Notes Regarding Sediment Toxicity (SEDTOX) Database

Table structures

The following tables describe the structure of the database management system developed for the SEDTOX database. Above each table are the names of the database tables and brief descriptions of the purpose. Following the database table names are "keys" which describe how unique records in the tables are defined. There are two sets of tables in the SEDTOX database system; one set for freshwater data and one set for marine data. The table structures for both sets are identical.

Site: Table to define general location
Key: Siteid

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
SITENAME	Char	40	Descriptive name for site
EPAREGION	Num	2, 0	Region for site location; 11 for Canada

Study: Provides basic information regarding the study (e.g. name, contact, etc.).
Key: Siteid+Studyid

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
STUDYID	Char	2	Study identifier
STUDYNAME	Char	40	Short name of study
CONTACT	Char	40	Contact source for data
SEDCHEM	Logical	1	Sediment chemistry data, Y or N?
SEDTOX	Logical	1	Sediment toxicity data, Y or N?

Studynot: Primarily a table for descriptive notes regarding the study design and method for recording data in the database. Information may include how replicates are recorded and any chemical sums calculated.
Key: Siteid+Studyid

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
STUDYID	Char	2	Study identifier
NOTES	Memo	10	Memo field data processing notes

Studyref: Contains information regarding the document which describes the study and data.
Key: Siteid+Studyid

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
STUDYID	Char	2	Study identifier
YEAR	Char	4	Year of publication
AUTHORS	Char	200	Authors, if published
TITLE	Char	160	Title, if published
SOURCE	Char	160	Citation or agency, if published

Station: Listing of stations for sediment chemistry, tissue chemistry, and bioassay sample collections.
Key: Siteid+Studyid+Stationid

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
STUDYID	Char	2	Study identifier
STATIONID	Char	6	Station identifier
LATITUDE	Num	12, 8	Latitude in decimal degrees, NAD83
LONGITUDE	Num	13, 8	Longitude in decimal degrees, NAD83
EST_STN	Char	8	How coordinates were established

Sample: Information regarding the sediment samples collected including stationid, sample date, depth (in centimeters). There should be records for true field samples and lab replicates.
Key: Siteid+Studyid+Stationid+Sampleid+Labrep

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
STUDYID	Char	2	Study identifier
STATIONID	Char	6	Station identifier
SAMPLEID	Char	2	Sample identifier
LABREP	Char	2	Lab replicate number
SAMPDATE	Char	8	Date sample collected as YYYYMMDD
SAMPTIME	Char	5	Time sample collected
UDEPTH	Num	8, 2	Top depth of sample from sed/water interface in cm
LDEPTH	Num	8, 2	Bottom depth of sample from sed/water interface in cm
TOC	Num	6, 2	Total organic carbon as percent
PCTFINES	Num	6, 2	Percent fines
UAN_PW	Num	10, 4	Unionized ammonia in porewater
H2S_PW	Num	10, 4	Hydrogen sulfide in porewater
EXSAMPID	Char	12	Investigator's sample identifier

Chem: Chemistry data associated with surface sediment samples.
Key: Siteid+Studyid+Stationid+Sampleid+Labrep+Chemcode

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
STUDYID	Char	2	Study identifier
STATIONID	Char	6	Station identifier
SAMPLEID	Char	2	Sample identifier
LABREP	Char	2	Lab replicate number
CHEMCODE	Char	10	Code for parameter name
CONC	Num	12, 5	Measured concentration
QUALCODE	Char	5	Assigned qualifier for concentration
UNITS	Char	6	Units of concentration for parameter
MEASBASIS	Char	2	Wet (WW) or dry weight (DW) indication
MISSINGVAL	Logical	1	Data missing, Y or N?

Biosumm: Mean results (of replicate data) for sediment bioassay.
Key: Siteid+Studyid+Stationid+Sampleid+Testid

(When necessary, series may be used in the key to distinguish multiple results for the same test using the same sample. Notes will be in the Studynot.dbf table to provide details.)

Note: Bioextra is a table identical to biosumm. The table contains data for additional tests that were not used for the sediment toxicity evaluations (see explanation provided at the end of the structure information).

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
STUDYID	Char	2	Study identifier
STATIONID	Char	6	Station identifier
SAMPLEID	Char	2	Sample identifier
TESTID	Char	12	Bioassay test code
GROUP	Char	2	Sample grouping
SERIES	Char	2	Bioassay test series number
EFFECTVAL	Num	7, 2	Measured effect value
SIGEFFECT	Logical	1	Was effect significant, Y or N?
NEG	Logical	1	Negative control sample, Y or N?
REF	Logical	1	Reference sample, Y or N?
STAT	Logical	1	Used for statistical comparison, Y or N?
CTRLADJ	Num	6, 2	Control-adjusted effect value
SIG_ORIGIN	Char	2	Code for toxic sample used by original study

Bmaster: Descriptives notes associated with bioassay tests where available.
Key: Siteid+Studyid+Testid

Note: Bmextra is a table identical to biosumm. The table contains information for additional tests that were not used for the sediment toxicity evaluations (see explanation provided at the end of the structure information).

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
STUDYID	Char	2	Study identifier
GROUP	Char	2	Sample grouping based on spatial or temporal
TESTID	Char	12	Bioassay test code
SPIKED	Logical	1	Sediment spiked with contaminant, Y or N?
TESTCOMM	Memo	10	Bioassay test comments

Qualify: Defines qualifiers used with chemical data
Key: Siteid+Studyid+Qualcode

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SITEID	Char	4	Site identifier
STUDYID	Char	2	Study identifier
QUALCODE	Char	5	Assigned qualifier code for concentration
QUALIFIERS	Char	30	Qualifiers used in original study
DESCRIPT	Char	80	Description of qualifiers used in study

Chemdict: Provides a unique list of chemical names and associated chemical codes which are used in the Chem table.
Key: Chemcode

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
CHEMCODE	Char	10	Code for parameter name
CHEMNAME	Char	40	Full chemical name
CHEMCLASS	Char	8	Chemical classification
CATEGORY	Char	8	Alternate chemical classification
SUBCATGY	Char	10	Subclassification for alternate chemical class
CHEMTOTAL	Char	10	Classification used for totaling chemicals
MOLWT	Num	7, 3	Molecular weight of chemical
CASNUM	Char	24	CAS number
UNITS	Char	6	Units of concentration for chemical (sed/tiss)
WA_UNITS	Char	6	Units of concentration for chemical in water media

Testdict: Provides a unique list of bioassay tests and associated test codes which are used in the Biosumm and Bmaster tables.
Key: Testid

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
TESTID	Char	12	Bioassay test code
MEDIUM	Char	15	Medium tested
MEDCODE	Char	2	Code for medium tested
GROUP	Char	20	Bioassay species grouping
ALTGROUP	Char	20	Alternate bioassay species grouping
SPECIES	Char	40	Bioassay organism
SPPCODE	Char	3	Code for bioassay organism
LHS	Char	10	Life history stage of bioassay organism
LHSCODE	Char	1	Code for life history stage
ENDPOINT	Char	30	Bioassay test endpoint
ENDCODE	Char	2	Code for test endpoint
DURATION	Char	10	Duration of test
DURCODE	Char	4	Code for test duration

Sqc: A table of sediment quality guidelines (sediment quality criteria (sqc)) by chemical
Key: Sqccode+Chemcode

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SQCCODE	Char	10	Sediment quality guideline code
CHEMCODE	Char	10	Code for parameter name
CONC	Num	10, 3	Guideline concentration
UNITS	Char	6	Units of concentration for SQC value
NORM	Char	2	Normalization factor

Sqcdict: A description of the sediment quality guideline sources.
Key: Sqccode

FIELD NAME	TYPE	WIDTH, DEC	DESCRIPTION
SQCCODE	Char	10	Sediment quality guideline code
SQCDESCR	Char	90	Description of sediment quality guideline
YEAR	Char	4	Reference year for SQC publication
AUTHORS	Char	160	Authors of the SQC publication
TITLE	Char	160	Title of the SQC publication
SOURCE	Char	160	Source reference for the SQC
COMMENT	Char	160	Comments about use of the SQC

Comments regarding Bioextra.dbf and Bmextra.dbf

The Bioextra.dbf table has the same structure as biosumm.dbf and contains results from bioassay tests which were not used in the evaluation due to the following reasons:

• In the marine data, some samples were run in two or more bioassay batches (refer to the series ID). A review of the data was conducted to try to determine which was the ?preferred? result from documentation (when available). The ?preferred? result was maintained in the biosumm table and the additional record(s) move to bioextra.dbf.
  
• In the freshwater data, the results from Hyalella azteca and Chironomus sp tests often had multiple growth endpoints (length and weight). Based on personal communication (C.G.Ingersoll of United States Geological Survey), the preferred growth endpoints were length data for Hyalella and weight data for Chironomus. However, if the preferred endpoint for growth was not available, the alternate endpoint was retained in the biosumm.dbf table. The additional endpoints that were not used for the analyses of growth responses were placed in the bioextra table. Therefore, data for Chironomus length and Hyalella weight can be found in bioextra.dbf.

Bmextra is a table which has the same structure as Bmaster.dbf and contains additional notes (when available) about the tests that are recorded in Bioextra.dbf. A Bmextra is only available for the freshwater data.

Other pages in this series

Predicting Sediment Toxicity