Dependency Path

Is there anyone who was able to parse a dependency path similar to the one provided in the paper? I need help…

Hi @Sarahrp @ddas I need to tag all MLBI participants but I can’t.

@2021-MLBI-L-S1 @2021-MLBI-P-S1

Please take a look at Wafaa’s query above.

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Hi @Wafaa

I’m from Team 5. We created a Dependency Matrix like this with the “typed dependency output” format from Stanford Dependency Parsing .

Rows: drug-gene & Columns: dependency relations.

We got 169 drug-gene pairs & 23 unique dependency relations iterating over 2000 medline sentences that we have extracted.

If a drug-gene pair is found by any of the dependency relations it will append 1 in the matrix otherwise 0.

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@Sourav_Naskar okay that sounds good. but does the EBC algorithm accept this matrix as input?

@Wafaa, @mtaruno @Sourav_Naskar: Colin will answer the queries from Teams 2 & 5 tomorrow 07/12 (the Monday 10am PST meeting). Hoping at least one member of your team can attend! If it is not possible for anyone to attend, Colin will cover it in the Wednesday meeting.

@CharlesIm, @ShravyaKairamkonda: the session 1 teams have some urgent queries that Colin will address tomorrow (07/12). Hopefully it will not take up too much time and the rest can be used by your team. It will also help your team to see where the session 1 teams are facing their challenges!

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Hi @Wafaa

We need input for the EBC algorithm like this

[ ‘drug, gene’, ‘[dependency path’], value] → [’(rc-160,igf-i)’, ‘[nsubj, reduced, dobj]’, 1.0]

For every drug-gene pair we will store all the dependency relations (with non zero values) as list which will be the dependency path & value will be 1.0 as the drug-gene pair is present.

@Sourav_Naskar The dependency path is not the same as dependency relation. let’s consider the following sentence:
CYP3A4 mRNA expression was significantly increased by rifampicin exposure in human hepatocytes.
the dependency relation between “rifampicin” and “CYP3A4” is “increasred”. which is the least common node between them in the dependency tree.
While the dependency path between the two words is : [amod, expression, nsubjpass, increased, agent, exposure,nn]
the dependency path is the one which I couldn’t extract, and apparently I need it as input for the EBC algorithm.

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