May 30, 2005BIONLP Lexical Issues in Anatomical Ontologies Sarah Luger www.xspan.org based on work with Stuart Aitken and Bonnie Webber.

Slides:



Advertisements
Similar presentations
Workshop Cross-species Mapping between Anatomical Ontologies: Terminological and Structural Support by Sarah Luger, Stuart.
Advertisements

Meiosis.
Lukas Blunschi Claudio Jossen Donald Kossmann Magdalini Mori Kurt Stockinger.
1 A Systematic Nomenclature for Embryo Anatomy MRC, Human Genetics Unit Heriot-Watt University, Dept. of Comp & EE, Albert Burger.
Chapter 27: Introduction to Animals.  Heterotrophy  Animals are heterotrophs – that is, they can not make their own food.  Most animals move from place.
Linking ontologies to one another and to the Cell Ontology with the COBrA ontology editor Jonathan Bard & Stuart Aitken Biomedical Science & Informatics.
Organs D. Crowley, 2007.
SC.912.L16.13 Describe the basic anatomy and physiology of the human reproductive system. Describe the process of human development from fertilization.
Classification of developing structures Developing structures are typically classified by developmental biologists according to their fate. If such terms.
UNDERSTANDING LINKAGE, AND GENETIC MAPPING. INTRODUCTION Each species of organism must contain hundreds to thousands of genes Yet most species have at.
Representing Part Relationships Between Developing Structures.
UNDERSTANDING LINKAGE, AND GENETIC MAPPING. INTRODUCTION Each species of organism must contain hundreds to thousands of genes –Yet most species have at.
The Inheritance of Complex Traits
6 September, 2006 Chapter 21 Methods: Model Systems I.
VERTEBRATE DISSECTION LAB 13 Rat Internal Anatomy - Excretory, Reproductive, Endocrine & Nervous Systems.
Developmental Neurobiology Fall 2005 Credit: Two Time: 1:30 PM-3:30 PM, Tuesday Place: 316, 3rd Floor, Nursing Building Instructors: 范明基 ( ), 簡正鼎.
Starter Check comments on marking. Complete task given. Remember to respond to marking on the sticker !
Scaffold Download free viewer:
Chapter 34 Endocrine and Reproductive Systems 34.3
Sponge: Set up Cornell Notes on pg. 19 Topic: Ch. 1 Organ Systems Essential Question: Choose an organ system. Describe the general functions of that organ.
Comparative Genomics of the Eukaryotes
PSY 2012 General Psychology Chapter 2: Biopsychology Samuel R. Mathews, Ph.D. Associate Professor The Department of Psychology The University of West Florida.
5.5 Multicellular Life KEY CONCEPT Cells work together to carry out complex functions.
Slides 1 to 73 Copyright © 2007 Pearson Education, Inc., publishing as Benjamin Cummings.
Multicellular Organisms. Tissue - a group of similar cells that together perform a specific function in an organism.
Gene Expression Databases: Where and When Dave Clements EuReGene and Mouse Atlas projects Medical Research Council Human Genetics.
Anatomy Basics Chapter 1
ENJOY LIFE! “Live life so completely that when death comes to you like a thief in the night, there will be nothing left for him to steal.” -unknown.
1 Major Themes of Anatomy and Physiology  Form and Function  Anatomy is the study of what and where  Physiology is the study of how and why.
Using String Similarity Metrics for Terminology Recognition Jonathan Butters March 2008 LREC 2008 – Marrakech, Morocco.
Taxonomy. Taxonomy: Defining groups of organisms based on similar characteristics. The result is a branching structure called the phylogenetic tree 4.
“Things that make you go Hmmmm….” “What happens if you get scared half to death twice?”
SEXUAL REPRODUCTION Chapter 4 lesson 1 Part 1.
Amphibians Chapter 40.
The Brain The Brain _______ ___________ ______________ ___________.
The Perceptual Process. Sensory Processing Bottom-Up (Data-Based): Analysis that begins with the sense receptors and works up to the brain’s integration.
Human Urinary and Reproductive Systems Salt Lake Community College Human Anatomy Laboratory.
 Examine two basic sources for implicit relevance feedback on the segment level for search personalization. Eye tracking Display time.
Linking Animal Models and Human Diseases Supported by NIH P41 HG002659, U54 HG004028, & R01 HG Cambridge University & the University of Oregon.
Introduction All living organisms share the following characteristics Growth Reproduction Movement Metabolism Copyright © 2007 Pearson Education, Inc.,
Terminology in Health Care and Public Health Settings
Collocations and Terminology Vasileios Hatzivassiloglou University of Texas at Dallas.
KEY CONCEPT Cells work together to carry out complex functions. 5.5 Multicellular Life.
Using the worksheet received today complete the first page. Use your HW to Label the steps of MEIOSIS, quite.
Chapter 2. From Complex Networks to Intelligent Systems in Creating Brain-like Systems, Sendhoff et al. Course: Robots Learning from Humans Baek, Da Som.
BMS 231: 2015/2016 ENDOCRINE SYSTEM DR SOBIA IKRAM DR AQEELA BANO DR SADIA FARHAN.
Spatial Smoothing and Multiple Comparisons Correction for Dummies Alexa Morcom, Matthew Brett Acknowledgements.
Nervous System Carries messages to and from the brain and spinal cord and all other parts of the body.
Evidence for Evolution Review of Natural Selection.
1 XSPAN: A Cross-Species Anatomy Network MRC, Human Genetics Unit Heriot-Watt University, Dept. of Comp & EE, Albert Burger.
Anatomy Ontologies & Potential Users: Bridging the Gap Ravensara Travillian European Bioinformatics Institute
BMS 231: 2015/2016 ENDOCRINE SYSTEM DR SOBIA IKRAM DR AQEELA BANO.
Aim #51: How do organisms create offspring through sexual reproduction?
Topical Analysis and Visualization of (Network) Data Using Sci2 Ted Polley Research & Editorial Assistant Cyberinfrastructure for Network Science Center.
Chapter 131 Normal Distributions. Chapter 132 Thought Question 2 What does it mean if a person’s SAT score falls at the 20th percentile for all people.
Human Neurobiology 217 Prof Stuart Bunt Prof. Stuart Bunt.
But Ma, how do all the body systems fit together?.
Organs. Organs To be able to label the organs of the human body To be able to label the organs of the human body Friday, September 30, 2016Friday, September.
IN Define Phenotype Define Genotype
Unit 4: Reproduction and Development
Warm Up #6 What is fertilization?.
The great variety of possible gene combinations in a
From: TopHat: discovering splice junctions with RNA-Seq
Reproduction.
Start-up for 12/8/14 Complete the word search regarding meiosis terminology. If you are the first person finished, let me know.
Notes: Introduction to 5 More Organ Systems
Opening Activity: May 25, 2016 Review the folder at your table. It has the following items for your work today: Evidence for Evolution Powerpoint Evidence.
WEEK 4 – Urinary and Reproductive Systems
Additional Example 2: Graphing Ordered Pairs Graph and label each point on a coordinate grid. A. L (3, 5) Start at (0, 0)
Meiosis Self Manager Reflective Learner Effective Participator
Presentation transcript:

May 30, 2005BIONLP Lexical Issues in Anatomical Ontologies Sarah Luger based on work with Stuart Aitken and Bonnie Webber

May 30, 2005BIONLP XSPAN Objectives To support access to tissue-based genetic information that is indexed by anatomy across species, via anatomy ontology integration. –homology relationships –function similarities –lineage relationships –cell types

May 30, 2005BIONLP A Mapping Problem Mouse Tail

May 30, 2005BIONLP A Mapping Problem C. Elegans Tail Mouse tail to C. elegans tail Same name, different function

May 30, 2005BIONLP A Mapping Problem In mouse: embryo/ organ system/ sensory organ/ eye/ optic stalk/ optic nerve In drosophila: larva/ larval organ system/ larval nervous system/ larval central nervous system/ larval brain/ medulla anlage/ optic nerve Mouse optic nerve to drosophila optic nerve –Same name, same function –The ontologies show different paths.

May 30, 2005BIONLP A Mapping Problem Identify and exploit relationships between tissues across the key model organisms given: –Mouse: 3559 anatomical parts –Drosophila: 506 anatomical parts –C. Elegans: 242 anatomical parts –Zebrafish: ~1200 anatomical parts –Human: 2328 anatomical parts Can their terminologies and anatomical ontogolies suggest what parts may be similar (homologous)?

May 30, 2005BIONLP Lexical Analysis Language processing: normalize, remove stop words, stemmed and lemmatized and then treated as unordered set Use more than the leaf label –Context, terms are not unique –Important terms spread across path The last term is weighted more than all prior terms combined. This filters out some “garbage” when comparing similar root-to-leaf paths with vastly different levels of specificity.

May 30, 2005BIONLP Weighting Example EMAPA.18237: Mouse/ embryo/ organ system/ sensory organ/ eye/ lens/ capsule EHDAA.9045: 100% match Human/ embryo/ organ system/ sensory organ/ eye/ lens/ capsule EHDAA.4727: 87% similar or 55/63 Human/ embryo/ organ system/ sensory organ/ eye/ lens vesicle/capsule

May 30, 2005BIONLP Weighting Example 1.EHDAA.9045: Human/ embryo/ organ system/ sensory organ/ eye/ lens/ capsule 2.EMAPA.18979: Mouse/ embryo/ organ system/ visceral organ/ reproductive system/ female/ ovary/ capsule 3.EMAPA.18679: Mouse/ embryo/ organ system/ visceral organ/ renal urinary system/ metanepheros/ excretory component/ cortex/ capsule

May 30, 2005BIONLP Methodology Use a similarity threshold to limit the number of results. Resultant pairs have one to many mappings: EMAPA: 18237EHDAA.9045 EMAPA: EHDAA.4727 Tissue pairs then structurally assessed by taking the ontologies as graphs with directed but unlabeled edges. –Examine intra-species relationships –Check relative positions of the terms between species –Judge comparisons as contradictory, supported, or no evidence.

May 30, 2005BIONLP Mouse-Human Results Threshold Matched Pairs Support 100% % 96% % 94% % This improvement follows from the larger set of lexical matches having more common terms near the top of the ontology, which permits paths that were previously being rejected.

May 30, 2005BIONLP Mouse-Human Results Mappings between human and mouse terms, where the x-axis represents thresholds of lexical similarity.

May 30, 2005BIONLP Human-Drosophila Results Fewer matches so we chose lexical similarity levels of 75%, 66% and 50%. Some contradictory mappings appear at 50%. The proportion of compatible mappings drops as the comparison threshold is reduced. An increase in mapping score is again observed.

May 30, 2005BIONLP Future Work Different name, same function –Introduces the need for synonym tables. Working with an anatomist to include synonyms in the mouse anatomy. –Zebrafish is also working on this. Discover more differences in ontology terms and free-text terms.

May 30, 2005BIONLP Ontologies, Mapping and Synonyms drosophila isa whole organism part of organ system isa reproductive system isa male reproductive system part of testis C. elegans part of organ system isa sex-associated system isa male-associated system isa male reproductive system isa male gonad gonad testis

May 30, 2005BIONLP COBrA: Ontology Mapping

May 30, 2005BIONLP COBrA: A GO editor hyperlink GO term data search

May 30, 2005BIONLP COBrA: A GO editor

May 30, 2005BIONLP Structural Analysis