Case 4: Entity Extraction

[djarecka]

This is the use case from the list in #23

This place will be to discuss ideas around the use case, especially around the 3 main components: ingestion, public view and feedback. Below are notes from our initial discussion on August 27.

Ingestion

• should be public
• we should be able to submit papers and a function (entity extraction) should be run
• perhaps feedback during the ingestion process

Public View

• we can group the entities, e.g., species, methods, datasets, software

Feedback

[tekrajchhetri]

Phase 1 of entity extraction is completed. StructSense has been integrated + user would be able to view the extracted data.

[djarecka]

Thanks @tekrajchhetri ! I've added things to discuss for this use case.

List of things to discuss:

• what is the acceptable time for entity extraction for:
  • simple text, e.g., abstract (~300 words)
  • short publication: 6-8 pages of text
  • longer publication: 20-40 pages
• usage of external services to extract pdf: benefits and possible issues
• how complete the list of the entities should be
• ontology mapping: should we add more ontologies? ontology_id and ontology_label is sometimes null
• what kind of feedback should be provided: mapping to ontology? labeling more entities?