Item Identification

Title: Column Notes for BioSampling Data from LHP Cruises
Status: In Work
Abstract:

Explanation of what each column could include in the bottomfish sampling data.

Keywords

Theme Keywords

Thesaurus Keyword
None Hawaiian
None Length
None species
None weight

Spatial Keywords

Thesaurus Keyword
None CNMI
None Guam
None Johnston
None Kona
None MHI
None NWHI
None Oahu
None Samoa

Physical Location

Organization: Pacific Islands Fisheries Science Center
City: Honolulu
State/Province: HI
Country: USA
Location Description:

NOAA IRC Ford Island Facility

Entity Information

Entity Type: Data Table
Active Version?: Yes
Schema Name: bfsamp.BFS_BFSAMP_MAIN_V
Description:

Biosampling data from LHP cruises.

Data Attributes

Attribute Summary

Rubric Score Primary Key? Name Type Description
100
cruiseNum VARCHAR The designator for the cruise, e.g. SE-16-01.
100
caughtDate DATE The date that the fish was processed in the lab or at sea. Generally, this is done on the same day it was caught.
100
location VARCHAR2 The island, region or location where the fish was caught.
100
species VARCHAR2 The 4-letter species code, common or latin name for the species. A separate entity in this same parent item can be used to cross reference species codes and their common or latin names.
100
fl_cm NUMBER The length of the fish in centimeters. Fork length is measured from the tip of the snout to the fork of the tail.
100
wt_kg NUMBER Body weight of the fish in kilograms before any extractions occurred (round weight).
100
macroSex CHAR Sex of the fish, F for female, M for male, U for unknown. Gonads that are immature are difficult to determine sex using the naked eye, when the sex is not definite, a U is put into this column.
100
gonadWt_g NUMBER Weight of the gonads in grams.
100
numOtos VARCHAR2 Were there otoliths extracted and saved from this fish, Yes or No? Or, the # of otos extracted between 0 and 2. Some cruises only indicated Y/N values.
100
Primary Key fishDatNum VARCHAR2 The unique fish data number assigned to each fish. This contains the abbreviated vessel name, vessel trip number, page number, line number, tag number, and species. After 2009, the page and line number were omitted from the fish data number. The composite cruise and fish id number. These are assigned in continuously increasing order as the cruise progresses, e.g. SE-16-01-101, SE-16-01-102 and should be unique.
100
ziptie VARCHAR2 The tag number assigned to each individual fish from each trip; used to correlate specimens with catch log. These should be unique, but shouldn't be assumed so (different cruises used varying methods; some didn't use the ziptie method at all).
100
notes VARCHAR Additional details about the fish and any of its collected parts.
100
LAT_DEG NUMBER The latitude degrees where the fish was caught.
100
LAT_MIN NUMBER The latitude minutes where the fish was caught.
100
LAT_DIR CHAR The latitude direction.
100
LONG_DEG NUMBER The longitude degrees of where the fish was caught.
100
LONG_MIN NUMBER The longitude minutes of where the fish was caught.
100
L_SAG NUMBER If the left sagitta was recovered successfully and was extracted intact, a 1 will be entered into this column. If the left sagitta was not extracted successfully, there will be a 0 in the row.
100
DORSAL_FIN_YN CHAR Was the dorsal fin collected from this fish, yes(Y) or no (N)? When LHP moved from Aiea to IRC, ALL these specimens were thrown away!
100
ANAL_FIN_YN CHAR Was the anal fin collected from this fish, yes(Y) or no (N)? When LHP moved from Aiea to IRC, ALL these specimens were thrown away!
100
GENETICS_YN CHAR Was tissue for genetics collected from this fish, yes(Y) or no (N)? Can most likely retain a sample for genetic analysis from other samples taken from the fish but if there is a yes in this column, a genetic sample was taken and put into DMSO or in a separate Ziploc for future analysis.
100
ISOTOPES_YN CHAR Were isotopes collected from this fish, yes(Y) or no (N)? When LHP moved from Aiea to the IRC ALL these specimens were thrown away!
100
STOMACH VARCHAR2 Was the Stomach or its contents collected from this fish? (STOMACH/CONTENTS/SPEW) If nothing from the stomach was collected then there will be an N in this column.
100
EYEBALLS_YN CHAR Were the eyeballs collected from this fish, yes(Y) or no (N)? When LHP moved from Aiea to IRC, ALL these specimens were thrown away!
100
otoLoc CHAR Once determined, the general physical location of any extracted otoliths.
100
Fisher_or_GVI_For RFPGrantOnly VARCHAR2 For ease of searching, I added this column to easily query fish purchased from individual fisherman (Fisher) or fish purchased from the wholesale buyer, Garden Valley Isle (GVI). These fish were purchased under the 2 year RFP starting July 2014-July 2016.
100
GONAD_YN VARCHAR2 Was a gonad extracted from this fish and is the whole gonad still available for further processing (jar is stored in Wet Archival Storage)? Yes or No? Created for querying purposes.
100
LEFT_Sagittae_Wt_G NUMBER The weight of the left sagittae otolith in grams. NOTE: Oven dried weights were obtained 2007-2013, however, it was found the difference between oven and air-dried weights was insignificant. From 2014 on, otoliths were not oven-dried, but weighed after air drying in scintillation vials for three or more days. Oven dried values can be found in the Otolith_Wts_Msmts Spreadsheet.
100
Otolith_Notes VARCHAR2 Any notes associated with both otoliths.
100
PIFG_ID_Num VARCHAR2 In October, 2015, a stock assessment fishing project began and fishermen participating in that project provided fish to the LHP for age and growth research. The PIFG ID# is the number on the zip tie tag number attached to the fish when brought to the IRC. This number should be able to link each fish to additional information recoded on the SAP PIFG fishing forms with data collected in the field.
100
Purchased_from_PIFG_YN VARCHAR2 For ease of searching, I added this column to easily query fish purchased from PIFG fishermen. They would bring in heads and gonads or juvenile bottomfish LHP asked them to arget at various times throughout the years. On occasion, PIFG asks for a summary of all fish brought in by PIFG.
100
Right_Sagittae_Notes VARCHAR2 Any notes associated with the right sagittae, Possible values for this column are noted below.

Attribute Details

cruiseNum

CC ID: 326128
Seq. Order: 1
Data Storage Type: VARCHAR
Max Length: 30
Required: Yes
Primary Key: No
Status: Active
Description:

The designator for the cruise, e.g. SE-16-01.

Null Value: NO

caughtDate

CC ID: 326130
Seq. Order: 2
Data Storage Type: DATE
Max Length: 8
Required: No
Primary Key: No
Status: Active
Description:

The date that the fish was processed in the lab or at sea. Generally, this is done on the same day it was caught.

Null Value: YES
Null Value Meaning:

The workup date was unkown or was not recorded.

location

CC ID: 326129
Seq. Order: 3
Data Storage Type: VARCHAR2
Max Length: 15
Required: Yes
Primary Key: No
Status: Active
Description:

The island, region or location where the fish was caught.

Null Value: NO

species

CC ID: 326124
Seq. Order: 4
Data Storage Type: VARCHAR2
Max Length: 4
Required: Yes
Primary Key: No
Status: Active
Description:

The 4-letter species code, common or latin name for the species. A separate entity in this same parent item can be used to cross reference species codes and their common or latin names.

Null Value: NO

fl_cm

CC ID: 326093
Seq. Order: 5
Data Storage Type: NUMBER
Max Length: 4
Required: No
Primary Key: No
Status: Active
Description:

The length of the fish in centimeters. Fork length is measured from the tip of the snout to the fork of the tail.

Null Value: YES
Null Value Meaning:

The length was not recorded.

wt_kg

CC ID: 326085
Seq. Order: 6
Data Storage Type: NUMBER
Max Length: 4
Required: No
Primary Key: No
Status: Active
Description:

Body weight of the fish in kilograms before any extractions occurred (round weight).

Null Value: YES
Null Value Meaning:

No weight was recorded.

macroSex

CC ID: 326122
Seq. Order: 7
Data Storage Type: CHAR
Max Length: 1
Required: Yes
Primary Key: No
Status: Active
Description:

Sex of the fish, F for female, M for male, U for unknown. Gonads that are immature are difficult to determine sex using the naked eye, when the sex is not definite, a U is put into this column.

Null Value: NO
Null Value Meaning:

If the sex is unknown or was not recorded, then a U should be put into the column.

Allowed Values: M, F, U

gonadWt_g

CC ID: 326099
Seq. Order: 8
Data Storage Type: NUMBER
Max Length: 6
Required: No
Primary Key: No
Status: Active
Description:

Weight of the gonads in grams.

Null Value: YES
Null Value Meaning:

Gonads were not extracted or gonads were not weighed; check notes.

numOtos

CC ID: 326114
Seq. Order: 9
Data Storage Type: VARCHAR2
Max Length: 2
Required: No
Primary Key: No
Status: Active
Description:

Were there otoliths extracted and saved from this fish, Yes or No? Or, the # of otos extracted between 0 and 2. Some cruises only indicated Y/N values.

Null Value: YES
Allowed Values: Y,N

fishDatNum

CC ID: 326092
Seq. Order: 10
Data Storage Type: VARCHAR2
Max Length: 30
Required: Yes
Primary Key: Yes
Status: Active
Description:

The unique fish data number assigned to each fish. This contains the abbreviated vessel name, vessel trip number, page number, line number, tag number, and species. After 2009, the page and line number were omitted from the fish data number. The composite cruise and fish id number. These are assigned in continuously increasing order as the cruise progresses, e.g. SE-16-01-101, SE-16-01-102 and should be unique.

Null Value: NO
Null Value Meaning:

Every fish MUST have a fish data number to associate it with additional data collected from that fish.

ziptie

CC ID: 326126
Seq. Order: 10
Data Storage Type: VARCHAR2
Max Length: 4
Required: Yes
Primary Key: No
Status: Active
Description:

The tag number assigned to each individual fish from each trip; used to correlate specimens with catch log. These should be unique, but shouldn't be assumed so (different cruises used varying methods; some didn't use the ziptie method at all).

Null Value: NO

notes

CC ID: 326095
Seq. Order: 12
Data Storage Type: VARCHAR
Max Length: 4000
Required: No
Primary Key: No
Status: Active
Description:

Additional details about the fish and any of its collected parts.

Null Value: YES
Null Value Meaning:

There was not additional information to report about the fish.

LAT_DEG

CC ID: 326103
Seq. Order: 15
Data Storage Type: NUMBER
Max Length: 2
Required: No
Primary Key: No
Status: Active
Description:

The latitude degrees where the fish was caught.

Null Value: YES
Null Value Meaning:

The latitude degrees is unknown or it was not recorded.

LAT_MIN

CC ID: 326105
Seq. Order: 16
Data Storage Type: NUMBER
Max Length: 6
Required: No
Primary Key: No
Status: Active
Description:

The latitude minutes where the fish was caught.

Null Value: YES
Null Value Meaning:

The latitude minutes is unknown or was not recorded.

LAT_DIR

CC ID: 326104
Seq. Order: 17
Data Storage Type: CHAR
Max Length: 1
Required: Yes
Primary Key: No
Status: Active
Description:

The latitude direction.

Null Value: NO
Null Value Meaning:

The latitude direction can be determined from other specimens provided by the same source.

Allowed Values: N, S
Default Value: N

LONG_DEG

CC ID: 326107
Seq. Order: 18
Data Storage Type: NUMBER
Max Length: 3
Required: No
Primary Key: No
Status: Active
Description:

The longitude degrees of where the fish was caught.

Null Value: YES
Null Value Meaning:

The longitude degrees is unknown or was not recorded.

LONG_MIN

CC ID: 326109
Seq. Order: 19
Data Storage Type: NUMBER
Max Length: 6
Required: No
Primary Key: No
Status: Active
Description:

The longitude minutes of where the fish was caught.

Null Value: YES
Null Value Meaning:

The longitude minutes is unknown or was not recorded.

L_SAG

CC ID: 326110
Seq. Order: 30
Data Storage Type: NUMBER
Max Length: 1
Required: Yes
Primary Key: No
Status: Active
Description:

If the left sagitta was recovered successfully and was extracted intact, a 1 will be entered into this column. If the left sagitta was not extracted successfully, there will be a 0 in the row.

Null Value: NO
Null Value Meaning:

There should always be a 1 or a 0 entered; the sagitta is either available or it isn't.

Allowed Values: 1, 0

DORSAL_FIN_YN

CC ID: 326089
Seq. Order: 34
Data Storage Type: CHAR
Max Length: 1
Required: Yes
Primary Key: No
Status: Active
Description:

Was the dorsal fin collected from this fish, yes(Y) or no (N)? When LHP moved from Aiea to IRC, ALL these specimens were thrown away!

Null Value: NO
Null Value Meaning:

There will always be a value; the dorsal spine either was or was not collected.

Allowed Values: Y, N
Default Value: Y

ANAL_FIN_YN

CC ID: 326083
Seq. Order: 35
Data Storage Type: CHAR
Max Length: 1
Required: Yes
Primary Key: No
Status: Active
Description:

Was the anal fin collected from this fish, yes(Y) or no (N)? When LHP moved from Aiea to IRC, ALL these specimens were thrown away!

Null Value: NO
Null Value Meaning:

Anal fin either was or was not collected however, anal fins are usually only collected from hapu'upu'puu.

Allowed Values: Y, N
Default Value: N

GENETICS_YN

CC ID: 326096
Seq. Order: 36
Data Storage Type: CHAR
Max Length: 1
Required: Yes
Primary Key: No
Status: Active
Description:

Was tissue for genetics collected from this fish, yes(Y) or no (N)? Can most likely retain a sample for genetic analysis from other samples taken from the fish but if there is a yes in this column, a genetic sample was taken and put into DMSO or in a separate Ziploc for future analysis.

Null Value: NO
Null Value Meaning:

Genetic tissue was or was not collected. If there is a "N" is this column, it is possible to collect genetic material from the dorsal spine or muscle tissue.

Allowed Values: Y, N
Default Value: Y

ISOTOPES_YN

CC ID: 326101
Seq. Order: 37
Data Storage Type: CHAR
Max Length: 1
Required: Yes
Primary Key: No
Status: Active
Description:

Were isotopes collected from this fish, yes(Y) or no (N)? When LHP moved from Aiea to the IRC ALL these specimens were thrown away!

Null Value: NO
Null Value Meaning:

Isotope tissue was or was not collected.

Allowed Values: Y, N

STOMACH

CC ID: 326125
Seq. Order: 38
Data Storage Type: VARCHAR2
Max Length: 30
Required: Yes
Primary Key: No
Status: Active
Description:

Was the Stomach or its contents collected from this fish? (STOMACH/CONTENTS/SPEW) If nothing from the stomach was collected then there will be an N in this column.

Null Value: NO
Null Value Meaning:

The stomach or its contents either were or were not collected.

Allowed Values: Stomach, Contents, Spew, N

EYEBALLS_YN

CC ID: 326090
Seq. Order: 39
Data Storage Type: CHAR
Max Length: 1
Required: Yes
Primary Key: No
Status: Active
Description:

Were the eyeballs collected from this fish, yes(Y) or no (N)? When LHP moved from Aiea to IRC, ALL these specimens were thrown away!

Null Value: NO
Allowed Values: Y, N
Default Value: N

otoLoc

CC ID: 326112
Seq. Order: 40
Data Storage Type: CHAR
Max Length: 500
Required: No
Primary Key: No
Status: Active
Description:

Once determined, the general physical location of any extracted otoliths.

Null Value: NO
Null Value Meaning:

The opercles either were or were not collected.

Allowed Values: Y, N

Fisher_or_GVI_For RFPGrantOnly

CC ID: 326094
Data Storage Type: VARCHAR2
Max Length: 10
Required: No
Primary Key: No
Status: Active
Description:

For ease of searching, I added this column to easily query fish purchased from individual fisherman (Fisher) or fish purchased from the wholesale buyer, Garden Valley Isle (GVI). These fish were purchased under the 2 year RFP starting July 2014-July 2016.

Null Value: YES
Null Value Meaning:

This fish wasn't purchased under this RFP.

Allowed Values: Fisher, GVI

GONAD_YN

CC ID: 326100
Data Storage Type: VARCHAR2
Max Length: 1
Required: No
Primary Key: No
Status: Active
Description:

Was a gonad extracted from this fish and is the whole gonad still available for further processing (jar is stored in Wet Archival Storage)? Yes or No? Created for querying purposes.

Null Value: Yes
Null Value Meaning:

whether or not there is still a whole gonad wasn't properly documented

Allowed Values: Y, N

LEFT_Sagittae_Wt_G

CC ID: 326106
Data Storage Type: NUMBER
Max Length: 5
Required: No
Primary Key: No
Status: Active
Description:

The weight of the left sagittae otolith in grams. NOTE: Oven dried weights were obtained 2007-2013, however, it was found the difference between oven and air-dried weights was insignificant. From 2014 on, otoliths were not oven-dried, but weighed after air drying in scintillation vials for three or more days. Oven dried values can be found in the Otolith_Wts_Msmts Spreadsheet.

Otolith_Notes

CC ID: 326115
Data Storage Type: VARCHAR2
Max Length: 50
Required: No
Primary Key: No
Status: Active
Description:

Any notes associated with both otoliths.

Null Value: YES
Null Value Meaning:

NO NOTES

PIFG_ID_Num

CC ID: 326117
Data Storage Type: VARCHAR2
Max Length: 10
Required: No
Primary Key: No
Status: Active
Description:

In October, 2015, a stock assessment fishing project began and fishermen participating in that project provided fish to the LHP for age and growth research. The PIFG ID# is the number on the zip tie tag number attached to the fish when brought to the IRC. This number should be able to link each fish to additional information recoded on the SAP PIFG fishing forms with data collected in the field.

Purchased_from_PIFG_YN

CC ID: 326118
Data Storage Type: VARCHAR2
Max Length: 1
Required: No
Primary Key: No
Status: Active
Description:

For ease of searching, I added this column to easily query fish purchased from PIFG fishermen. They would bring in heads and gonads or juvenile bottomfish LHP asked them to arget at various times throughout the years. On occasion, PIFG asks for a summary of all fish brought in by PIFG.

Null Value: YES
Null Value Meaning:

Wasn't properly documented whether or not fish was from PIFG.

Allowed Values: Y, N

Right_Sagittae_Notes

CC ID: 326121
Data Storage Type: VARCHAR2
Max Length: 20
Required: No
Primary Key: No
Status: Active
Description:

Any notes associated with the right sagittae, Possible values for this column are noted below.

Null Value: YES
Null Value Meaning:

No notes associated with otolith

Allowed Values: AA Sectioned Allen Andrews already sectioned the otolith B-CI Otolith is broken but the core is intact B-CNI- Otolith is broken and the core is not intact C Small portion of otolith is chipped; chip is insignificant RB Rostrum broken, but the core intact RC Rostrum is chipped SH Otolith shattered in multiple pieces; core not intact

Support Roles

Data Steward

CC ID: 326131
Date Effective From: 2008-01-01
Date Effective To:
Contact (Person): Sundberg, Meagan A
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: meagan.sundberg@noaa.gov
Phone: (808)725-5379
Business Hours: 7:30 a.m. - 4:00 p.m. M-F
Contact Instructions:

Email with questions.

Extents

Extent Group 1

Extent Group 1 / Time Frame 1

CC ID: 326133
Time Frame Type: Continuing
Start: 2005-01-01

Access Information

Security Class: Confidential
Security Classification System:

After permission is granted to view the dataset, a read-only view will be provided.

Data Access Policy:

Need to obtain clearance before this data is available for view.

Catalog Details

Catalog Item ID: 32857
Metadata Record Created By: Maia Kapur
Metadata Record Created: 2016-06-03 15:12+0000
Metadata Record Last Modified By: Joseph M O'Malley
Metadata Record Last Modified: 2020-03-06 15:09+0000
Metadata Record Published: 2020-03-06
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Next Review Date: 2021-03-07