The different types or sets of barcodes in BARCODE_DATA.
BARCODE_TYPES defines values for the Barcode_Type column in BARCODE_DATA.
A text string indicating the organization from whence this barcode type or set came. Usually this will be the name of the company that manufactured the barcodes.
This column may not be NULL. This column may not be empty, it must contain characters,
and it must contain at least one non-whitespace character.
A text string indicating the manufacturer's identifier(s) for this barcode type or set. Usually this will be one or more catalog numbers.
This column may not be NULL. This column may not be empty, it must contain characters,
and it must contain at least one non-whitespace character.
When a barcode type/set doesn't have a catalog
number, use N/A or something
similar.
The possible locales where tissue and nucleic acid samples can be stored or used.
INSTITUTIONS defines values for the Institution column in LOCATIONS, NUCACID_DATA, NUCACID_LOCAL_IDS, TISSUE_DATA, and TISSUE_LOCAL_IDS.
The value 1 has
special meaning to the system. It is used in the TISSUES, NUCACIDS, and NUCACIDS_W_CONC views to help populate each
view's respective LocalId_1 column.
The value 2 has
special meaning to the system. It is used in the TISSUES, NUCACIDS, and NUCACIDS_W_CONC views to help populate each
view's respective LocalId_2 column.
The different roles that a barcode might have for an input in a library.
LIBRARY_BARCODE_ROLES defines values for the LIBRARY_INPUT_BARCODES.Role column.
The value FWD
has a special meaning to the system. In the definition of the
LIBRARY_INPUTS view, this LIBRARY_INPUT_BARCODES.Role value is used when
gathering data about the "forward" barcode — e.g. the
i7/P7 barcode — applied to a library input.
The value REV
has a special meaning to the system. In the definition of the
LIBRARY_INPUTS view, this LIBRARY_INPUT_BARCODES.Role value is used when
gathering data about the "reverse" barcode — e.g. the
i5/P5 barcode — applied to a library input.
The different kits that may be used as part of a Creation_Method for a library.
LIBRARY_KITS defines values for NUCACID_CREATION_METHODS.Library_Kit.
The possible types of libraries.
LIBRARY_TYPES defines values for NUCACID_CREATION_METHODS.Library_Type.
The possible levels of confidence in the identity of a tissue sample.
MISID_STATUSES defines values for TISSUE_DATA.Misid_Status.
The possible methods for quantifying nucleic acid concentrations.
NUCACID_CONC_METHODS defines values for NUCACID_CONC_DATA.Conc_Method.
The value 1 has a
special meaning to the system. This is the only NUCACID_CONC_DATA.Conc_Method value that
indicates quantification by quantitative PCR ("qPCR"). Also,
this value is used in the definition of
the NUCACIDS_W_CONC view.
The value 2
has a special meaning to the system. This is the only NUCACID_CONC_DATA.Conc_Method value that
indicates quantification with a Nanodrop
spectrophotometer. Also, this value is used in the definition of
the NUCACIDS_W_CONC view.
The value 3 has
a special meaning to the system. This is the only NUCACID_CONC_DATA.Conc_Method value that
indicates quantification with a Qubit fluorometer. Also,
this value is used in the definition of
the NUCACIDS_W_CONC view and that of the LIBRARIES view.
The value
4 has a special
meaning to the system. This is the only NUCACID_CONC_DATA.Conc_Method value that
indicates quantification with a Bioanalyzer assay. Also,
this value is used in the definition of
the NUCACIDS_W_CONC view.
The value 5
has a special meaning to the system. This is the only NUCACID_CONC_DATA.Conc_Method value that
indicates quantification with a Quant-iT assay. Also, this
value is used in the definition of
the NUCACIDS_W_CONC view.
A boolean indicating whether quantifications with this method can appear as a library quantification in the LIBRARIES view.
This column may not be NULL.
The possible units used in quantifications of nucleic acid concentrations.
The values in this table are used by the convert_conc() to convert values from one unit to
another. This is possible only when both units are related.
The Reference column is
used to indicate that relatedness. It is a Unit value that is used as a
standard or point of reference for all the units in that
group. E.g. rows for the unit μM
(micromolar) and nM (nanomolar) might both
have a Reference of M (molar)[240].
The Conversion
column is a number that indicates how the Unit is related to
its Reference. Given a quantity whose unit is the Reference,
multiply that quantity by the Conversion to get a
concentration with that row's Unit. E.g. in a row with Unit
mM (millimolar) and Reference
M (molar), the Conversion should be
1000.
When the Unit and
Reference are equal, the
Conversion must be
1. When Unit and Reference are not equal,
the Conversion cannot be 1.
NUCACID_CONC_UNITS defines values for NUCACID_CONC_DATA.Unit and for the two "unit" parameters of the convert_conc() function.
The value NG/UL has a
special meaning to the system. This is the only NUCACID_CONC_DATA.Unit value that indicates
nanograms per microliter (ng/μL). Also, this value is
used in the NUCACIDS_W_CONC and LIBRARIES views to show several concentrations
in ng/μL.
The value NM has a
special meaning to the system. This is the only NUCACID_CONC_DATA.Unit value that indicates
nanomolarity (nanomoles/L). Also, this value is
used in the LIBRARIES view to show a concentration in
nanomolar.
The value PG/UL has a
special meaning to the system. This is the only NUCACID_CONC_DATA.Unit value that indicates
picograms per microliter (pg/μL). Also, this value is
used in the NUCACIDS_W_CONC view to show a
concentration in pg/μL.
The Unit used for reference when converting quantities to and from this row's Unit.
This column may not be NULL.
The possible methods for creating nucleic acid samples.
For the nucleic acid samples that are also libraries,
additional columns are included to record data that are
relevant only to library creation: Library_Kit and Library_Type. If a
method has one of these then it must have the other; these
columns must both be NULL or both non-NULL.
Methods with a Library_Kit and Library_Type value can
only be used with libraries. That is, if a sample in NUCACID_DATA has a Creation_Method with a non-NULL
Library_Kit and Library_Type in this table, then that sample's
NucAcid_Type must be
LIBRARY.
Each Library_Kit-Library_Type pair must be unique.
NUCACID_CREATION_METHODS defines values for NUCACID_DATA.Creation_Method.
A name or abbreviation indicating the materials, equipment, and procedure used to create this library.
This column may be NULL when the row is not a
creation method for libraries. This column may not be empty, it must contain characters,
and it must contain at least one non-whitespace character.
A name or abbreviation indicating what kind of library is created by this protocol.
This column may be NULL when the row is not a
creation method for libraries. This column may not be empty, it must contain characters,
and it must contain at least one non-whitespace character.
The possible nucleic acid sample types.
NUCACID_TYPES defines values for NUCACID_DATA.NucAcid_Type.
This column may not be empty, it must contain characters, and it must contain at least one non-whitespace character.
The value LIBRARY has
a special meaning to the system. This is the only NUCACID_DATA.NucAcid_Type value that indicates
the nucleic acid sample is a library. Nucleic acid samples
must have this value as their NucAcid_Type to be allowed in the
LIBRARY_DATA table.
The possible media used for storage/archiving of tissue samples.
STORAGE_MEDIA defines values for TISSUE_DATA.Storage_Medium.
This column may not be empty, it must contain characters, and it must contain at least one non-whitespace character.
The possible tissue sample types.
Some types of tissues, e.g. blood, cannot plausibly be collected after an individual has died or disappeared. Other tissue types may be collected during regular observation or sometime afterward, e.g. "skin" could be a puncture from a live animal or a patch of dry flesh from a found corpse. To validate the TISSUE_DATA.Collection_Date against the source individual's BIOGRAPH.Statdate, but also allow the flexibility to set different rules for different tissue types, this table includes the Max_After_Statdate column.
When the Max_After_Statdate column is not
NULL, all TISSUE_DATA rows that have this
row's Tissue_Type and that came from an individual in the main
population cannot have a Collection_Date that is more than
Max_After_Statdate days after
the individual's Statdate. That is,
tissue samples cannot be collected more than Max_After_Statdate days after the
individual's death/disappearance.
TISSUE_TYPES defines values for TISSUE_DATA.Tissue_Type.
A non-negative integer, indicating the maximum number of days that the Collection_Date of a TISSUE_DATA row with this Tissue_Type is allowed to exceed the source individual's BIOGRAPH.Statdate, if any.
This column may be NULL, indicating that the row's
Tissue_Type can be collected any number of days after the
Statdate.
[240] It's not necessary to go all the way back to the SI standard unit. If all your concentrations tend to be in nanomolar with the occasional picomolar, then both units could use nanomolar as their Reference and never bother going back to molar.