Annotation Mapping

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This page documents the recommended BioSQL-standard of mapping sequence annotations (through Bio* object models) to the BioSQL relational model.

Contents


GenBank

DIVISION column division in table bioentry
accession numbers secondary accession numbers go into bioentry qualifier value table. Primary accession maps to column accession in table bioentry
TITLE this is part of a publication reference, and should map to column title in table reference
VERSION in BioPerl we parse this apart into a version for the accession (which is column version in table bioentry) and the GI number, which maps to column identifier in table bioentry
REFERENCE table reference (and bioentry_reference for association with the bioentry)
KEYWORDS map to bioentry_qualifier_value
GI column identifier in table bioentry
SIZE if it is the length of the sequence, it should map to column length in table biosequence
DEFINITION column description in table bioentry
ORGANISM this is the organism and maps to the table taxon (and taxon_name), with a foreign key in bioentry pointing to the taxon
JOURNAL this is part of a reference, see 'references'
ACCESSION the primary accession, maps to column accession in table bioentry
LOCUS in the file itself this is an entire line consisting of multiple fields; BioPerl/bioperl-db maps the locus name (the first token after the literal token LOCUS) to column name in table bioentry
SOURCE this is the organism, see 'ORGANISM'
PUBMED this is part of a literature reference, and maps to a foreign key in the reference table (reference.dbxref) to a dbxref entry with PUBMED or PMID as the database and the pubmed ID as the accession
AUTHORS part of a literature reference, maps to column authors in table reference
TYPE if this is the alphabet, it maps to table biosequence, column alphabet
CIRCULAR this at present maps to bioentry_qualifier_value, though there are plans to make it a column in table biosequence.

GFF3

Work in progress - Use the information in this section at your own risk!

See biosql-list threads: Importing GFF3 files into a BioSQL database? following the SO's GFF3 specification and this blog entry.

Major Columns

The table below describes each column of the GFF3 file, where the content should reside in the BioSQL schema (if it is known), a summary of the field from the original GFF3 spec, and notes on the BioSQL mapping. The remaining columns should provide some indication of how this data is mapped into the various Bio-* language bindings (please add version numbers/binding model where known if you fill in these).

Column Number GFF Field Name BioSQL Table Column Description (summarised from GFF3 spec) Mapping Notes BioPerl BioJava BioPython BioRuby
1 seqid BIOENTRY accession Sequence Identifier The BioEntry being annotated.

Interpretation depends of GFF file's context

2 source TERM name The source is a free text qualifier intended to describe the algorithm

or operating procedure that generated this feature. In effect, the source is used to extend the feature ontology by adding a qualifier to the type creating a new composite type that is a subclass of the type in the type column.

BioSapiens have gone to some length to create a controlled vocabulary for the source term - but it is in no way complete (TODO).
3 type TERM name The SO provides the most complete type ontology, and type terms are constrained to be either: (a) a term from the "lite" sequence

ontology, SOFA; or (b) a SOFA accession number. The latter alternative is distinguished using the syntax SO:000000.

The content of the type field is, in practice, usually human readable rather than a term ID, and even worse - is usually some (un)controlled vocabulary often dictated by the source term.
4 & 5 start & end LOCATION start & end The start and end of the feature, in 1-based integer coordinates,

relative to the landmark given in column 1, where start <=end. For zero-length features, such as insertion sites, start equals end and the implied site is to the right of the indicated base in the direction of the landmark.

TODO This field is a source of ambiguity. Previous versions of GFF arbitrarily allow '-', or for start and end to indicate either non-positional annotation, or annotation with an undefined start or end. The BioSQL schema supports this (see LOCATION documentation) but BioPerl bindings do not (see this thread).

One way of handling this is to map non-positional features directly to bioentry attributes (name, description, dbxrefs, references) - but this approach is not feasible for all non-positional features.

6 score SEQFEATURE_QUALIFIER_VALUE value

The score of the feature, a floating point number. As in earlier versions of the format, the semantics of the score are ill-defined. It is strongly recommended that E-values be used for sequence similarity features, and that P-values be used for ab initio gene prediction features.

7 strand LOCATION strand The strand of the feature. + for positive strand (relative to the

landmark), - for minus strand, and . for features that are not stranded. In addition, ? can be used for features whose strandedness is relevant, but unknown.

8 phase LOCATION (?) TODO

For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon. In other words, a phase of "0" indicates that the next codon begins at the first base of the region described by the current line, a phase of "1" indicates that the next codon begins at the second base of this region, and a phase of "2" indicates that the codon begins at the third base of this region. This is NOT to be confused with the frame, which is simply start modulo 3.

For forward strand features, phase is counted from the start field. For reverse strand features, phase is counted from the end field.

The phase is REQUIRED for all CDS features.

This is a field specific to DNA. Most GFF files related to protein sequences specify PHASE as '0'. Some overload it in some way.
9 attributes See below See Below A list of feature attributes in the format tag=value. Multiple

tag=value pairs are separated by semicolons. URL escaping rules are used for tags or values containing the following characters: ",=;". Spaces are allowed in this field, but tabs must be replaced with the %09 URL escape.

The content of the attributes field can be used to specify a host of properties - it is frequently used to specify URLs, database accessions or addtional references associated with a feature. It is also essential for the representation of alignments.

TODO - Format below and merge in with interpretations from this blog entry

These tags have predefined meanings:

    ID	   Indicates the name of the feature.  IDs must be unique
	   within the scope of the GFF file.

    Name   Display name for the feature.  This is the name to be
           displayed to the user.  Unlike IDs, there is no requirement
	   that the Name be unique within the file.

    Alias  A secondary name for the feature.  It is suggested that
	   this tag be used whenever a secondary identifier for the
	   feature is needed, such as locus names and
	   accession numbers.  Unlike ID, there is no requirement
	   that Alias be unique within the file.

    Parent Indicates the parent of the feature.  A parent ID can be
	   used to group exons into transcripts, transcripts into
	   genes, an so forth.  A feature may have multiple parents.
	   Parent can *only* be used to indicate a partof 
	   relationship.

    Target Indicates the target of a nucleotide-to-nucleotide or
	   protein-to-nucleotide alignment.  The format of the
	   value is "target_id start end [strand]", where strand
	   is optional and may be "+" or "-".  If the target_id 
	   contains spaces, they must be escaped as hex escape %20.

    Gap   The alignment of the feature to the target if the two are
          not collinear (e.g. contain gaps).  The alignment format is
	  taken from the CIGAR format described in the 
	  Exonerate documentation.
	  (http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/exonerate
          ?cvsroot=Ensembl).  See "THE GAP ATTRIBUTE" for a description
	  of this format.

    Derives_from  
          Used to disambiguate the relationship between one
          feature and another when the relationship is a temporal
          one rather than a purely structural "part of" one.  This
          is needed for polycistronic genes.  See "PATHOLOGICAL CASES"
	  for further discussion.

    Note   A free text note.

    Dbxref A database cross reference.  See the section
	   "Ontology Associations and Db Cross References" for
	   details on the format.

    Ontology_term  A cross reference to an ontology term.  See
           the section "Ontology Associations and Db Cross References"
	   for details.

Multiple attributes of the same type are indicated by separating the
values with the comma "," character, as in:

       Parent=AF2312,AB2812,abc-3

Note that attribute names are case sensitive.  "Parent" is not the
same as "parent".

All attributes that begin with an uppercase letter are reserved for
later use.  Attributes that begin with a lowercase letter can be used
freely by applications.
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