Putting Semantics into the Semantic Web - Semantic Scholar

Outline Why Biological Semantics Matter Is the Semantic Web Structurally Sufficient? Towards Solutions

Putting Semantics into the Semantic Web: How Well Can It Capture Biology? Toni Kazic University of Missouri, Columbia

January 4, 2006

Toni Kazic University of Missouri, Columbia

Putting Semantics into the Semantic Web – PSB 2006


1

Why Biological Semantics Matter Purine Salvage — But They’re Pyrimidines! The Challenge

2

Is the Semantic Web Structurally Sufficient? Is a Simple Syntax Sufficient? Are an Implicit Semantics Effective? Does the Machinery Scale?

3

Towards Solutions Some Suggestions for Going Forward A Partial Solution Prospects




Purine Salvage — But They’re Pyrimidines! The Challenge

Are These Reactions the Same?






deoxyadenosine adenine deoxyinosine hypoxanthine






deoxyadenosine adenine deoxyinosine hypoxanthine





Rewriting Doesn’t Help Structurally, Either Using EC 2.4.2.6, a reaction officially “similar” to EC 2.4.2.4, try transforming EC 2.4.2.4 into KEGG’s reaction: thymidine +

phosphate thymine + 2-deoxy-α-D-ribose 1-phosphate





Rewriting Doesn’t Help Structurally, Either Using EC 2.4.2.6, a reaction officially “similar” to EC 2.4.2.4, try transforming EC 2.4.2.4 into KEGG’s reaction: thymidine +

phosphate thymine + 2-deoxy-α-D-ribose 1-phosphate

2-deoxy-D-ribosyl-base1 +

base2

base1 + 2-deoxy-Dribosyl-base2

deoxyadenosine +


thymine

adenine + thymidine




. . . and the Synonyms Aren’t Very Synonymous






blood platelet-derived endothelial cell growth factor gliostatins






blood platelet-derived endothelial cell growth factor gliostatins and what’s this got to do with purine metabolism, anyway?





It’s What’s Under the Hood (of the Words) That Counts! Humans rely on connotations, allusions, and imagery to interpret tokens and reconcile apparent contradictions.





It’s What’s Under the Hood (of the Words) That Counts! Humans rely on connotations, allusions, and imagery to interpret tokens and reconcile apparent contradictions. Automatically producing biologically incorrect (or worse, misleading) results isn’t helpful.





It’s What’s Under the Hood (of the Words) That Counts! Humans rely on connotations, allusions, and imagery to interpret tokens and reconcile apparent contradictions. Automatically producing biologically incorrect (or worse, misleading) results isn’t helpful. “Plausible answers” by definition must be biologically credible: deoxyadenosine adenine thymidine + phosphate thymine+ 2-deoxy-α-D-ribose 1-phosphate





It’s What’s Under the Hood (of the Words) That Counts! Humans rely on connotations, allusions, and imagery to interpret tokens and reconcile apparent contradictions. Automatically producing biologically incorrect (or worse, misleading) results isn’t helpful. “Plausible answers” by definition must be biologically credible: deoxyadenosine adenine thymidine + phosphate thymine+ 2-deoxy-α-D-ribose 1-phosphate Could the Semantic Web “understand” domain semantics? e. g., an enzymatic reaction 6= a drug reaction Toni Kazic University of Missouri, Columbia




the Semantic Web and its Denizens Are Languages!

Resources are mutually intelligible when they can translate each other’s domain semantics.






Resources are mutually intelligible when they can translate each other’s domain semantics. Translation requires that the domain semantics be adequately specified.






Resources are mutually intelligible when they can translate each other’s domain semantics. Translation requires that the domain semantics be adequately specified. Scalability requires automatic operations and distributed methodologies.






Resources are mutually intelligible when they can translate each other’s domain semantics. Translation requires that the domain semantics be adequately specified. Scalability requires automatic operations and distributed methodologies. Does the Semantic Web’s structure meet these requirements?




Is a Simple Syntax Sufficient? Are an Implicit Semantics Effective? Does the Machinery Scale?

Nesting Our Way to RDF (and Relatives) “thymidine and phosphate are converted into thymine and 2-deoxy-α-D-ribose 1-phosphate by the enzyme thymidine phosphorylase”



Nesting Our Way to RDF (and Relatives) “thymidine and phosphate are converted into thymine and 2-deoxy-α-D-ribose 1-phosphate by the enzyme thymidine phosphorylase” thymidine and phosphate }

*convert* }

*thymine and 2-deoxy-α-D-ribose *thymidine 1-phosphate phosphorylase }

}



Nesting Our Way to RDF (and Relatives) “thymidine and phosphate are converted into thymine and 2-deoxy-α-D-ribose 1-phosphate by the enzyme thymidine phosphorylase” thymidine and phosphate

*convert*

*thymine and 2-deoxy-α-D-ribose *thymidine 1-phosphate phosphorylase

} } } } P PP Q PP Q PP Q PP Q PP Q PP Q PP Q Q m P P m m

m




*convert*


} } } } P PP Q PP Q PP Q PP Q PP Q PP Q PP Q Q m P P m m }

reaction

m

}

catalyzes




*convert*


} } } } P PP Q PP Q PP Q PP Q PP Q PP Q PP Q Q m P P m m } P PP Q reaction PPP Q PP Q PP Q PP Q PP Q PP Q Q P m }

catalyzes Toni Kazic University of Missouri, Columbia




Enzymes Alter Semantics thymidine phosphorylase + thymidine + phosphate

thymidine phosphorylase•thymidine•phosphate

*convert*

*thymine and 2-deoxy-α-D-ribose 1-phosphate

}

} Q Q Q Q

Q Q Q Q m } m P PP Q reaction PPP Q PP Q PP Q PP Q PP Q PP QQ P }

catalyzes






thymidine phosphorylase•thymidine•phosphate

*convert* }

*thymine and 2-deoxy-α-D-ribose *thymidine 1-phosphate phosphorylase } Q Q Q

} Q

Q Q Q Q m } m P PP Q reaction PPP Q PP Q PP Q PP Q PP Q PP QQ P } }

catalyzes






thymidine phosphorylase•thymidine•phosphate thymidine and phosphate

*convert*


} } } } PP Q PP Q PP Q PP Q PP Q PP Q PP Q PP Q m P } } m P PP Q reaction PPP Q PP Q P Q PPP Q PP Q PP QQ P} } }

catalyzes






thymidine phosphorylase•thymidine•phosphate thymidine and phosphate

*convert*


} } } } PP Q PP Q PP Q PP Q PP Q PP Q PP Q PP Q m P } } m P PP Q reaction PPP Q PP Q P Q PPP Q PP Q PP QQ P} } }

catalyzes

Squeezing complex syntax into RDF means your resource’s “thymidine phosphorylase” may not be the same as mine! Toni Kazic University of Missouri, Columbia




The Semantic Web’s Semantics Are Implicit in Three Ways

definitions are in natural language – hence not very computable






definitions are in natural language – hence not very computable programs that use the RDF carry much of the semantics of the terms – hence less accessible to people building resources






definitions are in natural language – hence not very computable programs that use the RDF carry much of the semantics of the terms – hence less accessible to people building resources some semantics are intensional – hence programs are needed to produce the extensional semantics





The Problems of an Implicit Semantics

People have to read the definitions and other people’s code! How many developers speak biology, and vice versa?






People have to read the definitions and other people’s code! How many developers speak biology, and vice versa? People interpret the same term(s) differently. Are deoxyadenosine adenine and thymidine + phosphate

thymine + 2-deoxy-α-D-ribose 1-phosphate the same? Depends on your view of “same”.






People have to read the definitions and other people’s code! How many developers speak biology, and vice versa? People interpret the same term(s) differently. Are deoxyadenosine adenine and thymidine + phosphate

thymine + 2-deoxy-α-D-ribose 1-phosphate the same? Depends on your view of “same”. The semantics gets pushed onto the applications. Results from a resource that retrieves “related” reactions will be meaningless unless you know what it means by “related”.





Scaling Problems, Obvious and Otherwise

Pairs of resources translate, but n(n − 1) is not as nice as n parsers. People reading, understanding, and fitting other’s ontologies to their resources is very slow. Automatically drawing inferences can be combinatorially explosive — and how to filter the signal from the noise? And this isn’t a matter of “trust”.




Some Suggestions for Going Forward A Partial Solution Prospects

Ideas for a Richer Web Enrich the syntax Why not more parts of speech? And what do biologists mean when they talk, anyway?





Ideas for a Richer Web Enrich the syntax Why not more parts of speech? And what do biologists mean when they talk, anyway? Let biologists build They know what they mean and have a long history of defining terms. But how to prevent cacophony?





Ideas for a Richer Web Enrich the syntax Why not more parts of speech? And what do biologists mean when they talk, anyway? Let biologists build They know what they mean and have a long history of defining terms. But how to prevent cacophony? Make the semantics finely grained To avoid argument, avoid “big” ideas. How to ensure the uniqueness and elementariness of the axioms?





Ideas for a Richer Web Enrich the syntax Why not more parts of speech? And what do biologists mean when they talk, anyway? Let biologists build They know what they mean and have a long history of defining terms. But how to prevent cacophony? Make the semantics finely grained To avoid argument, avoid “big” ideas. How to ensure the uniqueness and elementariness of the axioms? Make the semantics computable Rather than overload set operations and AnnotationProperty, why not use a more expressive language?





Ideas for a Richer Web Enrich the syntax Why not more parts of speech? And what do biologists mean when they talk, anyway? Let biologists build They know what they mean and have a long history of defining terms. But how to prevent cacophony? Make the semantics finely grained To avoid argument, avoid “big” ideas. How to ensure the uniqueness and elementariness of the axioms? Make the semantics computable Rather than overload set operations and AnnotationProperty, why not use a more expressive language? Constrain inferences to improve scalability Use the semantics! How? Quality metrics for good inferences? Toni Kazic University of Missouri, Columbia




Glossa A formal language for defining the semantics of ideas, data, and computations. The semantics of constructs are computed from the semantics of their alphabet and grammatical rules. Glossa and its machinery live on top of existing resources, without requiring them to rewrite their semantics and schemata. Glossa has been demonstrated to produce interoperability (in a proof-of-concept way).





Glossa A formal language for defining the semantics of ideas, data, and computations. The semantics of constructs are computed from the semantics of their alphabet and grammatical rules. Glossa and its machinery live on top of existing resources, without requiring them to rewrite their semantics and schemata. Glossa has been demonstrated to produce interoperability (in a proof-of-concept way). The number of semiotes needed may be significantly larger than the terms in the GO — if so, keeping them straight will be hard. It’s not as user-friendly as ontologies are (yet). Toni Kazic University of Missouri, Columbia




Is the Semantic Web Wrong for Biological Computations?






Not necessarily the wrong vision, but a weak one.






Not necessarily the wrong vision, but a weak one. What is the right level or granularity?






Not necessarily the wrong vision, but a weak one. What is the right level or granularity? Usage is a problem for everyone and every technology.






Not necessarily the wrong vision, but a weak one. What is the right level or granularity? Usage is a problem for everyone and every technology. Something that understood semantics would help in maintain the Semantic Web — and we’ve come full circle to the underlying importance of the Semantic Web.





Thanks!

The organizers! Phani Chilukuri and Armani Valvo! The people who talked with me! The referees! The NIH (GM 56529)!





Thanks!

The organizers! Phani Chilukuri and Armani Valvo! The people who talked with me! The referees! The NIH (GM 56529)! AND YOU!



Putting Semantics into the Semantic Web - Semantic Scholar

Putting Semantics into the Semantic Web - Semantic Scholar

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