Why are graphs the future of biomedical research and what is the value of NLP here?

A small case study about:

How to speed up drug discovery with knowledge graphs and discover potential cures for diseases

In this case text mining is used to contextualize knowledge about:

- Genes
- Compounds
- Diseases
- Adverse drug effects
- Receptor bindings
Which text types are processed here? Medical literature, patient notes, electronic health records, clinical reports etc.

But how to start?

First you need to identify the different entities such as compounds, diseases, adverse drug effects and receptor bindings.
This is achieved through Natural Language Processing (NLP) and there are suitable pre-trained models for processing biomedical, scientific or clinical text like scispaCy

@spacy_io models for processing biomedical, scientific or clinical text
https://t.co/1EPFZCFwoc
Another library which is specialized in biomedical text is Spark NLP

@JohnSnowLabs

https://t.co/EYM8lIyuUp
The next challenge is to extract the different relations! Diseases are related to genes which are related to receptors and compounds can bind to these receptors.

Sounds simple at first but there are several problems that need to be solved
Problems to solve

1. Difficult to ingest and integrate complex networks of text mined outputs
2. Difficult to contextualize knowledge extracted from text with existing knowledge
3. Difficult to investigate insights in a scalable and efficient way
Fortunately, Grakn solves all our problems!

@GraknLabs

How it works is explained here: https://t.co/BCGDuWrVqA
To understand how NLP and graphs are used to link medical knowledge I recommend this talk on text mining and drug discovery at Novartis

Not quite up to date but aged very well

Connecting the Dots in Early Drug Discovery at Novartis
https://t.co/QNJt6q5IsU

More from All

You May Also Like

THE MEANING, SIGNIFICANCE AND HISTORY OF SWASTIK

The Swastik is a geometrical figure and an ancient religious icon. Swastik has been Sanatan Dharma’s symbol of auspiciousness – mangalya since time immemorial.


The name swastika comes from Sanskrit (Devanagari: स्वस्तिक, pronounced: swastik) &denotes “conducive to wellbeing or auspicious”.
The word Swastik has a definite etymological origin in Sanskrit. It is derived from the roots su – meaning “well or auspicious” & as meaning “being”.


"सु अस्ति येन तत स्वस्तिकं"
Swastik is de symbol through which everything auspicios occurs

Scholars believe word’s origin in Vedas,known as Swasti mantra;

"🕉स्वस्ति ना इन्द्रो वृधश्रवाहा
स्वस्ति ना पूषा विश्ववेदाहा
स्वस्तिनास्तरक्ष्यो अरिश्तनेमिही
स्वस्तिनो बृहस्पतिर्दधातु"


It translates to," O famed Indra, redeem us. O Pusha, the beholder of all knowledge, redeem us. Redeem us O Garudji, of limitless speed and O Bruhaspati, redeem us".

SWASTIK’s COSMIC ORIGIN

The Swastika represents the living creation in the whole Cosmos.


Hindu astronomers divide the ecliptic circle of cosmos in 27 divisions called
https://t.co/sLeuV1R2eQ this manner a cross forms in 4 directions in the celestial sky. At centre of this cross is Dhruva(Polestar). In a line from Dhruva, the stars known as Saptarishi can be observed.
The UN just voted to condemn Israel 9 times, and the rest of the world 0.

View the resolutions and voting results here:

The resolution titled "The occupied Syrian Golan," which condemns Israel for "repressive measures" against Syrian citizens in the Golan Heights, was adopted by a vote of 151 - 2 - 14.

Israel and the U.S. voted 'No'
https://t.co/HoO7oz0dwr


The resolution titled "Israeli practices affecting the human rights of the Palestinian people..." was adopted by a vote of 153 - 6 - 9.

Australia, Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No' https://t.co/1Ntpi7Vqab


The resolution titled "Israeli settlements in the Occupied Palestinian Territory, including East Jerusalem, and the occupied Syrian Golan" was adopted by a vote of 153 – 5 – 10.

Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No'
https://t.co/REumYgyRuF


The resolution titled "Applicability of the Geneva Convention... to the
Occupied Palestinian Territory..." was adopted by a vote of 154 - 5 - 8.

Canada, Israel, Marshall Islands, Micronesia, and the U.S. voted 'No'
https://t.co/xDAeS9K1kW