1. Marine Mammal Health Monitoring and Analyses Platform
DRAFT Documents: Discussion
Felimon Gayanilo
Systems Architect
Harte Research Institute, Texas A&M University Corpus Christi
ORCID:

2. System Overview
Marine Mammal Health Monitoring and Analysis Platform (MMHMAP): 3-year Strategic Plan ( )

3. Use Cases and scenario
Incidence Notification &
Data Flow

4. Use Cases and scenario
Reporting Requirements: Not established

5. System Overview
Marine Mammal Health Monitoring and Analysis Platform (MMHMAP): 3-year Strategic Plan ( )

6. System Architecture: Overview
Multi-tiered Architecture

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

8. 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 T13:10:00Z) 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.

9. 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

10. 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

11. 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.

12. 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

13. 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

14. Middle Tier Authenticator
Communicates with an OpenID Provider and returns user profile and
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

15. 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

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

17. Data Exchange

18. RP – Relying Party
OP – OpenID Provider

19. 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

20. 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.

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

22. 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

23. 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

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

25. Darwin Core What’s Next? Data Security and Risk Mitigation
Term
Definition
Reference
Comments
<?xml version="1.0"?> <rdf:RDF xmlns:rdf=" xmlns:owl=" xmlns:j.0=" xmlns:omv=" xmlns=" xmlns:rdfs=" xmlns:xsd=" xml:base=" > <rdf:Description rdf:about=" <Reference rdf:resource=" <Definition>increased excretion rate of albumin in the urine in the range of mg/g creatinine</Definition> <Category>Urinalysis</Category> <Vocabulary>Microalbumin</Vocabulary> <rdf:type rdf:resource=" </rdf:Description> <rdf:Description rdf:about=" <Reference rdf:resource=" <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=" </rdf:Description> <rdf:Description rdf:about=" <Reference rdf:resource=" <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=" </rdf:Description> <rdf:Description rdf:about=" <Reference rdf:resource=" <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
Vocabulary – words used in a particular sphere, marine mammals
Common vocabulary – required in an interdisciplinary efforts
Register
Register

26. 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

27. 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

28. TASK & Timeline

29. Marine Mammal Health Monitoring and Analyses Platform
Felimon Gayanilo
Systems Architect
Harte Research Institute, Texas A&M University Corpus Christi
ORCID:
Thank You