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Concomitant Ontology-driven
Patent and Non-Patent Literature
Searching in the Life Sciences
Denis Bayada / GQ Life Sciences
II-SDV Nice, 2016
Ontologies
Definition:
an ontology is a formal naming and
definition of the types, properties, and
interrelationships of entities
Most often a tree where each node
contains names.
Ontology in text searching :
Advantages / Disadvantages
Selecting a node will select all entries below
Pre-computed implies selecting a node immediately
shows you the number of hits
Selecting a high-level node means millions of terms
Bacteria
All terms need to be curated to avoid unwanted hits
Ontology-extracted Synonym Lists
Only using the terms at one level
A lot more flexible
No pre-computing (just normal indexing)
Easy to manually correct
User-based curation possible
User defined lists
It cannot use all terms below a node
OntologiesIn LifeQuest
In LifeQuest
Curation
Needs to be removed
Curated
CRISPR / CAS9
Known since the 80's in Bacteria.
Researchers have explored many different
applications of CRISPR/CAS9:
genetically modifying crops
eradicating viruses
screening for cancer genes
genome engineering
Genome editing: 2012 / 2013 2012:
Jinek, Doudna, Charpentier et al. develop CRISPR/Cas9, which can be programmed to recognize and target any DNA sequence.
2013: Cong, Zhang et al. show that CRISPR/Cas9 can precisely edit
DNA in human & mouse cells, and that a single CRISPR/Cas9 array can be programmed to edit several sites at once.
Tan et al. use CRISPR/Cas9 in pig, goat, and cattle cells.
Ran, Zhang et al. report that a technique called “double nicking,” which breaks both strands of DNA, can reduce CRISPR/Cas9 off-targeting by 50- to 1,500-fold.
Scientists use CRISPR/Cas9 to modify the genome of silkworm and frog embryos.
Patent battle Berkeley filed before Broad
Broad got an expedited review process
Broad’s granted
Provisionals were filed before
Right before AND after the American Invents Act cutoff date
Accusations of inequitable conduct
deception
misrepresentation
Berkeley vs. Broad Institute
Doudna/Charpentier vs. Zhang
Retrieving those documents
CRISPR and synonyms
Its variant called cas9
for the bacteria spcas9
Streptococcus pyogenes
Retrieving those documents
Adding species
Color coding
Blue for literature
Green for patents
Using WT cas9 in GenomeQuest
Filtered for QID>99% AND QID < 100%
Cas9 modified protein
GQ results in LQ
All together
Final result
Conclusion
Ontologies and synonym lists can be used
to search both Patent and Non-Patent
literature
Using biological sequences can help too
The ability of seeing it all together is very
useful
Link cited scientific literature and retrieved
scientific literature
Thank you