if we can include the XSLT in its own github repository to allow people external to CrossRef to contribute changes to it. I know that we are missing translation of some other important information, such as funding and full-text links.

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kjw Sep 30, 2014

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@jure I've put up our XSLT for NLM / JATS to CrossRef at http://github.com/CrossRef/jats-crossref-xslt. Not sure I have found the latest version but hopefully will get it up to date today.

Feel free to raise issues or even contribute additional translation.

Contributor

kjw commented Sep 30, 2014

@jure I've put up our XSLT for NLM / JATS to CrossRef at http://github.com/CrossRef/jats-crossref-xslt. Not sure I have found the latest version but hopefully will get it up to date today.

Feel free to raise issues or even contribute additional translation.

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mfenner Oct 8, 2014

@kjw thanks for looking into this, and for starting the new repo with the XSLT. My two cents regarding affiliation:

  • support affilation unique identifiers similar to what you do with FundRef and ORCID. Ringgold/ISNI is the emerging standard, although publishers are just starting to use them (but ORCID has for a year).
  • encourage publishers to deposit via JATS and polish this workflow as discussed above. This saves work for publishers also depositing to PubMed, but is increasingly used as the journal article standard XML outside of the life sciences.

mfenner commented Oct 8, 2014

@kjw thanks for looking into this, and for starting the new repo with the XSLT. My two cents regarding affiliation:

  • support affilation unique identifiers similar to what you do with FundRef and ORCID. Ringgold/ISNI is the emerging standard, although publishers are just starting to use them (but ORCID has for a year).
  • encourage publishers to deposit via JATS and polish this workflow as discussed above. This saves work for publishers also depositing to PubMed, but is increasingly used as the journal article standard XML outside of the life sciences.
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kjw Oct 14, 2014

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Agreed on both points, @mfenner. Ideally I would like affiliation, and in fact any other place an identifier is required, to accept any URN. We should be able to link a contributor to a Ringgold resolvable URI (they need to create them if they don't have them), a resolvable FundRef funder DOI, so on.

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kjw commented Oct 14, 2014

Agreed on both points, @mfenner. Ideally I would like affiliation, and in fact any other place an identifier is required, to accept any URN. We should be able to link a contributor to a Ringgold resolvable URI (they need to create them if they don't have them), a resolvable FundRef funder DOI, so on.

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kjw May 26, 2015

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Contributor affiliations now available. This data is being indexed at the moment. It will be available for DOIs registered from now, but only fully available for all DOIs (where we have the data) in a week or two once re-indexing is complete.

I agree with the plans for affiliation organisational IDs but I'm going to treat this issue as the need for existing affiliation info in the REST API.

Contributor

kjw commented May 26, 2015

Contributor affiliations now available. This data is being indexed at the moment. It will be available for DOIs registered from now, but only fully available for all DOIs (where we have the data) in a week or two once re-indexing is complete.

I agree with the plans for affiliation organisational IDs but I'm going to treat this issue as the need for existing affiliation info in the REST API.

@kjw kjw closed this May 26, 2015

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jure May 26, 2015

Fantastic! 👍
On tor., 26. maj 2015 at 21.10 Karl Jonathan Ward notifications@github.com
wrote:

Closed #4 #4.


Reply to this email directly or view it on GitHub
#4 (comment).

jure commented May 26, 2015

Fantastic! 👍
On tor., 26. maj 2015 at 21.10 Karl Jonathan Ward notifications@github.com
wrote:

Closed #4 #4.


Reply to this email directly or view it on GitHub
#4 (comment).

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mfenner May 26, 2015

Excellent!

mfenner commented May 26, 2015

Excellent!

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zjiang4 Feb 22, 2018

cr_journals(issn = c('1538-4640'),works=TRUE,facet="orcid:*")
When I execute this line, it only gives me 10 orcids...why that discrepancy happens?

zjiang4 commented Feb 22, 2018

cr_journals(issn = c('1538-4640'),works=TRUE,facet="orcid:*")
When I execute this line, it only gives me 10 orcids...why that discrepancy happens?

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