semantic web technology in support of bioinformatics for glycan expression amit sheth large scale...
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![Page 1: Semantic Web Technology in Support of Bioinformatics for Glycan Expression Amit Sheth Large Scale Distributed Information Systems (LSDIS) lab, Univ. of](https://reader036.vdocuments.site/reader036/viewer/2022062407/56649d4c5503460f94a298f9/html5/thumbnails/1.jpg)
Semantic Web Technology in Support of Bioinformatics for
Glycan Expression Amit Sheth
Large Scale Distributed Information Systems (LSDIS) lab, Univ. of Georgia
and Semagix, Inc.
W3C workshop on Semantic Web for Life Sciences, October 28, 2004, Cambridge MA
Thanks to Will York, Christopher Thomas, Satya Sanket Sahoo
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NIH Integrated Technology Resource for Biomedical Glycomics
Complex Carbohydrate Research Center The University of Georgia
Biology and Chemistry• Michael Pierce – CCRC (PI)• Al Merrill - Georgia Tech• Kelley Moremen - CCRC• Ron Orlando - CCRC• Parastoo Azadi – CCRC• Stephen Dalton – UGA Animal
Science
Bioinformatics and Computing•Will York - CCRC•Amit Sheth, Krys Kochut, John Miller; UGA Large Scale Distributed Information Systems Laboratory
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Quick Take• Comprehensive and deep domain ontology
– GlycO
• Process ontology to go beyond provenance– ProGlycO
• Semantic Annotation of Scientific data– Textual– Experimental, machine-generated, non-textual
• Tool for ontology visualization, querying,…• All open source, free
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Central Role of Ontology• Ontology represents agreement, represents
common terminology/nomenclature• Ontology is populated with extensive domain
knowledge or known facts/assertions• Key enabler of semantic metadata extraction from
all forms of content:–unstructured text (and 150 file formats)–semi-structured (HTML, XML) and –structured data
• Ontology is in turn the center price that enables–resolution of semantic heterogeneity –semantic integration–semantically correlating/associating objects and
documents
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Types of Ontologies (or things close to ontology)• Upper ontologies: modeling of time, space, process, etc• Broad-based or general purpose ontology/nomenclatures:
Cyc, CIRCA ontology (Applied Semantics), SWETO, WordNet ;
• Domain-specific or Industry specific ontologies– News: politics, sports, business, entertainment– Financial Market– Terrorism– Pharma– GlycO– (GO (a nomenclature), UMLS inspired ontology, …)
• Application Specific and Task specific ontologies– Anti-money laundering– Equity Research– Repertoire Management
Blue: Commercial ontologies developed by Semagix or its customers; Brown: open/public ontologies from LSDIS Lab, Univ. of Georgia
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Expressiveness Range: Knowledge Representation and Ontologies
Catalog/ID
GeneralLogical
constraints
Terms/glossary
Thesauri“narrower
term”relation
Formalis-a
Frames(properties)
Informalis-a
Formalinstance
Value Restriction
Disjointness, Inverse,part of…
Ontology Dimensions After McGuinness and FininOntology Dimensions After McGuinness and Finin
SimpleTaxonomies
Expressive
Ontologies
Wordnet
CYCRDF DAML
OO
DB Schema RDFS
IEEE SUOOWL
UMLS
GO
KEGG TAMBIS
EcoCyc
BioPAX
GlycOSWETO
Pharma
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Ontology can be very large
Semantic Web Ontology Evaluation Testbed – SWETO v1.4 is
• Populated with over 800,000 entities and over 1,500,000 explicit relationships among them
• Continue to populate the ontology with diverse sources thereby extending it in multiple domains, new larger release due soon
• Two other ontologies of Semagix customers have over 10 million instances, and requests for even larger ontologies exist
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GlycO statistics: Ontology schema can be large and complex
• 767 classes• 142 slots• Instances Extracted with Semagix Freedom:
– 69,516 genes (From PharmGKB and KEGG)– 92,800 proteins (from SwissProt)– 18,343 publications (from CarbBank and MedLine)– 12,308 chemical compounds (from KEGG)– 3,193 enzymes (from KEGG)– 5,872 chemical reactions (from KEGG)– 2210 N-glycans (from KEGG)
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GlycO
• is a focused ontology for the description of glycomics
• models the biosynthesis, metabolism, and biological relevance of complex glycans
• models complex carbohydrates as sets of simpler structures that are connected with rich relationships
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GlycO taxonomyThe first levels of the GlycO taxonomy
Most relationships and attributes in GlycO
GlycO exploits the expressiveness of OWL-DL.Cardinality constraints, value constraints, Existential and Universal restrictions on Range and Domain of properties allow the classification of unknown entities as well as the deduction of implicit relationships.
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Query and visualization
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A biosynthetic pathwayGNT-I
attaches GlcNAc at position 2
UDP-N-acetyl-D-glucosamine + alpha-D-Mannosyl-1,3-(R1)-beta-D-mannosyl-R2 <=>
UDP + N-Acetyl-$beta-D-glucosaminyl-1,2-alpha-D-mannosyl-1,3-(R1)-beta-D-mannosyl-$R2
GNT-Vattaches GlcNAc at position 6
UDP-N-acetyl-D-glucosamine + G00020 <=> UDP + G00021
N-acetyl-glucosaminyl_transferase_VN-glycan_beta_GlcNAc_9N-glycan_alpha_man_4
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The impact of GlycO
• GlycO models classes of glycans with unprecedented accuracy.
• Implicit knowledge about glycans can be deductively derived
• Experimental results can be validated according to the model
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Identification and Quantification of N-Identification and Quantification of N-glycosylationglycosylationCell Culture
Glycoprotein Fraction
Glycopeptides Fraction
extract
Separation technique I
Glycopeptides Fraction
n*m
n
Signal integrationData correlation
Peptide Fraction
Peptide Fraction
ms data ms/ms data
ms peaklist ms/ms peaklist
Peptide listN-dimensional arrayPeptide identificationand quantification
proteolysis
Separation technique II
PNGase
Mass spectrometry
Data reductionData reduction
Peptide identificationbinning
n
1
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ProglycOProglycO – Structure of the Process Ontology– Structure of the Process Ontology
Four structural components†:
Sample Creation
Separation (includes chromatography)
Mass spectrometry
Data analysis
†: pedrodownload.man.ac.uk/Domains.shtml
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Semantic Annotation of Scientific DataSemantic Annotation of Scientific Data
830.9570 194.9604 2580.2985 0.3592688.3214 0.2526
779.4759 38.4939784.3607 21.77361543.7476 1.38221544.7595 2.9977
1562.8113 37.47901660.7776 476.5043
ms/ms peaklist data
<ms/ms_peak_list>
<parameter instrument=micromass_QTOF_2_quadropole_time_of_flight_mass_spectrometer
mode = “ms/ms”/>
<parent_ion_mass>830.9570</parent_ion_mass>
<total_abundance>194.9604</total_abundance>
<z>2</z>
<mass_spec_peak m/z = 580.2985 abundance = 0.3592/>
<mass_spec_peak m/z = 688.3214 abundance = 0.2526/>
<mass_spec_peak m/z = 779.4759 abundance = 38.4939/>
<mass_spec_peak m/z = 784.3607 abundance = 21.7736/>
<mass_spec_peak m/z = 1543.7476 abundance = 1.3822/>
<mass_spec_peak m/z = 1544.7595 abundance = 2.9977/>
<mass_spec_peak m/z = 1562.8113 abundance = 37.4790/>
<mass_spec_peak m/z = 1660.7776 abundance = 476.5043/>
<ms/ms_peak_list>
Annotated ms/ms peaklist data
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Semantic annotation of Scientific Semantic annotation of Scientific DataData
Annotated ms/ms peaklist data
<ms/ms_peak_list>
<parameter
instrument=“micromass_QTOF_2_quadropole_time_of_flight_mass_spectrometer”
mode = “ms/ms”/>
<parent_ion_mass>830.9570</parent_ion_mass>
<total_abundance>194.9604</total_abundance>
<z>2</z>
<mass_spec_peak m/z = 580.2985 abundance = 0.3592/>
<mass_spec_peak m/z = 688.3214 abundance = 0.2526/>
<mass_spec_peak m/z = 779.4759 abundance = 38.4939/>
<mass_spec_peak m/z = 784.3607 abundance = 21.7736/>
<mass_spec_peak m/z = 1543.7476 abundance = 1.3822/>
<mass_spec_peak m/z = 1544.7595 abundance = 2.9977/>
<mass_spec_peak m/z = 1562.8113 abundance = 37.4790/>
<mass_spec_peak m/z = 1660.7776 abundance = 476.5043/>
<ms/ms_peak_list>
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Beyond Provenance…. Semantic Beyond Provenance…. Semantic AnnotationsAnnotations
Data provenance: information regarding the ‘place of origin’ of a data element
Mapping a data element to concepts that collaboratively define it and enable its interpretation – Semantic Annotation
Data provenance paves the path to repeatability of data generation, but it does not enable: Its (machine) interpretability Its computability (e.g., discovery)
Semantic Annotations make these possible.
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Identified and quantified
peptides
Specific cellularprocess
Lectin
Collection of N-glycan ligands
Collection ofBiosynthetic enzymes
Discovery of relationship between biological Discovery of relationship between biological entitiesentities
Fragment ofSpecific protein
GlycOProglycO
Gene Ontology (GO)
Genomic database (Mascot/Sequest)
The inference: instances of the class collection of Biosynthetic enzymes (GNT-V) are involved in the specific cellular process (metastasis).
p
r
o
c
e
s
s
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Dimensions of expressiveness
complexitybivalent Multivalued
discretecontinu
ous
Degre
e o
f Ag
reem
ent
Info
rmal
Sem
i-Form
al
Form
al
Expressiveness
XMLRDF
FOL withfunctions
Current Semantic
Web Focus
Futureresearch
Cf: Guarino, Gruber
RDFS/OWL
FOL w/o functions
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The downside
• That a structure is not valid according to the ontology could just mean that it is a new kind of structure that needs to be incorporated
• That a substance can be synthesized according to one pathway does not exclude the synthesis through another pathway
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Man9GlcNAc2
Glycan
is a
Glycosyl Transferase
is a
synthesizes
May Synthesize
Mannose
contains
transfers
May Synthesize
Lipid-mannosyl transferase
Probabilistic Relationships
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For more information
• http://lsdis.cs.uga.edu– Especially see Glycomics project– SWETO ontology
• http://www.semagix.com
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Backup slides
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Automatic Semantic Annotation of Text:Entity and Relationship Extraction
KB, statistical and linguistic
techniques
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Ontologies – many questions remain• How do we design ontologies with the constituent
concepts/classes and relationships?• How do we capture knowledge to populate
ontologies• Certain knowledge at time t is captured; but real
world changes• imprecision, uncertainties and inconsistencies
– what about things of which we know that we don’t know?
– What about things that are “in the eye of the beholder”?
• Need more powerful semantics
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What we need
• We need a formalism that can – express the degree of confidence that e.g. a
glycan is synthesized according to a certain pathway.
– express the probability of a glycan attaching to a certain site on a protein
– derive a probability for e.g. a certain gene sequence to be the origin of a certain protein
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What we want
• Validate pathways with experimental evidence. Many pathways still need to be verified.
• Reason on experimental data using statistical techniques such as Bayesian reasoning
• Are activities of iso-forms of biosynthetic enzymes dependent on physiological context? (e.g. is it a cancer cell?)
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How to power the semantics• A major drawback of logics dealing with
uncertainties is the assignment of prior probabilities and/or fuzzy membership functions.
• Values can be assigned manually by domain experts or automatically
• Techniques to capture implicit semantics– Statistical methods– Machine Learning