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