This presentation describes work in progress. it is about the formalization of laboratory protocols using ontologies and rules.

1. SMART Protocols: SeMAntic
RepresenTation for
Experimental Protocols
Olga Giraldo
ogiraldo@fi.upm.es
Ontology engineering group (OEG)
Universidad Politécnica de Madrid

2. Agenda
• What is a lab protocol
• Motivation
• Our general research question
• Our assumption
• Our propose
• Preliminary results
• Future work

3. What is a lab protocol
• Laboratory protocols are like cooking recipes
• They have ingredients: reagents and sample
• They have appliances: equipment,
• They have a total time
• They have a list of instructions,
• They have critical steps.
• The laboratory protocols are “the how to do” an
experiment.

4. Some problems in lab protocols
 some of them present
insufficient granularity,
 the instructions can be
imprecise or ambiguous due to
the use of natural language.
• Incubate the
centrifuge tubes in a
water bath.
• Incubate the samples
for 5 min with gentle
shaking.
• Rinse DNA briefly in
1-2 ml of wash.
• Incubate at -20C
overnight.

5. Why do we need to formalize and extract information from
lab protocols?
Because we want a recommendation system…
• That matches protocols according to my situation, for
instance
• samples I have,
• availability of equipment, reagents, lab conditions
• expertise
We also want content based information retrieval
• Meaningful sentences, sample used, purpose of the
protocol, applicability, critical steps, etc. Also,
identification of instructions
• Find all protocols for DNA extraction that have been used in
Oryza sativa that are suitable for processing a large number of
samples with a low execution time.
Motivation

6. Currently…
Semi-structured information
Unstructured information
How to formalize the information from laboratory
protocols as a knowledge base?
Ontologies + NLP tools

7. Our assumption
“Experimental protocols
are fundamental
information structures that
should support the
description of the
processes by means of
which results are
generated in experimental
research”

8. Our propose

9. Methods to represent and extract information
• Ontology model representing lab protocols
• Gazetteer-based method: use existing lists of named
entities
 Lists of proper nouns, which refer to real-life entities
• Rule-based approaches: write manual extraction rules
• Combination of the above

11. Ontology development

12. SMART Protocols - document
The Protocol as a document
sp:application of the protocol
sp:advantage of the protocol
sp:limitation of the protocol
sp:provenance of the protocol
sp:purpose of the protocol
sp:introduction section
sp:buffer list
sp:equipment and supplies list
sp:kit list
sp:primer list
sp:reagent list
sp:software list
sp:solution list
sp:materials section
exact:caution
sp:critical step
sp:hint
sp:pause point
sp:storage condition
sp:timing
sp:troubleshooting
sp:methods section
sp:experimental
protocol
iao:document iao:document part
iao:textual entity iao:data set
owl:subClassOf
ro:hasPart
ro:partOf
owl:subClassOf
owl:subClassOfowl:subClassOf
ro:hasPart
ro:hasPart
ro:hasPart
ro:partOf
ro:partOf
ro:partOf
owl:subClassOf owl:subClassOf
exact:alert message
owl:subClassOf
 Rhetorical and structural components (e.g. introduction, materials, and methods);
 Information like application of the protocol, advantages and limitations, list of reagents,
critical steps.

13. SMART Protocols - wf
sp:basic step of
DNA extraction
p-plan:Step
p-plan:Variable
sp:cell disruption
sp:plant tissue
Basic Steps of DNA Extraction
sp:DNA purification
obi:DNA extract
p-plan:hasInputVariable
p-plan:hasOutputVariable
p-plan:hasOutputVariable
owl:subClassOf
sp:digestion
reaction
sp:powdered tissue
owl:subClassOf owl:subClassOf
owl:subClassOf
p-plan:hasInputVariable
sp:digested
contaminant
p-plan:hasInputVariable
p-plan:hasOutputVariable
owl:subClassOfowl:subClassOfowl:subClassOfowl:subClassOf
bfo:isPrecededBy bfo:isPrecededBy
Representation of the workflow aspects in protocols
 implicit order in the instructions, following the input output structure.

14. SMART Protocols documentation
• SMART Protocols ontology is available here:
• http://vocab.linkeddata.es/SMARTProtocols/
• Paper accepted in the Linked Science 2014
(LISC2014)
• Authors: Giraldo O, Garcia A, Corcho O
• Title: SMART Protocols: SeMAntic RepresenTation for
Experimental Protocols
• Collocated with the 13th International Semantic Web
Conference (ISWC2014)
• http://xurl.es/smart_protocols

15. Linguistic pattern recognition

16. Classification of the protocols
• Our corpus of protocols was classified according to the
purpose.
DNA / RNA extraction
DNA amplification
Electrophoresis or sequencing of nucleic acids
Genetic transformation
• Identification of instructions common to a type of protocol
 Key steps in DNA extraction: cell disruption, digestion reaction and
DNA purification
≈ pasta recipe
Key steps of pasta recipe: boil water, add the pasta until it is cooked
and mix the sauce with the pasta.

17. Creation of gazetteer lists
 Lists containing keywords to find occurrences of these key words in
the text.

18. Creation of grammar rules (JAPE rules)
Rule: secondstep1
(
({Token.category == "CD"})
(({Token})[0,3])
({Token.category == "NN"})
(({Token})[0,3])
{digest_reaction_reagent.majorType == "reagents"}
(({Token})*)
({Token.string == "." })
):digestionreaction1
-->
:digestionreaction1.Digestionreaction1 = {type = "digestionreaction1"}
 To find occurrences of basic steps from lab protocols.

19. SMART Protocols in action
sp= smart protocols, ro= relation ontology
sp:experimental
protocol
sp:DNA extraction
protocol
sp:advantages
sp:sample
owl:subClassOf
rdf:type
sp:title of the protocol
sp:author entry
rdf:type
sp:hasAuthor
sp:hasTitle
rdf:type
ro:partOf
ro:partOf
sp:application
of the protocol
ro:partOf
rdf:type
rdf:type

20. SMART Protocols in action

21. Future work

22. Continue…
• Analysis of the protocols. Focus on the identification of
keywords and/or constructs in English –e.g. instructions,
actions.
• Writing rules.
• Executing, testing and debugging the rules.

23. Goal of the internship
To take advantage of the previous experiences
in the formalization of lab protocols and apply
them in a new OHSU-Elsevier project focused
on research data management systems.

24. Special thanks…
Olga Giraldo
ogiraldo@fi.upm.es
oxgiraldo@gmail.com
Ontology engineering group (OEG)
Universidad Politécnica de Madrid
Supervisors OEG’s colleagues
Thank you!!!
Oscar Corcho Alexander Garcia Daniel Garijo María Poveda Pablo Calleja