1999 West EMAP Histology

Metadata:


Identification_Information:
Citation:
Citation_Information:
Originator:
Southern California Coastal Water Research Project (SCCWRP)
Publication_Date: 20040402
Publication_Time: 20000402
Title: 1999 West EMAP Histology
Edition: 1.0
Publication_Information:
Publication_Place: Costa Mesa, California
Publisher:
Southern California Coastal Water Research Project (SCCWRP)
Online_Linkage: ftp://ftp.sccwp.org/pub/download
Description:
Abstract:
The presence of contaminants in estuaries has been identified in both the scientific and popular press as a major problem contributing to degraded ecological resources and restricted harvest of fish and shell fish resources due to human health concerns. Reducing contaminant inputs and concentrations , therefore, is often a major focus of regulatory programs for estuaries. Contaminants include both inorganic (primarily metals) and organic forms originating from many sources, including atmospheric depostion, freshwater inputs, land runoff and point sources. These sources are poorly characterized , except in the most well-studied estuaries. Most contaminants that are potentially toxic to indigenous biological resources tend to bind to particles , which ultimaltely are deposited at he bottom of estuaries. This binding changes the form of contaminants and removes them from the water column; consequently, contaminants accumulate in estuarine sediments. Sediment contaminant concentrations were measured to aid in interpretation of the spatial patterns observed in the condition of biolgical resources in the estuaries of the West Coast. EMAP monitoring efforts have focused on sediment contaminants rather than measurement of water column contaminants because concentrations of contaminants in sediments are less variable and the sediment integrates contaminant inputs to estuartis over time (i.e. months and years). Metals in the sediment are derived from anthropogenic sources or from natural geochemical processes of weathering and erosion of the earth's crust. The difficulty arises in identifying which portion of the total metal content of the sediment was due to natural processes and which was due to human activities. Several methods can be used to determine whether measured metal concentrations in estuarine sediments represent anthropogenically-enriched or natural conditions.
Purpose:
The purpose of this table is to contain all of the abundance data for trawl invertebrates collected by trawl in this project.
Supplemental_Information:
OVERVIEW: In 1999 the US EPA contracted the states of Washington, Oregon, and California to conduct a West Coast Estuary survey. There were 210 stations in the sample design, 18 of which were not able to be sampled for a total of 192 successful measurements. DATA TYPES: Grabs, Trawls, and Water Quality casts were conducted at each of the stations to yield Benthic infauna, Sediment Toxicity, Sediment Chemistry, Trawl Fish, Macro Invertebrate, Debris, water column characterization at one meter increments from surface to bottom, and sediment grain size data. These data types can be aggregated using the StationID variable in each table. Missing numerical values have been coded as -99 Missing text values have been coded as NR Missing date values have been coded as 01/Jan/1999 Missing time values have been coded as 23:00
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 19990701
Ending_Date: 19990831
Currentness_Reference: Sampling was conducted in the summer of 1999.
Status:
Progress: Complete
Maintenance_and_Update_Frequency: As needed
Spatial_Domain:
Description_of_Geographic_Extent: The west coast of the continental United States
Bounding_Coordinates:
West_Bounding_Coordinate: -124.70778
East_Bounding_Coordinate: -117.12895
North_Bounding_Coordinate: 48.31995
South_Bounding_Coordinate: 32.63867
Keywords:
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: None
Access_Constraints: None
Use_Constraints: Dataset credit required
Point_of_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Information Systems Manager
Contact_Organization: SCCWRP
Contact_Address:
Address_Type: mailing and physical address
Address: 3535 Harbor Blvd., Suite 110
City: Costa Mesa
State_or_Province: California
Postal_Code: 92626
Country: USA
Contact_Voice_Telephone: 714.755.3200
Contact_Facsimile_Telephone: 714.438.1016
Contact_Electronic_Mail_Address: im_contact@sccwrp.org
Hours_of_Service: 8:00 a.m. to 4:00 p.m. Monday Through Friday
Data_Set_Credit: National Marine Fisheries Northwest Office
Native_Data_Set_Environment: Microsoft Access Version 97

Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report: Coordinates accurate to within 100 ft
Logical_Consistency_Report:
These tables may all be joined using the StationID field
Completeness_Report:
Only fish and invertebrates with anomalies were reported in this table. It is a complete list of anomalies in this project.
Positional_Accuracy:
Horizontal_Positional_Accuracy:
Horizontal_Positional_Accuracy_Report:
The station locations were determined using a GPS and are accurate with in a radius of 100 ft
Vertical_Positional_Accuracy:
Vertical_Positional_Accuracy_Report: The depths expressed are accurate to 0.1 meters.
Lineage:
Methodology:
Methodology_Type: Field
Methodology_Description:
Gross External Fish Pathology Any fish pathologies (i.e. tumors) will photographed, then excised and placed into an orange labeled pathology cartridge, and put immediately into Dietrich’s solution. Excised tissue must include the entire pathology and some adjacent healthy tissue. Pathology information including cartridge number, fish species, size, station ID, trawl #, pathology location, description, and sample depth will be recorded onto the Cumulative Fish Pathology Log. Cartridge numbers are to begin with 00-1001 up to 00-1999. Up to 60 cartridges can be placed in a 2 L Dietrich’s Container. The pathology log will serve as the chain of custody form to be delivered with the samples at the end of field collection to Mark Meyers at NMFS/NOAA in Seattle.
Process_Step:
Process_Description: QA Checks Performed
Process_Date: 20000801

Spatial_Data_Organization_Information:

Spatial_Reference_Information:
Horizontal_Coordinate_System_Definition:
Geodetic_Model:
Horizontal_Datum_Name: North American Datum of 1983
Ellipsoid_Name: Geodedic Reference System 80
Semi-major_Axis: 6378137
Denominator_of_Flattening_Ratio:
298.257 4.2.2.1 Depth Datum Name:

Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label: tblHistoPath
Entity_Type_Definition: Table
Entity_Type_Definition_Source: West EMAP Information Mangement Plan
Attribute:
Attribute_Label: SampleDate
Attribute_Definition: The date the sample was collected
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 19990719
Range_Domain_Maximum: 19991014
Entity_Type:
Entity_Type_Label: tblHistoPath
Entity_Type_Definition: Table
Entity_Type_Definition_Source: West EMAP Information Mangement Plan
Attribute:
Attribute_Label: Species
Attribute_Definition: The species of animal with the anomaly
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Species
Enumerated_Domain_Value_Definition: The affected species
Enumerated_Domain_Value_Definition_Source: West EMAP Information Management Plan
Attribute:
Attribute_Label: Crangon nigircauda
Attribute_Definition: Grass Shrimp
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Fish Tissue Codes
Enumerated_Domain_Value_Definition:
list 12 Fish Tissue Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: Gasterosteus aculeatus
Attribute_Definition: Shrimp
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Fish Tissue Codes
Enumerated_Domain_Value_Definition:
list 12 Fish Tissue Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: Paralichthys californicus
Attribute_Definition: California halibut
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Fish Tissue Codes
Enumerated_Domain_Value_Definition:
list 12 Fish Tissue Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: Platichthys stellatus
Attribute_Definition: starry flounder
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Fish Tissue Codes
Enumerated_Domain_Value_Definition:
list 12 Fish Tissue Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: Pleuronectes vetulus
Attribute_Definition: English sole
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Fish Tissue Codes
Enumerated_Domain_Value_Definition:
list 12 Fish Tissue Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: Pleuronichthys ritteri
Attribute_Definition: spotted turbot
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Fish Tissue Codes
Enumerated_Domain_Value_Definition:
list 12 Fish Tissue Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Entity_Type:
Entity_Type_Label: tblHistoPath
Entity_Type_Definition: Table
Entity_Type_Definition_Source: West EMAP Information Mangement Plan
Attribute:
Attribute_Label: FishSequenceNumber
Attribute_Definition: A unique identifier for the animal
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Unrepresentable_Domain: A unique identifier for the animal
Entity_Type:
Entity_Type_Label: tblHistoPath
Entity_Type_Definition: Table
Entity_Type_Definition_Source: West EMAP Information Mangement Plan
Attribute:
Attribute_Label: SizeClass
Attribute_Definition: The length in centimeters of the animal
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: -9999
Range_Domain_Maximum: 10
Entity_Type:
Entity_Type_Label: tblHistoPath
Entity_Type_Definition: Table
Entity_Type_Definition_Source: West EMAP Information Mangement Plan
Attribute:
Attribute_Label: Anomaly
Attribute_Definition: A code for the anomaly from list 31
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: List 31 Fish Anomaly codes
Enumerated_Domain_Value_Definition: A coded list of anomalies
Enumerated_Domain_Value_Definition_Source: West EMAP Information Management Plan
Attribute:
Attribute_Label: Glugea spp xenoma
Attribute_Definition: Anomaly
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anomaly Codes
Enumerated_Domain_Value_Definition:
list 31 Anomaly Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: healed bite wound
Attribute_Definition: Anomaly
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anomaly Codes
Enumerated_Domain_Value_Definition:
list 31 Anomaly Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: no histopatholgy observed
Attribute_Definition: Anomaly
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anomaly Codes
Enumerated_Domain_Value_Definition:
list 31 Anomaly Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: parasitic copepod
Attribute_Definition: Anomaly
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anomaly Codes
Enumerated_Domain_Value_Definition:
list 31 Anomaly Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: parasitic isopod
Attribute_Definition: Anomaly
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anomaly Codes
Enumerated_Domain_Value_Definition:
list 31 Anomaly Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: trematode metacercariae
Attribute_Definition: Anomaly
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anomaly Codes
Enumerated_Domain_Value_Definition:
list 31 Anomaly Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Attribute:
Attribute_Label: X-cell pseudotumor
Attribute_Definition: Anomaly
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Anomaly Codes
Enumerated_Domain_Value_Definition:
list 31 Anomaly Codes
Enumerated_Domain_Value_Definition_Source:
West EMAP Information Plan

Entity_Type:
Entity_Type_Label: tblHistoPath
Entity_Type_Definition: Table
Entity_Type_Definition_Source: West EMAP Information Mangement Plan
Attribute:
Attribute_Label: SeverityIndex
Attribute_Definition: A code for the severity of the anomaly
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 2
Range_Domain_Maximum: 6
Entity_Type:
Entity_Type_Label: tblHistoPath
Entity_Type_Definition: Table
Entity_Type_Definition_Source: West EMAP Information Mangement Plan
Attribute:
Attribute_Label: DistributionIndex
Attribute_Definition:
A code for the amount of the animal covered by the anomlay
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 1
Range_Domain_Maximum: 5
Entity_Type:
Entity_Type_Label: tblHistoPath
Entity_Type_Definition: Table
Entity_Type_Definition_Source: West EMAP Information Mangement Plan
Attribute:
Attribute_Label: Comments
Attribute_Definition: Any additional comments
Attribute_Definition_Source: West EMAP Information Management Plan
Attribute_Domain_Values:
Unrepresentable_Domain: Additional remarks
Entity_Type:
Entity_Type_Label: tblHistoPath
Entity_Type_Definition: Table
Entity_Type_Definition_Source: West EMAP Information Mangement Plan
Attribute:
Attribute_Label: EMAP StationID
Attribute_Definition: The EMAP Station identifier
Attribute_Definition_Source: West EMAP Information Plan
Attribute_Domain_Values:
Unrepresentable_Domain: The EMAP Station identifier

Distribution_Information:
Distributor:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Information Systems Manager
Contact_Organization: SCCWRP
Contact_Address:
Address_Type: mailing and physical address
Address: 3535 Harbor Blvd., Suite 110
City: Costa Mesa
State_or_Province: California
Postal_Code: 92626
Country: USA
Contact_Voice_Telephone: 714.755.3200
Contact_Facsimile_Telephone: 714.438.1016
Contact_Electronic_Mail_Address: im_contact@sccwrp.org
Hours_of_Service: 8:00 a.m. to 4:00 p.m. Monday Through Friday
Distribution_Liability:
Although these data have been processed successfully on a computer system at SCCWRP, no warranty expressed or implied is made regarding the accuracy or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. This disclaimer applies both to individual use of the data and aggregate use with other data. It is strongly recommended that these data are directly acquired from a MLML server, and not indirectly through other sources which may have changed the data in some way. It is also strongly recommended that careful attention be paid to the contents of the metadata file associated with these data. MLML shall not be held liable for improper or incorrect use of the data described and/or contained herein.

Metadata_Reference_Information:
Metadata_Date: 20000801
Metadata_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Information Systems Manager
Contact_Organization: SCCWRP
Contact_Address:
Address_Type: mailing and physical address
Address: 3535 Harbor Blvd., Suite 110
City: Costa Mesa
State_or_Province: California
Postal_Code: 92626
Country: USA
Contact_Voice_Telephone: 714.755.3200
Contact_Facsimile_Telephone: 714.438.1016
Contact_Electronic_Mail_Address: im_contact@sccwrp.org
Hours_of_Service: 8:00 a.m. to 4:00 p.m. Monday Through Friday
Metadata_Standard_Name:
NBII Content Standard for National Biological Information Infrastructure Metadata
Metadata_Standard_Version: December 1995
Metadata_Time_Convention: local time
Metadata_Access_Constraints: None

Generated by mp on Wed Aug 11 09:45:18 2004