Robert Buels / Bio-Chado-Schema

Modules

Bio::Chado::Schema	standard DBIx::Class layer for the Chado database schema	0.05501
Bio::Chado::Schema::CellLine::CellLine
Bio::Chado::Schema::CellLine::CellLineCvterm
Bio::Chado::Schema::CellLine::CellLineCvtermprop
Bio::Chado::Schema::CellLine::CellLineDbxref
Bio::Chado::Schema::CellLine::CellLineFeature
Bio::Chado::Schema::CellLine::CellLineLibrary
Bio::Chado::Schema::CellLine::CellLinePub
Bio::Chado::Schema::CellLine::CellLineRelationship
Bio::Chado::Schema::CellLine::CellLineSynonym
Bio::Chado::Schema::CellLine::CellLineprop
Bio::Chado::Schema::CellLine::CellLinepropPub
Bio::Chado::Schema::Companalysis::Analysis	An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit
Bio::Chado::Schema::Companalysis::Analysisfeature	Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from th
Bio::Chado::Schema::Companalysis::Analysisfeatureprop
Bio::Chado::Schema::Companalysis::Analysisprop
Bio::Chado::Schema::Composite::AllFeatureNames
Bio::Chado::Schema::Composite::Dfeatureloc
Bio::Chado::Schema::Composite::FLoc
Bio::Chado::Schema::Composite::FType
Bio::Chado::Schema::Composite::FeatureContains	subject intervals contains (or is same as) object interval. transitive,reflexive
Bio::Chado::Schema::Composite::FeatureDifference	size of gap between two features. must be abutting or disjoint
Bio::Chado::Schema::Composite::FeatureDisjoint	featurelocs do not meet. symmetric
Bio::Chado::Schema::Composite::FeatureDistance
Bio::Chado::Schema::Composite::FeatureIntersection	set-intersection on interval defined by featureloc. featurelocs must meet
Bio::Chado::Schema::Composite::FeatureMeets	intervals have at least one interbase point in common (ie overlap OR abut). symmetric,reflexive
Bio::Chado::Schema::Composite::FeatureMeetsOnSameStrand	as feature_meets, but featurelocs must be on the same strand. symmetric,reflexive
Bio::Chado::Schema::Composite::FeatureUnion	set-union on interval defined by featureloc. featurelocs must meet
Bio::Chado::Schema::Composite::FeaturesetMeets
Bio::Chado::Schema::Composite::FnrType
Bio::Chado::Schema::Composite::FpKey
Bio::Chado::Schema::Composite::Gff3atts
Bio::Chado::Schema::Composite::Gff3view
Bio::Chado::Schema::Composite::Gffatts
Bio::Chado::Schema::Contact::Contact	Model persons, institutes, groups, organizations, etc.
Bio::Chado::Schema::Contact::ContactRelationship	Model relationships between contacts
Bio::Chado::Schema::Cv::CommonAncestorCvterm	The common ancestor of any two terms is the intersection of both terms ancestors. Two terms can have multiple common ancestors. Use total_pathdistance to get the least common ancestor
Bio::Chado::Schema::Cv::CommonDescendantCvterm	The common descendant of any two terms is the intersection of both terms descendants. Two terms can have multiple common descendants. Use total_pathdistance to get the least common ancestor
Bio::Chado::Schema::Cv::Cv	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.
Bio::Chado::Schema::Cv::CvCvtermCount	per-cv terms counts (excludes obsoletes)
Bio::Chado::Schema::Cv::CvCvtermCountWithObs	per-cv terms counts (includes obsoletes)
Bio::Chado::Schema::Cv::CvLeaf	the leaves of a cv are the set of terms which have no children (terms that are not the object of a relation). All cvs will have at least 1 leaf
Bio::Chado::Schema::Cv::CvLinkCount	per-cv summary of number of links (cvterm_relationships) broken down by relationship_type. num_links is the total # of links of the specified type in which the subject_id of the link is in the named c
Bio::Chado::Schema::Cv::CvPathCount	per-cv summary of number of paths (cvtermpaths) broken down by relationship_type. num_paths is the total # of paths of the specified type in which the subject_id of the path is in the named cv. See al
Bio::Chado::Schema::Cv::CvRoot	the roots of a cv are the set of terms which have no parents (terms that are not the subject of a relation). Most cvs will have a single root, some may have >1. All will have at least 1
Bio::Chado::Schema::Cv::Cvterm	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 c
Bio::Chado::Schema::Cv::CvtermDbxref	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_d
Bio::Chado::Schema::Cv::CvtermRelationship	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 depe
Bio::Chado::Schema::Cv::Cvtermpath	The reflexive transitive closure of the cvterm_relationship relation.
Bio::Chado::Schema::Cv::Cvtermprop	Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.
Bio::Chado::Schema::Cv::Cvtermsynonym	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
Bio::Chado::Schema::Cv::Dbxrefprop	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.
Bio::Chado::Schema::Cv::StatsPathsToRoot	per-cvterm statistics on its placement in the DAG relative to the root. There may be multiple paths from any term to the root. This gives the total number of paths, and the average minimum and maximum
Bio::Chado::Schema::Expression::Eimage
Bio::Chado::Schema::Expression::Expression	The expression table is essentially a bridge table.
Bio::Chado::Schema::Expression::ExpressionCvterm
Bio::Chado::Schema::Expression::ExpressionCvtermprop	Extensible properties for expression to cvterm associations. Examples: qualifiers.
Bio::Chado::Schema::Expression::ExpressionImage
Bio::Chado::Schema::Expression::ExpressionPub
Bio::Chado::Schema::Expression::Expressionprop
Bio::Chado::Schema::Expression::FeatureExpression
Bio::Chado::Schema::Expression::FeatureExpressionprop	Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.
Bio::Chado::Schema::General::Db	A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics a
Bio::Chado::Schema::General::DbDbxrefCount	per-db dbxref counts
Bio::Chado::Schema::General::Dbxref	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 uniquel
Bio::Chado::Schema::General::Project
Bio::Chado::Schema::General::Tableinfo
Bio::Chado::Schema::Genetic::Environment	The environmental component of a phenotype description.
Bio::Chado::Schema::Genetic::EnvironmentCvterm
Bio::Chado::Schema::Genetic::FeatureGenotype
Bio::Chado::Schema::Genetic::Genotype	Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.
Bio::Chado::Schema::Genetic::Phendesc	A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.
Bio::Chado::Schema::Genetic::PhenotypeComparison	Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.
Bio::Chado::Schema::Genetic::PhenotypeComparisonCvterm
Bio::Chado::Schema::Genetic::Phenstatement	Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genot
Bio::Chado::Schema::Library::Library
Bio::Chado::Schema::Library::LibraryCvterm	The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes librar
Bio::Chado::Schema::Library::LibraryDbxref
Bio::Chado::Schema::Library::LibraryFeature	library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".
Bio::Chado::Schema::Library::LibraryPub
Bio::Chado::Schema::Library::LibrarySynonym
Bio::Chado::Schema::Library::Libraryprop
Bio::Chado::Schema::Library::LibrarypropPub
Bio::Chado::Schema::Mage::Acquisition	This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.
Bio::Chado::Schema::Mage::AcquisitionRelationship	Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.
Bio::Chado::Schema::Mage::Acquisitionprop	Parameters associated with image acquisition.
Bio::Chado::Schema::Mage::Arraydesign	General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and
Bio::Chado::Schema::Mage::Arraydesignprop	Extra array design properties that are not accounted for in arraydesign.
Bio::Chado::Schema::Mage::Assay	An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.
Bio::Chado::Schema::Mage::AssayBiomaterial	A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).
Bio::Chado::Schema::Mage::AssayProject	Link assays to projects.
Bio::Chado::Schema::Mage::Assayprop	Extra assay properties that are not accounted for in assay.
Bio::Chado::Schema::Mage::Biomaterial	A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomate
Bio::Chado::Schema::Mage::BiomaterialDbxref
Bio::Chado::Schema::Mage::BiomaterialRelationship	Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.
Bio::Chado::Schema::Mage::BiomaterialTreatment	Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).
Bio::Chado::Schema::Mage::Biomaterialprop	Extra biomaterial properties that are not accounted for in biomaterial.
Bio::Chado::Schema::Mage::Channel	Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).
Bio::Chado::Schema::Mage::Control
Bio::Chado::Schema::Mage::Element	Represents a feature of the array. This is typically a region of the array coated or bound to DNA.
Bio::Chado::Schema::Mage::ElementRelationship	Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.
Bio::Chado::Schema::Mage::Elementresult	An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.
Bio::Chado::Schema::Mage::ElementresultRelationship	Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.
Bio::Chado::Schema::Mage::Magedocumentation
Bio::Chado::Schema::Mage::Mageml	This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.
Bio::Chado::Schema::Mage::Protocol	Procedural notes on how data was prepared and processed.
Bio::Chado::Schema::Mage::Protocolparam	Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.
Bio::Chado::Schema::Mage::Quantification	Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.
Bio::Chado::Schema::Mage::QuantificationRelationship	There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.
Bio::Chado::Schema::Mage::Quantificationprop	Extra quantification properties that are not accounted for in quantification.
Bio::Chado::Schema::Mage::Study
Bio::Chado::Schema::Mage::StudyAssay
Bio::Chado::Schema::Mage::Studydesign
Bio::Chado::Schema::Mage::Studydesignprop
Bio::Chado::Schema::Mage::Studyfactor
Bio::Chado::Schema::Mage::Studyfactorvalue
Bio::Chado::Schema::Mage::Studyprop
Bio::Chado::Schema::Mage::StudypropFeature
Bio::Chado::Schema::Mage::Treatment	A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.
Bio::Chado::Schema::Map::Featuremap
Bio::Chado::Schema::Map::FeaturemapPub
Bio::Chado::Schema::Map::Featurepos
Bio::Chado::Schema::Map::Featurerange	In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect t
Bio::Chado::Schema::Organism::Organism	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.
Bio::Chado::Schema::Organism::OrganismDbxref
Bio::Chado::Schema::Organism::Organismprop	Tag-value properties - follows standard chado model.
Bio::Chado::Schema::Phenotype::FeaturePhenotype
Bio::Chado::Schema::Phenotype::Phenotype	A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.
Bio::Chado::Schema::Phenotype::PhenotypeCvterm
Bio::Chado::Schema::Phylogeny::Phylonode	This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set im
Bio::Chado::Schema::Phylogeny::PhylonodeDbxref	For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.
Bio::Chado::Schema::Phylogeny::PhylonodeOrganism	This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more
Bio::Chado::Schema::Phylogeny::PhylonodePub
Bio::Chado::Schema::Phylogeny::PhylonodeRelationship	This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.
Bio::Chado::Schema::Phylogeny::Phylonodeprop
Bio::Chado::Schema::Phylogeny::Phylotree	Global anchor for phylogenetic tree.
Bio::Chado::Schema::Phylogeny::PhylotreePub	Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.
Bio::Chado::Schema::Pub::Pub	A documented provenance artefact - publications, documents, personal communication.
Bio::Chado::Schema::Pub::PubDbxref	Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...
Bio::Chado::Schema::Pub::PubRelationship	Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appe
Bio::Chado::Schema::Pub::Pubauthor	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.
Bio::Chado::Schema::Pub::Pubprop	Property-value pairs for a pub. Follows standard chado pattern.
Bio::Chado::Schema::Sequence::Cvtermsynonym
Bio::Chado::Schema::Sequence::Feature	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 domain
Bio::Chado::Schema::Sequence::FeatureCvterm	Associate a term from a cv with a feature, for example, GO annotation.
Bio::Chado::Schema::Sequence::FeatureCvtermDbxref	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 b
Bio::Chado::Schema::Sequence::FeatureCvtermPub	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 associati
Bio::Chado::Schema::Sequence::FeatureCvtermprop	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 f
Bio::Chado::Schema::Sequence::FeatureDbxref	Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.
Bio::Chado::Schema::Sequence::FeaturePub	Provenance. Linking table between features and publications that mention them.
Bio::Chado::Schema::Sequence::FeaturePubprop	Property or attribute of a feature_pub link.
Bio::Chado::Schema::Sequence::FeatureRelationship	Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be t
Bio::Chado::Schema::Sequence::FeatureRelationshipPub	Provenance. Attach optional evidence to a feature_relationship in the form of a publication.
Bio::Chado::Schema::Sequence::FeatureRelationshipprop	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
Bio::Chado::Schema::Sequence::FeatureRelationshippropPub	Provenance for feature_relationshipprop.
Bio::Chado::Schema::Sequence::FeatureSynonym	Linking table between feature and synonym.
Bio::Chado::Schema::Sequence::Featureloc	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 e.g. splice sites, insertion points wi
Bio::Chado::Schema::Sequence::FeaturelocPub	Provenance of featureloc. Linking table between featurelocs and publications that mention them.
Bio::Chado::Schema::Sequence::Featureprop	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.
Bio::Chado::Schema::Sequence::FeaturepropPub	Provenance. Any featureprop assignment can optionally be supported by a publication.
Bio::Chado::Schema::Sequence::IntronCombinedView
Bio::Chado::Schema::Sequence::IntronlocView
Bio::Chado::Schema::Sequence::ProteinCodingGene
Bio::Chado::Schema::Sequence::Synonym	A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.
Bio::Chado::Schema::Sequence::TypeFeatureCount	per-feature-type feature counts
Bio::Chado::Schema::Stock::Stock	Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a co
Bio::Chado::Schema::Stock::StockCvterm	stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.
Bio::Chado::Schema::Stock::StockDbxref	stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.
Bio::Chado::Schema::Stock::StockGenotype	Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.
Bio::Chado::Schema::Stock::StockPub	Provenance. Linking table between stocks and, for example, a stocklist computer file.
Bio::Chado::Schema::Stock::StockRelationship
Bio::Chado::Schema::Stock::StockRelationshipPub	Provenance. Attach optional evidence to a stock_relationship in the form of a publication.
Bio::Chado::Schema::Stock::Stockcollection	The lab or stock center distributing the stocks in their collection.
Bio::Chado::Schema::Stock::StockcollectionStock	stockcollection_stock links a stock collection to the stocks which are contained in the collection.
Bio::Chado::Schema::Stock::Stockcollectionprop	The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.
Bio::Chado::Schema::Stock::Stockprop	A stock 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. There is a unique
Bio::Chado::Schema::Stock::StockpropPub	Provenance. Any stockprop assignment can optionally be supported by a publication.
Bio::Chado::Schema::Util	utility functions shared by Bio::Chado::Schema objects

Bio::Chado::Schema::$mod_moniker	$info->{module_comment}
Bio::Chado::Schema::CellLine	For describing cell lines
Bio::Chado::Schema::Companalysis	Augments sequence module with descriptions of computational analyses and features resulting from those analyses
Bio::Chado::Schema::Composite	A collection of bridge codes that have multiple dependancies so they don't happily go where is most obvious
Bio::Chado::Schema::Contact	model persons, institutes, groups, organizations, etc
Bio::Chado::Schema::Cv	Controlled vocabularies and ontologies
Bio::Chado::Schema::Expression	transcript or protein expression data
Bio::Chado::Schema::General	General purpose tables, including dbxrefs
Bio::Chado::Schema::Genetic	Genotypes and mutant alleles
Bio::Chado::Schema::Library	For describing molecular libraries
Bio::Chado::Schema::Mage	Alternative expression module, based on MAGE model
Bio::Chado::Schema::Map	Non-sequence maps: genetic, radiation hybrid, cytogenetic, etc
Bio::Chado::Schema::Organism	Species data - does not include phylogeny
Bio::Chado::Schema::Phenotype	Entity-attribute-value phenotypic character descriptions
Bio::Chado::Schema::Phylogeny	For representing phylogenetic trees; the trees represent the phylogeny of some some kind of sequence feature (mainly proteins) or actual organism taxonomy trees
Bio::Chado::Schema::Pub	Bibliographic data on publications
Bio::Chado::Schema::Sequence	Sequence and sequence features, their localization and properties
Bio::Chado::Schema::Stock	For tracking stock collections

Bio-Chado-Schema

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