Alaska 

Fisheries Science 

Center 

National Marine 

Fisheries Service 

U.S DEPARTMENT OF COMMERCE 

AFSC PROCESSED REPORT 2009-01
 


Alaska Fisheries Science Center 

Essential Fish Habitat Data Inventory 

January 2009 

This report does not constitute a publication and is for information only. 

All data herein are to be considered provisional. 
This document should be cited as follows: 

McConnaughey, R. A., J. V. Olson, and M. F. Sigler. 2009. Alaska Fisheries 

Science Center essential fish habitat data inventory. AFSC Processed Rep. 

2009-01, 40 p. Alaska Fish. Sci. Cent., NOAA, Natl. Mar. Fish. Serv., 7600 Sand 

Point Way NE, Seattle WA 98115. 

Reference in this document to trade names does not imply endorsement by the 

National Marine Fisheries Service, NOAA. 
Notice to Users of this Document 

This document is being made available in .PDF format for the convenience of users; however, the 

accuracy and correctness of the document can only be certified as was presented in the original hard 

copy format. 

Alaska Fisheries Science Center 

Essential Fish Habitat Data Inventory 

by 

Robert A. McConnaughey1

, John V. Olson2, and Michael F. Sigler3

1

Alaska Fisheries Science Center 

Resource Assessment and Conservation Engineering Division 

7600 Sand Point Way NE 

Seattle WA 98115 

2

Alaska Regional Office 

Habitat Conservation Division 

222 West 7th Ave. 

Anchorage, AK 99513 

3

Alaska Fisheries Science Center 

Habitat and Ecological Processes Research Program 

17109 Point Lena Loop Road 

Juneau, AK 99801 

January 2009 
 
Contents 

Introduction........................................................................................................................................................1

Habitat Data Inventory .....................................................................................................................................2

Habitat Areas of Particular Concern: a case study of EFH habitat data. ..........................................................3

Delta submarine video archiving. .....................................................................................................................4

Estuaries database.............................................................................................................................................5

Essential Fish Habitat requirements for skate nurseries. ..................................................................................6

Alaska coastal mapping / Nearshore Fish Atlas of Alaska...............................................................................7

Effect of light intensity on vertical and spatial distribution of fish and their availability to bottom trawl 

and acoustic surveys......................................................................................................................................8

Nearshore habitat use in juvenile Pacific cod...................................................................................................9

Flatfish nursery function.................................................................................................................................10

Atka mackerel EFH. .......................................................................................................................................11

Habitat influence on rearing condition and overwinter survival of juvenile capelin (Mallotus villosus).......12

Bristol Bay reconnaissance.............................................................................................................................13

Bering Sea echosounder survey......................................................................................................................14

EBSSED sediment database. ..........................................................................................................................15

2006 FISHPAC experiment............................................................................................................................16

1996 TRAWLEX experiment.........................................................................................................................17

1997 TRAWLEX experiment.........................................................................................................................18

TRAWLEX BACI experiment. ......................................................................................................................19

Trawl-effect reduction tests. ...........................................................................................................................20

Multibeam habitat mapping in the Alaska region...........................................................................................21

Trawlability - AFSC survey single-beams......................................................................................................22

usSEABED. ....................................................................................................................................................23

Pacific ocean perch (Sebastes alutus) habitats. ..............................................................................................24

Aleutian Islands cooperative acoustic survey study. ......................................................................................25

Kodiak fishery interactions and fisheries oceanography studies. ...................................................................26

Atka mackerel tag release and recovery. ........................................................................................................27

Pacific cod Cape Sarichef localized depletion experiment.............................................................................28

Down to 50 m bathymetry. .............................................................................................................................29

Appendix A. Meeting agenda, participants and workshop minutes..................................................................31

Appendix B. Data management system example from the Mojave Desert.......................................................39

 iii
 
 

Introduction 

The Magnuson-Stevens Fishery Conservation and Management Act is the primary law regulating marine 

fisheries management in the United States. This Act includes a requirement to define the essential fish habitat 

(EFH) of all federally managed species. Since passage of the Act in 1996, scientists with the National Marine 

Fisheries Service’s Alaska Fisheries Science Center (AFSC) have conducted diverse research projects that 

address this requirement. In many cases, these studies have been published in the peer-reviewed scientific 

literature. However much of the data have not been assembled in a readily accessible and centralized location, 

thereby limiting their overall utility. 

In July 2005, the newly formed Habitat and Ecological Processes Research (HEPR) Program convened a 

meeting of AFSC staff to discuss EFH research in the Gulf of Alaska (GOA), Bering Sea (BS), and Aleutian 

Islands (AI) regions. Meeting participants identified creation of an AFSC habitat data inventory as a high 

priority. In particular, participants felt that a habitat data inventory would be useful for communicating AFSC 

habitat research and would also facilitate future data analyses and EFH research. 

A workshop was held 20-21 September 2007 at the AFSC in Seattle, Washington. Workshop objectives were 

to: (1) inventory habitat data sets; (2) promote collaborative use of these data through greater awareness and 

accessibility; and (3) informally discuss EFH research and management issues. The workshop was attended 

by 27 individuals representing five AFSC Divisions, the Alaska Regional Office, the North Pacific Fishery 

Management Council, the Alaska Department of Fish and Game and the environmental group Oceana. The 

workshop conveners were Bob McConnaughey, John Olson and Jon Heifetz. The meeting agenda, 

participants and minutes are found in Appendix A. 

Meeting participants presented summaries of the habitat data sets. Next, Eric Boerner of the AFSC’s National 

Marine Mammal Laboratory presented lessons learned and practical insights from a similar exercise to 

catalog and share terrestrial environmental data among various scientific and public user groups (Appendix 

B). This presentation was followed by a structured group discussion that was specific to the needs for 

improved awareness of and accessibility to Alaska EFH data. Finally, participants discussed practical issues 

such as the need for more and better metadata, the desirability of greater research collaboration, and possible 

methods for integrating habitat studies conducted at substantially different spatial scales. 
Habitat Data Inventory 

The habitat data sets were described following a standard format for this report. This inventory is the main 

product of the workshop and this report. The habitat data inventories begin on the next page. 

 2
Name of Project: Habitat Areas of Particular 

Concern: a case study of EFH habitat data. 

Region (GOA, BS, AI): GOA. 

Specific Location: Fairweather Grounds and 

Cape Ommaney. 

Data Types (Formats): Point (latitude, 

longitude) data of coral locations. 

Instruments/Devices Used For Collection:

DSV Delta. 

Summary of Project/Data: Concentrations of 

Primnoa sp. corals were documented during 

submersible groundfish surveys in the 1990s 

and subsequent directed research. Commercial 

fish species and in situ disturbances were 

observed in association with high relief corals. 

The 2004 Habitat Areas of Particular Concern 

(HAPC) selection process resulted in a closure 

of five discrete areas with known densities of 

Primnoa sp. Each area was considered as an 

HAPC based on the specific characteristics of 

each site. The Primnoa Coral Garden Marine 

Reserve prohibits any bottom contact fishing 

gear in a 13.5 nmi2

 area. A larger area was designated as HAPC for future research. 

Sampling Dates: 2001. 

Status of Project/Data Processing: Additional dives have occurred since the HAPC designation. 

References/Publications: 

(1) Heifetz, J. 2002. Coral in Alaska: distribution, abundance, and species associations. Hydrobiologia 471: 

19-27. 

(2) Krieger, K. J. 2001. Coral (Primnoa) impacted by fishing gear in the Gulf of Alaska. Pages 106-116 in J. 

H. M. Willison et al. (eds.). Proceedings of the first international symposium on deep-sea corals. Ecology 

Action Centre and Nova Scotia Museum, Halifax, Nova Scotia. 

(3) Krieger, K. J. and B. L.Wing. 2002. Megafauna associations with deepwater corals (Primnoa spp.) in the 

Gulf of Alaska. Hydrobiologia 471: 83-90. 

(4) Stone, R., J. Heifetz, and J. L. Freese. Unpublished HAPC proposals to the North Pacific Fishery 

Management Council for Cape Ommaney and Fairweather grounds. NOAA Fisheries, Alaska Fisheries 

Science Center, Auke Bay Laboratory, Juneau, Alaska. 

(5) Witherell, D. and C. Coon. 2001. Protecting gorgonian corals from fishing impacts. Pages 117-125 in J. 

H. M. Willison et al. (eds.). Proceedings of the first international symposium on deep-sea corals. Ecology 

Action Centre and Nova Scotia Museum, Halifax, Nova Scotia. 

Point of Contact: Cathy Coon, North Pacific Fishery Management Council, 907-271-2809, 

cathy.coon@noaa.gov. 

 3
Name of Project: Delta 

submarine video 

archiving. 

Region (GOA, BS, AI): 

GOA, BS, AI. 

Specific Location:

Various. 

Data Types (Formats):

Video, *.xls. 

Instruments/Devices 

Used For Collection:

Delta submarine. 

Summary of 

Project/Data: For about 

20 years scientists at the 

Auke Bay Laboratories 

have been using the Delta

submarine for a wide 

range of research projects. 

About 500 dives have been completed. The video collected during these projects provides valuable direct 

observations of seafloor habitat and biological attributes. This project is assembling a database that will 

include dive locations and basic biological and substrate information from each of the dives. To date, 

biological and substrate data have been processed for about 40% of the dives. If there is interest, the database 

may be expanded to include video collected from ROVs and/or video collected by other AFSC Divisions and 

programs. 

Sampling Dates: 1988-2006. 

Status of Project/Data Processing: In progress. 

References/Publications: None. 

Point of Contact: Jon Heifetz, ABL, 907-789-6054, jon.heifetz@noaa.gov. 

 4
Name of Project: Estuaries database. 

Region (GOA, BS, AI): GOA. 

Specific Location: Estuaries throughout 

southeast Alaska. 

Data Types (Formats): ACCESS 

database. 

Instruments/Devices Used For 

Collection: Fyke net, seine, trawl, and 

physical data devices. 

Summary of Project/Data: Since 1998 

estuaries throughout southeast Alaska 

have been sampled with several gear types 

to assess fish habitat utilization. Some 

estuaries were sampled multiple times 

within a year and over multiple years to 

determine temporal patterns of habitat use. 

The most common fish species 

encountered were yellowfin sole, chum 

and pink salmon, starry flounder, and 

Pacific herring. 

Sampling Dates: 1998 - present. 

Status of Project/Data Processing:

Ongoing. 

References/Publications: None. 

Point of Contact: Mitch Lorenz, ABL, 907-789-6036, mitch.lorenz@noaa.gov. 

 5
Name of Project: Essential Fish Habitat 

requirements for skate nurseries. 

Region (GOA, BS, AI): Eastern Bering Sea. 

Specific Location: Shelf-slope interface. 

Data Types (Formats): Biological data in 

Excel spreadsheets including depth, location, 

and bottom and sea-surface temperature. A 

single trackline through a nursery site 

recorded with digital video. 

Instruments/Devices Used For Collection:

Bottom trawl, Sea-bird SBE 39, bottom 

sounder. 

Summary of Project/Data: Six skate nursery 

sites were located and mapped using bottom 

trawls during 2004-2006. All sites occurred 

along the shelf slope interface between 135 

and 380 meters. The bottom was relatively 

flat sandy-muddy bottom with no evident 

relief or attached benthic invertebrates for all 

sites. Nursery sites were all small in area and 

possessed areas of highly concentrated egg 

cases. We collected egg case density, location 

(latitude and longitude), bottom depth, and temperature data, as well as species composition, length data and 

diet composition of selected predatory species. In summer of 2006, Craig Rose gathered digital video from a 

single camera-sled tow through an area of the Alaska Skate Nursery (AKS). 

2

180°W 175°W

170°W

170°W

165°W

55°N

55°N

60°N

60°N

175°W

165°W

180°0'0"W

170°0'0"W

170°0'0"W

60°0'0"N

60°0'0"N

Nursery Site Designations

AKN = Alaska Skate North

AKM = Alaska Skate Middle 

AKS = Alaska Skate South

BNN = Bering Skate North

BNS = Bering Skate South

ALS = Aleutian Skate South

Figure 1. 

Alaska

Eastern 

Bering 

Sea

AKS

ALS

BNS

AKM 

AKN

BNN

2

180°W 175°W

170°W

170°W

165°W

55°N

55°N

60°N

60°N

175°W

165°W

180°0'0"W

170°0'0"W

170°0'0"W

60°0'0"N

60°0'0"N

Nursery Site Designations

AKN = Alaska Skate North

AKM = Alaska Skate Middle 

AKS = Alaska Skate South

BNN = Bering Skate North

BNS = Bering Skate South

ALS = Aleutian Skate South

Figure 1. 

Alaska

Eastern 

Bering 

Sea

AKS

ALS

BNS

AKM 

AKN

BNN

Sampling Dates: 1 June 2004 – 3 July 2006. 

Status of Project/Data Processing: Initial process complete and analysis in progress. 

References/Publications: 

(1) Hoff, G. R. 2007. Reproductive biology of the Alaska skate, Bathyraja parmifera, with regard to nursery 

sites, embryo development and predation. Ph.D. dissertation, University of Washington, School of 

Aquatic and Fishery Sciences, Seattle. 160 p. 

(2) Hoff, G. R. 2008. A nursery site of the Alaska skate (Bathyraja parmifera) in the eastern Bering Sea. 

Fish. Bull., U.S. 106: 233-244. 

(3) Hoff, G. R. In Press. Embryo developmental events and the egg case of the Aleutian skate Bathyraja 

aleutica (Gilbert) and the Alaska skate Bathyraja parmifera (Bean). Journal of Fish Biology. xx; xx-xx. 

(4) Hoff, G. R. 2009. Skate Bathyraja spp. egg predation in the eastern Bering Sea. Journal of Fish Biology. 

74:250-269. 

(5) Hoff, G. R. 2008. A nursery site of the Alaska skate (Bathyraja parmifera) in the eastern Bering Sea. 

Fishery Bulletin. 106:233-244. 

Point of Contact: Gerald R. Hoff, RACE Division, 206-526-4580, jerry.hoff@noaa.gov.

 6
Name of Project: Alaska 

coastal mapping / Nearshore 

Fish Atlas of Alaska. 

Region: GOA, BS, AI, Arctic. 

Data Types (Formats): Lowaltitude, geo-referenced aerial 

video and still photography, 

biophysical habitat 

classifications, and beach seine 

catch data. 

 

Instruments/Devices Used For 

Collection: Helicopter, fixed 

wing aircraft, differential GPS, 

digital cameras, standard beach 

seine. 

Summary of Project/Data:

Alaska’s coastline is currently being mapped using the ShoreZone habitat classification system. The first 

phase of ShoreZone involves flying the coastline during minus tide windows and acquiring geo-referenced 

imagery. The second phase is the biophysical mapping where the imagery is analyzed for geomorphology and 

biological characteristics (e.g., eelgrass meadows, kelp beds). The third phase transfers the imagery and 

biophysical mapping data to an interactive online database for the public. The ShoreZone website is also used 

as a spatial platform for hosting additional datasets such as the Nearshore Fish Atlas of Alaska. The Fish 

Atlas database is linked to the ShoreZone website and contains 10 years of nearshore catch data (beach seine). 

Nearly 600,000 fish representing 98 species have been captured in over 800 seine hauls. Some of the most 

abundant species captured, mostly as juveniles, include walleye pollock, Pacific sand lance, Pacific herring, 

and salmon. 

Sampling Dates: ShoreZone (2001 to present); Fish Atlas (1998 to present). 

Status of Project/Data Processing: ShoreZone (see figure); Fish Atlas (up-to-date thru 2007). 

References/Publications: 

(1) Johnson, S. W., A. D. Neff, and J. F. Thedinga. 2005. An atlas on the distribution and habitat of common 

fishes in shallow nearshore waters of southeastern Alaska. U. S. Dep. Commer., NOAA Tech. Memo. 

NMFS-AFSC-157. 89 p. 

(2) http://www.fakr.noaa.gov/maps/szintro.htm

(3) http://www.fakr.noaa.gov/habitat/fishatlas/

Point of Contact: 

ShoreZone—Mandy Lindeberg, ABL, 907-789-6616, mandy.lindeberg@noaa.gov. 

Fish Atlas—Scott Johnson, ABL, 907-789-6063, scott.johnson@noaa.gov.

 7
Name of Project: Effect of 

light intensity on vertical and 

spatial distribution of fish and 

their availability to bottom trawl 

and acoustic surveys. 

Region (GOA, BS, AI): GOA, 

BS, AI. 

Specific Location: AFSC 

groundfish survey areas. 

Data Types (Formats):

Relative light intensity (in terms 

of downward irradiance) levels on scale from 0 – 255. 

Instruments/Devices Used For Collection: MK-9 Wildlife Computer tag. 

Summary of Project/Data: Project goals are assessment of the effects of light intensity and light penetration 

on the vertical and horizontal distributions of walleye pollock and their availability to bottom trawl and 

hydroacoustic surveys. Currently, these surveys are used as independent estimates of abundance, but our 

results may provide the means to integrate the results from these surveys and establish a relationship between 

light penetration and availability of walleye pollock to bottom trawls. If this relationship is established, it has 

the potential to reduce uncertainty in biomass estimates from the stock assessment model for walleye pollock 

in the EBS and to increase our understanding of pollock stock dynamics. In addition, the effect of light 

intensity and light penetration on the feeding success and degree of cannibalism (either through changes in 

horizontal or vertical distribution (prey availability), or through prey detection or selectivity (feeding 

behavior)), may affect the output of multi-species models that support management advice in the Ecosystem 

Considerations chapter of the Stock Assessment and Fisheries Evaluation Report provided to the North 

Pacific Fishery Management Council. 

Sampling Dates: Summer 2004-2007. 

Status of Project/Data Processing: EBS data from years 2004-2006 have been processed. GOA and AI data 

have not been processed and are stored in raw files. 

References/Publications: 

Kotwicki, S., A. De Robertis, P. von Szalay, and R. Towler. In press. The effect of light intensity on the 

availability of walleye pollock (Theragra chalcogramma) to bottom trawl and acoustic surveys. Can. J. 

Fish. Aquat. Sci. 

Point of Contact: Stan Kotwicki, RACE Division, 206-526-6614, stan.kotwicki@noaa.gov.

 8
Name of Project: Nearshore habitat 

use in juvenile Pacific cod. 

Region (GOA, BS, AI): GOA. 

Specific Location: Kodiak Island 

nearshore and embayments. 

 

Data Types (Formats): Monochrome 

video (digital tape), demersal beach 

seine and beam trawl (Excel). Other 

biological data include predator 

abundance, co-occurring juvenile 

gadid distribution and frozen 

specimens. 

Instruments/Devices Used For 

Collection: Baited camera; demersal 

beach seine; beam trawl; temperature, 

salinity, oxygen probes. 

Summary of Project/Data: Nearshore surveys of age-0 and -1 year old Pacific cod have been conducted 

over 2 years across multiple nearshore habitats and depths in coastal embayments around Kodiak Island. 

Seine surveys have 1) identified important habitats for age-0 cod in the nearshore; 2) provided a relative 

estimate of year-class strength; and 3) been an effective means of collecting juvenile cod for live transport to 

the Fisheries Behavior and Ecology Program laboratory at the Hatfield Marine Science Center in Newport, 

OR. Baited camera surveys have complemented these surveys by extending sampling into deep water and 

complex habitats that are not available to the seine. Baited camera video (DV tapes) is analyzed under several 

pre-established indices to provide a relative estimate of abundance stratified by depth zone and habitat type 

(e.g., Laminaria, eelgrass, etc.). In 2006, we were able to explain ontogenetic changes in habitat use of age-0 

gadids (Pacific cod, saffron cod, and walleye pollock) on a categorical level. In 2007, we are analyzing field 

data on a diel, seasonal and annual basis. It is clear that this temporal component to juvenile cod habitat use is 

extremely dynamic, largely the consequence of year-class strength, ontogenetic changes in habitat preference 

and changes in the physical environment (e.g., temperature, light level). 

Sampling Dates: Baited camera – July-August 2006 and July-October 2007; Seines – July-August 2006 and 

July-October 2007; Beam trawls – July-August 2006. Physical measures for same dates. 

Status of Project/Data Processing: Seine and trawl samples are fully processed. Video records have been 

processed for 2006; 2007 records presently are being analyzed. 

References/Publications:

(1) Laurel, B. J., A. W. Stoner, C. H. Ryer, T. P. Hurst, and A. A. Abookire. 2007. Comparative habitat 

associations in juvenile Pacific cod and other gadids using seines, baited cameras and laboratory 

techniques. J. Exp. Mar. Biol. Ecol. 351: 42-55. 

(2) Stoner, A. W., B. J. Laurel, and T. P. Hurst. 2008. Using a baited camera to assess relative abundance of 

juvenile Pacific cod: field and laboratory trials. J. Exp. Mar. Biol. Ecol. 354: 202-211. 

Point of Contact: Benjamin Laurel, RACE Division, 541-867-0197, ben.laurel@noaa.gov.

 9
Name of Project: Flatfish nursery function. 

Region (GOA, BS, AI): GOA. 

Specific Location: Kodiak nearshore and 

embayments. 

 

Data Types (Formats): (1) Monochrome 

video (digital tape and DVD), sediment grain 

size, bathymetry, trawl results (Excel and GIS 

coverages) (all high spatial resolution). (2) 

Other biological data – predator abundance, 

flatfish growth and predation rates (northern 

rock sole). 

Instruments/Devices Used For Collection:

Towed camera sled; beam trawl; sediment 

grab; temperature, salinity, oxygen probes or 

recorders. 

Summary of Project/Data: Beam trawling 

has been conducted during the summer season for 7 years at five sites believed to be representative for 

northern rock sole, Pacific halibut and other flatfish species in the GOA. To evaluate qualitative 

characteristics of the habitat, intensive video-camera coverages were acquired for three nurseries, with 

coarser-scale coverage for the surrounding shelf areas. Video tapes are analyzed for bed formations, sediment 

characteristics, and structural elements of the habitat (e.g., pits, algae, invertebrates). Spatially-explicit models 

were developed for the first year of the descriptive study. Seasonal and interannual variation in habitat 

utilization is now under analysis. The descriptive investigation is being supplemented by field experiments to 

evaluate spatial variation in flatfish growth and mortality. We believe that nursery function is best defined by 

the intersection of physical habitat characteristics, with larval supply and the biological processes affecting 

high growth and survival – and not by simple nominal descriptors of bottom type. 

Sampling Dates: Trawl samples - June through October 2002 to 2007; Towed camera – July 2002; July 

2003; June, July, August, September 2004; August 2005; July 2006; Physical measures for same dates; Field 

experiments for growth, mortality, etc. - summer 2005, 2006, 2007. 

Status of Project/Data Processing: Trawl samples, sediment and depth coverages fully processed. Video 

records processed for 2002, 2003; subsequent years under analysis. 

References/Publications:

(1) Hurst, T. P. and A. A. Abookire. 2006. Temporal and spatial variation in potential and realized growth 

rates of age-0 northern rock sole. J. Fish Biol. 68: 905-919. 

(2) Spencer, M. L., A. W. Stoner, C. H. Ryer, and J. E. Munk. 2005. A towed camera sled for estimating 

abundance of juvenile flatfishes and habitat characteristics: comparison with beam trawls and divers. 

Estuar. Coast. Shelf Sci. 64: 497-503. 

(3) Stoner, A. W., M. L. Spencer, and C. H. Ryer. 2007. Flatfish-habitat associations in Alaska nursery 

grounds: use of continuous video records for multi-scale spatial analysis. J. Sea Res. 57: 137-150. 

Point of Contact: Allan Stoner, RACE Division, 541-867-0165, al.stoner@noaa.gov.

 10
Name of Project: Atka mackerel EFH. 

Region (GOA, BS, AI): AI, GOA. 

Specific Location: Various locations along 

AI and GOA continental shelf. 

 

Data Types (Formats): Mini-DV video 

with time 

and GPS overlays, depth, and temperature. 

High-resolution multibeam bathymetry and 

backscatter snippets (.xtf) are also available 

for a single spawning and nesting ground 

near Dutch Harbor, AK. 

Instruments/Devices Used For Collection: 

Towed video drop camera (various camera 

and light combinations depending on light 

conditions) with real-time video feed and 

variable-speed electronic winch, SONY DVG300 

mini-DV recorder, Sea-bird SBE-39, Intuitive 

Circuits GeoStamp, Garmin GPS, and Globe 

plotting software. 

DD

DDDDDD DD DD D

DDDDD

DDDDDDDDDDD DDDDDDDDDDDDD D D DD DD

DDD

DDD

DD DD DDDD D D

180° 175°W 170°W 165°W 160°W 155°W

48°N

50°N

52°N

54°N

56°N

58°N

60°N

ALASKA

Summary of Project/Data: The objectives of this 

research were to locate and characterize the general 

spawning and nesting habitat of Atka mackerel 

(Pleurogrammus monopterygius) in Alaska and 

determine the geographic distribution and depth 

range of spawning and nesting sites. 

Sampling Dates: June to October 2004. 

Status of Project/Data Processing: Initial 

processing completed. Further analysis of habitat from videotapes is in progress. 

References/Publications: 

(1) Lauth, R. R., S. W. McEntire, and H. H. Zenger. 2007. Geographic distribution, depth range, and 

description of Atka mackerel (Pleurogrammus monopterygius) nesting habitat in Alaska. Alaska Fish. 

Res. Bull. 12: 164-185. 

(2) Lauth, R. R. and D. M. Blood. 2007. Description of embryonic development of Atka mackerel 

(Pleurogrammus monopterygius). Fish. Bull., U.S. 105: 571–576. 

(3) Lauth, R. R., J. Guthridge, D. Nichol, S. W. McEntire, and N. Hillgruber. 2007. Timing and duration of 

mating and brooding periods of Atka mackerel (Pleurogrammus monopterygius) in the North Pacific 

Ocean. Fish. Bull., U.S. 105: 560-570. 

(4) http://doc.nprb.org/web/04_prjs/f0417_final_report.pdf.

Point of Contact: Robert R. Lauth, RACE Division, 206-526-4121, bob.lauth@noaa.gov.

 11
Name of Project: Habitat influence on rearing 

condition and overwinter survival of juvenile 

capelin (Mallotus villosus). Glacier

Bay Berners

Bay

Fritz Cove

Admiralty I

Chichigof I

Juneau

Glacier

Bay Berners

Bay

Fritz Cove

Admiralty I

Chichigof I

Juneau

Region (GOA, BS, AI): GOA. 

Specific Location: Berners Bay, Auke Bay 

and Glacier Bay in southeastern Alaska. 

Data Types (Formats): Fish abundance from 

acoustic backscatter along predefined survey 

tracks. Oceanographic data collected by CTD. 

Zooplankton with a single net. 

Instruments/Devices Used For Collection:

Acoustic data collected with 38 kHz Simrad 

EK60 echosounder system, targets identified 

with midwater trawl. Physical oceanographic 

data collected with a CTD equipped with 

temperature, salinity, turbidity, light, pH and 

fluorometry sensors. 

Summary of Project/Data: We are collecting data describing the relative abundance, size (length, wet mass) 

and proximate composition (protein, lipid, water, ash and energy) of juvenile capelin and eulachon. In 

addition we are collecting physical (temperature, conductivity, turbidity, pH, light) and biological 

oceanographic (chlorophyll-a, relative zooplankton abundance) data. Matched data sets are being collected 

from different bays in southeastern Alaska. Ultimately the data describing oceanographic conditions will be 

compared with measures of abundance, growth and energetic condition to evaluate habitat characteristics 

conducive to increased recruitment. Oceanographic data are collected along a stratified grid. 

Sampling Dates: 1 October 2007 – 1 April 2009. 

 

Status of Project/Data Processing: Data and samples have been collected, samples are being processed. 

Oceanographic data have been downloaded from the CTD. 

References/Publications: None, project is still underway. 

Point of Contact: Johanna Vollenweider, ABL, 907-789-6612, johanna.vollenweider@noaa.gov.

 12
Name of Project: Bristol Bay 

reconnaissance. 

Region (GOA, BS, AI): BS. 

Specific Location: Bristol Bay, 

eastern Bering Sea continental 

shelf. 

Data Types (Formats): (1) 

High-resolution digital sidescan 

sonar data (.xtf) and georeferenced backscatter images 

(GeoTIFF); (2) sediment grain 

size (.xls); (3) analog video (Hi8); (4) CTD (.cap ASCII text). 

Instruments/Devices Used For 

Collection: (1) Klein 5410; (2) 

van Veen grab sampler; (3) drop 

camera; (4) Sea-bird SBE 19 

Plus. 

Summary of Project/Data: Seafloor habitats in the eastern Bering Sea were surveyed in June-July 2002 

using a high-resolution sidescan sonar deployed from the F/V Ocean Explorer. The reconnaissance effort was 

centered on an uncharted 2,750 km2

 area of central Bristol Bay. A 150 m swath of backscatter and 

bathymetric data were collected along survey lines totaling nearly 1,110 km. Imagery was systematically 

groundtruthed using an underwater video camera (8 sites) and van Veen grab sampler (22 sites). The 

backscatter data have been processed using QTC Sideview software and were also classified by a marine 

geologist. 

Sampling Dates: 28 June 2002 – 4 July 2002.

Status of Project/Data Processing: Fully processed. 

References/Publications: 

(1) Yeung, C. and McConnaughey, R. A. 2008. Using acoustic backscatter from a sidescan sonar to explain 

fish and invertebrate distributions: a case study in Bristol Bay, Alaska. ICES J. Mar. Sci. 65: 242–254. 

(2) Bornhold, B. D., C. V. Jay, R. A. McConnaughey, G. Rathwell, K. Rhynas, and W. Collins. 2006. Walrus 

foraging marks on the seafloor in Bristol Bay, Alaska – a reconnaissance survey. Geo-Marine Letters 25: 

293-299. 

(3) http://www.afsc.noaa.gov/RACE/groundfish/hrt/sonar.htm. 

(4) http://oceanexplorer.noaa.gov/projects/alaskatools01/alaskatools01.html. 

Point of Contact: Bob McConnaughey, RACE Division, 206-526-4150, bob.mcconnaughey@noaa.gov.

 13
Name of Project: Bering Sea 

echosounder survey. 

Region (GOA, BS, AI): BS. 

Specific Location: 

Continental shelf of the 

eastern Bering Sea. 

 

Data Types (Formats): (1) 

georeferenced soundings 

(ASCII text); (2) QTC View - 

processed echo returns from 

the seabed (Q-values and 

classes in ASCII text). 

Instruments/Devices Used 

For Collection: Simrad EK500 split-beam calibrated 

echosounder (38 kHz, 120 

kHz) connected to a Quester 

Tangent Corporation ISAH-S 

waveform recorder. 

Summary of Project/Data: Seafloor habitats in the eastern Bering Sea were surveyed in June-August 1999 

using a calibrated split-beam echosounder deployed by the NOAA ship Miller Freeman. Approximately 6 

million echo returns from the seafloor were simultaneously collected at two frequencies (38 and 120 kHz) 

during a routine hydroacoustic fishery survey. A total of 16,700 km of EBS seabed was sampled. Numerical 

parameters were extracted from the digitized echo returns using QTC View software and then reduced to 

principal components (Q-values). A new application of the Bayesian Information Criterion identified 14 

distinct acoustic bottom types in the 38 kHz data. 

Sampling Dates: 14 June – 3 August 1999. 

Status of Project/Data Processing: Fully processed. 

References/Publications: 

(1) Preston, J. M, A. C. Christney, W. T. Collins, R. A. McConnaughey, and S. E. Syrjala. 2004. 

Considerations in large-scale acoustic seabed characterization for mapping benthic habitats. ICES CM 

2004/T:13, 8 p. 

(2) McConnaughey, R. A. and S. E. Syrjala. 2009. Statistical relationships between the distributions of 

groundfish and crabs in the eastern Bering Sea and processed returns from a single-beam echosounder. 

ICES J. Mar. Sci. 66. 

(3) http://www.afsc.noaa.gov/RACE/groundfish/hrt/echosounder.htm. 

(4) http://www.afsc.noaa.gov/RACE/surveys/cruise_archives/cruises1999/results_MF1999-09.pdf. 

(5) Quester Tangent Corporation. June 2004. Revised final report: QTC VIEWTM acoustic seabed 

classification, Bering Sea, Miller Freeman 1999. Document Number: DRP NOAA 0005.R00. 148 p. 

Point of Contact: Bob McConnaughey, RACE Division, 206-526-4150, bob.mcconnaughey@noaa.gov.

 14
Name of Project:

EBSSED sediment 

database. 

Region (GOA, BS, 

AI): BS. 

Specific Location:

Continental shelf of 

the eastern Bering 

Sea, delimited by the 

boundaries of the 

annual RACE bottom 

trawl survey. 

 

Data Types 

(Formats):

Granulometric data 

and categorical 

textures (.dbf). 

Instruments/Devices 

Used For Collection:

Miscellaneous grab 

samplers and corers. 

Summary of Project/Data: EBSSED is a compilation of historical point-sample sediment data (n=2,587) 

from all available sources at the time of publication. Textural data in the database are of two main types: (1) 

standardized statistics characterizing sample grain size distribution based on laboratory measurements 

(granulometric data), including percent composition by size grades (e.g., gravel, sand, mud) and size 

distribution parameters (e.g., mean size); and (2) sample descriptions from less exacting, more subjective 

visual/tactile observations, usually made in the field, establishing size-grade constituents. Each record 

includes information about the original samples, including location, water depth and sampling gear used. 

 

Sampling Dates: 1934 – 1997. 

Status of Project/Data Processing: Currently 2,587 samples. New samples added when available. 

References/Publications: 

(1) Smith, K. R. and R. A. McConnaughey. 1999. Surficial sediments of the eastern Bering Sea continental 

shelf: EBSSED database documentation. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-104, 

41 p. (http://www.afsc.noaa.gov/Publications/AFSC-TM/NOAA-TM-AFSC-104.pdf). 

(2) McConnaughey, R. A. and K. R. Smith. 2000. Associations between flatfish abundance and surficial 

sediments in the eastern Bering Sea. Can. J. Fish. Aquat. Sci. 57: 2410-2419. 

Point of Contact: Bob McConnaughey, RACE Division, 206-526-4150, bob.mcconnaughey@noaa.gov.

 15
Name of Project: 2006 FISHPAC 

experiment. 

Region (GOA, BS, AI): BS. 

Specific Location: Bristol Bay, eastern 

Bering Sea continental shelf. 

 

Data Types (Formats): (1) multibeam 

bathymetry and backscatter snippets 

(.xtf and Caris); (2) high-resolution 

sidescan sonar backscatter (.xtf); (3) 

optical backscatter data (.xtf); (4) sound 

velocity profiles (.svp ASCII text); (5) 

light levels (proprietary hexadecimal). 

Instruments/Devices Used For 

Collection: (1) Reson 8111-ER 

multibeam echosounder (50 kHz); (2) 

Reson 8160 multibeam echosounder (100 kHz); (3) Klein 5410 sidescan sonar (455 kHz); (4) Klein 7180 

long-range sidescan sonar with integrated multibeam echosounder (180 kHz); (5) 38 kHz vertical incidence 

echosounder (on Klein 7180 towfish); (5) SEABOSS sediment grab/camera system; (6) TACOS towed video 

sled; (7) FFCPT sediment probe with sound velocity profiler; (8) MVP sound velocity profiler; (9) ECO 

triplet backscattering meter; (10) Mk9 light-level logger. 

Summary of Project/Data: NOAA ship Fairweather surveyed six 260 km tracklines on the Bering Sea shelf 

during July-August 2006. Five different sonar systems were used to acquire acoustic backscatter and 

bathymetry data at depths ranging from 20 to 160 m. The five systems included two hull-mounted multibeam 

echosounders, a high-resolution interferometric sidescan sonar, and a prototype long-range sidescan sonar 

with an independent single beam echosounder. Groundtruth samples of sediment, infauna, and still/video 

images were collected during one of three passes along each trackline. Additional sensors provided 

continuous measurements of dissolved organics, chlorophyll-a, total particulate concentrations, and light 

levels in the study area. 

Sampling Dates: 13 July 2006 – 23 August 2006. 

Status of Project/Data Processing: Fully processed – Reson 8111 bathymetry, Klein 5410 backscatter, 

sediment granulometrics, infauna, sound velocity profiles. Processing ongoing – bathymetry and backscatter 

from Reson 8160 and Klein 7180; optical backscatter; light levels. 

References/Publications: 

(1) Lomnicky, J., R. A. McConnaughey, C. Yeung, K. R. Smith, and M. Amend. 2008. Hydrography through 

the eyes of a fish – can acoustic backscatter be used to classify benthic fish habitat? Proceedings of the 

U.S. Hydro 2007 Conference, The Hydrographic Society of America. 

(2) Lomnicky, J. and R. A. McConnaughey. 2008. Integrating charting and acoustic habitat research. Sea 

Tech. 49(8): 10-15. 

(3) Yeung, C., M-S. Yang, and R. A. McConnaughey. In review. Polychaete community in southeastern 

Bering Sea in relation to groundfish distribution and diet. 

(4) http://www.afsc.noaa.gov/RACE/surveys/cruise_archives/cruises2006/results_FW-FISHPAC2006.pdf. 

(5) http://www.afsc.noaa.gov/RACE/groundfish/hrt/fishpac.php. 

Point of Contact: Bob McConnaughey, RACE Division, 206-526-4150, bob.mcconnaughey@noaa.gov.

 16
Name of Project: 1996 TRAWLEX experiment. 

Region (GOA, BS, AI): BS. ALASKA 

Specific Location: Bristol Bay, eastern Bering Eastern Sea continental shelf. Bering 

Sea 

 Area 512 CHPZ1 

Data Types (Formats): (1) Standardized epifauna 

catches, temperatures, depths (RACEBASE), (2) Trawl Effort Hi-8 analog video (tapes digitized to DVD). 0 

Low 

Medium 

High Instruments/Devices Used For Collection: (1) Very High 

Eastern 83-112 bottom trawl modified with tickler N

W E chain and liner, (2) net-mounted MBT, (3) Osprey 

model OE1373 low-light analog video camera. S 

Summary of Project/Data: In 1996, epifauna populations were characterized in heavily fished and unfished 

areas in northern Bristol Bay during a July-August 1996 cruise involving the FV Aldebaran and the FV 

Arcturus. Quantitative estimates for 92 invertebrate taxa were obtained at 84 1-nmi2

 stations (n=42 pairs) 

straddling the northeastern boundary of the Crab and Halibut Protection Zone 1 (management area 512, which 

is now contained within the Bristol Bay Nearshore Closure Area). This area is relatively shallow (41-49 m), 

sandy and has strong tidal currents. Stations within the closed area had never been fished with commercial 

bottom trawls based on a review of historical fishing effort and foreign/domestic fishery regulations. A selfcontained color video camera was attached to the top bridle of the trawl and provided landscape imagery of 

the seabed (5 sites). 

Sampling Dates: 30 July – 6 August 2006. 

Status of Project/Data Processing: Fully processed epifauna samples and archived video. 

References/Publications: 

(1) http://www.afsc.noaa.gov/RACE/surveys/cruise_archives/docs1996.htm 

(2) McConnaughey, R. A., K. Mier, and C. B. Dew. 2000. An examination of chronic trawling effects on 

soft-bottom benthos of the eastern Bering Sea. ICES J. Mar. Sci. 57: 1377-1388. 

(3) McConnaughey, R. A., S. E. Syrjala, and C. B. Dew. 2005. Effects of chronic bottom trawling on the size 

structure of soft-bottom benthic invertebrates. Pages 425-437 in P. W. Barnes and J. P. Thomas (eds.). 

Benthic habitats and the effects of fishing. American Fisheries Society, Symposium 41, Bethesda, 

Maryland. 

Point of Contact: Bob McConnaughey, RACE Division, 206-526-4150, bob.mcconnaughey@noaa.gov. 

17 
Name of Project: 1997 TRAWLEX 

experiment. 

Region (GOA, BS, AI): BS. ALASKA 

Specific Location: Bristol Bay, eastern Bering Eastern 

Bering Sea continental shelf. Sea 

Area 512 

 

Data Types (Formats): (1) Infauna abundance 

(.xls); (2) sidescan sonar imagery (ArcView Trawl Effort 

0

project). Low 

Medium 

High Instruments/Devices Used For Collection: (1) Very High 

N

0.05 m2 Sutar van Veen grab sampler; (2) Klein 

2000 sidescan sonar (100/500 kHz) with 3.5 kHz W 

S 

E 

sub-bottom profiler. 

Summary of Project/Data: AFSC and U.S. Geological Survey (USGS) scientists characterized benthic 

habitats in northern Bristol Bay during a July-August 1997 cruise on the FV Golden Dawn. The primary study 

area straddled the northeast boundary of management area 512, a relatively shallow (41-49 m), sandy and 

high-current area closed to bottom trawling. Infauna were collected from adjacent untrawled and heavily 

trawled stations using a Sutar van Veen grab sampler (n=25 pairs). Sidescan (188 line-km) and video (22 linekm) transects oriented across the boundary explored seabed features. Additional infauna sampling (n=28) and 

sidescan/video surveys were conducted farther south in the closed area (depths 59-72 m). 

Sampling Dates: 28 July – 15 August 2007. 

Status of Project/Data Processing: Fully processed infauna samples and sidescan images. 

References/Publications: 

(1) http://www.afsc.noaa.gov/RACE/surveys/cruise_archives/cruises1997/results_GD1997-02.pdf

(2) McConnaughey, R. A., K. Mier, and C. B. Dew. 2000. An examination of chronic trawling effects on 

soft-bottom benthos of the eastern Bering Sea. ICES J. Mar. Sci. 57: 1377-1388. 

(3) McConnaughey, R. A., S. E. Syrjala, and C. B. Dew. 2005. Effects of chronic bottom trawling on the size 

structure of soft-bottom benthic invertebrates. Pages 425-437 in P. W. Barnes and J. P. Thomas (eds.). 

Benthic habitats and the effects of fishing. American Fisheries Society, Symposium 41, Bethesda, 

Maryland. 

(4) Marlow, M. S., A. J. Stevenson, H. Chezar, and R. A. McConnaughey. 1999. Tidally generated sea-floor 

lineations in Bristol Bay, Alaska. Geo-Marine Letters 19: 219-226. 

Point of Contact: Bob McConnaughey, RACE Division, 206-526-4150, bob.mcconnaughey@noaa.gov. 

18 
 

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164° 162° 160° 158° 156° 154° 

Name of Project: 

TRAWLEX BACI 

experiment. 

Region (GOA, BS, 58° 58° AI): BS. 

154° 

Specific Location: 

Bristol Bay, eastern 

Bering Sea 

continental shelf. 

Data Types
 

(Formats): (1)
 

standardized 56°
 56° 

epifauna catches,
 

temperatures,
 

depths
 

(RACEBASE), (2)
 

infauna (.xls), (3)
 

sediment
 

granulometrics and
 

chemistry (.xls), (4)
 

sidescan sonar
 

backscatter (.xtf), (5) CTD.
 

Instruments/Devices Used For Collection: (1) Eastern 83-112 bottom trawl modified with tickler chain and 

liner, (2) net-mounted MBT, (3) 0.1 m2 

van Veen grab sampler, (4) Klein 5410 sidescan sonar, (5) Sea-bird 

SBE 19 Plus. 

Summary of Project/Data: In 2001, six pairs of 10-mi long research corridors were sampled from the FV 

Ocean Explorer to investigate the effects of an experimental disturbance with a commercial bottom trawl. 

Quantitative assessments of epifauna and infauna populations were undertaken before and after trawling. 

Sediment samples were collected and processed for possible changes in grain size and chemical 

characteristics (organic carbon, nitrogen). Sidescan sonar surveys were also conducted before and after 

trawling. All corridors were revisited in 2002 to monitor recovery. The experimental design will 

accommodate one additional sampling event. 

Sampling Dates: (1) 15 June – 15 July 2001, (2) 18 June – 6 July 2002. 

Status of Project/Data Processing: All processing completed. 

References/Publications: 

(1) http://www.afsc.noaa.gov/RACE/surveys/cruise_archives/cruises2001/results_OE2001-01.pdf. 

(2) http://www.afsc.noaa.gov/RACE/groundfish/hrt/impact.htm. 

Point of Contact: Bob McConnaughey, RACE Division, 206- 526-4150, bob.mcconnaughey@noaa.gov. 

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164° 162° 160° 158° 156° 

Sediment texture 

gravel #S

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Trawlex01 study area 

CHPZ1 

50 m isobath 

Bristol Bay, Alaska 

19
 
Name of Project: Trawl-effect 

reduction tests. 

Region (GOA, BS, AI): BS. 

Specific Location: Eastern 

Bering Sea shelf. 

 

Data Types (Formats): Video, 

DIDSON (sonar imagery). 

Instruments/Devices Used For 

Collection: Strobe-lighted video 

camera and DIDSON sonar 

mounted on a towed benthic sled. 

Summary of Project/Data:

Benthic sled observations of trawl 

tracks. Trawl sweeps modified to 

test whether sweep modification 

reduces seafloor effects. Four test 

locations (letters on figure) plus opportunistic sled tows at survey sites, boundaries of fishing closures 

(circles) and a skate nursery (square). Site A had sled tows 1–2 days, 1 week, 1 month and 1 year after trawl 

tows. 

Sampling Dates: 23 May - 7 June 2005 (all sites on figure); 19 June - 3 July 2006 (site A only). 

Status of Project/Data Processing: DIDSON processing to determine location of trawl component tracks 

(doors, sweeps, footrope) and video counts of animals in different conditions by component. Video 

processing complete for 2005 sites A and D and partial for 2006 site A. 

References/Publications: Reports to North Pacific Fishery Management Council. 

Point of Contact: Craig Rose, RACE Division, 206-526-4128, craig.rose@noaa.gov.

 20
Name of Project: Multibeam habitat mapping 

in the Alaska region. 

Region (GOA, BS, AI): GOA, BS, AI. 

Specific Location: Various. 

 

Data Types (Formats): NA. 

Instruments/Devices Used For Collection:

Multibeam sonar. 

 Summary of Project/Data: Seafloor habitat 

maps have been created using high-resolution 

multibeam bathymetry with co-registered 

backscatter at various locations throughout the 

Alaska Region. Most of the mapping in the 

GOA is in the form of “postage stamps” 

ranging in size from 27 km2

 to 790 km2. Some 

of this mapping was in cooperation with the 

Alaska Department of Fish and Game and the 

University of Alaska Fairbanks. Such mapped 

sites in the GOA were generally selected in 

the areas of fisheries for rockfish (Sebastes

spp.). The selection of specific sites to map 

was influenced by budget and logistical 

constraints that in some cases limited the 

fishery-habitat mapping to areas near 

concurrent areas being mapped by NOAA’s 

Office of Coast Survey. In contrast for the 

Aleutian Islands, a systematic design was used 

to select sites to map that enabled a relatively 

substantial area of seafloor to be 

characterized. In theory such a systematic 

design allows extrapolation to unmapped 

areas. 

Sampling Dates: 2001-2003. 

Status of Project/Data Processing: Habitat typing of all maps except for AI has been completed. 

References/Publications: 

Shotwell, S. K., J. Heifetz, D. L. Courtney, and H. G. Greene. 2008. Mapping marine benthic habitat in the 

Gulf of Alaska: Geological habitat, fish distributions, and fishing intensity. Pages 349-368 in B. J. Todd 

and H.G. Greene (eds.). Mapping the seafloor for habitat characterization. Geological Association of 

Canada. Special Publication 47. 

Point of Contact: Jon Heifetz, ABL, 907-789-6054, jon.heifetz@noaa.gov. 

 21
Name of Project: Trawlability 

- AFSC survey single-beams. 

Region (GOA, BS, AI):

GOA. 

Specific Location: GOA 

bottom trawl survey area. 

 

Data Types (Formats): ES60 

and EK60 single-beam files 

(*.raw), EK-60 split-beam 

files. 

Instruments/Devices Used 

For Collection: Simrad ES60, 

EK60 single-beam 

echosounders. EK60 splitbeam echosounder. 

 

Summary of Project/Data:

The map shows approximately 

100,000 km of single-beam 

acoustic vessel tracks for the 2002 NOAA ship John N. Cobb survey, the 2003 and 2005 Gulf of Alaska 

bottom trawl vessels, four MACE cruises, 2 FOCI cruises, and the 2007 split-beam cruise on the NOAA ship 

Oscar Dyson. Quality varies widely but depth can usually be discerned. Data need to be smoothed to 

eliminate vessel motion and then integrated with the slope map for more complete coverage. There are also 

other single-beam transect data sets available from the NOAA National Geophysical Data Center (NGDC) 

and the USGS but they have not been proofed. 

Sampling Dates: 2002-present. 

Status of Project/Data Processing: Attempting to locate and acquire data. Editing and analysis has not 

begun. 

References/Publications: None. 

Point of Contact: Mark Zimmermann, RACE Division, 206-526-4119, mark.zimmermann@noaa.gov

 22
Name of Project: usSEABED.

Region (GOA, BS, AI): All. 

Specific Location: Alaskan EEZ. 

 

Data Types (Formats): Commadelimited text files and shapefiles on CD 

and web-based USGS publication; also 

searchable online ArcIMS database. Full 

FGDC-compliant metadata provided for 

usSEABED data files and all source 

data sets. 

Instruments/Devices Used For 

Collection: Lead-lines, grabs, cores, 

dredges, trawls, video and other 

groundtruthing methods. 

Summary of Project/Data: USGS-led 

initiative to collate all seafloor surficial groundtruthing information into a data-mined relational database. 

Numeric values for verbal descriptions are provided through the application of fuzzy set theory to geologic 

language; these data can be combined with more typical lab-based analytical data to increase seafloor 

coverage. Information provided includes: texture (GSSC), color, grain-size, geochemical or geophysical 

parameters, constituents (geologic and biologic); that is, whatever data were collected or can be inferred from 

the samples themselves. On map, brown dots are locations with verbal descriptions and orange dots are 

locations with numeric, laboratory-derived descriptions. 

Sampling Dates: 19 July 1888 to present. 

Status of Project/Data Processing: USGS Data Series publication "usSEABED: Pacific Coast (Alaska, 

Hawaii) Offshore Surficial-Sediment Data Release." 2008. For sediment contributions contact Jane Reid, 

USGS, jareid@usgs.gov. 

References/Publications: 

(1) For viewing seabed datasets see: http://coastalmap.marine.usgs.gov/regional/contusa/index.html. 

(2) For a description of the usSEABED database as currently published for the US. Pacific coast (2006), 

Atlantic coast (2005), and Gulf of Mexico and Caribbean (2006) see: http://walrus.wr.usgs.gov/usseabed/. 

(3) For a description of the seabed software see: Jenkins, C. J. 1997. Building offshore soils databases. Sea 

Tech. 38(12): 25-28. 

Point of Contact: Mark Zimmermann, RACE Division, 206-526-4119, mark.zimmermann@noaa.gov

 23
Name of Project: Pacific 

ocean perch (Sebastes 

alutus) habitats. 

Region (GOA, BS, AI):

AI. 

Specific Location:

Islands of Four 

Mountains and Samalga 

Pass, continental shelf. 

 

Data Types (Formats):

High resolution 

multibeam sonar data 

(.xtf) and georeferenced 

bathymetry images (.tiff); 

digital sidescan sonar 

data (.xtf) and 

georeferenced backscatter 

images (.tiff); analog and 

HD video (all in digital 

format – DVD). 

nstruments/Devices Used For Collection: Simrad SM2000, Klein 3000. 

e 

ntified and managed from large-scale mapping 

tudies that can discriminate mixed boulders and habitat. 

ampling Dates: 1 June – 24 August 2004. 

tatus of Project/Data Processing: Completed. 

(1) cean perch 

(2) ions and 

(3) erwater video 

es. 27: 947-957. 

) http://project.nprb.org/view.jsp?id=cb4ac4f5-390c-44fb-953e-c466816cd30c. 

Point of Contact: Chris Rooper, RACE Division, 206-526-4689, chris.rooper@noaa.gov. 

I

Summary of Project/Data: This study examined a nursery area for juvenile Pacific ocean perch (POP, 

Sebastes alutus) in the Aleutian Islands. Five study sites were mapped using sidescan and multibeam sonar,

and three were groundtruthed using underwater video. The video images were used to classify the seafloor 

into substrate types. Juvenile POP were found predominantly in mixed sand and boulder substrate within on

body length of complex structure such as boulders, coral or sponges. The distribution of juvenile POP also

suggest their essential habitats may be relatively easily ide

s

S

S

References/Publications: 

 Rooper, C. N., J. L. Boldt, and M. Zimmermann. 2007. An assessment of juvenile Pacific o

(Sebastes alutus) habitat use in a deepwater nursery. Estuar. Coast. Shelf Sci. 75:371-380. 

 Boldt, J. L., and C. N. Rooper. In review. An examination of links between feeding condit

energetic content of juvenile Pacific ocean perch in the Aleutian Islands. Fish. Oceanogr. 

 Rooper, C. N. and M. Zimmermann. 2007. A bottom-up methodology for integrating und

and acoustic mapping for seafloor substrate classification. Cont. Shelf R

(4) http://www.afsc.noaa.gov/race/groundfish/habitat/POP/pop_intro.htm. 

(5

 24
Name of Project: Aleutian 

Islands cooperative acoustic 

survey study. 

Region (GOA, BS, AI): AI. 

Specific Location: Central 

Aleutians; Atka Island 

(2006); 173°W longitude to 

179°W longitude (2007). 

 

Data Types (Formats):

Text files; Excel. 

Instruments/Devices Used 

For Collection: CTD. 

Summary of Project/Data:

Temperature, salinity and 

depth data were collected at 

sites throughout the study 

area. 

Sampling Dates: 

(1) 10 March – 5 April 2006. 

(2) 19 March – 21 April 2007. 

Status of Project/Data Processing: Project is on-going. 2006 data report is in review and 2007 data are 

being processed. 

References/Publications: None at this time. 

Point of Contact: 

Libby Logerwell, REFM Division, 206-526-4231, libby.logerwell@noaa.gov. 

Steve Barbeaux, REFM Division, 206-526-4211, steve.barbeaux@noaa.gov. 

 25
Name of Project: Kodiak fishery interactions and fisheries 

oceanography studies. 

Region (GOA, BS, AI): GOA. 

Specific Location: East coast of Kodiak Island. 

 

Data Types (Formats): Text, Excel, Access. 

Instruments/Devices Used For Collection: Sea-bird SBE 

9 Plus, MBT, XBT (expendable bathythermograph), 

continuous “sea chest” sampling, drifters, Tucker trawl 

(2005 only). 

Summary of Project/Data: Oceanographic data were 

collected near Kodiak Island from the NOAA ship Miller 

Freeman. Depth, temperature and salinity (SBE only) data 

were collected at numerous sites. Water samples were 

taken for chlorophyll and nutrient analysis. Continuous sea 

surface temperature, salinity and fluoresence data were 

also collected (with water samples for chlorophyll and 

nutrient analysis). Drifters were also released. 

Sampling Dates:

(1) 9-17 August 2000. 

(2) 9-30 August 2001. 

(3) 16 August – 4 September 2002. 

(4) 15 August – 4 September 2004. 

(5) 5 August – 14 September 2005. 

(6) 13 August – 6 September 2006. 

Status of Project/Data Processing: Projects are complete. Data from 2000-2004 have been published in 

peer-reviewed journals. 2005 and 2006 data have undergone preliminary analyses. 

References/Publications: 

(1) Hollowed, A. B., C. D. Wilson, P. J. Stabeno, and S. A. Salo. 2007. Effect of ocean conditions on the 

cross-shelf distribution of walleye pollock (Theragra chalcogramma) and capelin (Mallotus villosus). 

Fish. Oceanogr. 16: 142-154. 

(2) Logerwell, E. A., P. J. Stabeno, C. D. Wilson, and A. B. Hollowed. 2007. The effect of oceanographic 

variability and interspecific competition on juvenile pollock (Theragra chalcogramma) and capelin 

(Mallotus villosus) distributions on the Gulf of Alaska shelf. Deep Sea Res. II 54: 2849-2868. 

Point of Contact: 

Libby Logerwell, REFM Division, 206-526-4231, libby.logerwell@noaa.gov. 

Anne Hollowed, REFM Division, 206-526-4223, anne.hollowed@noaa.gov. 

 26
Name of Project: Atka 

mackerel tag release and 

recovery. 

Region (GOA, BS, AI): AI. 

Specific Location: Seguam 

Pass, Tanaga Pass, Amchitka 

Island, Kiska Island. 

 

Data Types (Formats): Text 

files, Excel files. 

Instruments/Devices Used For 

Collection: Net-mounted MBT, 

SBE45, SCUFA (SelfContained Underwater 

Fluorescence Apparatus). 

Summary of Project/Data:

Oceanographic data were 

collected at several locations along the Aleutian Islands from chartered fishing vessels. Temperature-depth 

data were collected with a MBT on nearly all tag release and recovery hauls. Temperature, salinity and 

fluorescence were collected continuously from surface water during tag release cruises only. Water samples 

were filtered and analyzed for chlorophyll to convert fluorescence data into chlorophyll biomass. 

Sampling Dates: Tag release cruises: (1) 10 June - 15 July 2002; (2) 12-26 July 2003; (3) 8-24 July 2006. 

Tag recovery cruises: (1) 23-28 August 2002; (2) 30 September – 12 October 2002; (3) 5-31 October 2003; 

(4) 7-23 October 2004; (5) 11 October - 1 November 2006. 

Status of Project/Data Processing: Project is on-going. Most data are in raw (text file) format. Some have 

been organized into Excel spreadsheets. 

References/Publications: 

McDermott, S. F., L. W. Fritz, and V. Haist. 2005. Estimative movement and abundance of Atka mackerel 

(Pleurogrammus monopterygius) with tag-release-recapture data. Fish. Oceanogr. 14 (Suppl. 1): 113-130. 

Point of Contact: 

Libby Logerwell, REFM Division, 206-526-4231, libby.logerwell@noaa.gov. 

Susanne McDermott, REFM Division, 206-526-4417, susanne.mcdermott@noaa.gov. 

 27
Name of Project: Pacific cod Cape 

Sarichef localized depletion experiment. 

Region (GOA, BS, AI): BS. 

Specific Location: Cape Sarichef. 

 

Data Types (Formats): Text files. 

Instruments/Devices Used For 

Collection: CTD (with dissolved oxygen, 

turbidity and light sensors), current meter. 

Summary of Project/Data:

Oceanographic data were collected nearby 

Unimak Pass. A CTD and current meter were deployed in a small “mooring cage” to collect near bottom data 

continuously throughout the study dates. 

Sampling Dates: 

(1) 27 December 2002 – 10 January 2003. 

(2) 15-31 March 2003. 

(3) 27 December 2003 – 10 January 2004. 

(4) 15-31 March 2004. 

(5) 5-19 January 2005. 

(6) 15-31 March 2005. 

Status of Project/Data Processing: Project is complete. Data have undergone preliminary analysis. 

References/Publications: 

Conners, M. E., and P. Munro. 2008. Effects of commercial fishing on local abundance of Pacific cod (Gadus 

macrocephalus) in the Bering Sea. Fish. Bull., U.S. 106:281-292. 

Point of Contact: 

Libby Logerwell, REFM Division, 206-526-4231, libby.logerwell@noaa.gov. 

Peter Munro, REFM Division, 206-526-4292, peter.munro@noaa.gov. 

 

 28
Name of Project: Down to 50 m 

bathymetry. 

Region (GOA, BS, AI): GOA, 

BS, AI. 

Specific Location: Alaska and 

surrounding areas. 

Data Types (Formats): Polygon 

– shapefile and geodatabase. 

ported it. 

Instruments/Devices Used For 

Collection: Off-the-shelf base 

data. Hydrographic survey. 

Trackline Geophysics. 

Summary of Project/Data: This 

Alaska bathymetric dataset was 

built using base data from 

Trackline Geophysics, 

hydrographic surveys, and filled 

in with ETOPO2 data. The 

process included creating higher 

resolution polygons where the 

trackline and hydrographic data sup

The final data product has two main attributes: the spatial resolution of the data (incrementally from 50 – 

1500 meters) and the depth by 1/10 of a meter. The Trackline Geophysics data remained uncorrected in this 

process. This dataset was last updated in June 2005. We have plans to update this dataset with the additional 

Trackline and hydrographic data that has become available. 

Sampling Dates: Data through March 2005. 

Status of Project/Data Processing: Complete. 

References/Publications: None. 

Point of Contact: Steve G. Lewis, National Marine Fisheries Service, Alaska Region, 907-586-7858, 

steve.lewis@noaa.gov

 29
 
Appendix A. Meeting agenda, participants, and workshop minutes. 

AGENDA 

Day Time Activity Facilitator 

Thursday 08:30 Coffee 

20 September 09:00 Welcome / Plan for the day Bob McConnaughey 

09:10 Workshop objectives Mike Sigler 

09:30 Oral presentations of data worksheets Bob McConnaughey

 12:30 Lunch 

13:30 Workshop products overview Bob McConnaughey 

13:40 Lessons learned about centralizing data Eric Boerner 

 14:10 Product-related discussions Mike Sigler 

 17:00 Wrap-up / Friday overview Bob McConnaughey 

Friday 08:30 Coffee 

21 September 09:00 Welcome / Plan for the day Bob McConnaughey 

09:10 Round table discussions Bob McConnaughey 

Lunch (1 hour) 

14:00 Wrap-up and Assignments Bob McConnaughey 

Time Permitting ShoreZone presentation (15 min) Scott Johnson 

________________________________________________________________________________________

 31
PARTICIPANTS 

Name Affiliation 

Steve Barbeaux AFSC, REFM, Seattle, WA 

Jan Benson AFSC, OMI, Seattle, WA 

Eric Boerner AFSC, NMML, Seattle, WA 

Cleo Brylinsky ADF&G, Sitka, AK 

Liz Chilton AFSC, RACE, Kodiak, AK 

Liz Conners AFSC, REFM, Seattle, WA 

Cathy Coon NPFMC, Anchorage, AK 

Guy Fleischer AFSC, RACE, Seattle, WA 

Angie Greig AFSC, REFM, Seattle, WA 

Jon Heifetz AFSC, ABL, Juneau, AK 

Jerry Hoff AFSC, RACE, Seattle, WA 

Scott Johnson AFSC, ABL, Juneau, AK 

Stan Kotwicki AFSC, RACE, Seattle, WA 

Jon Kurland AKRO, HCD, Juneau, AK 

Ben Laurel AFSC, RACE, Newport, OR 

Bob Lauth AFSC, RACE, Seattle, WA 

Steve Lewis AKRO, Juneau, AK 

Mandy Lindeberg AFSC, ABL, Juneau, AK 

Bob McConnaughey AFSC, RACE, Seattle, WA 

John Olson AKRO, HCD, Anchorage, AK 

Jeep Rice AFSC, ABL, Juneau, AK 

Phil Rigby AFSC, ABL, Juneau, AK 

Kalei Shotwell AFSC, ABL, Juneau, AK 

Mike Sigler AFSC, HEPR, Juneau, AK 

Jon Warrenchuk Oceana, Juneau, AK 

Cynthia Yeung AFSC, RACE, Seattle, WA 

Mark Zimmermann AFSC, RACE, Seattle, WA 

________________________________________________________________________________________ 

Abbreviations: Alaska Fisheries Science Center (AFSC), Alaska Department of Fish and Game (ADF&G), 

Alaska Regional Office (AKRO), Auke Bay Laboratories (ABL), Habitat and Ecological Processes Research 

Program (HEPR), Habitat Conservation Division (HCD), National Marine Mammal Laboratory (NMML), 

North Pacific Fishery Management Council (NPFMC), Operations Management and Information Division 

(OMI), Resource Assessment and Conservation Engineering Division (RACE), Resource Ecology and 

Fisheries Management Division (REFM).

 32
MINUTES 

Bob McConnaughey opened the workshop by addressing the plan for the day. The overall goal of the 

workshop is to discuss how to derive the maximum benefit from any data that may be collected, and the stated 

workshop objectives. We want to promote a discussion of where we’ve been, where we are, and where we go 

from here. Bringing this group of scientists together should enable three things: (1) to learn about the datasets 

provided by attendees and catalog other datasets that may be available; (2) to develop a plan for promoting 

collaborative use of data through greater awareness; and (3) to bring scientists involved in habitat research 

together to get to know one another. 

Mike Sigler stated that the purpose of the workshop is to communicate to each other what databases are 

available or that are used by scientists in the Alaska Region to support habitat research. The outcome of the 

workshop will be a Processed Report published through the AFSC, available both in hardcopy and online. 

The participants described 23 habitat data sets. The presentations are listed below in the order presented. The 

title of the data set is followed by the presenter. In addition, this information is described in the “Habitat Data 

Inventory” section of this workshop report following a standard format. Included in each section are questions 

raised during the ensuing group discussion. 

1. Habitat Areas of Particular Concern – a Case Study of EFH Habitat Data 

Cathy Coon, NPFMC 

 

This presentation was based on the use of coral and habitat data collected by Bob Stone, Ken Krieger, and Jon 

Heifetz in dives in SE Alaska. Working with the North Pacific Fishery Management Council and NMFS, 

three areas in SE Alaska were closed to bottom contact fishing gear to protect sensitive coral habitat. This 

closure was based on in situ observation of Primnoa thickets and rockfish from submersibles and also utilized 

multibeam data. These closures were a result of management actions taken by NMFS and NPFMC during the 

Essential Fish Habitat Environmental Impact Statement and illustrate how scientific datasets are utilized by 

managers. 

Q: How to keep management (NMFS, NPFMC) and AFSC aware of what each is doing? 

2. Delta Submarine Video Archiving 

Jon Heifetz, ABL 

Since 1988, 373 Delta dives have been conducted in Alaska, predominately in SE Alaska (260) but also in 

Kodiak (50) and the Aleutian Islands (63). The dives presented are those conducted by the Marine Fish 

section at ABL. A contractor was hired to analyze the video data and collect information such as start/end 

times, scientist name, purpose of dive, camera angle, navigation, depth min/max, stock assessment, slope, 

dominant habitat type, species table, abundance category, and navigation files. Data formats are VHS, Hi8 

analog, and Hi8 digital. 40% of the tapes have been completed, but approximately $15k and 6 months of time 

is required to finish the remaining 60%. It has proven difficult to find someone to process video files, as it is 

very time intensive and tedious. 

Q: Could these data be added to Fish Atlas? 

Q: Could locations/status be added to data sheets, even for unprocessed data? 

Q: Could datasets include image captures? 

Q: How much public access should be granted to these data? 

 33
3. Multibeam Habitat Mapping in the Alaska Region 

Kalei Shotwell, ABL 

A multibeam database collaboration between AFSC, UAF, OSU, ADFG, and NMFS containing imagery and 

backscatter; organized into Point of Contact, region, depth range, area, XYZ, and including information about 

how the data were produced. For AFSC data, approximately 16,000 km2

 of 390,000 km2 of the data have 

already been processed. AFSC data will be incorporated into NOS/NGDC data sets. Extrapolating processed 

data into unsurveyed areas is a goal of the program. 

Q: Have extrapolated data been groundtruthed at this time? 

Q: Does backscatter and bathymetry actually give you good habitat maps? 

4. Habitat Influence on Rearing Condition and Overwinter Survival of Juvenile Capelin (Mallotus 

villosus) 

Mandy Lindeberg, ABL 

A 2-year project studying juvenile capelin, utilizing acoustics, plankton tows, and surveys. Energetics and 

physiological studies are included. There are three study sites: Glacier Bay, Berners Bay, and Fritz Cove. 

Data collected will eventually be compared with measures of abundance, growth and energetic condition to 

evaluate habitat characteristics conducive to increased recruitment of capelin. 

Q: Studies of capelin don’t deal with hard (physical) boundaries, which is required for EFH designation. 

Q: Is there a way to designate habitat for the water column? 

Q: Acoustic files are huge and storage is a problem – how to solve? 

5. Essential Fish Habitat Requirements for Skate Nurseries 

Jerry Hoff, RACE 

Six skate nurseries in the Bering Sea were identified and mapped using bottom trawl survey data. Nurseries 

generally occur along the 200 m contour, usually in flat sandy-muddy bottom with little relief. Nursery sites 

tended to be small and contained large numbers of egg cases. 

Q: If the data exists in Excel format now, is it possible to put into RACEBASE format? 

Q: Are nursery sites discrete? 

Q: Are they vulnerable to fishing? 

6. Effect of Light Intensity on Vertical and Spatial Distribution of Fish and Their Availability to 

Bottom Trawl and Acoustic Surveys 

Stan Kotwicki, RACE 

Assess the effect of light intensity and penetration on the distribution of walleye pollock. Data are mainly 

from the Bering Sea, less from the Gulf of Alaska. The objective of this work is to establish a relationship 

between light penetration and the availability of pollock to trawls, which could allow scientists to reduce 

uncertainty in pollock biomass estimates. 

7. Nearshore Habitat Use in Juvenile Pacific Cod 

Benjamin Laurel, RACE 

This HEPR-funded project looks at smaller nearshore sites sampled with beach seines and baited cameras. 

Age-0 and -1 Pacific cod have been collected for 2 years at several sites around Kodiak Island. Data have 

been analyzed on a diel, season, and annual basis, leading to conclusions relating habitat use to year classstrength, ontogenetic changes in habitat preference and changes in the physical environment. 

 34
Q: Sampling in rough bottoms is difficult – how do you standardize? 

Q: How do you archive tapes? 

8. Atka Mackerel EFH 

Bob Lauth, RACE 

Towed video drop camera to locate and characterize the general spawning and nesting habitat of Atka 

mackerel in the AI. Research supported with EFH and NPRB funds. The drop cameras being used are 

designed for extremely rugged bottoms. 125 drops have been performed. Issues are storage – 1 hour of 

footage is 15GB. 

Q. How do you process and present data to the public? 

9. Estuaries Database 

Jon Heifetz, ABL 

Visit nearshore sites several times over scales of seasons and years to index variability. The most common 

fish species sampled have been yellowfin sole, chum and pink salmon, starry flounder, and Pacific herring. 

Q: Links between this project and ShoreZone and Fish Atlas? 

10. Alaska Coastal Mapping / Nearshore Fish Atlas 

Mandy Lindeberg/Scott Johnson, ABL 

ShoreZone is a biophysical mapping protocol for intertidal areas. Washington and British Columbia are done. 

30,000 km of Alaska have been mapped. Integrated with Fish Atlas. First phase involved flying coastline 

during a minus tide window and acquiring georeferenced images. The second phase is the biophysical 

mapping. The third phase involves an online website. 

Q: How much duplicative information from ESI maps, NOS, etc? 

Q: Can this type of project contain data on marine mammals as well? 

11. Trawlability – AFSC Survey Single-Beams 

Mark Zimmermann, RACE 

5 by 5 km grid cells have been marked good/bad trawls since 1990. 20,000-22,000 total grid cells, ~1,300 are 

bad, ~1,400 good, and the rest are presently unknown. Once a cell is designated as “bad” it is taken off the list 

of trawlable locations. Slope, rockiness, and snags are recorded. Midrange (100-200 m) strata were generally 

more trawlable than shallow (<100 m) or deeper (>300 m) strata. Overall strata are 75% trawlable on average. 

Q: Part of RACEBASE? 

Q: How often do they get to new grid cells? 

12. Bristol Bay Reconnaissance 

Bob McConnaughey, RACE 

Seafloor habitats in central Bristol Bay were surveyed with sidescan sonar. Imagery was groundtruthed using 

video camera and van Veen grab sampler. Acoustic data compared to AFSC bottom trawl survey data. 

Processed acoustics explained between 9-54% of variability in miscellaneous groundfish and benthic 

invertebrate species found in the study area. 

Q: How are data stored? Digital tape, DVDs, georeferenced TIFFs. 

 35
13. Bering Sea Echosounder Survey 

Bob McConnaughey, RACE 

Seafloor habitat in the eastern Bering Sea surveyed using a split-beam echosounder. Total of 9,000 nautical 

miles (16,700 km) of EBS seabed was sampled. Acoustic and other habitat data were compared to AFSC 

bottom trawl survey data. Overall, Generalized Additive Models explained 28-77% of variability in 

abundance for a variety of groundfish and benthic invertebrate species over a 23-year period, including a 

marginal contribution of 2–13% by the acoustic predictors. 

14. EBSSED Sediment Database 

Bob McConnaughey, RACE 

A compilation of historical point-sample sediment data (2,587 samples). Samples were reduced to broad 

textural categories but all original data were retained within records. 

Q: Can we use sediment/acoustic data to identify EFH? Acoustic data are easier to collect than sediments over 

large areas. This sediment database is assembled from many different sources. 

15. 2006 FISHPAC Experiment 

Bob McConnaughey, RACE 

Experimental comparison of various acoustic systems for quantitative characterization of groundfish habitat. 

Prototype long-range sidescan was designed for broader coverage at lower resolution. More tests to follow. 

Q: Have you been getting repeatable results from single/multibeam? 

Q: Are acoustic data affected by directionality? 

16. 1997 TRAWLEX Experiment 

Bob McConnaughey, RACE 

AFSC/USGS characterized benthic habitats in northern Bristol Bay. Heavily trawled areas compared to 

untrawled areas. Infauna sampling from 1 nmi2

 grid. 

17. Trawlex BACI Experiment 

Bob McConnaughey, RACE 

Investigated effects of experimental disturbance with commercial bottom trawl in six pairs of experimentalcontrol corridors each 10-mile (18.5 km) long. Experiment may continue in 2009. 

18. Pacific ocean perch (Sebastes alutus) habitats 

Mark Zimmermann, RACE 

Looked at high- versus low-relief habitat for juvenile POP at five 1 km by 10 km sites. Utilized grab samples, 

plankton nets, fishtraps as well as video. 

19. Trawl Effort Reduction Tests 

Bob McConnaughey, RACE 

Disks on trawl sweeps studied with video sled for habitat impact reduction. 

 36
20. Flatfish Nursery Function 

Al Stoner, RACE 

Beam trawl sampling at five sites over 7 years, video sampling as well. Augmented with lab work. 

Q: How do you use O2 and salinity? Not much variability. 

Q: How do you use nesting models? Run the models in different bins. 

21. Trawlability – AFSC Survey with Single-Beam 

Mark Zimmermann, RACE 

Attempting to utilize vessel track data in GOA. Pitch and roll corrections needed for data quality. 

Q: Talk with MACE? 

Q: Calibrations with bottom trawl survey? 

22. usSEABED 

Mark Zimmermann, RACE 

Collaborating with USGS for 10 years. 200,000 data points overall. Converting database - can take video 

data. ArcIMS interface. 

23. Down to 50 m Bathymetry 

Steve Lewis, AKRO 

Tracklines, hydrographic, and ETOPO data assembled into one nested database. Resolutions are from 50 to 

1,500 m. Project is integrating all possible data sources. 

 37
 
Appendix B. Data management system example from the Mojave Desert. 

Summary of Eric Boerner’s presentation describing the data management system developed for the Mojave 

Desert Ecosystem Program (MDEP).

The objective of the MDEP was to use GIS and the internet to gather and share data dynamically and regionwide through an interactive database with real-time data capabilities. Temporal and spatial analysis could be 

completed at an ecosystem scale. 

The basic intention was to get data organized and centralized. This was a regional collaboration by six 

agencies – Department of the Interior, National Park Service, State of California, U.S. Fish and Wildlife 

Service, United States Geological Survey, and the Department of Defense – to gather data in the Mojave 

region. However, a method to assemble and condense vast amounts of data into a streamlined, usable system 

was necessary. 

Another concern was the ability to allow various levels of access to different user groups. Some of the data 

collected was proprietary or could be disseminated only to other agencies rather than the public. Database 

programs allow you to restrict access in many ways. Eric’s suggestion for the AFSC’s EFH data was to use 

SQL rather than Oracle as the database because many of the required administrative issues are simpler in 

SQL. 

The Mojave project had a staff of 6 people for 3 years, funded at approximately $1,000,000 per year. Creating 

a comprehensive ecosystem database is not cheap. 

The steps in this process were as follows: 

1. Identify available data and data types. 

The collaborating agencies provided data to the MDEP, which cataloged and checked the quality of the data. 

Standards were set for accuracy and completeness of the data, and metadata were required. Data included GIS 

files, databases, spreadsheets, documents, imagery, and photos. 

2. Find complementary data sets from outside sources. 

Partner agencies were queried to determine data needs. These data were gathered gratis or through data 

grants, and in rare cases, purchased with joint MDEP funds. 

3. Determine data collaboration roles. 

It was important to establish data collaboration roles before the MDEP was developed. Questions regarding 

who contributed, used, and administered the system were answered. 

4. Evaluate server, storage, and database requirements. 

Forward thinking is important in planning a large database. The MDEP outgrew the data storage capabilities 

within 2 years, effectively doubling storage. Overbuild your data storage capacity. 

5. Consider methods of distribution. 

The original intent was to distribute the MDEP on 15 CDs. Hard copies of the data quickly became outdated, 

however. A centralized website was developed to provide data directly to users. 

6. Build the data portal interface. 

 39
 40

The database contained two components. Non-spatial data (web pages, images, photos, documents) were 

housed in a MySQL database, and spatial data were accessed through an ArcSDE/Oracle database. 

7. Create data visualization tools. 

Allowing users to simply access the data required the creation of visualization tools. These tools allow previewing of large data sets. The use of a GIS frontend allowed the viewing of spatial data in the web interface. 

8. Assign user and group policies. 

Some data contained within the MDEP is considered sensitive, so access restrictions were required. Individual 

and group policies were implemented, allowing data to be restricted or shared within or between groups. 

Since coming to AFSC-NMML, Eric has been working on the Polar Ecosystem Program Seal Telemetry 

Database. The emphasis of this project is to centralize data to increase effectiveness and analysis speed and 

reduce data errors and redundant data. 

NMML houses many diverse collections of data, both spatially and multi-species. Much of this data is housed 

either on an AFSC server or individual workstations as Access or Excel files. Multiple copies are created by 

scientists, creating data versioning issues. 

With the use of a centralized database, it is possible for a field scientist to upload data collected from field 

computers through MS Infopath to that database at some interval. Those data are available to scientists as a 

single “cleaned” dataset, but the original data remain intact. Those original data are imported into the database 

with the use of scripting, which automates the process. Users query the database through SQL 2005.