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| - | Many people want to know how to name their modules. We have tried to organize things under top level names that logically separate the datatypes or functionality. Most of the [[BioPerl]] modules focus on sequence analysis and related data, here is a table of a summary of namespace and the associated functionality.
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| - | {| border="1" cellspacing="0" cellpadding="4"
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| - | | Namespace
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| - | | Description
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| - | | {{PM|Bio::AlignIO}}
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| - | | [[Multiple sequence alignment]] input and output
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| - | | Bio::Align
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| - | | Alignment data functions including distance functions and misc utilities
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| - | |-
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| - | | Bio::Annotation
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| - | | Annotation data objects for Comments, DBLinks, OntologyTerms, References
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| - | |-
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| - | | Bio::Assembly
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| - | | Assembly objects
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| - | | {{PM|Bio::Biblio}}
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| - | | Bibliographic objects
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| - | | Bio::Cluster
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| - | | Clusters like groups of sequences from a family or [[UniGene]] clusters
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| - | |-
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| - | | {{PM|Bio::ClusterIO}}
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| - | | Cluster format input and output like unigene
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| - | | Bio::CodonTable
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| - | | Codon Usage Tables
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| - | | Bio::Coordinate
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| - | | Tools for mapping coordinates between different coordinate systems (like genomic to protein or CDS to genomic)
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| - | | Bio::DB
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| - | | A collection of database interfaces including {{PM|Bio::DB::GenBank}}, {{PM|Bio::DB::SwissProt}}, {{PM|Bio::DB::Fasta}}, {{PM|Bio::DB::GFF}}, {{PM|Bio::DB::Taxonomy}}
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| - | | Bio::Das
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| - | | Some [[DAS]] interfaces (implementations in this namespace are in other modules, see [[CPAN]])
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| - | | Bio::Event
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| - | | Event handling interfaces defined
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| - | | Bio::Expression
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| - | | Expression data interfaces defined
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| - | | Bio::Factory
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| - | | Factory interfaces for a number of different functionality - this is where the interfaces are defined only.
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| - | | Bio::FeatureIO
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| - | | New system for processing feature data ([[GFF]], BED)
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| - | |-
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| - | | Bio::Graph
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| - | | A (perhaps outdated) Graph interface and implementation for feature graphs and network representation
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| - | | {{PM|Bio::Graphics}}
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| - | | Interface for rendering graphics, basis for [[Gbrowse]] track rendering.
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| - | | Bio::Index
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| - | | A set of modules for building local indexed files for fast [[wp:Random access|random access]] to a sequences in file. Some conflict between whether modules should go in here or Bio::DB
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| - | | Bio::LiveSeq
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| - | | Bio::Location
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| - | | Locations are for representing locations in sequence typically. These include non-consecutive locations (Split) and those with undefined start or stop (Fuzzy).
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| - | | Bio::Map
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| - | | Represent biological maps like genetic maps and physical maps which are ultimately just an ordering of markers.
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| - | | Bio::Matrix
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| - | | Matricies of either sequence distances and substitution matricies.
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| - | | Bio::Ontology
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| - | | Ontology data representation ([[wp:Directed_acyclic_graph|DAG]])
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| - | | Bio::OntologyIO
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| - | | Parsing ontology data (GO, OBO)
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| - | |-
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| - | | Bio::Phenotype
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| - | | Phenotypic data representation (typically data from [[OMIM]])
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| - | | Bio::Root
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| - | | The key definitions in [[BioPerl]] objects including error handling and basic inheritance
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| - | | Bio::Search
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| - | | Key objects for parsing database sequence search results as parsed by {{PM|Bio::SearchIO}}, this includes [[Module:Bio::Search::HSP::HSPI|HSP]], [[Module:Bio::Search::Hit::HitI|Hit]] and
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| - | [[Module:Bio::Search::Result::ResultI|Result]] objects
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| - | | {{PM|Bio::SearchIO}}
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| - | | Parsing database sequence search results
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| - | | {{PM|Bio::Seq}}
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| - | | Sequence object extensions
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| - | |-
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| - | | {{PM|Bio::SeqIO}}
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| - | | Sequence input and output
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| - | |-
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| - | | Bio::Structure
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| - | | PDB and other protein sequence structure data parsing and representation
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| - | | Bio::Symbol
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| - | | An antiquitated set of objects for representing the symbols for sequence alphabets
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| - | | {{PM|Bio::Taxonomy}}
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| - | | Representation of the taxonomy hierarchy
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| - | |-
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| - | | Bio::Tools
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| - | | This is grabbag of modules whose function ranges from [[Phylogenetics]] to [[Gene prediction]] tools. A more [http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Tools/toc.html comprehensive list] of Bio::Tools functionality needs to be written...
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| - | | Bio::Tree
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| - | | Phylogenetic tree data objects and construction tools
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| - | | {{PM|Bio::TreeIO}}
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| - | | Parsing phylogenetic tree data in several formats.
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| - | | Bio::Variation
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| - | | TODO
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| - | |}
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| - | ==Avoiding conflicts with non-BioPerl modules==
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| - | Of course BioPerl is not the only package producing modules which fall in the <tt>Bio</tt> namespace. It is important to look in [[CPAN]] to see what other module names are already used. If you are a developer and want to put a new module in the namespace try and not use the namespaces we have already used to avoid confusion and collisions between our package and yours. If you plan to use a particular directory or module name we are happy to avoid using it if you just send and email to the [[Mailing lists]].
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| - | [[Category:Developer resources]]
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