Species ID Project
Data Set (DS) | NMFS Office Of Sustainable Fisheries (OSF)GUID: gov.noaa.nmfs.inport:28654 | Updated: October 17, 2023 | Published / External
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Summary
Short Citation
NMFS Office Of Sustainable Fisheries, 2025: Species ID Project, https://www.fisheries.noaa.gov/inport/item/28654.
Full Citation Examples
Up to 10 individuals of a fin fish, shark, and crustacean species are collected and morphologically identified by Southeast Fisheries Science Center. Water-soluble sarcoplasmic proteins are extracted from the tissue; proteins are analyzed by microfluidic electrophoresis (Agilent Bioanalyzer 2100) to generate species-specific protein patterns. The protein patterns are entered into a database to determine which are the most abundant for each species. The proteins that are seen in all 10 individuals are transferred to the excel pattern matching library database that uses NSIL designed formulas to calculate the range of each protein (+/- 1.5 to 3%) and compare an unknown protein to pattern to those in the pattern matching library.
Distribution Information
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CSV - Comma Separated Values (Text)
The database is only accessible through the facility's network and protected from public access by a firewall.
Child Items
Type | Title |
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Entity | Species Protein Repeatability |
Contact Information
Point of Contact
Jon Bell
jon.bell@noaa.gov
Metadata Contact
Shannara Lynn
shannara.lynn@noaa.gov
228-549-1730
Extents
Most species come from all areas of the Gulf of Mexico. However, so samples are shipped from other areas such as Hawaii
2011 - Present
Item Identification
Title: | Species ID Project |
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Short Name: | Species ID |
Status: | In Work |
Abstract: |
Up to 10 individuals of a fin fish, shark, and crustacean species are collected and morphologically identified by Southeast Fisheries Science Center. Water-soluble sarcoplasmic proteins are extracted from the tissue; proteins are analyzed by microfluidic electrophoresis (Agilent Bioanalyzer 2100) to generate species-specific protein patterns. The protein patterns are entered into a database to determine which are the most abundant for each species. The proteins that are seen in all 10 individuals are transferred to the excel pattern matching library database that uses NSIL designed formulas to calculate the range of each protein (+/- 1.5 to 3%) and compare an unknown protein to pattern to those in the pattern matching library. |
Purpose: |
The pattern matching library is designed to hold the highly abundant proteins extracted from tissue collected from 10 individuals of a species and compare an unknown pattern for identification. |
Notes: |
Specimens are collected and identified by the Southeast Fisheries Science center. Protein pattern analysis is is conducted by NMFS OSF National Seafood Inspection Laboratory. |
Keywords
Theme Keywords
Thesaurus | Keyword |
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UNCONTROLLED | |
None | Protein patterns |
None | Species ID |
Physical Location
Organization: | NMFS Office Of Sustainable Fisheries |
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City: | Pascagoula |
State/Province: | MS |
Country: | USA |
Data Set Information
Data Set Scope Code: | Data Set |
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Maintenance Frequency: | Continually |
Data Presentation Form: | Table (digital) |
Entity Attribute Overview: |
Species name, Species-specific protein masses, Sample protein masses, total # proteins, # of protein matches, Sample total of # of proteins, Library sample protein quantity ration, and similarity score. |
Distribution Liability: |
All the proteins in the library are from authenticated species and the most abundant with-in 10 individuals. |
Data Set Credit: | Shannara Lynn, Courtney Ford, Calvin Walker, Cheryl Lassiter |
Support Roles
Data Steward
Date Effective From: | 2011 |
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Date Effective To: | |
Contact (Person): | Lassitter, Cheryl |
Address: |
3209 Frederic Street Pascagoula, MS 39567 |
Email Address: | Cheryl.Lassitter@noaa.gov |
Phone: | 228-762-7402 |
Fax: | 228-762-7144 |
Distributor
Date Effective From: | 2015 |
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Date Effective To: | |
Contact (Person): | Bell, Jon |
Address: |
1315 East-West Highway, 13th Floor Silver Spring, MD 20910 |
Email Address: | jon.bell@noaa.gov |
Metadata Contact
Date Effective From: | 2011 |
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Date Effective To: | |
Contact (Person): | Lynn, Shannara |
Address: |
3209 Frederic Street Pascagoula, MS 39567 |
Email Address: | shannara.lynn@noaa.gov |
Phone: | 228-549-1730 |
Point of Contact
Date Effective From: | 2011 |
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Date Effective To: | |
Contact (Person): | Bell, Jon |
Address: |
1315 East-West Highway, 13th Floor Silver Spring, MD 20910 |
Email Address: | jon.bell@noaa.gov |
Extents
Currentness Reference: | as samples arrive and are processed |
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Extent Group 1
Extent Group 1 / Geographic Area 1
Description |
Most species come from all areas of the Gulf of Mexico. However, so samples are shipped from other areas such as Hawaii |
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Extent Group 1 / Time Frame 1
Time Frame Type: | Continuing |
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Start: | 2011 |
Access Information
Security Class: | Unclassified |
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Data Access Procedure: |
The database is only assessable by being in the facility and use of a CAC card to sign-in to any facility computer. The IT coordinator assigns which personnel in the facility can enter into each network folder. |
Data Access Constraints: |
The database is only accessible through the facility's network and protected from public access by a firewall. |
Distribution Information
Distribution 1
Download URL: | https://noaa-fisheries-hq.data.socrata.com/Seafood-Safety/Species-Protein-Repeatability/ub94-pbzc |
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Distributor: | |
File Name: | Species ID |
File Date/Time: | 2017-03-01 00:00:00 |
File Type (Deprecated): | .csv |
Distribution Format: | CSV - Comma Separated Values (Text) |
Technical Environment
Description: |
2010 Microsoft Excel |
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Data Quality
Representativeness: |
The number of proteins in the pattern matching library are species specific. |
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Accuracy: |
Individuals are authenticated morphologically by a fisheries biologist, documented and photographed for outside review. |
Analytical Accuracy: |
Protein size can be affected by many differing environmental factors. Due to this variation, a protein size range (+/- 1.5 to 3%) is used. |
Quantitation Limits: |
The number of proteins in the pattern matching library are species specific. |
Bias: |
If the individual is misidentified (morphologically), the protein patterns can shift in the wrong direction or some high abundant protein can be excluded that should not. |
Comparability: |
Each species in the library is compared to the library and others of that species not used as one of the to individuals is compared to verify the accuracy of the library. |
Completeness Measure: |
The ideal number of species-specific proteins is greater than five. The highest amount of proteins extracted is 16 and then decreased to only include those observed in all 10 individuals. |
Precision: |
Protein size can be affected by many differing environmental factors. Due to this variation, a protein size range (+/- 1.5 to 3%) is used. |
Analytical Precision: |
Protein size can be affected by many differing environmental factors. Due to this variation, a protein size range (+/- 1.5 to 3%) is used. |
Field Precision: |
On other analyses have been performed for comparison. |
Sensitivity: |
The pattern matching library compares all proteins of an unknown to the species specific proteins with-in the range (+/- 1.5 to 3%). |
Detection Limit: |
The height threshold is initially set to 5FU and raised incrementally for each individual to remove insignificant proteins until the total number of proteins is less than 16 |
Completeness Report: |
Only proteins that are seen in all 10 individuals, and above the height threshold of 5FU are inserted into the pattern matching library. |
Conceptual Consistency: |
Always. |
Quality Control Procedures Employed: |
The highly abundant proteins are determined, entered into the pattern matching library that performs the +/- 1.5 to 3% calculation and transcribed into a second worksheet to remove rounding extensions. All parts are checked by a second laboratory personnel. |
Data Management
Have Resources for Management of these Data Been Identified?: | Yes |
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Approximate Percentage of Budget for these Data Devoted to Data Management: | Unknown |
Do these Data Comply with the Data Access Directive?: | Yes |
Is Access to the Data Limited Based on an Approved Waiver?: | No |
If Distributor (Data Hosting Service) is Needed, Please Indicate: | NA |
Approximate Delay Between Data Collection and Dissemination: | immediate to 1 week |
If Delay is Longer than Latency of Automated Processing, Indicate Under What Authority Data Access is Delayed: |
NA |
Actual or Planned Long-Term Data Archive Location: | Other |
If World Data Center or Other, Specify: | servers collect and backup the data to servers to Maryland |
Approximate Delay Between Data Collection and Archiving: | 13 months |
How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?: |
Limited access and QA |
Lineage
Lineage Statement: |
A specimen is caught and recorded on the vessel as its location, date and condition. After the specimen is brought to NSIL, it is identified by a fisheries biologist and the data recorded on the vessel is recorded into the database. The specimen is process and the number of vials is recorded. |
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Child Items
Rubric scores updated every 15m
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Type | Title |
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Entity | Species Protein Repeatability |
Catalog Details
Catalog Item ID: | 28654 |
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GUID: | gov.noaa.nmfs.inport:28654 |
Metadata Record Created By: | Shannara Lynn |
Metadata Record Created: | 2015-11-12 13:49+0000 |
Metadata Record Last Modified By: | SysAdmin InPortAdmin |
Metadata Record Last Modified: | 2023-10-17 16:12+0000 |
Metadata Record Published: | 2018-03-23 |
Owner Org: | OSF |
Metadata Publication Status: | Published Externally |
Do Not Publish?: | N |
Metadata Last Review Date: | 2018-03-23 |
Metadata Review Frequency: | 1 Year |
Metadata Next Review Date: | 2019-03-23 |