Item Identification

Title: Necropsy
Short Name: Necropsy
Status: In Work
Abstract:

.

Keywords

Theme Keywords

Thesaurus Keyword
None Hawaiian monk seal
None health and disease program
None hmsrp
None necropsy
None pathology
None PIFSC
None protected species
None PSD

Spatial Keywords

Thesaurus Keyword
None Hawaiian Archipelago
None pacific region

Physical Location

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

1845 Wasp Blvd., Bldg 176, Honolulu, HI 96818

Entity Information

Entity Type: Data Table
Active Version?: Yes
Description:

.

Data Attributes

Attribute Summary

Rubric Score Primary Key? Name Type Description
100
DATE Date Date seal found dead.
100
SEAL_ID Varchar2 Permanent Seal ID of the seal.
100
TEMP_ID Varchar2 Temp ID of the seal (for example, a temporary bleach number, only valid for one island/year).
100
ATOLL NUMBER Atoll/island where seal found dead. Kaula 08 Lehua 09 Nihoa 10 Johnston Atoll 11 Niihau 12 Kauai 13 Oahu 14 Molokai 15 Lanai 16 Maui 17 Kaho’olawe 18 Hawaii (Big Island) 19 Necker 20 French Frigate Shoals 30 Laysan 40 Lisianski 50 Pearl and Hermes Reef 60 Midway 70 Kure 80 Other 99
100
SIZE Varchar2 Size of the seal. Pups of the year P0 = Fetus/premature pup P = Nursing pup. P1 = Nursing pup, wrinkles. Full term . P2 = Nursing pup, no wrinkles, black P3 = Nursing pup, blimp, black or reddish brown (prior to molt) P4 = Nursing pup, blimp, molting P5 = Nursing pup, blimp, molted (not all pups reach P5 before weaning) PW = Prematurely weaned/undersized weaned pup (< 90cm girth at weaning). W = weaned pup I = Immature J = Juvenile J1 = Juvenile I (smaller juvenile) J2 = Juvenile II (larger juvenile) S = Subadult S3 = Subadult III (smaller subadult) S4 = Subadult IV (larger subadult) A = Adult
100
SEX Varchar2 Sex of the seal (M = male; F = female; U = unknown).
100
TYPE Varchar2 Type of specimen collected. AB = abscess AD = adrenal AF = abdominal fluid AG = active fishing gear (ex. Hooks) AQ = aqueous humor BB = blubber biopsy (should have subtype either TX or FA) BC = blood cells (remainder in tube after removing plasma or serum) BI = bile BL = blubber (blubber chunk) BR = brain BS = blood smear BU = buffy coat BY = bycatch (DNA) BX = biotoxin (blood card test) CF = chest fluid CS = cerebral spinal fluid ES = eye swab EY = eye FE = feces (collected from GIT, as opposed to excreted scat or fecal loop) FL = feces obtained with fecal loop GB = gall bladder GI = gastrointestinal tract taken anywhere from pharynx to anus GS = genital swab HF = pericardial fluid HC = histopathology cassettes HL = hepatic lymph nodes HS = histopathology slides HT = heart IL = inguinal lymph nodes KI = kidney LI = liver LN = lymph node LU = lung MD = marine debris MI = milk ML = mesenteric lymph nodes MN = mediastinal lymph nodes MO = molt MS = medulla spinalis (spinal cord) MU = muscle NM = nasal mites NS = nasal swab NT = necropsy tissue (tissues from all organs) OO = otolith ON = other necropsy (non-tissue samples) OR = oral swab OS = other swab OT = other (describe in notes section on back of form) PA = parasites PC = placenta PF = peritoneal fluid PL = the 'pluck': heart, trachea, lungs and associated glands PN = pulmonary lymph nodes PS = plasma RS = rectal swab RT = whole reproductive tract of female or male SC = scat (excreted feces) SE = serum (collected in serum separator tube for serology) SI = small intestine SK = skeletal (bones or teeth)-specify sub-type SL = spleen SM = sub-mandibular lymph SN = skin SP = spew SS = sub-scapular lymph ST = stomach contents TE = testes TP = tissue plug (from both live and dead animals) TS = throat swab UB = urinary bladder UM = umbilicus UR = urine VH = vitreous humor VI = vibrissae WA = water WB = whole blood (old code = BL for whole blood) WC = whole carcass WH = whole heart
100
GROSS_FINDINGS Varchar2 Findings at gross necrospy.
100
MICROSCOPY Varchar2 Histopathology slide review findings.
100
NOTES Varchar2 Additional comments from lab report and/or field or other pertinent notes.
100
Slide_Review_AFIP Varchar2 Histopathology slide review findings for tissues examined at Armed Forces Institute of Pathology.
100
MANAGEMENT Varchar2 Comments from lab regarding management related to findings.
100
DIAGNOSES Varchar2 Histopathology findings.
100
COMMENTS_REMARKS Varchar2 Additional comments from lab report and/or field or other pertinent notes.

Attribute Details

DATE

CC ID: 381164
Seq. Order: 1
Data Storage Type: Date
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Date seal found dead.

General Data Type: Date

SEAL_ID

CC ID: 381165
Seq. Order: 2
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Permanent Seal ID of the seal.

General Data Type: Varchar2

TEMP_ID

CC ID: 381166
Seq. Order: 3
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Temp ID of the seal (for example, a temporary bleach number, only valid for one island/year).

General Data Type: Varchar2

ATOLL

CC ID: 381167
Seq. Order: 4
Data Storage Type: NUMBER
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Atoll/island where seal found dead.

Kaula

08

Lehua

09

Nihoa

10

Johnston Atoll

11

Niihau

12

Kauai

13

Oahu

14

Molokai

15

Lanai

16

Maui

17

Kaho’olawe

18

Hawaii (Big Island)

19

Necker

20

French Frigate Shoals

30

Laysan

40

Lisianski

50

Pearl and Hermes Reef

60

Midway

70

Kure

80

Other

99

General Data Type: NUMBER

SIZE

CC ID: 381168
Seq. Order: 5
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Size of the seal.

Pups of the year

P0 = Fetus/premature pup

P = Nursing pup.

P1 = Nursing pup, wrinkles. Full term .

P2 = Nursing pup, no wrinkles, black

P3 = Nursing pup, blimp, black or reddish brown (prior to molt)

P4 = Nursing pup, blimp, molting

P5 = Nursing pup, blimp, molted (not all pups reach P5 before weaning)

PW = Prematurely weaned/undersized weaned pup (< 90cm girth at weaning).

W = weaned pup

I = Immature

J = Juvenile

J1 = Juvenile I (smaller juvenile)

J2 = Juvenile II (larger juvenile)

S = Subadult

S3 = Subadult III (smaller subadult)

S4 = Subadult IV (larger subadult)

A = Adult

General Data Type: Varchar2

SEX

CC ID: 381169
Seq. Order: 6
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Sex of the seal (M = male; F = female; U = unknown).

General Data Type: Varchar2

TYPE

CC ID: 381170
Seq. Order: 7
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Type of specimen collected.

AB = abscess

AD = adrenal

AF = abdominal fluid

AG = active fishing gear (ex. Hooks)

AQ = aqueous humor

BB = blubber biopsy (should have subtype either TX or FA)

BC = blood cells (remainder in tube after removing plasma or serum)

BI = bile

BL = blubber (blubber chunk)

BR = brain

BS = blood smear

BU = buffy coat

BY = bycatch (DNA)

BX = biotoxin (blood card test)

CF = chest fluid

CS = cerebral spinal fluid

ES = eye swab

EY = eye

FE = feces (collected from GIT, as opposed to excreted scat or fecal loop)

FL = feces obtained with fecal loop

GB = gall bladder

GI = gastrointestinal tract taken anywhere from pharynx to anus

GS = genital swab

HF = pericardial fluid

HC = histopathology cassettes

HL = hepatic lymph nodes

HS = histopathology slides

HT = heart

IL = inguinal lymph nodes

KI = kidney

LI = liver

LN = lymph node

LU = lung

MD = marine debris

MI = milk

ML = mesenteric lymph nodes

MN = mediastinal lymph nodes

MO = molt

MS = medulla spinalis (spinal cord)

MU = muscle

NM = nasal mites

NS = nasal swab

NT = necropsy tissue (tissues from all organs)

OO = otolith

ON = other necropsy (non-tissue samples)

OR = oral swab

OS = other swab

OT = other (describe in notes section on back of form)

PA = parasites

PC = placenta

PF = peritoneal fluid

PL = the 'pluck': heart, trachea, lungs and associated glands

PN = pulmonary lymph nodes

PS = plasma

RS = rectal swab

RT = whole reproductive tract of female or male

SC = scat (excreted feces)

SE = serum (collected in serum separator tube for serology)

SI = small intestine

SK = skeletal (bones or teeth)-specify sub-type

SL = spleen

SM = sub-mandibular lymph

SN = skin

SP = spew

SS = sub-scapular lymph

ST = stomach contents

TE = testes

TP = tissue plug (from both live and dead animals)

TS = throat swab

UB = urinary bladder

UM = umbilicus

UR = urine

VH = vitreous humor

VI = vibrissae

WA = water

WB = whole blood (old code = BL for whole blood)

WC = whole carcass

WH = whole heart

General Data Type: Varchar2

GROSS_FINDINGS

CC ID: 381173
Seq. Order: 10
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Findings at gross necrospy.

General Data Type: Varchar2

MICROSCOPY

CC ID: 381174
Seq. Order: 11
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Histopathology slide review findings.

General Data Type: Varchar2

NOTES

CC ID: 381175
Seq. Order: 12
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Additional comments from lab report and/or field or other pertinent notes.

General Data Type: Varchar2

Slide_Review_AFIP

CC ID: 381176
Seq. Order: 13
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Histopathology slide review findings for tissues examined at Armed Forces Institute of Pathology.

General Data Type: Varchar2

MANAGEMENT

CC ID: 381177
Seq. Order: 14
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Comments from lab regarding management related to findings.

General Data Type: Varchar2

DIAGNOSES

CC ID: 381178
Seq. Order: 15
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Histopathology findings.

General Data Type: Varchar2

COMMENTS_REMARKS

CC ID: 381179
Seq. Order: 16
Data Storage Type: Varchar2
Max Length: 22
Required: No
Primary Key: No
Status: Active
Description:

Additional comments from lab report and/or field or other pertinent notes.

General Data Type: Varchar2

Support Roles

Data Steward

CC ID: 381190
Date Effective From: 2015-12-03
Date Effective To:
Contact (Person): Kashinsky, Lizabeth
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: lizabeth.kashinsky@noaa.gov
Phone: (808)725-5719

Distributor

CC ID: 381191
Date Effective From: 2015-12-03
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Phone: 808-725-5300
URL: http://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Metadata Contact

CC ID: 381192
Date Effective From: 2015-12-03
Date Effective To:
Contact (Person): Johanos, Thea C
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: thea.johanos-kam@noaa.gov
Phone: (808)725-5709

Originator

CC ID: 381193
Date Effective From: 2007-10-22
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Phone: 808-725-5300
URL: http://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Point of Contact

CC ID: 381194
Date Effective From: 2007-10-22
Date Effective To:
Contact (Person): Kaufman, Angela C
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: angie.kaufman@noaa.gov
Phone: (808)725-5708

Point of Contact

CC ID: 381195
Date Effective From: 2007-10-22
Date Effective To:
Contact (Person): Kashinsky, Lizabeth
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: lizabeth.kashinsky@noaa.gov
Phone: (808)725-5719

Access Information

Security Class: Unclassified
Data Access Policy:

NMFS/PIFSC, Protected Species Division, Hawaiian Monk Seal Research Program Data Access, Sharing, and Dissemination Guidelines

Data Access Procedure:

Data are available by following the URL provided in this metadata record. The requester is asked to submit a request to Lizabeth Kashinsky (Lizabeth.Kashinsky@noaa.gov) and work with her and other PIFSC Hawaiian Monk Seal Research Program staff to assure proper use of this data.

Data Access Constraints:

NMFS/PIFSC, Protected Species Division, Hawaiian Monk Seal Research Program Data Access, Sharing, and Dissemination Guidelines

Data Use Constraints:

Use of the data set will ideally be cleared with NMFS/PIFSC, Protected Species Division. These data are PRELIMINARY and have not be completely screened for accuracy. NOAA can not be held liable for use of these data in a manner other than for perusal of preliminary data. The developers of these data are concerned with assuring its proper use. Before data are used to draw specific scientific conclusions, potential users are requested to contact NMFS/PIFSC, Protected Species Division for background on the data. Acknowledgement of the data should be cited. Different versions of the dataset may exist. The user must be sure to use the appropriate data set for the time period of interest. While efforts have been made to ensure that these data are accurate and reliable, NOAA cannot assume liablility for any damages or misrepresentation caused by any inaccuracies in the data or as a result of changes to the data caused by system transfers.

Catalog Details

Catalog Item ID: 36798
Metadata Record Created By: Vikram Khurana
Metadata Record Created: 2017-02-14 16:14+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2019-06-04 13:14+0000
Metadata Record Published: 2017-02-14
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Next Review Date: 2018-02-15