Knowledge maps: connecting the dots in the literature landscape

Together to the next level

Connecting the dots in the literature landscape

Wynand AlkemaNIZO Food Research Ede

Computational Design & Discovery RU Nijmegen


The age of big data

Source: http://bigdatadiary.com/networks-strain-to-keep-pace-with-data-explosion/


Get connected

http://www.cs.ubc.ca/~welu/woss2012/

Stay informed

Get acquainted

Share your thoughts

Learn from each other


Social connections


Scientific connections

http://informatics.indiana.edu/rocha/figures/IPP_3_clusters_labels.jpg


Connection knowledge islands

• Structured information can be read and processed by computers.

• Connections– Hyperlinks and hypertext– Structured vocabularies– RFD triples– Graphical representation


Connecting unstructured text

Lots of knowledge available in libraries, patents and on the web.

Use text mining to harvest that knowledge

Exponentially growing

Right information at the right time

Actionable knowledge

Business decision

Hypothesis generation

Text Mining


• PUBMED library• 22 million papers, largest open access collection• Growing with 1 paper per minute• More than a 1.5 billion searches per year

www.ncbi.nlm.nih.gov/pubmed

What is it all about?


Food-focused text mining: A Dutch initiative


Connecting knowledge

• Which knowledge is available in the literature? What do we know?

• How can we connect knowledge to start learning more?


Streptococcus

>1200 articles

Information retrieval

Information extraction

What is known about Streptococcus?


Word clouds as knowledge hubs

Bacillus anthracis> 4000 scientific papers

Staphylococcus aureus> 70000 scientific papers

Chlamydia> 1200 scientific papers


Word clouds as knowledge hubs


Can word clouds be connected?

• Which word clouds have overlapping words and themes?

• Word clouds are visual representations of an underlying matrix with word frequencies in articles that describe a topic

• Matrix of frequencies can be clustered. Identify which concepts share the same set of keywords.


New probiotics for Clostridium perfringens

• Clostridium perfringens is a food spoilage organism

• Third most common cause of food poisoning

• It is found in common intestinal/gut flora of humans

• It can cause diarrhea, vomiting and fever.

• Can we develop probiotics against this bacterium?

Public Health Image Library (PHIL)#2995CDC/ Don Stalons

C. perfringens


Probiotics

• Friendly bacteria• Stimulate the immune system• Improve gut health• Compete with the pathogenic bacteria• Contains

– Lactobacillus – Lactococcus

NIZO/Dr. Kleerebezem

Lactobacillus


Connecting information

Potential probiotic organisms

Analyze the concepts/keywords that are in each article.

Make groups of articles that contain the same concepts.


Literature Landscape of Clostridium and potential probiotics

Lactococcus lactis

Lactobacilli

Clostridiumperfringens

Individual articles


Lactococcus lactis

Lactobacilli

Clostridiumperfringens

Individual articles

Literature Landscape of Clostridium and potential probiotics


What are the papers about?


New applications for existing drugs

• Drugs maybe withdrawn because of – lack of efficacy for a certain disease– competition– ……

• Can we find new applications for these drugs (drug repositioning) with the use of text mining?

Photo by Sage Ross (ragesoss.com), from Wikimedia Commons. Creative Commons Attribution-Share Alike 3.0 Unported.


Novel drug use : Recommender Systems

Milnacipran is used for treatment of pain

Milnacipran can be used for treatment of obsessive compulsive disorder

Connected in literature


Acknowledgements

Computational Design & Discovery

Wilco Fleuren

Marijn Sanders

Jacob de Vlieg

Rene van Schaik

Tina Ritschl

Stefan Verhoeven

Jos Boekhorst


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Knowledge maps: connecting the dots in the literature landscape

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