Marine Mammal Health Monitoring and Analyses Platform DRAFT Documents: Discussion Felimon Gayanilo Systems Architect Harte Research Institute, Texas A&M University Corpus Christi email: fgayanilo@tamu.edu ORCID: 0000-0003-0520-5737

System Overview Marine Mammal Health Monitoring and Analysis Platform (MMHMAP): 3-year Strategic Plan (2015-2017) https://www.mmc.gov/wp-content/uploads/MMHMAP-Vision-Document-Final.pdf

Use Cases and scenario Incidence Notification & Data Flow

Use Cases and scenario Reporting Requirements: Not established

System Overview Marine Mammal Health Monitoring and Analysis Platform (MMHMAP): 3-year Strategic Plan (2015-2017) https://www.mmc.gov/wp-content/uploads/MMHMAP-Vision-Document-Final.pdf

System Architecture: Overview Multi-tiered Architecture

Dependencies External DBs (e.g. WoRMS) for taxonomic referencing

Persistent Record Identifier “urn:” <NID>”:”<NSS> <org>:<eId>:<aId>.<aIdn>:<lId>:<rId>.<rIdn> _________________________________________ Described in “Data Capture and Encoding” NID -> Namespace Identifier NSS -> Namespace Specific String <org> an abbreviated label of the organization or individual reporting the event; <eId> local identifier used by the reporting <org>. If the <org>do not maintain a local identifier, label identifying the person recording the event, or a period the event started can be used and the format, yyy-mm-ddThh:mm:ssZ may be used (e.g. 2017-03-01T13:10:00Z) in it stead; <aId>this is the animal ID. If animal identifier system is not maintained by , a formatted string or sequential numbers, starting with ‘001’ can be used; <aIdn> sequential number from 1 to identify specific animals (default is ‘1’) recorded on an event. The only time this number increment is if the returns to be recorded; <lId> this is similar to but is in reference to the label for the laboratory where the tissue sample or other materials from were sent for analyses; <rId> this is the identifier given to laboratory results. If does not maintain record identifier, a formatted string of sequential numbers may be used; and <rIdn> this is a sequential number starting from ‘1’ that references a results document.

Independent DBs User Registry will contain only the following: Username (OpenID uname) User details (OpenID supplied) Data access level (default: public level and can be modified only by the administrator) User audit on system access

Independent DBs Laboratory Registry will be initialized with the following: Laboratory ID Laboratory details (name, address, contact person and details, alternate contact person and details) NOTE: can be modified only by the administrator

Independent DBs National DB of HealthMAP data is designed to initially mirror a regional system (Gulf of Mexico) and can be scaled to consolidate data from other regions. This feature will not be available in the initial phases.

Middle Tier Data Ingest Validate data using a predefined Schematron following the recommended data schema Save captured and forwarded data by user interfaces Coordinates with System Alerts and Messaging to send messages to appropriate users and auditing tables for changes on the databases

Middle Tier Data Report Generator Provides a repository of SQL statements and allows the listing to be extended and managed (add, delete, edit) Generates an XML file based on SQL command and when applicable, following the proposed data schema or extended version when required Coordinates with System Alerts and Messaging to send status reports to appropriate modules

Middle Tier Authenticator Communicates with an OpenID Provider and returns user profile and email Updates the audit table to log user behavior within the system Stores and retrieve the data access level of the user based on the uReg and starts a persistent session until the user logs out, the interface is closed or no actions detected after an hour

Data Exchange Standard & BASE MODULES Data Capture Data View Data Browse … <xml> request/<xml> Data Ingest Data Report Generator … <xml> <xml> Core DB … NSDB WoRMS DIVER

see http://data.gcoos.org/mmhmap/ Data Schema Standardized data exchange schema (XSD) Darwin Information Typing Architecture (DITA) equivalent is also available. Schema Link: http://data.gcoos.org/mmhmap/xml/1.0/ Documentation: see http://data.gcoos.org/mmhmap/

Data Exchange

RP – Relying Party OP – OpenID Provider

Application Layer Data Browse: Table view of results from a user defined SQL Data View: Interactive map display of points, group of points, etc. System Alerts and Messaging: Interface to display messages, message forwarding, and interface for apps to receive notifications. Data Capture: Internet-based (browser) data collection forms Data Services: ID generator/validator, update lists, statistics

Application Layer Packages Data Browse Data View System Alerts and Messaging Data Capture  Data Services Common Features All packages in the application layer are web-based (on-line), user-interactive, and database controlled. Off-line version also available.

Application Layer Data Capture Taking advantage of online services (e.g. interactive map and location detection) BLOB or image storage

What’s NEXT? Data Security and Risk Mitigation  Data Access Protocol Data Security and Risk Mitigation  Vocabulary and Standards HealthMAP Organization SDA Change Management Data Access Designation Capabilities Read BAI and health categories Edit/Add BAI and health categories Read detailed health data Edit/Add detailed health data Initialize DB and manage users Level 1 Public ●   Level 2 Full Read Access Level 3 Researcher/ Collaboratora ●b Level 4 Administrative a Same read access as Level 2 but also read access to datasets they are collaborators on that may not yet be public, and full read/write access to their own data sets. b Write access is limited to only the data they own/provide

What’s Next? Data Security and Risk Mitigation  Physical Redundancy Data Security and Risk Mitigation  Vocabulary and Standards HealthMAP Organization SDA Change Management Domain Rollover Function

What’s Next? Data Security and Risk Mitigation  Vocabulary and Standards HealthMAP Organization SDA Change Management Response Process

Darwin Core What’s Next? Data Security and Risk Mitigation Term Definition Reference Comments <?xml version="1.0"?> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:j.0="http://mmisw.org/ont/mmi/20081020/ontologyMetadata/" xmlns:omv="http://omv.ontoware.org/2005/05/ontology#" xmlns="https://xdomes.org/ont/mmhmap/lab_procedures/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xml:base="https://xdomes.org/ont/mmhmap/lab_procedures" > <rdf:Description rdf:about="https://xdomes.org/ont/mmhmap/lab_procedures/microalbumin"> <Reference rdf:resource="https://www.ncbi.nlm.nih.gov/pubmed/15538104"/> <Definition>increased excretion rate of albumin in the urine in the range of 30-299 mg/g creatinine</Definition> <Category>Urinalysis</Category> <Vocabulary>Microalbumin</Vocabulary> <rdf:type rdf:resource="https://xdomes.org/ont/mmhmap/lab_procedures/varTerm"/> </rdf:Description> <rdf:Description rdf:about="https://xdomes.org/ont/mmhmap/lab_procedures/urobilinogen"> <Reference rdf:resource="http://www.merriam-webster.com/medical/urobilinogen"/> <Definition>any of several chromogens that are reduction products of bilirubin and yield urobilins on oxidation</Definition> <Category>Urinalysis</Category> <Vocabulary>Urobilinogen</Vocabulary> <rdf:type rdf:resource="https://xdomes.org/ont/mmhmap/lab_procedures/varTerm"/> </rdf:Description> <rdf:Description rdf:about="https://xdomes.org/ont/mmhmap/lab_procedures/ketones"> <Reference rdf:resource="http://www.merriam-webster.com/dictionary/ketones"/> <Definition>any of a class of organic compounds (as acetone) characterized by a carbonyl group attached to two carbon atoms</Definition> <Category>Urinalysis</Category> <Vocabulary>Ketones</Vocabulary> <rdf:type rdf:resource="https://xdomes.org/ont/mmhmap/lab_procedures/varTerm"/> </rdf:Description> <rdf:Description rdf:about="https://xdomes.org/ont/mmhmap/lab_procedures/trematode"> <Reference rdf:resource="http://www.dictionary.com/browse/trematode"/> <Definition>any parasitic platyhelminth or flatworm of the class Trematoda, havingone or more external suckers; fluke.</Definition> <Category>Parasitology</Category> <Vocabulary>Trematode</Vocabulary> Transform RDF Define Terms What’s Next? Darwin Core Common terms to maximize re-usability Align & Enrich Transform RDF Data Security and Risk Mitigation Vocabulary and Standards  HealthMAP Organization SDA Change Management https://xdomes.org/ont/mmhmap/lab_procedures Vocabulary – words used in a particular sphere, marine mammals Common vocabulary – required in an interdisciplinary efforts Register Register

What’s Next? Controlled vocabulary Disaster Recovery Plan Executive Office (MMC, MMHMAP National Coordinator) Software & Network Data Capture & Quality Outreach & Education Advisory Committee (NOAA IOOS, Fisheries, MMC, Private Sect) Controlled vocabulary Disaster Recovery Plan HealthMAP Organizational Support  SDA Change Management Executive Office (MMHMAP National Coordinator + Office Assistant): Monitor and coordinate all MMHMAP activities Advisory Committee: Meet regularly or as necessary to review the program and its activities, and provide recommendations to strengthen the program Software & Network: Ensure that the functional requirements of the system are developed and maintained Data Capture & Quality: Continually review data collection activities and procedures to develop standards across the community Outreach & Education: Establish awareness of the program and assist in the deployment of the technologies that will emanate from the program

What’s Next? Controlled vocabulary Disaster Recovery Plan Change Management Controlled vocabulary Disaster Recovery Plan HealthMAP Organizational Support SDA Change Management  Changing the design to either meet a change in requirement or additional functions, needs to go through a process. Ad hoc decisions should be avoided

TASK & Timeline http://data.gcoos.org/mmhmap/MMHMAP_6_Task_and_Module_Implementation.pdf

Marine Mammal Health Monitoring and Analyses Platform Felimon Gayanilo Systems Architect Harte Research Institute, Texas A&M University Corpus Christi email: fgayanilo@tamu.edu ORCID: 0000-0003-0520-5737 Thank You