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Slides from talk: NLP tales in Biomedicine Auckland MeetUp group, June 2014 http://www.meetup.com/Natural-Language-Processing-in-NZ/events/184030662/ Mining text to answer biomedical questions is a fascinating applied research area. The biomedical domain is one of the first 'big data' domains. It attracts people from the domain itself passionate to answer pressing scientific questions as well as computer scientists and linguists who see a domain with great standards, resources and numerous applications. During this talk I will give you a brief overview of different NLP problems in the biomedical domain and I'll make comparisons to mainstream NLP applications (e.g., search) and other, more commercial domains (e.g., voice of customer). My aim is to introduce you to a domain with state of the art solutions, free high-quality resources and well developed methodologies. If I inspire anyone to work on challenging biomedical problems, will be a bonus!
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NLP Tales in Biomedicine
Anna Divoli@annadivoli
nelshami.deviantart.com
Auckland NLP MeetUp June 2014
Biology recap
Traits DiscussionsDNA > Genes > Proteins > Phenotype: Function > Emotions
Disease Medical Notes (scientific literature)
Information of interestGenes / 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…
imp.princeton.edu/static//css/images/network.png
Information of interestGenes / 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: GOCHEBI…
Medical:UMLSSNOMED CTIDC…
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 FreeLTR: Long Term Relationship
better to use domain specific resources in occassions like this
Search
Search
Search
Search
Search
Search
Search
Search
Search
Social Biomedicine
NewsPatient ForumsBlogsTwitter…
Social Biomedicine
NewsPatient ForumsBlogsTwitter…
Social Biomedicine
NewsPatient ForumsBlogsTwitter…
Social Biomedicine
NewsPatient ForumsBlogsTwitter…
344 online forum posts on DepressionSource: www.patient.co.ukDate: July 2013
Social Biomedicine
NewsPatient ForumsBlogsTwitter…
344 online forum posts on DepressionSource: www.patient.co.ukDate: July 2013
Social Biomedicine
NewsPatient ForumsBlogsTwitter…
344 online forum posts on DepressionSource: www.patient.co.ukDate: July 2013
Social Biomedicine
NewsPatient ForumsBlogsTwitter…
344 online forum posts on DepressionSource: www.patient.co.ukDate: 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.shtmlhttp://www.nactem.ac.uk/resources.php
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