User:Dirac/Altmetric

Goal:

• First: make a link between all the Wikidata elements with a DOI and their corresponding altmetric ID.
• Secondary: use Wikidata element with altmetric, but no DOI, to retrieve the DOI and enter in WD

Element in Wikidata with

• DOI: 26,694,908
• altmetric ID: 12759 (52 with no DOI)

Next steps

• Send email to altmetric to inform them of the request
• Dump of ~26M element ID from Linked Data Fragment, with their corresponding DOI (is it possible?)
• Filter for those that fits the right format for DOI
• Find what the result is when there is no entry for the corresponding DOI in altmetrics
• How to find DOI when we already have altmetric using their API

Altmetric ID

Answer received by Altmetric:

[...] there is a bit of a problem in that the Altmetric IDs are not designed to be persistent IDs. With that in mind, it would be fairly inefficient for you and for our API if you kept those IDs up to date all the time.

I would suggest instead building the URL in the following way:
www.altmetric.com/details/doi/ [doi] - just replace [doi] with the relevant article DOI. It will lead to a details page as long as we have a record for that item. If we do not have a record for the item, it will simply lead to a page stating that we have not received any attention for the item yet. This will be a much easier and more reliable way to link to the Altmetric details page.

Considerations posted on Altmetric ID property discussion page.

Pseudo code

• For every DOI:
  • Check if the corresponding WD element already have an altmetric ID
  • If not, fetch the JSON
  • If the altmetric exits, add it in a column
• Output: CSV with [Q, DOI, altmetric]

Requests / Lists

All DOI

• LDF request for elements with a DOI (>26 millions)

Element with Altmetric ID

# Element with altmetric defined
SELECT ?item ?itemLabel  ?altMetric ?DOI WHERE {
  ?item wdt:P5530 ?altMetric .
  
  # Display DOI if any
  OPTIONAL { ?item wdt:P356 ?DOI. }

  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

Try it!

Scientific papers with Altmetric ID but no DOI

# Scientific paper with altmetric
SELECT ?item ?itemLabel  ?altMetric WHERE {
  # Scientific paper
  ?item wdt:P31 wd:Q13442814.
  ?item wdt:P5530 ?altMetric .
  
  # That doesn't have a a DOI
  FILTER NOT EXISTS { ?item wdt:P356 ?DOI } 

  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

Try it!

Article CC-BY with a DOI but no Altmetrics

# Scientific paper with DOI and CC-BY license
SELECT ?item ?itemLabel ?DOI ?altMetric WHERE {
  # Scientific paper
  ?item wdt:P31 wd:Q13442814.
  # CC-BY
  ?item wdt:P275 wd:Q20007257 .
  
  # with DOI
  ?item wdt:P356 ?DOI .
  
  # That doesn't have an altmetric
  FILTER NOT EXISTS { ?item wdt:P5530 ?altMetric } 

  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

Try it!

Code

Bookmarklet

javascript:((function(){var%20a;a=function(){var%20a,b,c,d,e;b=document,e=b.createElement("script"),a=b.body,d=b.location;try{if(!a)throw%200;c="d1bxh8uas1mnw7.cloudfront.net";if(typeof%20runInject!="function")return%20e.setAttribute("src",""+d.protocol+"//"+c+"/assets/content.js?cb="+Date.now()),e.setAttribute("type","text/javascript"),e.setAttribute("onload","runInject()"),a.appendChild(e)}catch(f){return%20console.log(f),alert("Please%20wait%20until%20the%20page%20has%20loaded.")}},a(),void%200})).call(this);

This bookmarklet is a call to this Javascript:
https://d1bxh8uas1mnw7.cloudfront.net/assets/content.js

Altmetric API

It is possible to get the altmetric ID with the help of a DOI by using their API. This will result in a JSON file.

To get the corresponding altmetric ID for the DOI 10.1098/rstb.2003.1449:

curl -s https://api.altmetric.com/v1/doi/10.1098/rstb.2003.1449 | \
	jq .altmetric_id

Download the data

Generate URLs:

 for i in `seq 1 1000`;do echo  "https://query.wikidata.org/bigdata/ldf?accept=application/rdf+xml&subject=&predicate=http%3A%2F%2Fwww.wikidata.org%2Fprop%2Fstatement%2FP356&object=&page=$i" >> list.txt;done

Download the data and concatenate the result in a text file:

wget -i list.txt -O 1-1000.html -o log/1-1000.txt

Identify URLs with errors:

 grep ERROR fichier.log -B 3 | sed 's/.*https/https/g' | grep https

Extract the element id:

grep "wds\:" 1-1000.html  | grep -v prefix | sed 's/wds\://g' | sed 's/\-.*//g' > Q1-1000.txt

Extract DOI:

grep "\:P356" 1-1000.html |  sed 's/^[^"]*"//g' | sed 's/".*//g' > DOI_1-1000.txt

Check if they have the same number of lines:

wc -l Q1-1000.txt DOI_1-1000.txt

Combine Q element and DOI in one file:

paste Q1-1000.txt DOI_1-1000.txt | column -c 2  > Q_DOI_1-1000.txt

Find the line index of DOI that does not have the proper syntax:

egrep -v -n "10\.[[:digit:]]{4,9}/.+" Q_DOI_1-1000.txt | cut -d : -f 1 > improper-DOI-indices_1-1000.txt

Remove the index of the improper indices:

cp Q_DOI_1-1000.txt Q_DOI-valid_1-1000.txt;for ligne in `tac improper-DOI-indices_1-1000.txt`;do sed -i ${ligne}d Q_DOI-valid_1-1000.txt;done

Get the AltMetric for each valid DOI, if any:

for DOI in `head -n 100 Q_DOI-valid_1-1000.txt | awk '{print $2}'`; do
  if curl --head --silent --fail https://api.altmetric.com/v1/doi/${DOI} 2> /dev/null;
    then
       ALT=`curl -s https://api.altmetric.com/v1/doi/10.1098/rstb.2003.1449 | \
   jq .altmetric_id`
          echo "Altmetric found"
          echo $DOI, $ALT
  else
    echo $DOI "not found!"
  fi
done

See also

Wikidata

Properties:

• DOI (P356)
• Altmetric DOI (P5530)

Example:

• Reference ranges for estradiol, progesterone, luteinizing hormone and follicle-stimulating hormone during the menstrual cycle (Q44275619)
• In Altmetric

External

• Vidéo de Scilabus Plus
• API Altmetric