Species ID Project
NMFS Office Of Sustainable Fisheries
Data Set
(DS)
| ID: 28654
| Published / External
Created: 2015-11-12
|
Last Modified: 2023-10-17
Project (PRJ) | ID: 28592
ID: 28654
Data Set (DS)
* Discovery• First Pass
» Metadata Rubric
Item Identification
* » Title | Species ID Project |
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Short Name | Species ID |
* Status | In Work |
Creation Date | |
Revision Date | |
• Publication Date | |
* » 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. |
Other Citation Details | |
• Supplemental Information | |
DOI (Digital Object Identifier) | |
DOI Registration Authority | |
DOI Issue Date |
Keywords
Theme Keywords
Thesaurus | Keyword |
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None | Protein patterns |
None | Species ID |
Temporal Keywords
Thesaurus | Keyword |
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* Spatial Keywords
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Stratum Keywords
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Instrument Keywords
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Platform Keywords
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Physical Location
• » Organization | NMFS Office Of Sustainable Fisheries |
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• » City | Pascagoula |
• » State/Province | MS |
• Country | USA |
• » Location Description |
Data Set Information
* Data Set Scope Code | Data Set |
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• Data Set Type | |
• Maintenance Frequency | Continually |
Maintenance Note | |
» 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. |
Entity Attribute Detail Citation | |
Entity Attribute Detail URL | |
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
* » Support Role | Data Steward |
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* » Date Effective From | 2011 |
Date Effective To | |
Person | Lassitter, Cheryl |
Address |
3209 Frederic Street Pascagoula, MS 39567 |
Email Address | Cheryl.Lassitter@noaa.gov |
Phone | 228-762-7402 |
Fax | 228-762-7144 |
Mobile | |
URL | |
Business Hours | |
Contact Instructions |
* » Support Role | Distributor |
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* » Date Effective From | 2015 |
Date Effective To | |
Person | Bell, Jon |
Address |
1315 East-West Highway, 13th Floor Silver Spring, MD 20910 |
Email Address | jon.bell@noaa.gov |
Phone | |
Fax | |
Mobile | |
URL | |
Business Hours | |
Contact Instructions |
* » Support Role | Metadata Contact |
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* » Date Effective From | 2011 |
Date Effective To | |
Person | Lynn, Shannara |
Address |
3209 Frederic Street Pascagoula, MS 39567 |
Email Address | shannara.lynn@noaa.gov |
Phone | 228-549-1730 |
Fax | |
Mobile | |
URL | |
Business Hours | |
Contact Instructions |
* » Support Role | Point of Contact |
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* » Date Effective From | 2011 |
Date Effective To | |
Person | Bell, Jon |
Address |
1315 East-West Highway, 13th Floor Silver Spring, MD 20910 |
Email Address | jon.bell@noaa.gov |
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* » Contact | |
* Contact Instructions |
Extents
Currentness Reference | as samples arrive and are processed |
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Extent Group 1
Extent Description |
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Extent Group 1 / Geographic Area 1
* » W° Bound | |
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* » E° Bound | |
* » N° Bound | |
* » S° Bound | |
* » Description |
Most species come from all areas of the Gulf of Mexico. However, so samples are shipped from other areas such as Hawaii |
Extent Group 1 / Vertical Extent
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Extent Group 1 / Time Frame 1
* » Time Frame Type | Continuing |
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* » Start | 2011 |
End | |
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Description |
Spatial Information
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Spatial Representation
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TIN Representation Used? | |
Stereo Model Representation Used? | |
Video Representation Used? |
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Vector Representation
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Surface Object Present? | |
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Reference Systems
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Access Information
Data License | |
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Data License URL | |
Data License Statement | |
* » Security Class | Unclassified |
* Security Classification System | |
Security Handling Description | |
• Data Access Policy | |
» 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. |
• Data Use Constraints | |
Metadata Access Constraints | |
Metadata Use Constraints |
Distribution Information
Start Date | |
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» Download URL | https://noaa-fisheries-hq.data.socrata.com/Seafood-Safety/Species-Protein-Repeatability/ub94-pbzc |
Distributor | |
File Name | Species ID |
Description | |
File Date/Time | 2017-03-01 00:00:00 |
File Type (Deprecated) | .csv |
Distribution Format | CSV - Comma Separated Values (Text) |
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Archive Information
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URL | |
Description | |
DOI | |
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URLs
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Activity Log
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Issues
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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. |
Horizontal Positional Accuracy | |
Vertical Positional Accuracy | |
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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Sources
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Acquisition Information
Instruments
Instrument Unavailable Reason |
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Identifier | |
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Docucomp UUID | |
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Platforms
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FAQs
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Child Items
Rubric scores updated every 15m
Score | Type | Title |
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Entity (ENT) | Species Protein Repeatability | |
Related Items
Item Type | Relationship Type | Title |
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Catalog Details
Catalog Item ID | 28654 |
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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 Workflow State | Published / External |
Metadata Last Review Date | 2018-03-23 |
Metadata Review Frequency | 1 Year |
Metadata Next Review Date | 2019-03-23 |
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