Enhanced Biological Sampling Data

This is a database of a variety of biological, reproductive, and energetic data collected from fish on the continental shelf in the northwest Atlantic Ocean. Species sampled in this database thus far include winter flounder, yellowtail flounder, summer flounder, haddock, cusk, Atlantic wolffish, and Atlantic herring. Data are collected from fish provided principally from fishermen participating in the NECRP Study Fleet. Some fish are taken from other NECRP research studies, and a small number from NEFSC surveys and surveys by MADMF and URI GSO. The catch location data is provided in views from the relevant FVTR, SVDBS, or other tables for a few cooperative research or external programs. The biological data includes general physical data (weights, lengths, organ weights, macroscopic maturity stage), age data, and other reproductive data. Measures collected from preserved gonad samples includes data for estimation of fish fecundity (oocyte counts and diameters) and from grading gonad histology for determination of maturity and seasonal reproductive status. In addition, relative measures of energetic condition are collected (including tissue wet weight and dry weights and bioimpedance data), and for some fish food habits data were collected in the first 18 months of data collection.

To supplement and expand beyond the standard biological data collected during NEFSC trawl surveys with greater detail and broader seasonal representation in order to improve the data collected on surveys and to provide additional information in support of stock assessments.

It is highly recommended that any users of this data consult with the POC of this data set. Data collection and auditing for some data types (histology, fecundity, and age particularly) have a long delay relative to initial sample collection, and some tables are still under development. There have been some minor modifications to protocols as well. Therefore, data could be misinterpreted or contain errors. Users should be aware of the caveats before use.

Data access is restricted, contact Dave McElroy.

NEFSC Data Access Procedure:

1. Formal request in writing usually to the data owner/contact or Center Director;

2. Requester is contacted by data owner to review and verify the request content and details for data delivery options.

3. If data is confidential then owner will determine if the data may be released to the requester;

4. If data can be released, the data is downloaded and packaged for delivery electronically; or the requester may be directed to where the data is available online.

Most of the fish capture locations come from the fishermen's commercial fishing locations and are imported from FVTR tables. These locations are protected proprietary information of the fishermen. Access is constrained by the same policies as all the FVTR data at the NEFSC.

NEFSC Data Access Constraint:

If data is stored on an internal NEFSC network, the requester may not have direct access to query the data unless they are also authorized for network access.

It is highly recommended that any users of this data consult with the POC of this data set prior to use for a better understanding of the data and its limitations.

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Most general fish and energetics data are initially entered through an application express (APEX) form into the oracle database. Some of the subsequent fecundity data are collected using macros in ImageJ and ObjectJ software, from which the data are output into .txt files. These .txt files are loaded into oracle through the APEX form. Histology data is recorded on paper when read at the microscope and input into the database or spreadsheets later. The scheme and data format is still being worked out for some species, so not all this data is loaded in Oracle tables currently. Image files for whole mount oocyte samples are collected using the proprietary Leica software that comes with the Leica dissecting scope. Some data auditing and derived data products are produced using R statistical software.

Most data are of higher precision when collected on site in the Woods Hole lab, but for the small number of fish sampled while at sea there is slightly less precision in the measurements. For lengths ± 0.1 cm in lab or 1 cm at sea. For whole fish ± 0.1 g in lab or 1 g at sea. For organ weights ± 0.1 or 0.001 g in lab or 1 g at sea. Fecundity ovarian subsamples are measured to ± 0.0001g. Oocyte diameters are measured ± 1 µm. Energetic tissue samples are weight to nearest ±0.001 g. Gonad or other lengths are taken to nearest mm. Fish are aged to the nearest year. Age samples are processed and examined using the same equipment and protocols used for age samples from all other programs at the NEFSC.

Some of the tables and data are incomplete. Some information is not in the Oracle tables (mostly histology and some oocyte image data) as the table design is incomplete and the data formats and variables are still under development. The reproductive data collection protocols and types are species specific and are changed as more is learned about each species. Data are continuously being collected and audited. Some values are still changing for older data as further analyses and audits identify errors, or as protocols improve. Some of the reproductive and age sample processing is labor intensive and so there is a long delay between initial sampling and final data availability.

The APEX form used to enter the data contains numerous data quality control restrictions. Some of these mandate specific data be collected or fit specified formats and levels of precision. Many of the variables collected also have warning prompts to users for data outside of the ranges typically observed for a particular species.

Data are backed up and stored on a schema on sole or several computers on site in the Woods Hole lab that are backed up following the standard routines for all data at the NEFSC. The database also has data editing access limited to those principally collecting and auditing the data routinely.

Fish samples are collected by cooperative research programs. Data were initially collected for the first 6 months of this program by hand on data sheets. The application express (APEX) form and oracle database were developed specifically for this project and began use in July 2010. Development of the software particular to the unique data for this project continues. Some tables are still in the developmental stage for some of the more unusual data types, and data is only partially loaded into Oracle tables.