A New Method of Examining Coral Reef Ecosystems: A First Use of Genomic and Bioinformatics Techniques Indiana University School of Informatics Capstone.

A New Method of Examining Coral Reef Ecosystems: A First Use of Genomic and Bioinformatics Techniques Indiana University School of Informatics Capstone Project Christopher Rosenthal Claudia Johnson (Geobiology) Mehmet Dalkilic (Bioinformatics) Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Outline Motivation Introduction What is an ecosystem Data
Biotic components Flow of energy in one direction Recycling of energy Toxic components Flow of energy between ecosystems Data Architecture (Microsoft) Programming Algorithm Results Screen Shots Discussion Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Motivation Coral Reef Ecosystem Research Background
Claudia Johnson (Geology) Mehmet Dalkilic (Bioinformatics) Susan Morse Coleman (HCI/d) Studied coral reef ecosystems first hand in the Dominican Republic Interface and Design Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Motivation Overview of Geobiology
Research generally focused on a single ecosystem - Coral Reefs Data is usually reported in raw form Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Example Study by Halpern et al 2008
20 different ecosystems around the world 17 data sets of anthropogenic drivers Coral reef, mangrove, seagrass, rocky reef, shallow soft bottom, hard shelf, soft shelf, hard slope, soft slope, hard deep, soft deep, seamounts, pelagic waters, deep waters Nutrient Input, Nonpoint organic pollution, Nonpoint non-organic pollution, Direct Human, Demersal destructive fishing, Sea temperature, UV, Ocean acidification, Species Invasion, Commercial Activity, Benthic Structures Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Motivation Applying Bioinformatics
Even though Bioinformatics is in its infancy a lot of information and a lot of methodologies have been acquired by studying genomes Biogeology is generally done on a much larger scale because the Earth itself can be thought of as the “DNA” of “Biogeoinformatics” (University of Kansas Geological Survey) Name coined in a project of analyzing geospatial, taxonomic, and environmental data for a group of marine invertebrates Metagenomics is an example of a bioinformatics methodologies based on environmental genomes Metagenomics Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Introduction Geologists have recently begun looking for complex relationships in their data to discover trends A word on temporal extent There exists millions of years of uncollected and unevaluated amounts of data Can Bioinformatics approaches be applied to geological analysis of ecosystems? What can ontologies tell us about coral reef ecosystems? What can coral genomes tell us about the coral reef diseases? Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Introduction What is an Ontology? Forming Relationships of Data
Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Introduction DDont – Data Driven Ontologies (Costello et al)
Bloom – Data Driven Ontologies for Coral Reef Disease and Genomic Ontologies An example of a Data-Driven Ontology (DDOnt). The network of yeast genes (A) selected as a subnetwork of the bioPIXIE integrated gene network is used along with the Gene Ontology biological process annotations to synthesize the DDOnt (B) using the BuildOntology algorithm. The edge colors in B are discussed in Section 3.2. The root node in the ontology is designated by the teal arrow. The orange nodes in A are the genes that have been annotated with the rosette of terms in B designated by the red arrow. This rosette of terms are potentially novel relationships between biological processes where the parent node is response to DNA damage stimulus (GO: ). Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Introduction What genes correspond to which diseases?
What does the functionality of these genes tell us about the environmental stressors present in the ecosystem? Northwestern University Functional Disease Ontology Server Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Introduction In particular, humans contain many of the same immune system genes as corals (Kortschak et al) Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Introduction (Kortschak et al)

What is an Ecosystem? Biotic Components Primary producers (herbivores)
Plants and algae Secondary consumers (mid-level carnivores) Tertiary consumers (top predator in food chain) Decomposers (bacteria and fungus) Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

What is an Ecosystem? Flow of energy in one direction
Sun -> producers -> consumers Marine Sulfur vents -> producers -> consumers Subterranean heat -> ? -> ? Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

What is an Ecosystem? Recycling of energy
Decomposers and primary consumers break down “waste” into nutrients Dead biomass or returns to soil to be used by primary consumers Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

What is an Ecosystem? Toxic components
Non-organic (Human made poisons) Poisons Factory waste Organic Fertilizer runoff into water streams causing algae blankets Natural disasters Volcanoes Wild fires Earthquakes etc Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

What is an Ecosystem? Flow of energy between ecosystems
Overlapping of biotic components between adjacent ecosystems Migrating consumers on land or by water Nutrient flow down rivers or along ocean currents Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Application Saturday, September 22, 2018
Paper in Submission to Geoinformatics Conference

Data Data Global Coral Disease Database Philippines Caribbean
Australia Red Sea Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Data Data National Oceanic Data Center – World Ocean Database (WODselect) Caribbean Australia Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Data Paper in Submission to Geoinformatics Conference
Coral Diseases White band disease Patchy necrosis Ring syndrome Necrotic patch syndrome Abnormal development Tissue necrosis Cancer growth Hyperplasmic tumours White syndrome Pink spots Pink blotch syndrome Thin dark line Orange patch Disease White pox lesions Yellowing disease Porites ulcerative white spot disease Tumours Dark spots disease Other disease White pox White Band Disease type I Corallliphila abbreviata, gastrapod predator Atramentous necrosis White band disease type II Black Patch Disease Skeleton eroding band Epizootic Cyanobacteria, Scytonema sp. Yellow Band Disease Brown Band Disease Dark band No disease observed at time of survey Dark band syndrome White spot Bleaching disease Red plague syndrome Neoplasia White disease Fungal disease Plague Blistering necrosis Red band disease Fast tissue necrosis White line disease Aspergillosis Pink line syndrome Yellow Band Disease - Atlantic Purple band Hyperplasia Red band disease II Vibrio coralyticus disease Black Band Disease Disease unspecified White plague Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Data Paper in Submission to Geoinformatics Conference
Acropora divaricata Acropora gemmifera Astreopora spp. Acropora polystoma Porites attenuata Madrepora annularis Eusmilia fastigiata Turbinaria reniformis Porites porites Favia fragum Pocillopora damicornis Acropora cytherea Acropora hyacinthus Acropora microphthalma Platygyra sinensis Favia favus Montipora informis Platygyra spp. Favia stelligera Acropora monticulosa Montipora patula Acropora palifera Lobophytum batarum Acropora humilis Helioseris cucullata Acropora formosa Goniopora columna Agaricia lamarcki Acropora cervicornis Madracis decactis Pavona spp. Astreopora myriophthalma Meandrina meandrites Colpophyllia breviserialis Favia valenciennesii Echinopora gemmacea Porites harrisoni Montipora verrucosa Favites pentagona Stephanocoenia michelinii Favia pallida Podabacia crustacea Diploria spp Diploastrea spp. (null) Favia spp. Cyphastrea microphthalma Acropora nobilis Gorgonia flabellum Platygyra daedalea Acropora squarrosa Echinopora spp. Acropora clathrata Mycetophyllia lamarckiana Acropora capillaris Montipora florida Acropora microclados Acropora pharaonis Montastraea faveolata Lobophyllia corymbosa Madracis mirabilis Millepora alcicornis Leptoria phrygia Acanthastrea spp. Montastraea annularis Acropora variabilis Turbinaria mesenterina Acropora downingi Agaricia humilis Acropora solitaryensis Millepora spp. Seriatopora spp. Acropora robusta Leptoseris mycetoseroides Goniastrea pectinata Acropora sarmentosa Acropora spp. Porites spp. Alveopora gigas Cyphastrea chalcidicum Agaricia agaricites Manicina areolata Acropora valencennesii Mycedium elephantotus Pseudopterogorgia americana Diploria clivosa Acropora millepora Symphyllia radians Platygyra lamellina Mycedium spp. Diploria strigosa Colpophyllia natans Pavona gigantea Montipora spp. Acropora florida Porites lichen Montipora aequituberculata Leptoseris cucullata Oulophyllia spp. Pocillopora spp. Goniastrea retiformis Gorgonia ventalina Pocillopora verrucosa Lobophyllia spp. Pocillopora meandrina Turbinaria radicalis Mussa angulosa Stylophora pistillata Siderastrea radians Acropora valida Stephanocoenia intersepta Porites astreoides Dichocoenia stokesii Mycetophyllia ferox Favia matthaii Goniopora somaliensis Porites lutea Plexaura homomalla Platygyra pini Agaricia tenuifolia Acropora palmata Porites divaricata Fungia spp. Madrepora kauaiensis Hydnophora microconos Pocillopora eydouxi Siderastrea siderea Acropora prolifera Acropora virgata Acropora austera Porites furcata Turbinaria frondens Acropora intermedia Pachyseris gemmae Dendrogyra cylindrus Montastraea cavernosa Montipora tuberculosa Millepora complanata Oculina patagonica Porites compressa Isophyllastrea rigida Goniopora stokesi Montastraea spp. Solenastrea bournonii Madrepora cavernosa Montastraea franksi Diploria labyrinthiformis Acropora hemprichii Acropora tenuis Acropora aspera Psammocora spp. Porites nodifera Leptoseris glabra Stylophora spp. Echinophyllia aspera Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Data Coral Genomes The Marine Genomics Project Ensembl
Montastraea annularis Porites porites Montastraea faveolata Porites astreoides Oculina varicosa Acropora palmata Ensembl Acropora millepora Porites lobata Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Architecture Programming (Microsoft) Web browser ASP.NET C# Server
Talk about the architecture, database layer, interface layer (through the web), internet to computer, computer to database and to Virtual Earth, logic, Server MS SQL Database Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Results Data Entry: 7808 – lines of disease
57848 – line of environmental ~ 4,000 – corresponding geographical matches Almost all data from the Caribbean latitude longitude disease temperature_C salinity_psu oxygen_ml_l phosphate_m_mol_l silicate_m_mol_l nitrate_m_mol_l pH Alkalinity (meq/l) Tritium (TU) Helium (nM) Argon (nM) Neon (nM) 11.83 -66.75 Purple band 11.77 -66.71 Dark spots disease 1.8671 18.15 -65.3 White band disease Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Results Data Entry Paper in Submission to Geoinformatics Conference

Results Specification of parameters

Results Coral Reef Disease Ontology

Discussion and Notes The lack of genomic data presents limited interpretation of on going analyses by our group We will eliminate the data entry portion and just read straight from the database Gene Ontology is speculative until further distinguishing data is available – More genomic and environmental data Better normalization techniques The structure will evolve as the data collected evolves Different ontological “engines” – Cosine comparisons and “Semantic Weight” Temporal extent will add dimension to the interpretation HCI contribution will improve usability and interpretation of results Different ontological engines can be chosen in our coding interface Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Thank You Claudia Johnson (Geology) Mehmet Dalkilic (Bioinformatics)
Susan Morse Coleman (HCI/d) School of Informatics Saturday, September 22, 2018 Paper in Submission to Geoinformatics Conference

Questions? Paper in Submission to Geoinformatics Conference

A New Method of Examining Coral Reef Ecosystems: A First Use of Genomic and Bioinformatics Techniques Indiana University School of Informatics Capstone.

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A New Method of Examining Coral Reef Ecosystems: A First Use of Genomic and Bioinformatics Techniques Indiana University School of Informatics Capstone.

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Presentation on theme: "A New Method of Examining Coral Reef Ecosystems: A First Use of Genomic and Bioinformatics Techniques Indiana University School of Informatics Capstone."— Presentation transcript:

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