SchemaSpy Analysis of cxgn.public |
Generated by SchemaSpy |
| Generated by SchemaSpy on Wed May 20 01:40 EDT 2009 | |
| Database Type: PostgreSQL - 8.1.11 |
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XML Representation Insertion Order Deletion Order (for database loading/purging scripts) |
106 Tables and 6 Views:
Total rows: 8,360,496
| Table | Children | Parents | Rows | Comments |
|---|---|---|---|---|
| analysis | 2 | 10 | ||
| analysisfeature | 2 | 0 | ||
| analysisprop | 2 | 0 | ||
| ara_annotation | 30,693 | |||
| ara_domain | 117,089 | |||
| ara_evidef | 12 | |||
| ara_family | 0 | |||
| ara_gfp_ms | 3,412 | |||
| ara_go_term | 0 | |||
| ara_interactome_all | 37,235 | |||
| ara_interactome_unique | 39,347 | |||
| ara_intron | 141,466 | |||
| ara_map | 31,226 | |||
| ara_myristoylation | 437 | |||
| ara_pmidlink | 0 | |||
| ara_prefix_info | 0 | |||
| ara_properties | 30,693 | |||
| ara_scop | 31,959 | |||
| ara_sequence | 30,693 | |||
| ara_signalp | 30,693 | |||
| ara_targetp | 30,693 | |||
| ara_users | 0 | |||
| blastwatch_queries | 1 | 103 | ||
| blastwatch_results | 1 | 7,019 | ||
| bug | 1 | |||
| clone_feature | 1 | 1,547 | linking table between genomic.clone and the chado feature table, showing which features in the feature table are the sequences of clones in the clone table | |
| clone_in_silico_digestion | 1 | 0 | ||
| clone_in_silico_digestion_bands | 1 | 0 | ||
| cv | 2 | 23 | A controlled vocabulary or ontology. A cv is composed of cvterms (aka terms, classes, types, universals - relations and properties are also stored in cvterm)) and the relationships between them |
|
| cvterm | 32 | 2 | 44,067 | A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships |
| cvterm_dbxref | 2 | 50,441 | In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation. |
|
| cvterm_pub_ranking | 2 | 164,937 | ||
| cvterm_relationship | 3 | 63,508 | A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement all SUBJs REL some OBJ is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax" |
|
| cvtermpath | 4 | 0 | The reflexive transitive closure of the cvterm_relationship relation. For a full discussion, see the file populating-cvtermpath.txt in this directory |
|
| cvtermprop | 2 | 4,205 | Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format | |
| cvtermsynonym | 2 | 33,552 | A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, -T cell- as a synonym for -T lymphocyte- |
|
| cxgn_bac_pipeline_genbank_log | 29 | |||
| cxgn_bac_pipeline_loading_log | 25,413 | |||
| cxgn_bac_pipeline_processing_log | 832,083 | |||
| cxgn_indexedlog_test_feel_free_to_delete_me | 50 | |||
| db | 1 | 190 | A database authority. Typical dbs in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this sortened form, which is unique within the bioinformatics and biomedical realm. **TODO** - add support for URIs, URNs (eg LSIDs). We can do this by treating the url as a uri - however, some applications may expect this to be resolvable - to be decided |
|
| dbxref | 9 | 1 | 660,961 | A unique, global, public, stable identifier. Not necessarily an eXternal reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table <T>_dbxref). A dbxref is generally written as <DB>:<ACCESSION> or as <DB>:<ACCESSION>:<VERSION>. |
| dbxrefprop | 2 | 0 | Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop | |
| enzyme_restriction_sites | 8,933 | |||
| family | view | |||
| family_build | view | |||
| family_member | view | |||
| feature | 11 | 3 | 358,674 | A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more |
| feature_cvterm | 3 | 3 | 0 | Associate a term from a cv with a feature, for example, GO annotation |
| feature_cvterm_dbxref | 2 | 0 | Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details | |
| feature_cvterm_pub | 2 | 0 | Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column |
|
| feature_cvtermprop | 2 | 0 | Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank |
|
| feature_dbxref | 2 | 359,892 | links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id | |
| feature_pub | 2 | 0 | Provenance. Linking table between features and publications that mention them | |
| feature_relationship | 2 | 3 | 0 | features can be arranged in graphs, eg exon part_of transcript part_of gene; translation madeby transcript if type is thought of as a verb, each arc makes a statement [SUBJECT VERB OBJECT] object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature) -- we include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we cant always do this - eg transpliced genes. its also useful for quickly getting implicit introns |
| feature_relationship_pub | 2 | 0 | Provenance. Attach optional evidence to a feature_relationship in the form of a publication | |
| feature_relationshipprop | 1 | 2 | 0 | Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts |
| feature_relationshipprop_pub | 2 | 0 | Provenance for feature_relationshipprop | |
| feature_synonym | 3 | 346,683 | Linking table between feature and synonym | |
| featureloc | 1 | 2 | 0 | The location of a feature relative to another feature. IMPORTANT: INTERBASE COORDINATES ARE USED.(This is vital as it allows us to represent zero-length features eg splice sites, insertion points without an awkward fuzzy system). Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (eg a gene that has been characterized genetically but no sequence/molecular info is available). NOTE ON MULTIPLE LOCATIONS: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. the column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (ie non-self) locations only; i.e. nothing should be located relative to itself |
| featureloc_pub | 2 | 0 | Provenance of featureloc. Linking table between featurelocs and publications that mention them | |
| featureprop | 1 | 2 | 4,002 | A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible |
| featureprop_pub | 2 | 0 | Provenance. Any featureprop assignment can optionally be supported by a publication | |
| forward_amplicon_sequence_information | 20 | |||
| forward_amplicon_sequence_markers | 1,473 | |||
| fpc_band | 1 | 2,777,795 | each row is a band in a gel lane or capillary run | |
| fpc_build | 2 | 1 | 8 | each row represents a run of the fpc contig building program, with a result file, linked to a bunch of fingerprints that it uses, and containing a bunch of fpc contigs |
| fpc_build_fpc_fingerprint | 2 | 132,482 | links fpc fingerprints to the builds that use them | |
| fpc_contig | 1 | 1 | 44,343 | each row is an contig in an fpc build, linked to clones it contains via fpc_contig_clone table |
| fpc_contig_clone | 1 | 397,028 | links fpc contigs with the clones that are a part of them | |
| fpc_fingerprint | 2 | 132,482 | each row is a lane in a gel or a single capillary run of a single clone | |
| fpc_series | 1 | 2 | each row here is one fpc build series, like "China FPC builds". captures when different fpc builds are different versions of the same build | |
| gff3atts | view | |||
| gff3view | view | |||
| gffatts | view | |||
| glossary | 178 | |||
| image | 5 | 15,751 | ||
| image_experiment | 1 | 539 | ||
| image_fish_result | 1 | 6,719 | ||
| image_individual | 1 | 8,146 | ||
| image_locus | 1 | 74 | ||
| itag_loading_log | 13 | |||
| locus_pub_ranking | 1 | 302,243 | ||
| locus_pub_ranking_validate | 1 | 18 | ||
| marker_names | 7,223 | |||
| materialized_view | 1 | |||
| organism | 8 | 1 | 54 | The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module |
| organism_dbxref | 2 | 128 | ||
| organism_relationship | 3 | 0 | ||
| organismpath | 3 | 0 | ||
| organismprop | 2 | 0 | tag-value properties - follows standard chado model | |
| phenotype | 1 | 4 | 13,242 | |
| phenotype_cvterm | 2 | -1 | ||
| project | 0 | |||
| pub | 18 | 1 | 12,944 | A documented provenance artefact - publications, documents, personal communication |
| pub_curator | 1 | 21 | ||
| pub_dbxref | 2 | 12,943 | Handle links to eg, pubmed, biosis, zoorec, OCLC, mdeline, ISSN, coden... |
|
| pub_relationship | 3 | 0 | Handle relationships between publications, eg, when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub (I think these three are it - at least for fb) |
|
| pubabstract | 1 | 12,942 | ||
| pubauthor | 1 | 54,885 | an author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors. | |
| pubprop | 2 | 0 | Property-value pairs for a pub. Follows standard chado pattern - see sequence module for details | |
| resource_file | 20 | each row defines a composite dataset, downloadable at the url cxgn-resource://name, that is composed of other downloadable datasets, according to the expression column. See CXGN::Tools::Wget for the accompanying code | ||
| signalp | 273,015 | |||
| synonym | 1 | 1 | 346,683 | A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features |
| tableinfo | 0 | |||
| tag | 2 | 18 | ||
| tag_experiment | 1 | 0 | ||
| tag_image | 2 | 10,321 | ||
| tmp_gff_load_cache | -1 | |||
| unigene_dbxref | 1 | 20,994 | ||
| unigene_relations | 107,825 | |||
| unigene_signalp | 145,954 |