[ALIAS_GROUP 1](#alias_group)

[ALLELE 2](#allele)

[ANOMALY 2](#anomaly)

[CHROMOSOME_MAP 3](#chromosome_map)

[HAP_MEMBER 4](#hap_member)

[HAPLOTYPE 4](#haplotype)

[INDIVIDUAL 5](#individual)

[INTERVAL 6](#interval)

[LABORATORY 7](#laboratory)

[MAP_MEMBER 8](#map_member)

[MAPPING 8](#mapping)

[MAPPING_INTERVAL 9](#mapping_interval)

[MAPPING_LOCATION 10](#mapping_location)

[MAPPING_RECOMBINATION 11](#mapping_recombination)

[MARKER_ALIAS 12](#marker_alias)

[MARKER_TYPING 13](#marker_typing)

[METHOD 14](#method)

[NON_INHERITANCE 15](#non_inheritance)

[PAIRWISE_LINKAGE 15](#pairwise_linkage)

[PANEL 16](#panel)

[PEDIGREE 16](#pedigree)

[PERSON 17](#person)

[POLYMORPHISM_TYPE 18](#polymorphism_type)

[RECOMBINATION 18](#recombination)

[REFERENCE_MAP 19](#reference_map)

[REFERENCE_MAP_PEDIGREE 19](#reference_map_pedigree)

[TYPING 20](#typing)

[VARIANT_TYPE 21](#variant_type)

# 

# ALIAS_GROUP

## Description:

Represents an official group of aliases for markers. An example would
be: GENBANK. When a user enters a Marker Alias for a Marker Typing, he
must also specify the Alias Group for that Marker Alias.

## Relationships:

An ALIAS_GROUP consists of zero to many MARKER_ALIASes.

## Fields:

  ------------- ---------------------------------------------------------
  AGNAME        The name of this group.

  ------------- ---------------------------------------------------------

# ALLELE

## Description:

Represents one allele of a particular marker.

## Relationships:

An ALLELE relates to exactly one MARKER_TYPING.

An ALLELE is the first allele of one to many TYPINGs.

An ALLELE is the second allele of one to many TYPINGs.

## Fields:

  ------------------- ---------------------------------------------------
  ALLELE_ID           Automatically generated primary key.

  ALLELE_SYMBOL       This is the identifier that the Mapping Tool will
                      use for this Allele during its calculations. It is
                      assigned automatically by the LPL.

  ALLELE_IDENT        The common name for this Allele. This is the
                      identifier for this Allele that was used in the
                      Laboratory that generated the Marker Typing to
                      which this Allele corresponds.

  ACCESSION_NUM       Foreign key referencing a MARKER_TYPING.

  FREQUENCY           The frequency of this Allele within the population
                      of individuals that was used to generate the Marker
                      Typing to which this Allele corresponds. It is
                      calculated by the LPL upon import of the Marker
                      Typing data.
  ------------------- ---------------------------------------------------

# ANOMALY

## Description:

An Anomaly is something exceptional about a certain Typing. This table
is a lookup table containing a standard set of Anomaly symbols and their
meanings.

## Relationships:

An ANOMALY is associated with zero to many TYPINGs.

Fields:

  --------------------- -------------------------------------------------
  ANOMALY_SYMBOL        A single character symbol that represents this
                        Anomaly.

  MEANING               A short description of the meaning associated
                        with a symbol.
  --------------------- -------------------------------------------------

# 

# CHROMOSOME_MAP

## Description:

Represents a collection of markers in a particular order on a particular
chromosome.

## Relationships:

A CHROMOSOME_MAP is a part of exactly one REFERENCE_MAP.

A CHROMOSOME_MAP consists of one to many MAP_MEMBERs.

A CHROMOSOME_MAP consists of one to many INTERVALs.

A CHROMOSOME_MAP consists of zero to many HAPLOTYPEs.

## Fields:

  ----------------------- -----------------------------------------------
  CHROMOSOME_MAP_ID       Primary key. Automatically generated.

  REFERENCE_MAP_ID        Foreign key. The ID of the REFERENCE_MAP to
                          which this CHROMOSOME_MAP belongs.

  CHRNUMBER               The number of this chromosome (1-23)

  FEMALE_LIK              The likelihood that this map is correct as
                          calculated by the MappingTool using a female
                          sex-specific parameter.

  MALE_LIK                The likelihood that this map is correct as
                          calculated by the MappingTool using a male
                          sex-specific parameter.

  AVERAGE_LIK             The likelihood that this map is correct as
                          calculated by the MappingTool using a
                          sex-averaged parameter.

  CHRFEMALE_LEN           The length of this map in Centimorgans as
                          calculated by the MappingTool using a female
                          sex-specific parameter.

  CHRMALE_LEN             The length of this map in Centimorgans as
                          calculated by the MappingTool using a male
                          sex-specific parameter.

  CHRAVERAGE_LEN          The length of this map in Centimorgans as
                          calculated by the MappingTool using a
                          sex-averaged parameter.

  CNOTES                  Arbitrary amount of text.
  ----------------------- -----------------------------------------------

# HAP_MEMBER

## Description:

Represents a marker that is a member of a particular haplotype on a
particular chromosome.

A HAP_MEMBER is a MAP_MEMBER that is part of a HAPLOTYPE on a
CHROMOSOME_MAP.

## Relationships:

A HAP_MEMBER is a MAP_MEMBER.

A HAP_MEMBER is a part of exactly one HAPLOTYPE.

## Fields:

  ------------------- ---------------------------------------------------
  HAP_MEMBER_ID       Primary key. Automatically generated.

  MAP_MEMBER_ID       Foreign key. The ID of the MAP_MEMBER that is part
                      of a HAPLOTYPE.

  HAPLOTYPE_ID        Foreign key. The ID of the HAPLOTYPE of which this
                      HAP_MEMBER is a part.

  HORDER              This HAP_MEMBER\'s order within the HAPLOTYPE.
  ------------------- ---------------------------------------------------

# HAPLOTYPE

## Description:

Represents a group of markers on a chromosome map that are always
inherited together.

## Relationships:

A HAPLOTYPE is associated with exactly one CHROMOSOME_MAP.

A HAPLOTYPE consists of one to many HAP_MEMBERs.

## Fields:

  ----------------------- -----------------------------------------------
  HAPLOTYPE_ID            Primary Key. Automatically generated.

  CHROMOSOME_MAP_ID       Foreign key. ID of CHROMOSOME_MAP to which this
                          HAPLOTYPE is associated.
  ----------------------- -----------------------------------------------

# INDIVIDUAL

## Description:

An Individual represents a particular sample of DNA (from a particular
individual).

## Relationships:

An INDIVIDUAL is a member of exactly one PEDIGREE.

An INDIVIDUAL is produced by exactly one LABORATORY.

An INDIVIDUAL is described by zero to many TYPINGs.

An INDIVIDUAL causes zero to many NONINHERITANCES.

## Fields:

  -------------------- --------------------------------------------------
  INDIVIDUAL_ID        Primary key. Automatically generated.

  SAMPLE_ID            The ID used to refer to this SAMPLE by the
                       LABORATORY that produced this SAMPLE. This ID is
                       unique within the context of a LABORATORY.

  LNAME                Foreign key. The name of the LABORATORY that
                       produced this particular SAMPLE.

  PEDIGREE_ID          The ID of the PEDIGREE of which this INDIVIDUAL is
                       a member.

  PEDIDENT             The common name of the PEDIGREE of which this
                       INDIVIDUAL is a member.

  MATSAMPLE_ID         The SAMPLE_ID of this INDIVIDUAL\'s mother.

  PATSAMPLE_ID         The SAMPLE_ID of this INDIVIDUAL\'s father.

  MATINDIVIDUAL_ID     Foreign key. ID of this INDIVIDUAL's mother.

  PATINDIVIDUAL_ID     Foreign key. ID of this INDIVIDUAL's father.

  SEX                  MALE, FEMALE, or UNKNOWN

  PROBAND_STATUS       Whether or not this INDIVIDUAL was the proband in
                       a disease study. (0 = FALSE or 1 = TRUE).

  INDEPENDENT          Indicates whether this INDIVIDUAL should be used
                       to calculate the allele frequency and
                       heterozygosity. Either 'TRUE' or 'FALSE'.
  -------------------- --------------------------------------------------

## Notes:

The MATSAMPLE_ID and PATSAMPLE_ID fields are present in this table for
efficiency's sake.

# INTERVAL

## Description:

Represents a section of a chromosome that is delimited either by two
markers or a marker and one of the terminal ends of the chromosome. The
interval is determined by the markers that are present in a particular
chromosome map. It is not a feature of the chromosome that the map
represents.

## Relationships:

An INTERVAL is associated with exactly one CHROMOSOME_MAP.

An INTERVAL is flanked toward the pter by zero or one MAP_MEMBER.

An INTERVAL is flanked toward the qter by zero or one MAP_MEMBER.

An INTERVAL has zero to many RECOMBINATIONs.

An INTERVAL is associated with zero to many MAPPING_INTERVALs.

## Fields:

  ----------------------- -----------------------------------------------
  INTERVAL_ID             Primary key. Automatically generated.

  CHROMOSOME_MAP_ID       Foreign key. ID of CHROMOSOME_MAP to which this
                          INTERVAL is associated.

  INUMBER                 The order of this INTERVAL on the
                          CHROMOSOME_MAP.

  FLANK_MARKERA           Foreign key. The ID of the MAP_MEMBER that
                          flanks this INTERVAL toward the pter. If it is
                          NULL then this INTERVAL is flanked by the pter.

  FLANK_MARKERB           Foreign key. The ID of the MAP_MEMBER that
                          flanks this INTERVAL toward the qter. If it is
                          NULL then this INTERVAL is flanked by the qter.

  IMALE_LENGTH            The length of this interval in Centimorgans as
                          calculated by the mapping tool using a
                          sex-specific male parameter.

  IFEMALE\_ LENGTH        The length of this interval in Centimorgans as
                          calculated by the mapping tool using a
                          sex-specific female parameter.

  IAVERAGE\_ LENGTH       The length of this interval in Centimorgans as
                          calculated by the mapping tool using a
                          sex-averaged parameter.

  IMALE_REC_FRAC          The male recombination fraction for this
                          interval.

  IFEMALE\_ REC_FRAC      The female recombination fraction for this
                          interval.

  IAVERAGE\_ REC_FRAC     The average recombination fraction for this
                          interval.
  ----------------------- -----------------------------------------------

# LABORATORY

## Description:

A LABORATORY is the source of samples which represent INDIVIDUALs. It is
also the source of MARKER_TYPING data. Finally, a PERSON, who imports or
types MARKER_TYPINGs and PEDIGREE data, belongs to a LABORATORY.

## Relationships:

A LABORATORY produces zero to many INDIVIDUALs.

A LABORATORY is the place to which zero to many PERSONs belong.

A LABORATORY is source of zero to many MARKER_TYPINGs.

## Fields:

  ------------------ ----------------------------------------------------
  LABORATORY_ID      Primary key. The official name of the Laboratory.

  LNAME              Official name of laboratory.

  STREET_ADDRESS     

  CITY               

  STATE              

  POSTAL_CODE        

  COUNTRY            
  ------------------ ----------------------------------------------------

# MAP_MEMBER

## Description:

Represents a marker that is a member of a chromosome map.

## Relationships:

A MAP_MEMBER is a MARKER_TYPING.

A MAP_MEMBER is a member of exactly one CHROMOSOME_MAP.

A MAP_MEMBER flanks the pter side of exactly one INTERVAL.

A MAP_MEMBER flanks the qter side of exactly one INTERVAL.

A MAP_MEMBER is the marker that flanks the pter side of zero to many
likely MAPPING_LOCATIONs.

A MAP_MEMBER is the likely marker that flanks the qter side of zero to
many likely MAPPING_LOCATIONs.

A MAP_MEMBER is the marker that flanks the pter side of zero to many
best MAPPING_LOCATIONs.

A MAP_MEMBER is the marker that flanks the qter side of zero to many
best MAPPING_LOCATIONs.

A MAP_MEMBER is associated with zero to many HAP_MEMBERs.

## Fields:

  ----------------------- -----------------------------------------------
  MAP_MEMBER_ID           Primary key. Automatically generated.

  ACCESSION_NUM           The ID of the MARKER_TYPING that is a member of
                          a CHROMOSOME_MAP.

  CHROMOSOME_MAP_ID       The ID of the CHROMOSOME_MAP_ID of which this
                          MAP_MEMBER is a member.

  MORDER                  This marker's order within the CHROMOSOME_MAP.
  ----------------------- -----------------------------------------------

# MAPPING

## Description:

Represents a set of data describing the mapping of a marker onto a
particular reference map. The marker may map to more that one chromosome
in the reference map.

## Relationships:

A MAPPING describes exactly one MARKER_TYPING.

A MAPPING is associated with zero to many MAPPING_LOCATIONs.

A MAPPING is associated with zero to many MAPPING_INTERVALs.

A MAPPING is associated with zero to many PAIRWISE_LINKAGEs.

A MAPPING is associated with exactly one REFERENCE_MAP.

A MAPPING is QCed by zero or one PERSON.

A MAPPING may have zero to many REPORTS.

## Fields:

  ---------------------- ------------------------------------------------
  MAPPING_ID             Primary key. Automatically generated.

  ACCESSION_NUM          Foreign key. The ID of the MARKER_TYPING
                         represented by this MAPPING.

  REFERENCE_MAP_ID       Foreign key. The ID of REFERENCE_MAP to which
                         the MARKER_TYPING represented by this MAPPING
                         has been mapped.

  DATE_MAPPED            The date on which the MARKER_TYPING was mapped
                         onto the REFERENCE_MAP.

  DATE_QCED              The date on which the data describing this
                         mapping was viewed and approved by someone.

  QC_PERSON              Foreign key. The unique ID of the PERSON that
                         QCed this set of data.

  QC_NOTE                Description provided by the QC_PERSON.

  LINKAGE_SUFFICIENT     Whether or not there was sufficient linkage
                         between this marker and some map member to
                         assign this marker to at least one chromosome.
                         Either 'TRUE' or 'FALSE'.
  ---------------------- ------------------------------------------------

# MAPPING_INTERVAL

## Description:

Represents the interval on a chromosome within which a marker has been
mapped.

## Relationships:

A MAPPING_INTERVAL is associated with exactly one MARKER_TYPING.

A MAPPING_INTERVAL is associated with exactly one INTERVAL.

A MAPPING_INTERVAL has zero to many MAPPING_RECOMBINATIONS.

## Fields:

+-----------------------+----------------------------------------------+
| MAPPING_INTERVAL_ID   | Primary key. Automatically generated.        |
+-----------------------+----------------------------------------------+
| ACCESSION_NUM         | Foreign key. The ID of the mapped            |
|                       | MARKER_TYPING.                               |
+-----------------------+----------------------------------------------+
| INTERVAL_ID           | Foreign key. The ID of the INTERVAL to which |
|                       | the MARKER_TYPING has been mapped.           |
+-----------------------+----------------------------------------------+
| LIKELIHOOD            | The log10 likelihood that the test marker    |
|                       | maps to this interval. This number is        |
|                       | calculated by the MappingTool.               |
+-----------------------+----------------------------------------------+
| INTERVAL_EXPANSION    | \*\*\* The name of this field should be      |
|                       | changed to MAP_EXPANSION. It was not changed |
|                       | in this release because it was mistake in    |
|                       | the model was found so late in development.  |
|                       |                                              |
|                       | The difference between the length of the map |
|                       | before the test marker is inserted and the   |
|                       | length of the map after the test marker is   |
|                       | inserted.                                    |
+-----------------------+----------------------------------------------+
| LENGTH1               | The length between the inserted marker and   |
|                       | the flanking marker toward the pter.         |
+-----------------------+----------------------------------------------+
| LENGTH2               | The length between the inserted marker and   |
|                       | the flanking marker toward the qter.         |
+-----------------------+----------------------------------------------+
| MMALE_LENGTH          | The length of this map in Centimorgans as    |
|                       | calculated by the mapping tool using a       |
|                       | sex-specific male parameter.                 |
+-----------------------+----------------------------------------------+
| MFEMALE_LENGTH        | The length of this map in Centimorgans as    |
|                       | calculated by the mapping tool using a       |
|                       | sex-specific female parameter.               |
+-----------------------+----------------------------------------------+
| MAVERAGE_LENGTH       | The length of this map in Centimorgans as    |
|                       | calculated by the mapping tool using a       |
|                       | sex-averaged parameter.                      |
+-----------------------+----------------------------------------------+

## Notes:

INTERVAL_LIKELIHOOD, MMALE_LENGTH, MFEMALE_LENGTH, and MAVERAGE_LENGTH
all concern the entire CHROMOSOME_MAP, not just the INTERVAL.

Expansion and length information are filled in for only the insertion
interval.

# MAPPING_LOCATION

## Description:

Represents both the likely and best span on a chromosome map onto which
a marker has been mapped. These spans may include one or more intervals.

## Relationships:

A best MAPPING_LOCATION is flanked on the pter side by zero or one
MAP_MEMBER.

A best MAPPING_LOCATION is flanked on the qter side by zero or one
MAP_MEMBER.

A likely MAPPING_LOCATION is flanked on the pter side by zero or one
MAP_MEMBER.

A likely MAPPING_LOCATION is flanked on the qter side by zero or one
MAP_MEMBER.

A MAPPING_LOCATION is associated with exactly one MARKER_TYPING.

## Fields:

  ------------------------- ---------------------------------------------
  MAPPING_LOCATION_ID       Primary key. Automatically generated.

  ACCESSION_NUM             Foreign key. The ID of the mapped
                            MARKER_TYPING.

  LIKELY_MARKERA            The ID of the MAP_MEMBER on the pter end of
                            the likely MAPPING_LOCATION. If NULL, then it
                            is flanked by the pter.

  LIKELY_MARKERB            The ID of the MAP_MEMBER on the qter end of
                            the likely MAPPING_LOCATION. If NULL, then it
                            is flanked by the qter.

  BEST_MARKERA              The ID of the MAP_MEMBER on the pter end of
                            the best MAPPING_LOCATION. If NULL, then it
                            is flanked by the pter.

  BEST_MARKERB              The ID of the MAP_MEMBER on the qter end of
                            the best MAPPING_LOCATION. If NULL, then it
                            is flanked by the qter.
  ------------------------- ---------------------------------------------

# MAPPING_RECOMBINATION

## Description:

Represents a recombination that exists after the test marker has been
inserted into the chromosome map. For a particular MAPPING, there may be
more or less MAPPING_RECOMBINATIONs than RECOMBINATIONs.

## Relationships:

A MAPPING_RECOMBINATION occurs between zero to two MARKER_TYPINGs.

## Fields:

  ------------------------------ ----------------------------------------
  MAPPING_RECOMBINATION_ID       Primary key. Automatically generated.

  INDIVIDUAL_ID                  Foreign key. The ID of the INDIVIDUAL
                                 that cause the RECOMBINATION.

  GENDER                         Indicates if the recombination is
                                 maternal or paternal. Has a value of
                                 \'P\' or \'M\'.

  ADDITION_RECOMBINATION         Whether the recombination is new. 'TRUE'
                                 or 'FALSE'.

  MARKERA                        Foreign key. The accession num of the
                                 marker toward the pter.

  MARKERB                        Foreign key. The accession num of the
                                 marker toward the qter.

  MAPPING_INTERVAL_ID            Foreign key.
  ------------------------------ ----------------------------------------

## Notes:

MAPPING_INTERVAL has been left in the current schema but it no longer
makes sense. A recombination occurs between markers that are not
necessarily the flanking markers of an INTERVAL. The MAPPING_INTERVAL_ID
is needed still to allow one to figure out which MAPPING a certain
MAPPING_RECOMBINATION belongs to.

# MARKER_ALIAS

## Description:

A marker may be represented by any number of MARKER_TYPINGs. However, a
MARKER_TYPING represents exactly one marker (in reality). But, the
marker that a particular MARKER_TYPING represents may have any number of
aliases. So, the situation could arise that two difference markers could
by chance have the same alias, which means that two MARKER_TYPINGs that
represent difference markers could also have the same alias.

For this reason, a MARKER_TYPING is given an accession number by the LPL
upon import. To accommodate the reality of aliases, each marker typing
may have any number of MARKER_ALIASes. However, each MARKER_ALIAS record
corresponds to exactly one MARKER_TYPING record even though two
different MARKER_TYPINGs may have associated MARKER_ALIASes that
happened to have the same value in the alias column of the MARKER_ALIAS
record.

## Relationships:

A MARKER_ALIAS is associated with exactly one MARKER_TYPING.

A MARKER_ALIAS is a member of zero or one ALIAS_GROUP.

## Fields:

  ---------------------- ------------------------------------------------
  MARKER_ALIAS_ID        Primary key. Automatically generated.

  ACCESSION_NUM          Foreign key. The accession number of the Marker
                         Typing to which this Marker Alias corresponds.

  AGNAME                 Foreign key. The name of the Alias Group to
                         which this Marker Alias belongs.

  ALIAS                  The value of this Marker Alias.
  ---------------------- ------------------------------------------------

# MARKER_TYPING

## Description:

A marker typing represents data about the pattern of inheritance of a
marker within a population of individuals. The LPL uses this data to
determine the relative position of the represented marker on a
chromosome map.

## Relationships:

A MARKER_TYPING is typed by exactly one PERSON.

A MARKER_TYPING is imported by exactly one PERSON.

A MARKER_TYPING comes from exactly one LABORATORY.

A MARKER_TYPING consists of one to many TYPINGs.

A MARKER_TYPING has one to many MARKER_ALIASes.

A MARKER_TYPING is of exactly one VARIANT_TYPE.

A MARKER_TYPING is produced using exactly one METHOD.

A MARKER_TYPING is of exactly one POLYMORPHISM_TYPE.

A MARKER_TYPING is associated with zero to many MAPPINGs.

A MARKER_TYPING has one to many ALLELEs.

A MARKER_TYPING is associated with zero to many NONINHERITANCEs.

A MARKER_TYPING may have zero to many REPORTs.

## Fields:

  ---------------------- ------------------------------------------------
  ACCESSION_NUM          Primary key. Automatically generated.

  MARKER_NAME            The common name for the maker represented by
                         this data. It is the name that the importing
                         person used when importing this Marker Typing.

  LNAME                  The name of the Laboratory that produced this
                         Marker Typing.

  PROJECT_ID             The ID of the project that produced this Marker
                         Typing.

  DATE_IMPORTED          The date on which this data was imported into
                         the LPL.

  DATE_MAPPED            The date on which this Marker Typing was mapped
                         to a particular Reference Map.

  DATE_QCED              The date on which this Marker Typing data was
                         QC\'ed.

  DATE_TYPED             The date on which this data was originally
                         produced in the laboratory.

  IMPORTER               Foreign key. The ID of the Person that imported
                         this data.

  TYPER                  Foreign key. The ID of the Person that typed
                         this data.

  MNAME                  Foreign key. The name of the Method used to
                         produce this data. For example: RFLP, SS, MALDI,
                         etc\...

  VNAME                  Foreign key. A values such as \'genotype\',
                         \'phenotype\', \'haplotype\', etc\... This value
                         is taken for the Variant Type table.

  PTYPE                  Foreign key. A values such as \'trinucleotide\',
                         dinucleotide\', ect.. taken from the
                         Polymorphism Type table.

  LOCKED_TYPING          Whether or not this Marker Typing may be mapped
                         or qc\'ed. Either \'TRUE\' or \'FALSE\'.

  MPUB_STATUS            Whether or not this data has been published.
                         Either \'TRUE\' or \'FALSE\'.

  NIM                    The number of informative meioses as calculated
                         by the mapping tool.

  HETZYG_LAB             The percentage heterozygosity as calculated by
                         the source Laboratory.

  HETZYG_LINK            The percentage heterozygosity as calculated by
                         the LPL.

  NUM_ALLELES            The number of alleles for the marker that this
                         data represents.

  MOTIF                  A string like: AAAA\[CA\]6CCC

  TYPING_RELIABILITY     Indicates how easy this MARKER_TYPING was to
                         score according to the source LABORATORY.

  MNOTES                 

  LABORATORY_ID          Foreign key. The ID of the LABORATORY that
                         produced this MARKER_TYPING.
  ---------------------- ------------------------------------------------

# METHOD

## Description:

This is a lookup table. Contains the names of the methods available to
produce a Marker Typing.

## Relationships:

A METHOD is used to generate zero to many MARKER_TYPINGS.

## Fields:

  ---------------- ------------------------------------------------------
  MNAME            Primary key. The name of this method.

  ---------------- ------------------------------------------------------

# NON_INHERITANCE

## Description:

This is a case in which an INDIVIDUAL belonging to a particular PEDIGREE
has an ALLELE that could not have been inherited according to normal
Mendelian inheritance.

## Relationships:

A NONINHERITANCE is caused by exactly one INDIVIDUAL.

A NONINHERITANCE is associated with exactly one MARKER_TYPING.

## Fields:

  ----------------------------------- -----------------------------------
  NONINHERITANCE_ID                   Primary key. Automatically
                                      generated.

  ACCESSION_NUM                       Foreign key. The ID of the
                                      MARKER_TYPING with which this is
                                      associated

  INDIVIDUAL_ID                       Foreign key. The ID of the
                                      INIDIVIDUAL that caused this.
  ----------------------------------- -----------------------------------

# PAIRWISE_LINKAGE

## Description:

This represents a significant linkage between a test marker and a marker
that is the member of a chromosome map.

## Relationships:

A PAIRWISE_LINKAGE is associated with exactly one MAPPING.

A PAIRWISE_LINKAGE is associated with exactly one MAP_MEMBER.

## Fields:

  ----------------------- -----------------------------------------------
  PAIRWISE_LINKAGE_ID     Primary key. Autmatically generated.

  MAPPING                 Foreign key. The ID of the test MAPPING record
                          which in turn corresponds to a MARKER_TYPING.

  MAP_MEMBER_ID           The ID of the MAP_MEMBER to which significant
                          linkage was found.

  PFEMALE_REC_FRAC        The female recombination fraction. A floating
                          point number.

  PMALE_REC_FRAC          The male recombination fraction. A floating
                          point number.

  PAVERAGE_REC_FRAC       The average recombination fraction. A floating
                          point number.

  LOD_SCORE               Indicates the strength of linkage between a
                          MARKER_TYPING and a MAP_MEMBER.
  ----------------------- -----------------------------------------------

# PANEL

## Description:

A Panel is the source of a group of Pedigrees. The CEPH Panel is a
well-known Panel.

## Relationships:

A PANEL is a group of one to many PEDIGREEs.

## Fields:

  ------------------- ---------------------------------------------------
  PNAME               Primary key. The name of the PANEL.

  ------------------- ---------------------------------------------------

# PEDIGREE

## Description:

Pedigree is a collection of Individuals. It represents inheritance data
concerning a group of related individuals.

## Relationships:

A PEDIGREE is part of exactly one PANEL.

A PEDIGREE is a group of one to many INDIVIDUALS.

A PEDIGREE is associated with zero to many REFERENCE_MAP_PEDIGREEs.

## Fields:

  ------------------- ---------------------------------------------------
  PEDIGREE_ID         Primary key. Automatically generated.

  PEDIDENT            The common name for this Pedigree, assigned by the
                      Panel.

  PNAME               Foreign key. This Pedigree\'s Panel\'s name

  DATE_IMPORTED       The date on which this collection of data was
                      imported into the LPL system.

  IMPORTER            Foreign key. The ID of the Person who imported this
                      set of data.

  PNOTES              
  ------------------- ---------------------------------------------------

# PERSON

## Description:

A Person can:

-import Pedigree and Marker Typing data

-be the one that produced (typed) a particular Marker Typing

Persons belong to Laboratories.

## Relationships:

A PERSON belongs to exactly one LABORATORY.

A PERSON imports zero to many PEDIGREEs.

A PERSON types zero to many MARKER_TYPINGs.

A PERSON imports zero to many MARKER_TYPINGs.

## Fields:

  ----------------- -----------------------------------------------------
  PERSON_ID         Primary key. Automatically generated.

  FIRST_NAME        

  LAST_NAME         

  LNAME             Foreign key. The ID of the LABORATORY to which this
                    PERSON belongs.

  PHONE_NUMBER      
  ----------------- -----------------------------------------------------

# POLYMORPHISM_TYPE

## Description:

## Relationships:

A POLYMORPHISM_TYPE is associated with zero to many MARKER_TYPINGs.

## Fields:

  ------------- ---------------------------------------------------------
  PTYPE         Primary key. The name of the POLYMORPHISM_TYPE.

  ------------- ---------------------------------------------------------

# RECOMBINATION

## Description:

Represents one recombination that exists between to markers on a
chromosome map before the test marker is inserted.

## Relationships:

A RECOMBINATION is associated with zero to two MARKER_TYPINGs.

A RECOMBINATION is associated with exactly one INDIVIDUAL.

## Fields:

  ----------------------- -----------------------------------------------
  RECOMBINATION_ID        Primary key. Automatically generated.

  INTERVAL_ID             Foreign key. The ID of the INTERVAL on which
                          the RECOMBINATION occurred.

  INDIVIDUAL_ID           Foreign key. The ID of the INDIVIDUAL that
                          cause the RECOMBINATION.

  GENDER                  Whether the recombination came from the
                          paternal side. TRUE or FALSE.

  RMATERNAL               Whether the recombination came from the
                          maternal side. TRUE or FALSE.

  CHROMOSOME_MAP_ID       Foreign key. The ID of the CHROMOSOME_MAP on
                          which this recombination occurs.
  ----------------------- -----------------------------------------------

# REFERENCE_MAP

## Description:

A collection of chromosome maps.

## Relationships:

A REFERENCE_MAP is associated with 23 CHROMOSOME_MAPs.

A REFERENCE_MAP is associated with zero to many REFERENCE_MAP_PEDIGREEs.

## Fields:

  -------------------- --------------------------------------------------
  REFERENCE_MAP_ID     Primary key. Automatically generated.

  RNAME                The name of this REFERENCE_MAP.

  VERSION              

  RPUB_STATUS          Whether or not this map has been published. Either
                       \'TRUE\' or \'FALSE\'.

  RTYPE                The type of this reference map. Values such as
                       'skeletal', 'recmin', 'reference'.

  AVAILABLE_ONLINE     Indicates whether or not the flat files for this
                       reference map are available to the system. If not,
                       this reference map is not available to map
                       against. Either 'TRUE' or 'FALSE'.
  -------------------- --------------------------------------------------

# REFERENCE_MAP_PEDIGREE

## Description:

A PEDIGREE that has been used to generate the data for a REFERENCE_MAP.
Not all pedigree data associate with all MARKER_TYPINGS that make up a
REFERENCE_MAP is used in the actual mapping, only the PEDIGREEs listed
in this table.

## Relationships:

A PEDIGREE_REFERENCE_MAP is associated with exactly one REFERENCE_MAP.

A PEDIGREE_REFERENCE_MAP is associated with exactly one PEDIGREE.

## Fields:

  ----------------------------------- -----------------------------------
  PEDIGREE_REFERENCE_MAP_ID           Primary key. Automatically
                                      generated.

  REFERENCE_MAP_ID                    Foreign key. The ID of the
                                      REFERENCE_MAP.

  PEDIGREE_ID                         Foreign key. The ID of the
                                      PEDIGREE.
  ----------------------------------- -----------------------------------

# REPORT

## Description:

A binary version of a particular type of report.

## Relationships:

A REPORT is of particular REPORT_TYPE.

A REPORT concerns exactly one MARKER_TYPING

A REPORT concerns exactly one MAPPING.

## Fields:

  ----------------------------------- -----------------------------------
  REPORT_ID                           Primary key. Automatically
                                      generated

  REPORT_TYPE                         Foreign key. References
                                      REPORT.RTYPE

  MAPPING_ID                          Foreign key. The MAPPING that this
                                      REPORT is about.

  ACCESSION_NUM                       Foreign key. The MARKER_TYPING that
                                      this REPORT is about.

  DATE_CREATED                        Date on which this REPORT was
                                      generated.

  REPORT                              The binary form of this REPORT.
  ----------------------------------- -----------------------------------

# REPORT_TYPE

## Description:

This is a lookup table. It lists the names of available types of
reports. In the current system, there are three types of reports:
DESCRIBE, MAP, QC.

## Relationships:

There are zero to many REPORTS of a particular REPORT_TYPE.

## Fields:

  ----------------------------------- -----------------------------------
  RTYPE                               The report type.

  ----------------------------------- -----------------------------------

# TYPING

## Description:

A Typing represents genotype information for one Individual.

## Relationships:

A TYPING is part of exactly one MARKER_TYPING.

A TYPING has zero or one first ALLELE.

A TYPING has zero or one second ALLELE.

A TYPING represents exactly one INDIVIDUAL.

A TYPING has zero or one ANOMALY.

## Fields:

  -------------------- --------------------------------------------------
  TYPING_ID            Primary key. Automatically generated.

  INDIVIDUAL_ID        Foreign key. The ID of the Individual represented
                       by this TYPING.

  ACCESSION_NUM        Accession number of Marker Typing of which this
                       Typing is a part.

  ALLELE_A             Foreign key. The ID of the first ALLELE in this
                       genotype.

  ALLELE_B             Foreign key. The ID of the second ALLELE in this
                       genotype.

  ALLELE_A_SYMBOL      This is the identifier that the Mapping Tool will
                       use for the first Allele in this genotype during
                       its calculations. It is assigned by the LPL.

  ALLELE_B_SYMBOL      This is the identifier that the Mapping Tool will
                       use for the second Allele in this genotype during
                       its calculations. It is assigned by the LPL.

  ALLELE_A_IDENT       The common name for this Allele. This is the
                       identifier for the first Allele in this genotype
                       that was used in the Laboratory that generated the
                       Marker Typing to which this Allele corresponds.

  ALLELE_B_IDENT       The common name for this Allele. This is the
                       identifier for the second Allele in this genotype
                       that was used in the Laboratory that generated the
                       Marker Typing to which this Allele corresponds.

  ANOMALY_SYMBOL       Foreign key. One of the anomaly_symbols from the
                       Anomaly table.

  TNOTES               Arbitrary amount of notes.
  -------------------- --------------------------------------------------

## Notes:

The ALLELE_X_SYMBOL and ALLELE_X_IDENT fields are present in this table
for the sake of efficiency.

# USER_INFO

## Description:

This table contains user names for the purpose of authentication.

## Fields:

  ----------------------------------- -----------------------------------
  USER_NAME                           The user name that the user enters
                                      when logging into the system.

  INTERNAL_UNAME                      The user name that is used by the
                                      system to do authentication. In the
                                      current system, LDAP is used, so
                                      this name is the user's LDAP user
                                      name.

  ACTIVE                              Whether or not the user is active.
                                      Either 'TRUE' or 'FALSE'. Only
                                      active users may log into the
                                      system.
  ----------------------------------- -----------------------------------

# VARIANT_TYPE

## Description:

This is a lookup table. Contains values such as: genotype, phenotype,
haplotype.

## Relationships:

A VARIANT_TYPE is associated with zero to many MARKER_TYPINGs.

## Fields:

  ------------- ---------------------------------------------------------
  VTYPE         Primary key. The name of this VARIANT_TYPE.

  ------------- ---------------------------------------------------------