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NLP Tales in Biomedicine
Anna Divoli
@annadivoli
nelshami.deviantart.com
Auckland NLP MeetUp June 2014
Biology recap
Traits Discussions
DNA > Genes > Proteins > Phenotype: Function > Emotions
Disease Medical Notes
(scientific literature)
Information of interest
Genes / Proteins  specific information for database annotation
Gene names:
tinman, lilliputian, dreadlocks, lush, cheap date, methuselah, Van Gogh, maggie, brainiac, grim,
reaper, cleopatra, swiss cheese, ken and barbie, kenny, out cold, lava lamp, hamlet, sonic
hedgehog, werewolf, half pint, fucK, drop dead, chardonnay, agnostic, I’m not dead yet…
NLP Tales in Biomedicine (introductory presentation for the Auckland NLP MeetUp group by Anna Divoli)
NLP Tales in Biomedicine (introductory presentation for the Auckland NLP MeetUp group by Anna Divoli)
imp.princeton.edu/static//css/images/network.png
Information of interest
Genes / Proteins  relationships & network building
www.frontiersin.org/files/Articles/77923
Proteins: their sub-cellular location, their structure, the conditions of
their expression, their interactions, disease associations…
Disease – Drug: interactions, adverse effects, secondary indications…
Other entities: organs/tissues, metabolites/chemicals, phenotypes…
Detecting: methodologies & findings in experimental papers, paradigm
shifts…
Systems for specific: diseases, pathways, drug targets, organisms…
Examples of information of interest
Don Swanson’s ABC model:
dietary fish oil
reduction of: blood viscosity, platelet
aggregability, vascular reactivity
Raynaud’s disease
- Swanson, D. R. (1986). Fish oil, Raynaud's syndrome and undiscovered
public knowledge. Perspectives in Biology and Medicine, 30(1): 7-18.
- Swanson, D. R. (1987). Two medical literatures that are logically but
not bibliographically connected. Journal of the American Society for
Information Science 38: 228-233.
Literature-based Discovery:
Text mining!
causes
ameliorates
Don Swanson’s ABC model:
dietary fish oil
reduction of: blood viscosity, platelet
aggregability, vascular reactivity
Raynaud’s disease
- Swanson, D. R. (1986). Fish oil, Raynaud's syndrome and undiscovered
public knowledge. Perspectives in Biology and Medicine, 30(1): 7-18.
- Swanson, D. R. (1987). Two medical literatures that are logically but
not bibliographically connected. Journal of the American Society for
Information Science 38: 228-233.
Literature-based Discovery:
Text mining!
causes
ameliorates
Ontologies
OBO Foundry:
GO
CHEBI…
Medical:
UMLS
SNOMED CT
IDC…
MeSH
Search
Search
Search query: SAF LTR
Looking for: interactions between SAF and viral LTR elements
(SAF is a transcription factor, LTR stands for ‘long terminal repeat’)
but also:
SAF: Single And Free
LTR: Long Term Relationship
 better to use domain specific resources in occassions like this 
Search
Search
Search
Search
Search
Search
Search
Search
Search
Social Biomedicine
News
Patient Forums
Blogs
Twitter
…
Social Biomedicine
News
Patient Forums
Blogs
Twitter
…
Social Biomedicine
News
Patient Forums
Blogs
Twitter
…
Social Biomedicine
News
Patient Forums
Blogs
Twitter
…
344 online forum posts on Depression
Source: www.patient.co.uk
Date: July 2013
Social Biomedicine
News
Patient Forums
Blogs
Twitter
…
344 online forum posts on Depression
Source: www.patient.co.uk
Date: July 2013
Social Biomedicine
News
Patient Forums
Blogs
Twitter
…
344 online forum posts on Depression
Source: www.patient.co.uk
Date: July 2013
Social Biomedicine
News
Patient Forums
Blogs
Twitter
…
344 online forum posts on Depression
Source: www.patient.co.uk
Date: July 2013
Citation Analysis
From:
clinical meta-analysis…
to:
detect information for
knowledge
augmentation and
summarization…
Citation Analysis
From:
clinical meta-analysis…
to:
detect information for
knowledge
augmentation and
summarization…
Citation Analysis
From:
clinical meta-analysis…
to:
detect information for
knowledge
augmentation and
summarization…
Growing field: publications over the past 20 years
“text mining” ontology
Summary
Entities – Relationships/Interactions
Resources: Databases, Ontologies, Corpora…
Networks: Systems Biology, Translational Medicine, Literature-based Discovery
End Users – Search
Social Biomedicine
Citation analysis
… and this is just a 30 min introduction…
Resources
Databases (from genes to literature):
http://www.ncbi.nlm.nih.gov/
http://www.ebi.ac.uk/services
Ontologies & Linked Data:
http://www.obofoundry.org/
http://www.nlm.nih.gov/research/umls/
http://linkedlifedata.com/
Corpora:
http://compbio.ucdenver.edu/ccp/corpora/obtaining.shtml
http://www.nactem.ac.uk/resources.php

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NLP Tales in Biomedicine (introductory presentation for the Auckland NLP MeetUp group by Anna Divoli)