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2012 Deep Sea Guide Project Update

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by Brian Schlining on 27 February 2013

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Transcript of 2012 Deep Sea Guide Project Update

A Little History 2009 - Feasibility Study for MBARI Biodiversity Initiative “There are several ways that we might go about building a biodiversity baseline for the deep-sea communities of Monterey Bay. [...]" 2010 - Biodiversity Initiative “The immediate objective of the Initiative is to develop a biodiversity baseline for the deep waters off Monterey." 2010 - Video Annotation Analysis and Presentation “Discussions with the Biodiversity Initiative researchers have indicated that the analyses of video annotations are critical first steps to establishing a baseline for biodiversity research” “We are proposing to aggregate existing analysis created for other projects and systematically apply them to the video annotations.” “In order to provide access to the data products, we are proposing to create a web-based interface, dubbed the Deep Sea Guide.” The MBARI Deep-sea Guide A Walkthrough of an Analysis Video Annotations VideoArchiveSet VideoArchive VideoFrame Observation Association CameraData PhysicalData CameraDeployment Recorded Date 3,516,852 3,516,852 Latitude
Longitude
Depth 3,509,256 3,758,647 Concept Name 22,958 4,585 4,661 Link 1,102,242 Expedition Data Merge VARS with Expedition CamlogData 27,000,000+ RovctdData 40,000,000+ RovctdBinData 5,500,000+ CleanNavData 40,000,000+ RawNavData 46,000,000+ Merged nightly

'Smart' code.
Uses best available data
Checks for clean data if raw data was previously used. PhysicalData Latitude
Longitude
Depth 3,509,256 CameraData CamlogData 27,000,000+ RovctdData 40,000,000+ CleanNavData 40,000,000+ Creating a Depth Histogram Actinopoda Acantharea Heliozoa Radiolaria Phaeodaria Polycystina Knowledgebase Phaeoconchia Phaeocystina ... ... ... ... Coelodendridae Concharidae Astracanthidae Aulacanthidae ... Collodaria Nassellaria ... ... ... ... ... Astrostrobiidae Cannobotryidae ... Collozoida Read Annotations Create Data 'Artifacts' Filter for Duplicates Filter by 'Zones' Start Register in DSG Database Association Link 1,102,242 Since August 8, 1988 TAPE SET: V1688
CONCEPT: Grimpoteuthis
LINK: identity-reference | self | 1 Current zones:
Global (i.e. unfiltered)
Greater Monterey Bay

Zones can be created on request:
Baja
Hawaii
Midwater 1 station
etc. Typically a zone is some spatial bounds but we can use anything as a zone:
Altitude (i.e. only benthic annotations)
Time (start and end dates)
or any combination of parameters Normalize by Effort Preparing the Data V0001
T0001
D0001
...
V3668
T1163
D0332 List all Dives Read Start and End Dates T1163

2001-12-20 14:52:15Z
2001-12-20 21:56:15Z Fetch best navigation data CleanNavData 40,000,000+ RawNavData 46,000,000+ Estimate duration of Navigation
datum 1. Calculate dt between each
record
2. Toss out outlier values
3. Use mean(dt) as duration Why do we need the Deep-sea Guide? 2 files x 4261 Concepts = 8522 x 2 Zones = 17044 x 2 = 34088
(normalized) repeat for other data products: = a lot of files It would be handy to 'google' for data ... x ... and see thumbnails of available data Metadata would be nice too. and maybe the data's parent data as well The Good Stuff ... The Deep-sea Guide is written in Scala Why Scala? 1. Runs on Java Virtual Machines VARS is written in Java.
The DSG reuses VARS libraries.
Saves lots of development time. 2. Concise syntax 4. Fast 5. Easy to parallelize It takes 6 hours to generate ~116,000 data products The Deep-sea Guide Architecture 1. Contributors Engineer:
Brian Schlining

Video Lab:
Nancy Jacobsen Stout
Kyra Schlining
Susan von Thun
Linda Kuhnz
Lonny Lundsten Scientists:
Charlie Paull
Steve Haddock

Interns:
Erica Curles
Hana Hashim Built Around a Micro-framework Scalatra 1. provides routing
2. Excellent templating and layouts
3. Deploys on MBARI infrastructure request DeepSeaGuide.scala http://seaspray.shore.mbari.org:8082/dsg/search/concept/grimp
http://seaspray.shore.mbari.org:8082/dsg/view/concept/Grimpoteuthis
http://seaspray.shore.mbari.org:8082/dsg/images/concept/Grimpoteuthis
http://seaspray.shore.mbari.org:8082/dsg/plots/concept/Grimpoteuthis
http://seaspray.shore.mbari.org:8082/dsg/annotated/images/concept/Grimpoteuthis Transformer Map("searchterm" -> "pname",
"resultcount" -> 20,
"results" -> List(
Map("primaryimagelink" -> "http://foo/bar/someimage.png,
"viewlink" -> "/view/concept/pname",
"primaryname -> "pname",
"taxa" -> "<ul class="tree><li>1</li><li>2</li><li>3</li></ul>",
"alternate_names" -> "foo, bar, but-not-pname", // OPTIONAL
"rank" ->supersubgenus" // OPTIONAL
)) TemplateEngine <!DOCTYPE html>
<html>
<head>
<link rel="stylesheet" href="../../assets/styles/reset.css"/>
<link rel="stylesheet" href="../../assets/styles/core.css"/>
<link rel="stylesheet" href="../../assets/styles/no_nav_interior.css"/>
<link rel="stylesheet" href="../../assets/styles/searchresults.css"/>
<title>MBARI's Deep Sea Guide</title>
</head>
<body>

<!--
Map("searchterm" -> "pname",
"resultcount" -> 20,
"results" -> List(
Map("primaryimagelink" -> "http://foo/bar/someimage.png,
"viewlink" -> "/view/concept/pname",
"primaryname -> "pname",
"taxa" -> "<ul class="tree><li>1</li><li>2</li><li>3</li></ul>",
"alternate_names" -> "foo, bar, but-not-pname", // OPTIONAL
"rank" ->supersubgenus" // OPTIONAL
))
-->

<header>
<h1>{{resultcount}} results for "<span class="{{class}}">{{searchterm}}</span>"</h1>
</header>
<div id="search_results">
<div class="searchhead">
<span class="h_image">Primary Image</span>
<span class="h_name">Name</span>
<span class="h_tax">Taxonomy</span>
</div>

{{#results}}
<div class="result">
<span class="image">
<a href="{{viewlink}}" target="_blank">
<img src="{{primaryimagelink}}" />
</a>
</span>
<span class="allnames">
<a href="{{viewlink}}">
<span class="{{class}}"><span class="primary_name">{{primaryname}}</span> </span>
</a>
<p>
{{#alternate_names}} <!-- HIDE alternate names if none are found -->
<span class="italics">Also known as:</span>
<span class="alternate_names">{{alternate_names}}</span>
{{/alternate_names}}
</p>
</span>
<span class="short_tax">
<span class="taxa">{{taxa}}</span>
{{#rank}} <!-- HIDE rank if it's not found -->
<p>
<span class="italics">Rank:</span>
<span class="rank">{{rank}}</span>
</p>
{{/rank}}
</span>
</div>
{{/results}}

</div>
<!-- <span class="navigator" wicket:id="navigator">[dataview navigator]</span> -->

</body>
</html> seaspray.shore.mbari.org seadog.wf.mbari.org Future Work 1. Data product validation
2. Additional data products
3. Schedule products to update every week
4. Improve the user interface
5. Link to external taxonomy authorities
6. Add pages for dive quality control Feedback is welcome!
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