|SchemaSpy Analysis of pub.mgd||Generated by
|Generated by SchemaSpy on Fri Jan 09 10:52 EST 2015|
|Database Type: PostgreSQL - 9.3.5||
Insertion Order Deletion Order (for database loading/purging scripts)
|Table / View||Children||Parents||Columns||Rows||Comments|
|acc_accession||1||4||13||28,764,832||Master Accession table; stores all internal (MGI) and external accession numbers for any accessionable object. Each accession number has a prefix (non-numeric) part and a numeric part. Accession numbers are assigned to a specific object (_Object_key) within a specific data set (_MGIType_key), to a specific logical database (_LogicalDB_key). Accession numbers which are designated as private (1) are not dispalyed or searchable via the Web. Preferred accession numbers are the *primary* accession numbers for a given object.
See ACC_AccessionMax, ACC_AccessionReference.
|acc_accessionmax||4||2||Stores the current maximum numeric part for the ''J:'' and ''MGI:'' prefixes. Set maximum field to 0 when initializing a new record. When a new ACC_Accession record is added, maxNumericPart is incremented and ACC_Accession.numericPart is assigned that value.
|acc_accessionreference||4||6||7,577,799||Accession Reference table; A record in this table is the reference for a specific Accession number.
|acc_actualdb||3||11||114||Defines physical location, by URL, of an external data resource. Used to dynamically construct HTML links for the Web interface.
Detail table of ACC_LogicalDB.
|acc_logicaldb||3||2||8||166||Defines a logical entity to which to attach accession numbers. Examples include: Sequence DB, MGI, RIKEN, etc.. After a logical entity is defined, multiple URLs (actual database objects) may be attached to the logical object. Master table of ACC_ActualDB.|
|acc_mgitype||21||2||10||38||Controlled vocabulary table of all accessionable object types in the system. Accessionable objects will be assigned MGI accession numbers during inserts.
|all_allele||13||10||20||793,729||A record in this table represents one Allele. An Allele is any of the alternative forms of a gene occupying a given locus; any one of several mutational forms of a gene. In MGI, allelic variants are associated with phenotypes. See ALL_Marker_Assoc.
A transgenic Allele will contain a Strain of Origin, and a new Strain can then be bred from this trangene. This new Strain will be associated with the transgenic allele (see PRB_Strain, PRB_Strain_Marker). For example, see TR11000/MMRRC/UC-Davis. For example: MGI:4847055/Tg(Foxi2-EGFP)HX217Gsat, strain of origin: FVB/NTac. New Strain: MGI:5003868/STOCK Tg(Foxi2-EGFP)HX217Gsat/Mmucd associated with MGI:5003868/Tg(Foxi2-EGFP)HX217Gsat via PRB_Strain/PRB_Strain_Marker.
|all_allele_cellline||4||7||918,534||A record in this table represents the association between an Allele and a Cell Line. The type of Cell Line associated with the Allele depends on the Allele Type. See ALL_CellLine.|
|all_allele_mutation||2||4||743,977||A record in this table represents the Molecular Mutation for a specific Allele. An Allele can have 0 or more Molecular Mutations.|
|all_cellline||4||5||10||942,685||A record in this table represents a parental or a mutant ES Cell Line.|
|all_cellline_derivation||1||8||13||2,779||A record in this table represents the Derivation of a Cell Line. See ALL_CellLine.|
|all_cre_cache||7||23||26,855||A record in this table represents the cached values of a Cre Allele (that may/may not contain Assay information). See ALL_Allele, GXD_Assay, allcacheload/allelecrecache.csh.|
|all_knockout_cache||4||12||257||A record in this table represents a Deltagen or Lexicon knockout.|
|all_label||1||8||1,516,165||A record in this table represents an Allele Label (current symbol, current name, synonym). This table is a cache table of all ''labels'' for a given Allele...representing the different ways in which a user may search for a particular Allele. This table is loaded via the alllabelload product.|
|all_marker_assoc||7||10||454,340||A record in this table represents the association between a Marker and an Allele. This table will eventually take the place of the ALL_Allele._Marker_key column. For now, ALL_Marker_Assoc and ALL_Allele._Marker_key are kept in sync. See ALL_Allele.|
|bib_books||1||8||323||A record in this table represents the Book attributes of a BIB_Refs record. This table is only populated if BIB_Refs.refType = BOOK.|
|bib_citation_cache||1||11||210,503||A record in this table represents a unique Reference. This table is a cache table of all References in MGI. This table is loaded via the mgicacheload product. See mgicacheload/bibcitation.csh.|
|bib_dataset||1||2||10||11||A record in this table represents a MGI DataSet. Each DataSet corresonds to a curatorial area within MGI and enables us to index References to particular curatorial areas. Examples are Molecular Segments, Mapping, Gene Ontology.|
|bib_dataset_assoc||4||8||341,718||A record in this table represents the association between a DataSet and a Reference.|
|bib_notes||1||5||12,487||A record in this table represents a 255-character segment of a Reference s note.|
|bib_refs||35||3||21||210,503||A record in this table represents a journal article, book or personal communication.|
|bib_reviewstatus||1||4||3||A record in this table represents a Review Status vocabulary term.|
|crs_cross||4||3||19||4,491||Controlled vocabulary table for all Mapping Cross descriptions.
See MLD_Matrix, CRS_Matrix.
|crs_matrix||2||2||8||28,009||Defines a row in a Matrix of a Mapping Panel Cross.|
|crs_progeny||1||7||3,610||Defines Progeny for Mapping Panel Cross.
See CRS_Matrix, CRS_References, CRS_Typings.
|crs_references||3||5||7,596||Defines References used in Mapping Panel Cross.
See CRS_Matrix, CRS_Progeny, CRS_Typings.
|crs_typings||2||6||63,596||Defines haplotype typings for Mapping Panel Cross.
See CRS_Matrix, CRS_Progeny, CRS_References.
|dag_closure||6||10||1,447,724||A record in this table represents an ancestor/descendent pair within a DAG. It caches data for performance reasons. Two
common queries of a DAG are:
1. retrieve all the descendents of a node
2. retrieve all the ancestors of a node
This table provides a mechanism for performing such queries within one SQL statement.
|dag_dag||6||2||7||42||A record in this table represents a specific DAG.|
|dag_edge||3||8||156,891||A record in this table represents an edge of a DAG, the relationship between 2 nodes.|
|dag_label||4||4||9||A record in this table represents a ''label'' for a Node or an Edge. A ''label'' is an attribute of the Note or Edge
which may be specific to a given DAG. A ''label'' is not necessarily something which is printed.
|dag_node||3||2||6||91,174||A record in this table represents a specific Node within a DAG. The _Object_key/DAG_DAG._MGIType_key combination
identifies the specific Node object. In the case of a GO DAG, this is a specific Vocabulary Term.
The DAG_DAG._MGIType_key identifies the type of object (a Vocabulary Term) and the _Object_key identifies the
|go_tracking||4||8||102,497||A record in this table represents the GO Tracking history for a specific Gene (_Marker_key).|
|gxd_allelegenotype||5||8||100,591||A record in this table represents the association between an Allele, a Genotype and a Marker. This is a cache table which is derived from GXD_AllelePair.|
|gxd_allelepair||10||14||80,345||Defines Allele Pair for Genotype object. Each pair specifies two alleles, both of which must be associated with the same marker. Allele Pairs may be homozygous, heterzygous or hemizygous. For hemizygous Allele Pairs, Allele 2 is null.
|gxd_antibody||3||6||11||5,655||Defines an accessionable Antibody object. An antibody is a protein produced by cells of the immune system that binds to an antigen.|
|gxd_antibodyclass||1||4||13||Controlled vocabulary table for all Antibody Classes. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_antibodymarker||2||4||5,823||Defines relationship between Antibodies and Markers. Antibodies can recognize the product of one or more markers.
|gxd_antibodyprep||1||3||6||9,046||Defines the Antibody preparation for an expression assay. The Antibody preparation specifies the antibody and detection system used. The detection is a combination of a Secondary Antibody and a labelling material.
See GXD_Assay, GXD_Antibody, GXD_Secondary, GXD_Label.
|gxd_antibodytype||1||4||4||Controlled vocabulary table of all Antibody Types. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_antigen||1||3||9||4,625||Defines an accessionable Antigen object. An antigen is a protein or fragment of a protein derived from a specific source.|
|gxd_assay||6||9||12||70,125||A record in this table represents the high level definition of a Gene Expression experiment; the type of Assay, the Reference, the Marker of interest, the Probe used to detect the Marker or Reporter Gene, the Antibody used to detect the Marker or Reporter Gene, the Reporter Gene, and the Image Pane. A Reporter Gene is a benign gene which is knocked-in to report the expression of the mouse gene. It is only applicable when Assay Type is ''In situ reporter (knock in)'', ''In situ reporter (transgenic)'' and ''Recombinase reporter''. These three assay types may use a nucleotide probe (has a Probe Prep), an antibody (has an Antibody Prep) or direct detection (has neither a Probe Prep nor an Antibody prep). Not all records in this table are in the GXD_Expression table. Assay Type ''In situ reporter (transgenic)'' assays are excluded because they do not examine the expression of endogenous genes. Assay Type ''Recombinase reporter'' assays are excluded because they do not examine gene expression. See GXD_Specimen, GXD_GelLane.|
|gxd_assaynote||1||5||35,146||Assay Notes. An Assay may have 0 more notes. Notes are stored in chunks of 255, ordered by sequenceNum.|
|gxd_assaytype||3||6||12||Controlled vocabulary table for all Assay types. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_embeddingmethod||1||4||8||Controlled vocabulary table for all Embedding Methods. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_expression||5||17||1,498,935||A cache table of redundant Assay results whose purpose is to make the most common kinds of queries more efficient. Primarily used by the Web interface. Loaded by a stored procedure which is executed from the GXD_Assay insert/update triggers.
|gxd_fixationmethod||1||4||18||Controlled vocabulary table for all Fixation Methods. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_gelband||2||7||245,928||Defines a Gel Band for a given Gel Lane and Gel Row. A band is assigned a strength.
See GXD_GelLane, GXD_GelRow, GXD_Strength.
|gxd_gelcontrol||1||4||14||Controlled vocabulary table for all Gel Control designations.
|gxd_gellane||1||4||16||221,131||Defines a Gel Lane. A Gel Assay is represented as a 2-D matrix with some number of columns (GXD_GelLane) and some number of rows (GXD_GelRow, GXD_GelBand). Lanes have sequence numbers for ordering and labels to describe lane content. The information associated with a Gel Lane corresponds to the way the gel was prepared in the lab. Source material is derived from one or more tissues in an animal. Tissues are described through reference to the anatomical dictionary. Animals are described via their genotype, age and sex. Minimal information is recorded for control lanes.
See GXD_Assay, GXD_Genotype, GXD_GelLaneStructure, GXD_GelRNAType.
|gxd_gellanestructure||2||4||199,498||Defines a relationship between a Gel Lane and an Anatomical Structure. A Gel Lane can correspond to one or more Anatomical Structures.
See GXD_GelLane, GXD_Structure.
|gxd_gelrnatype||1||4||4||Controlled vocabulary table for all Gel RNA Types. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_gelrow||1||2||8||29,166||Defines a Gel Row. A Gel Row corresponds to a particular size of band (GXD_GelBand) and includes attributes for size, units and optional notes. Band sizes are automatically sorted in decreasing order via the Editorial Interface.
See GXD_GelLane, GXD_GelBand.
|gxd_gelunits||1||4||7||Controlled vocabulary table for all Gel Row Size Units. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_genotype||7||4||9||61,778||Defines Genotype of animal used for Gel Lane or Specimen using Strain information.
See GXD_GelLane, GXD_Specimen, GXD_AllelePair.
|gxd_index||5||10||167,001||A record in this table represents a GXD ''index'' relationship between a Reference and a Marker. Precusor to fully coding a GXD paper. All records in the GXD Index may or may not be entered into the GXD Assay table. See GXD_Index_Stages.|
|gxd_index_stages||4||7||408,021||A record in this table represents the Assays and Stages present in a given Index (Reference/Marker pair). See GXD_Index.|
|gxd_insituresult||2||3||8||1,242,414||Defines an In Situ Specimen Result. For each Specimen defined, one or more results can be recorded. Each result contains the anatomical structure(s), signal strength, pattern of expression within the structure(s) and optional notes. One or more
Image Panes may also be associated with a result.
See GXD_Specimen, GXD_Strength, GXD_Pattern, GXD_InSituResultImage, GXD_ISResultStructure.
|gxd_insituresultimage||2||4||1,152,915||Defines relationship between an In Situ Result and an Image Pane. One In Situ Result can have one or more Image Panes associated with it.
See GXD_InSituResult, GXD_ImagePane.
|gxd_isresultstructure||2||4||1,300,731||Defines relationship between an In Situ Result and an Anatomical Structure. One In Situ Result can have one or more Anatomical Structures associated with it.
See GXD_InSituResult, GXD_Structure.
|gxd_label||2||4||36||Controlled vocabulary table for all Probe Prep and Antibody Prep Labels. Includes Not Applicable (-2) and Not Specified (-1).
See GXD_AntibodyPrep, GXD_ProbePrep.
|gxd_pattern||1||4||15||Controlled vocabulary table for all In Situ Result Expression Patterns. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_probeprep||1||4||8||59,022||Defines the Probe preparation for an expression assay. The Probe preparation specifies the probe used, final type (DNA, RNA) and the label used to visualize the probe.
See GXD_Assay, PRB_Probe, GXD_ProbeSense, GXD_Label, GXD_LabelCoverage, GXD_Visualization.
|gxd_probesense||1||4||4||Controlled vocabulary table for all Probe Prep Hybridizations. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_secondary||1||4||5||Controlled vocabulary table for all Antibody Prep Secondary Antibodies. Includes Not Applicable (-2) and Not Specified (-1).
|gxd_specimen||1||4||16||274,414||Defines an In Situ Assay Specimen. A Specimen is described in terms of its genotype, sex, age and the methods used to prepare the sample. If multiple animals within one reference have identical genotypes and preparation procedures, then they can be collectively represented by a single Specimen object.
See GXD_Assay, GXD_EmbeddingMethod, GXD_FixationMethod, GXD_Genotype.
|gxd_strength||2||4||10||Controlled vocabulary table for all Gel Band and In Situ Result Strengths. Includes Not Applicable (-2) and Not Specified (-1).
See GXD_GelBand, GXD_InSituResults.
|gxd_structure||7||4||14||19,579||Master table of Anatomical Dictionary.
See GXD_StructureClosure, GXD_StructureName, GXD_TheilerStage.
|gxd_structureclosure||2||4||125,137||The closure table allows one to find all substructures or superstructures of a given node in one query.
|gxd_structurename||1||1||6||24,259||Official and Synonym table for Anatomical Structures. If the GXD_StructureName._StructureName_key equals GXD_Structure._StructureName_key, then this is the *official* name of the symbol. All other ''names'' are synonyms. See GXD_Structure.|
|gxd_theilerstage||1||1||8||28||Defines the Theiler Stages, one for each developmental stage defined in the Theiler system. Each stage has a ''stage'' attribute, which is an integer from 1 to 28, an approximate mapping to DPC values, and a short description of the main anatomical developments for the stage.
|gxd_visualizationmethod||1||4||11||Controlled vocabulary table for all Probe Prep Visualization Methods. Includes Not Applicable (-2) and Not Specified (-1).
|hmd_assay||1||5||14||Controlled vocabulary table for all Homology Assays. Includes Not Specified (-1).|
|hmd_class||2||3||19,357||Defines a primary key for grouping together homologies which are concluded to be related based on a common species/symbol pair. Through transitive associations, similar homology records are assigned the same Homology Class identifier.
|hmd_homology||3||2||5||40,799||Defines a Homology. A Homology is defined by a reference which reports similarity between 2 or more markers within multiple species. This table records the Homology Class and Reference.
See HMD_Class, HMD_HomologyMarker.
|hmd_homology_assay||2||4||70,607||Defines all of the Assays associated with a given Homology assertion. Every assay applies to every homologous pair in the assertion.
See HMD_Homology, HMD_Assay.
|hmd_homology_marker||1||4||147,780||Defines all of the Markers which belong to a defined Homology. A homology usually consists of two or more Markers from different species. There are *single* homologies in the database, but these are being reviewed and may be removed.
|hmd_notes||1||5||78||Homology Notes. A Homology may have 0 more notes. Notes are stored in chunks of 255, ordered by sequenceNum.|
|img_cache||7||16||7,636||A record in this table represents the cached value of an Image. See mgicacheload/imgcache.csh.|
|img_image||4||7||13||227,298||A record in this table represents a full size or thumbnail Image. If the X dimension (width) and Y dimension (height) are non-null, then an Image file is associated with the Image (via the PIX accession ID).|
|img_imagepane||4||1||9||322,849||A record in this table represents an Image Pane. An Image hast at least one Image Pane.|
|img_imagepane_assoc||4||9||15,817||A record in this table represents an association between an Image Pane and an MGI Object (allele, genotype). At most one association for a given MGI object can be primary.|
|map_coord_collection||1||2||7||13||A record in this table represents one Coordinate Map Collection; an ordered set of Coordinate Maps. A Coordinate Map Colllection can contain Coordinate Maps of different Map Types.|
|map_coord_feature||4||11||939,524||A record in this table represents a feature on a coordinate map (MAP_Coordinate).|
|map_coordinate||2||6||15||245||A record in this table represents one Coordinate Map; a set of Coordinate Map Features of the specified Units for the specified Object. The Object can be an MGI object (Chromosome or Sequence), or a non-MGI object (in which case the _Object_key and _MGIType_key are null). A Coordinate Map can belong to at most one Collection.|
|mgi_columns||1||6||1,650||A record in this table represents the comments for table columns.|
|mgi_dbinfo||8||1||This table has one and only one record which contains information about the database such as the public version name, the product name, the last time the database was dumped.|
|mgi_emaps_mapping||7||19,230||A record in this table represents a mapping between an accession ID, e,g, Anatomical Dictionary term ID, and an EMAPS term ID.
See EMAPS vocab: VOC_Term._Vocab_key = 91
|mgi_measurement||1||5||76,379||A record in this table represents the measurement for a particular type of statistic|
|mgi_note||1||4||8||2,037,857||A record in this table represents a Note of a specific type (_NoteType_key) for a specific object (_Object_key) of a specific object type (_Object_key) with a specific privacy setting.|
|mgi_notechunk||3||7||2,806,900||A record in this table represents a 255-character segment of a specific Note object (defined in MGI_Note).|
|mgi_notetype||1||3||8||44||A record in this table represents a Note Type.|
|mgi_organism||13||2||7||51||A record in this table represents an Organism.|
|mgi_organism_mgitype||4||6||122||A record in this table represents the relationship between an Organism and a MGI Type; what Organisms are valid for a given MGI Type. An Organism can be associated with one or more MGI Types. This enables us to generate a list of Organisms by MGI Type. Examples are Orthology, Molecular Segment , GXD Antigen, GXD Antibody, Sequence, Marker.|
|mgi_refassoctype||1||3||8||28||A record in this table represents a Reference Association Type (e.g. General, Original).|
|mgi_reference_assoc||5||9||5,832,981||A record in this table repesents an association between a Reference of a specific type (_RefAssocType_key, e.g. Original) and a specific database object (_Object_key, e.g. Sequence A12345 ) of a specific object type (_MGIType_key, e.g., Sequence, Marker/Sequence Association).|
|mgi_relationship||1||7||12||4,594,829||A record in this table represents a relationship, of a particular category, between any two objects with an MGI Type. For example a relationship between two Markers or a relationship between an Allele and a Marker.
|mgi_relationship_category||1||8||12||4||A record in this table defines a category (type) of relationship between two objects, allowing us to encapsulate data that is standard across all relationships of this type.
|mgi_relationship_property||4||9||27,204,637||A record in this table represents ordered properties, or name-value pairs, for a relationship
|mgi_roletask||4||7||87||A record in this table represents a Role/Task association.|
|mgi_set||1||3||8||41||A record in this table represents a Set.|
|mgi_setmember||3||8||5,329||A record in this table represents the ordered member of a specific Set.|
|mgi_statistic||2||6||69||A record in this table represents one type of statistic for which we would ilike to record numeric measurements. See MGI_Measurement.|
|mgi_statisticsql||1||3||96||Each statistic (see MGI_Statistic) can have an associated SQL statement that is used to compute a measurement. That SQL statement may be split into multiple records in this table, with each record being one chunk of text to be concatenated together.|
|mgi_synonym||4||10||420,835||A record in this table repesents a Synonym of a specific type (_SynonymType_key, e.g. Exact) and a specific database object (_Object_key, e.g. Marker Kit ) of a specific object type (_MGIType_key, e.g., Marker). The Synonym may also have a Reference associated with it.|
|mgi_synonymtype||4||10||31||A record in this table represents a Synonym Type (e.g. Exact) for a specific Object Type. The Object may be of a specific Organism (for example, Marker, Mouse).|
|mgi_tables||1||6||204||A record in this table represents the comments for a table.|
|mgi_translation||3||9||3,660||A record in this table represents the Translation between a ''bad name'' and the corresponding MGI object (the ''good name'') of a specific Translation Type.|
|mgi_translationtype||1||4||10||17||A record in this table represents a Translation Type.|
|mgi_user||169||4||9||238||A record in this table represents a valid MGI user login.|
|mgi_userrole||3||7||338||A record in this table represents a Role/User association.|
|mlc_marker||3||5||1,322||A record in this table represents the relationship between a MLC entry and a Marker used within the MLC entry text.|
|mlc_reference||3||5||3,764||A record in this table represents a Reference used for annotating the MLC entry of a Marker.|
|mlc_text||2||1||7||389||Textual descriptions for phenotypic Markers. Contains special markup for Web conversion to HTML links. Refer to Editing Interface Requirements document on MLC for details on the markkup supported and for information regarding the _edit tables.|
|mld_assay_types||1||4||91||Controlled vocabulary table for all Mapping Assays. Includes a blank (-1) Assay, which is used ilike a ''Not Specified'' vocabulary record.
|mld_concordance||3||10||11,827||Defines Concordance values for Hybrid Experiment. The Concordance table contains results for either Markers or Chromosomes. Concordance values are stored as integers which represent the number of Hybrid cells recording the presence/absence of a particular Marker/Chromosome in the Concordance table vs. the presence/absence of the Marker being tested for linkage: -/- (neither present), -/+ (linkage Marker present), +/- (Marker/Chromosome present), +/+ (both present).
Detail of MLD_Hybrid.
|mld_contig||1||1||8||2,054||Defines CONTIG Experiment for MIT Physical Mapping data. Each Contig has a name and an indication (minLink) of the minimum number of common hits required to assemble YACs into the Contig. For the MIT data, the value in this field is either 1 or 2. Each Contig is labelled with the minimum and maximum cM position of markers within the Contig. When printing the Contigs for a chromosome, the Contigs should be ordered by the mincm field. The Contig tables are loaded via a load script and there is no Editorial Interface for modifying this data.
See MLD_ContigProbe, MLD_Hit, PRB_Probe.
|mld_contigprobe||2||5||14,342||Defines the STS order within a Contig. A Contig can have one or more Probes/STS's associated with it.
Detail of MLD_Contig, PRB_Probe.
|mld_expt_marker||4||10||191,952||Defines relationship between an Experiment and a Marker reported for that Experiment. An Experiment may have one or more Markers associated with it.
|mld_expt_notes||1||5||45,884||Mapping experiment notes.|
|mld_expts||14||1||7||22,283||Defines a Mapping Experiment for a specific Reference. A Reference may have one or more Experiments associated with it. Each Experiment within a specific Reference is assigned an Experiment Type and and Experiment Tag value (CROSS-1). The currently supported Experiment Types are: CONTIG, CROSS, FISH, HYBRID, IN SITU, MAP, RI, TEXT.|
|mld_fish||1||2||12||1,429||Defines FISH (Fluorescence In Situ Hybridization) Experiment. FISH Experiments use fluorescein tags to detect the hybridization of probes with metaphase chromosomes. This suggests the chromosome and band assignment of the marker to which the probe hybrdizes.
Master of MLD_FISH_Region.
|mld_fish_region||2||7||77||Defines number of single and double signal hits by chromosomal region for a specific FISH Experiment.
Detail of MLD_FISH.
|mld_hit||3||5||50,872||Defines hits between Probes and Targets for MIT Physical Mapping data. Each Probe and each Target is a Molecular Segment in PRB_Probe. Each hit is associated with an Experiment. In the case of MIT data, each _Probe_key points to an STS,
and each _Target_key points to a YAC.
Detail of MLD_Expts, PRB_Probe.
|mld_hybrid||1||1||5||651||Defines HYBRID Experiment; stores the band assignment determined by the experiment.
Master for MLD_Concordance.
|mld_insitu||1||2||12||449||Defines IN SITU Experiment. In Situ Experiments use a DNA or RNA probe to detect the presence of the complementary DNA sequence in cloned bacterial or cultured eukaryotic cells. This suggests the chromosome and band assignment of the marker to which the probe hybridizes.
Master of MLD_ISRegion.
|mld_isregion||2||6||2,523||Defines number of grain counts by chromosomal region for a specific In Situ Experiment.
Detail of MLD_InSitu.
|mld_matrix||1||2||8||6,925||Defines CROSS Experiment. Cross Experiments may use a well-defined Cross or a one-time only mating of two strains.
The Editorial Interface constructs the female and male genotypes based on the number of Markers used in the Experiment and the allele abbreviations designated for the Cross.
See MLD_MC2point, MLC_MCDataList, CRS_Cross.
|mld_mc2point||2||8||10,047||Defines 2 Point data for Cross Experiments. 2 Point data records typing of animals for specified pairs of Markers.
Detail of MLD_Matrix.
|mld_mcdatalist||2||6||30,247||Defines Haplotype data for Cross Experiments. Haplotype data records haplotypes and number of offspring for Experimental Markers designated as having Haplotype data (MLD_Expt_Marker.matrixData = 1).
Detail of MLD_Matrix.
|mld_notes||1||5||1,711||Mapping Notes for a specific Reference.|
|mld_ri||1||5||3,501||Defines RI (Recombinant Inbred and Recombinant Congenic) Experiment. RI Experiments use well-defined recombinant inbred and recombinant congenic strains to provide linkage mapping information.
See MLD_RI2Point, MLD_RIData, RI_RISet.
|mld_ri2point||2||9||524||Defines 2 Point data for RI Experiments. 2 Point data records typing of animals for specified pairs of Markers and specified RI Sets.
Detail of MLD_RI.
|mld_ridata||1||6||12,779||Defines Haplotype data for RI Experiments. Haplotype data records strain distribution pattern for Experimental Markers for each animal in the RI set.
Detail of MLD_RI.
|mld_statistics||3||10||27,147||Defines Statistics generated from Haplotype and 2 Point data. Generated automatically based on Experiment Type (CROSS or RI) and Cross Type (if Experiment is a CROSS).
|mrk_alias||2||4||590||Defines Aliases for Markers. Aliases must be valid Markers and should have the same chromosome value as the aliased Marker. This is enforced within the Editorial Interface. A Marker may have one or more Aliases associated with it.
|mrk_anchors||1||4||192||Defines Anchor Markers for construction of Web Mini-Map on Marker detail form.
|mrk_chromosome||3||8||364||A record in this table represents an ordered Chromosome for the specified Organism (Species). See MRK_Marker.|
|mrk_class||1||4||34||Controlled vocabulary table for all Marker Classes. Includes Not Applicable (-2) and Not Specified (-1).
|mrk_classes||2||4||6,161||Defines relationship between MLC Marker and MLC Class descriptions. A Marker may have on or more MLC Classes associated with it.
|mrk_cluster||1||4||10||25,999||A record in this table defines a relationship between a set of markers. This table was designed to represent Homology clusters to allow multiple markers per organism to be in a cluster and has been generalized by including a cluster type, a source and an accession ID
|mrk_clustermember||2||4||187,074||A record in this table defines an ordered set of members of a marker cluster.
|mrk_current||2||4||161,342||Defines relationship between a Marker and its Current Symbol(s). A Marker may have one or more current symbols associated with it. Usually there is only one current symbol for a marker. But, if a marker is split, then each of the new symbols will be assigned as a current symbol of the split symbol.
|mrk_event||1||4||8||Controlled vocabulary of Marker Nomenclature events.|
|mrk_eventreason||1||4||9||Controlled vocabulary of Marker Nomenclature Event Reasons|
|mrk_history||7||12||223,469||A record in this table represents a nomenclature event in the life of a Marker. A nomenclature event is defined by the event itself (rename, merge, split, etc.), the reason for the event, date of the event, reference (J:).|
|mrk_homology_cache||5||6||147,780||A record in this table represents the cached value of the homology class of a specific Marker. See mrkcacheload/mrkhomology.csh.|
|mrk_label||3||11||2,082,355||A record in this table represents the cached value of a label (name, synonym, symbol) for a Marker. Examples: [priority = 1, label type = ''MS'', label name = ''current symbol''], [priority = 2, label = ''MN'', label name = ''current name''].
See mrkcacheload/mrklabel.csh for complete list.
|mrk_location_cache||4||19||209,018||A record in this table represents the cached value of a Marker and its genetic and physical location. See mrkcacheload/mrklocation.csh.|
|mrk_marker||50||6||13||508,835||A record in this table represents a Marker (gene, dna segment, complex/cluster). Mouse Markers have MGI Accession IDs. Non-mouse Markers (human, rat, etc.) are also stored in this table.|
|mrk_mcv_cache||3||9||331,084||A record in this table represents the cached value of a Marker and its Feature Types. See MRK_Marker. See mrkcacheload/mrkmcv.csh.|
|mrk_mcv_count_cache||2||6||45||A cache of the current number of markers annotated to a given Feature Type Vocab Term (formerly known as Marker Category Vocabulary)|
|mrk_notes||1||5||12,379||A record in this table represents a 255 chunk of note for a Marker.|
|mrk_offset||1||5||261,267||Defines Marker centimorgan (cM) offsets from three different sources: MGD (0), Chromosome Committee (1) and MIT (2).
Offset value of -1.0 designates syntenic marker. Offset value of -999.9 designates withdrawn or reserved marker. All mouse symbols have an MGD offset.
|mrk_omim_cache||8||29||12,771||A record in this table represents the cached value of a mouse genotype/allele/OMIM annotation or a human marker/OMIM annotation. See mrkcacheload/mrkomim.csh.|
|mrk_reference||2||8||1,349,436||A record in this table represents a unique association between a Marker and a Reference. This is a cache table that is rebuilt nightly by the mrkcacheload product. It represents a union of unique Marker/Reference associations from all data sets in MGI (Orthology, Expression, Mapping, Alleles, GO Annotations, etc.).|
|mrk_status||1||4||5||Controlled vocabulary table for all Marker Statuses (approved, withdrawn).
|mrk_types||4||4||9||Controlled vocabulary table for all Marker Types.
|prb_alias||3||7||45,026||Defines synonyms for Probe names referred to in a specific Reference.
See PRB_Reference, PRB_Probe.
|prb_allele||1||3||8||64,250||Defines relationship between an RFLV (marker/endonuclease pair), an allele ''symbol'', and a fragment size.
See PRB_RFLV, PRB_Allele_Strain, PRB_Reference.
|prb_allele_strain||4||6||138,911||Defines relationship between a defined RFLV Allele (PRB_Allele) and a Strain. An RFLV Allele may have one or more Strains associated with it.
See PRB_Allele, PRB_RFLV, PRB_Strain.
|prb_marker||5||8||1,073,968||Defines relationship between a Probe and a Marker. Relationship values: H = hybridizes to, E = encodes, A = amplifies, M = MIT Physical Mapping data, P = putative (ESTs). A Probe can have one or more Markers associated with it.
See PRB_Probe, MRK_Marker.
|prb_notes||1||5||111,544||A record in this table represents a 255 chunk of note for a Molecular Segment.|
|prb_probe||9||6||16||2,160,579||Defines an accessionable Molecular Segment object. Master table for all Molecular Segments: Single-stranded DNA or RNA molecules of specific base sequence, labeled either radioactively or immunologically, that are used to detect the complementary base sequence by hybridization.
Master for PRB_Marker, PRB_Reference.
|prb_ref_notes||1||5||2,329||A record in this table represents a 255 chunk of note for a Molecular Segment Reference.|
|prb_reference||3||4||9||2,855,810||Defines relationship between a Probe and a Reference. A Probe may have one or more References associated with it. Accession numbers can be associated with Probes using the Reference object in conjunction with the ACC_AccessionReference table.
|prb_rflv||1||4||8||22,684||Defines a relationship between a Marker and an Endonuclease for a specific Probe Reference. Variations exist between individuals in DNA fragment sizes cut by specific restriction enzymes; polymorphic sequences that result in RFLPs are used as markers on both physical maps and genetic linkage maps. RFLPs are usually caused by mutation at a cutting site.
Detail of PRB_Reference.
|prb_source||3||10||19||61,686||Defines the biological context from which a Probe is derived, e.g., species, strain, tissue, etc. Some sources are well-defined ''libraries''. Every Probe has one and only one Source.
|prb_strain||13||4||11||39,999||A record in this table represents a unique strain or genetic background. Accession IDs for Strains (MGI, JRS, EMMA, MMRC, etc.) are stored in the ACC_Accession table.|
|prb_strain_genotype||4||8||14,558||A record in this table represents a Strain/Genotype association. An association is qualified using the _Qualifier_key. A Strain can have 0 or more Genotypes associated with it.|
|prb_strain_marker||6||9||33,246||A record in this table represents a Strain/Marker/Allele association. An associations is qualified using the _Qualifier_key. A Strain can have 0 or more Marker/Allele pairs associated with it.
A Strain may be created as the result of a mutation (transgenic allele), in which case the transgenic allele is associated with the newly bred Strain using this table. For example: MGI:4847055/Tg(Foxi2-EGFP)HX217Gsat, strain of origin: FVB/NTac. New Strain: MGI:5003868/STOCK Tg(Foxi2-EGFP)HX217Gsat/Mmucd associated with MGI:5003868/Tg(Foxi2-EGFP)HX217Gsat via PRB_Strain/PRB_Strain_Marker.
|prb_tissue||1||5||571||Controlled vocabulary table for all Tissues. Includes Not Applicable (-2) and Not Specified (-1).|
|ri_riset||1||2||9||40||A record in this table represents the definition of a Recombinant Inbred Strain.|
|ri_summary||2||6||9,583||A record in this table represents the RI haplotypes for a given RI Set and a given Marker.|
|ri_summary_expt_ref||1||5||12,716||A record in this table defines the Experiment and Reference for an RI Summary record. There is one or more RI_Summary_Expt_Ref records per RI_Summary record.|
|seq_allele_assoc||6||9||854,157||A record in this table represents the association between an Allele and a Sequence.|
|seq_coord_cache||4||13||882,552||A record in this table represents the Sequence coordinate for an Assembly Sequence. See seqcacheload/seqcoord.csh.|
|seq_description_cache||3||6||1,063,936||A record in this table represents the description of a Sequence that is annotated to a mouse Marker or mouse Molecular Segment. See seqcacheload/seqdescription.csh.|
|seq_genemodel||4||9||115,052||A record in this table represents additional information about Gene Model Sequences.|
|seq_genetrap||6||10||906,842||A row in this table represents additional information about Gene Trap sequences.|
|seq_marker_cache||10||18||1,750,918||A record in this table represents the cached value of the annotation between a mouse Marker and a Sequence. See seqcacheload/seqmarker.csh.|
|seq_probe_cache||5||8||2,171,607||A record in this table represents the cached value of the annotation between a mouse Molecular Segment and a Sequence. See seqcacheload/seqprobe.csh.|
|seq_sequence||11||7||18||13,002,056||A record in this table represents a specific Sequence object.|
|seq_sequence_assoc||5||8||281,968||A record in this table represents the association between two Sequences objects. For example, a Gene Model Sequence can be associated with its protein or transcript sequence.|
|seq_sequence_raw||3||13||13,002,056||A record in this table represents the raw attributes of a Sequence.|
|seq_source_assoc||4||7||13,002,056||A record in this table represents the relationship between a Sequence and a Molecular Source (PRB_Source).|
|voc_allele_cache||3||261,526||A record in this table represents the cached value of the association between an Allele and an Annotation Type. The Annotation Types are VOC_AnnotType: 1002:Mammalian Phentype/Genotype, 1006:OMIM/Genotype. The cache is loaded from mgicacheload/vocallele.csh which calls stored procedures in mgddbschema/procedure (VOC_Cache_Alleles, VOC_Cache_MP_Alleles, VOC_Cache_OMIM_Alleles).|
|voc_annot||1||2||7||1,115,664||A record in this table represents the Annotation between a Vocabulary Term and an Object of type specified by the Annotation Type. There is one Annotation per Object/Term/Annotation Type/isNot. See VOC_AnnotType.|
|voc_annot_count_cache||5||74,412||A record in this table represents a cached value of the number of objects (of a given type) with annotations (of a given type) to a given vocabulary term.|
|voc_annotheader||5||12||149,674||A record in this table represents the unique use of a Header term for a specific annotated Object of a specific Annotation Type. A set of records grouped by Annot Type/Object represents the ordered list of Header terms for an annotated Object of a specific Annotation Type.|
|voc_annottype||2||4||8||15||A record in this table defines an Annotation Type. Each Annotation instance specifies its type (VOC_Annot). An Annotation Type specifies an Object type (_MGIType_key), the Vocabulary to which an Object of that type is being annotated (_Vocab_key), and the Evidence Vocabulary (_EvidenceVocab_key) used to annotate the Object of the specified type. An Object which is to be annotated (a Marker or a Genotype) is an accessionable object which requires an entry in ACC_MGIType.|
|voc_evidence||1||5||9||1,021,765||A record in this table represents one evidence statement which supports one Annotation. There can be one or more Evidence records per Annotation. Although the schema supports zero or more Evidence records per Annotation, editorially at least one Evidence record is required per Annotation.|
|voc_evidence_property||4||10||775,415||A record in this table represents the association between an Annotation Evidence record and a Property. This stores the contextual data of a particular Annotation row. Each stanza that occurs in a given Annotation experiment (row) is stored as separate contextual data within the Annotation experiment. Each individual stanza is treated as a distinct contextual set of data that is associated with the proper Annotation row.|
|voc_go_cache||2||5||42,334||A record in thie table represents the cached value of the GO Terms, the GO DAG and GO accession ids. See mgicacheload/vocgo.csh.|
|voc_marker_cache||1||3||1,898,539||A record in this table represents a cached value of the association between a Marker, a Term and an Annotation Type. The Annotation Types are GXD_Structure: 'AD': VOC_AnnotType: 1000:GO/Marker, 1003:InterPro/Marker, 1002:Mammalian Phenotype/Genotype, 1005:OMIM/Genotype, 1006:OMIM/Human Marker, 1007:PIRSF/Marker. The cache is loaded from mgicacheload/vocmarker.csh which refers to stored procedues in mgddbschema/procedure (VOC_Cache_Markers, VOC_Cache_Anatomy_Markers, VOC_Cache_MP_Markers, VOC_Cache_OMIM_Markers, VOC_Cache_Other_Markers).|
|voc_term||75||3||10||146,773||A record in this table represents a Vocabulary Term for a specific Vocabulary. There is one big bucket of Terms for each Vocabulary. A Term can appear in 0 or more DAGS within the same Vocabulary. Remember that a Term is an accessionable object, so there is a corresponding entry for this table in ACC_MGIType.|
|voc_term_emapa||4||8||6,268||A record in this table represents additional information about EMAPA (abstract mouse) structured vocabulary terms. Each term has a starting and ending Theiler stage and a default parent (or NULL if root term).
See VOC_Term._Vocab_key = 90
|voc_term_emaps||5||8||27,982||A record in this table represents additional information about EMAPS (Theiler stage specific) structured vocabulary terms. Each term has a Theiler stage, an EMAPA term and a default parent (or NULL if root term).
See VOC_Term._Vocab_key = 91
|voc_text||1||5||61,361||A record in this table represents textual information of a Vocabulary Term. The Term's definition and example are part of the textual information. This implements one unlimited-length note per Term and each record represents one 255-char chunk of the note.|
|voc_vocab||9||2||8||93||A record in this table represents a Vocabulary. Different versions of the same Vocabulary are represented by records with different names (as in GO 1.0, GO 2.0, etc).|
|voc_vocabdag||2||4||42||A record in this table represents an ownership relationship of a Vocabulary over a DAG. A Vocabulary can have many DAGS, but a DAG can belong to at most one Vocabulary.|
|wks_rosetta||1||6||64||A record in this table represents the relationship between a Marker in the WK Silvers book and a Marker in MGI.|