How to Extract PubMed Articles and Apply Mesh Terms

About Mesh Tagger

• Mesh Tagger is used to return PubMed articles, classify, and return, and apply Mesh Term tags and similar articles. 
• Mesh Tagger calls an API from PubMed. For more information see https://id.nlm.nih.gov/mesh/swagger/ui. 
• MeSH (Medical Subject Headings) is the NLM-controlled vocabulary thesaurus used for indexing articles for PubMed
• To learn more about MeSH, also see https://www.nlm.nih.gov/bsd/disted/meshtutorial/introduction/index.html.
• The API for Mesh information and Similar Documents on PubMed uses: https://meshb.nlm.nih.gov/MeSHonDemand

Install the Mesh Tagger

How to Add the Mesh Tagger Component to a Pipeline

1. To add the Mesh Tagger component to a pipeline in AutoClassifier, see the generic component installation instructions here: How to Add Components to Pipelines.
2. Select "Mesh Tagger" as your component when you are instructed to add your component in the "How to Add a Component" section. 
3. Click Apply.
4. Configure your component as specified below:

Mesh Tagger Pipeline Configuration

• Api Endpoint:
  • Specify the API endpoint.
  • This is public.
• PubMed Article Url Format:
  • A template you can use for the URL.
  • You can also use this format to access the document in PubMed.
• Input Property:
  • The name of the metadata to be used for processing.
  • For example body
• Max Character Length:
  • The maximum number of characters used as text for the API request.
  • For example 5000
  • Note that the Mesh API is slower for larger number of character.
  • It is recommended not to exceed 5000.
  • The maximum value allowed by the API is 10000
• Send raw response as metadata:
  • Output from Python API in JSON format. 

Output Properties

Property	Type	Description
PubMedSimilarArticles	Text – Multi	Includes - from PubMed- multiple: Article IDs URLs Article Titles
PubMedMeshTerms	Text – Multi	Example: 'Human', 'Glucose tolerance test', 'Weight Loss'