Triples extraction/relations identification about kgmednli HOT 5 OPEN

Yes, I would also like to know how did you guys get this triples?

from kgmednli.

Yes, I would also like to know how did you guys get this triples?

have a look at this.
https://www.ncbi.nlm.nih.gov/books/NBK9679/
https://skr3.nlm.nih.gov/SemMedDB/dbinfo.html

from kgmednli.

Hi all,

Thank you for the interest in the paper. I hope my answer will provide you with the information in detail.
We generate the sub-graph of UMLS specific to the dataset i.e. we use the premise and hypothesis sentences in the MedNLI dataset and run a Named Entity Recognition tool specific to UMLS: MetaMap. MetaMap helps identify UMLS concepts referred to in the text. The input to the metamap is thus the premise and hypothesis sentences in the MedNLI dataset and output are the UMLS entities present in the sentences.

UMLS has two primary sources: The Metathesaurus and the Semantic Network. The Semantic Network contains categories for the concepts present in the UMLS Metathesaurus and provides a relationship between these Semantic categories. Using the Metathesaurus, we extract the entity and through the Semantic Network we get the category of the entity and thereby, we get the relations between the entities. This creates a relevant sub-KG of the entire UMLS KG.

While the triples data is not available right now, I hope this process helps. Please feel free to ask any further questions!

from kgmednli.

For a text :: Hello doctor, I am suffering from coughing, throat infection from last week.

I am getting these kb tripes for the entity throat infection ::

[('throat infection', 'associated_with', 'suffering'), ('throat infection', 'result_of', 'suffering'), ('throat infection', 'associated_with', 'Coughing'), ('throat infection', 'co-occurs_with', 'suffering'), ('throat infection', 'manifestation_of', 'suffering'), ('throat infection', 'complicates', 'suffering'), ('throat infection', 'associated_with', 'gargle'), ('throat infection', 'occurs_in', 'suffering'), ('throat infection', 'process_of', 'suffering'), ('throat infection', 'degree_of', 'suffering'), ('throat infection', 'affects', 'suffering')]

Did you also get the same kind of triples?

from kgmednli.

Hi Deeksha,

I'm facing the same issue but I think I've made some headway in this. As Soumyah mentioned, UMLS provides 2 main knowledge sources Metathesaurus & Semantic N/w. If you see this (https://www.nlm.nih.gov/research/umls/implementation_resources/query_diagrams/er1.html) the Metathesaurus provides relations b/w concepts (CUI's). However, the issue is with the relationship labels (such as RO, RB, etc.) They aren't descriptive and you're thus left with RELA. Hence you can use RELA to connect concepts through the Metathesaurus and use Soumyah's advice for connecting them via the Semantic N/w. This is the best I could come up with.

I'm working on writing a tutorial for extracting triples in the way mentioned.

from kgmednli.