WormBase Model:Sequence
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This is a huge class with many deprecated elements.
Model
///////////////////////////////////////////////////////////////////////
//
// ?Sequence class
//
// Stores: genomic DNA objects (chromosomes, superlinks, and clones)
// cDNAs (ESTs, OSTs, mRNAs)
// sequences from other species (e.g. targets of BLAT_NEMATODE)
//
///////////////////////////////////////////////////////////////////////
?Sequence DNA UNIQUE ?DNA UNIQUE Int // Int is the length
// if you want to register a length without a DNA sequence, then use a dummy sequence object, e.g. "-"
// This ensures that when a real sequence appears, its length dominates.
SMap S_parent UNIQUE Canonical_parent UNIQUE ?Sequence XREF Genomic_non_canonical
Genomic_parent UNIQUE ?Sequence XREF Nongenomic
AGP_parent UNIQUE ?Sequence XREF AGP_fragment // added to hold briggsae data [krb 020726]
S_child Gene_child ?Gene XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // maximal extent of Gene objects
CDS_child ?CDS XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // For ?CDS class [031104 krb]
Transcript ?Transcript XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // for ?Transcript class [021126 krb]
Pseudogene ?Pseudogene XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // For ?Pseudogene class [030801 krb]
Transposon ?Transposon XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // for transposons [020128 dl]
Genomic_non_canonical ?Sequence XREF Canonical_parent UNIQUE Int UNIQUE Int #SMap_info
Nongenomic ?Sequence XREF Genomic_parent UNIQUE Int UNIQUE Int #SMap_info // for Lincoln RNAi [010226 dl]
PCR_product ?PCR_product XREF Canonical_parent UNIQUE Int UNIQUE Int #SMap_info // for Lincoln RNAi [010226 dl]
Operon ?Operon XREF Canonical_parent UNIQUE Int UNIQUE Int #SMap_info // for Operon data [dl]
AGP_fragment ?Sequence XREF AGP_parent Int UNIQUE Int #SMap_info // for Briggsae data [020726 krb]
Allele ?Variation XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // SMapped Allele class [021217 krb]
Oligo_set ?Oligo_set XREF Canonical_parent UNIQUE Int UNIQUE Int #SMap_info //added for Oligo_set class
Feature_object ?Feature XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // dl feature play
Feature_data ?Feature_data XREF Sequence UNIQUE Int UNIQUE Int #SMap_info
Homol_data ?Homol_data XREF Sequence UNIQUE Int UNIQUE Int #SMap_info
Structure From Source UNIQUE ?Sequence XREF Subsequence
Source_exons Int UNIQUE Int // start at 1
// WARNING: is this still needed when ?CDS class is present???
Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int
Overlap_right UNIQUE ?Sequence XREF Overlap_left UNIQUE Int // potentially use Overlap_right integer for auto-linking
Overlap_left UNIQUE ?Sequence XREF Overlap_right
Gap_right UNIQUE Int Text // 000909 dl added to track gap sizes
Clone_left_end ?Clone XREF Clone_left_end UNIQUE Int
Clone_right_end ?Clone XREF Clone_right_end UNIQUE Int
Flipped
DB_info Database ?Database ?Database_field UNIQUE ?Accession_number XREF Sequence
Protein_id ?Sequence UNIQUE Text UNIQUE Int // DB_info tag added [011030 krb]
Secondary_accession ?Accession_number XREF Sequence
DB_remark ?Text #Evidence // EMBL/Genbank
Keyword ?Keyword // EMBL/Genbank
DB_annotation ?Database UNIQUE ?LongText
EMBL_dump_info #EMBL_dump_info
Origin From_database UNIQUE ?Database UNIQUE Int // release number
From_author ?Author XREF Sequence
From_laboratory UNIQUE ?Laboratory
Genetic_code UNIQUE ?Genetic_code // krb 030506
Date DateType Text // Text for comments on operation
Date_directory UNIQUE Text // date of this version for cosmids, changed sdm 000731 to text
Life_stage UNIQUE ?Life_stage // to capture details of ESTs that are from different libraries
Species UNIQUE ?Species
Library UNIQUE ?Library
Strain UNIQUE ?Strain
Anatomy_term ?Anatomy_term // life-stage and tissues that the sequence comes from
Analysis UNIQUE ?Analysis // analysis or project that produced this set of data
Read_coverage UNIQUE Float // average read-coverage in a short-read cluster sequence
Visible Title UNIQUE ?Text
Matching_CDS ?CDS XREF Matching_cDNA #Evidence // to link ESTs/mRNAs to CDS
Matching_transcript ?Transcript XREF Matching_cDNA #Evidence // to link ESTs/mRNAs to RNA genes
Matching_pseudogene ?Pseudogene XREF Matching_cDNA #Evidence // to link ESTs/mRNAs to Pseudogenes
Clone ?Clone XREF Sequence
GO_term ?GO_term XREF Sequence ?GO_code #Evidence
Gene ?Gene XREF Other_sequence // for where mRNAs etc. correspond to a gene
Paired_read ?Sequence XREF Paired_read // dl 020110
Reference ?Paper XREF Sequence
Expr_pattern ?Expr_pattern XREF Sequence
RNAi ?RNAi XREF Sequence
Confidential_remark ?Text
Remark ?Text #Evidence
// tag2 system: names of all objects following next tag are shown in the
// general annotation display column as "tag:objname"
Properties Genomic_canonical Gene_count UNIQUE Int // added tag for dot name tracking [020128 dl]
Briggsae_canonical
Genomic // added tag to define genomic sequences not from the consortium
cDNA cDNA_EST
EST_5 // Indicate whether this is a 5' or 3' read [010423 dl]
EST_3
Capped_5 // Indicates capped 5' end - for Lincoln [06/12/01 krb]
TSL_tag // Indicates a short RT-PCR product for TSL detection [030220 dl]
EST_consensus // Designates this object as a consensus
// if RNA tag, acedb outputs U in place of T in sequence output
RNA UNIQUE mRNA UNIQUE Processed_mRNA //
Unprocessed_mRNA
tRNA Type UNIQUE Text // ck1 [030926] krb
Anticodon UNIQUE Text //
rRNA UNIQUE Text
snRNA UNIQUE Text
snoRNA UNIQUE Text // [030102 krb]
scRNA UNIQUE Text
miRNA UNIQUE Text // [020306 kj]
ncRNA UNIQUE Text // true non-coding RNA molecules
Ignore #Evidence // tag to flag problem Sequence objects to avoid certain analysis [031120 krb]
Show_in_reverse_orientation // Draw 3' reads in reverse orientation [010423 dl]
Status Received UNIQUE DateType
Library_construction UNIQUE DateType
Shotgun UNIQUE DateType
Shotgun_complete UNIQUE DateType
Contiguous UNIQUE DateType
Finished UNIQUE DateType
Submitted UNIQUE DateType
Annotated UNIQUE DateType
Archived UNIQUE DateType UNIQUE Text // Date Disk
Match_type UNIQUE Match_with_function
Match_without_function
// These are designed specifically for measuring
// statistics. What you match should be listed in
// Brief_id, Remark etc. The aim now is to use Brief_id
// exactly for what you would like a half-line summary to
// contain, for making tables etc.
Link // Enable gene curation of link genes [020805 krb]
Splices Confirmed_intron Int Int #Splice_confirmation
Predicted_5 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
Predicted_3 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
Cluster_information Contains_reads ?Sequence XREF Contained_in_cluster // Links cluster contig and
Contained_in_cluster ?Sequence XREF Contains_reads // individual reads
Map ?Map XREF Sequence #Map_position // use in particular for Genomic_canonical
Interpolated_map_position UNIQUE ?Map UNIQUE Float // For updated CDS-based interpolated map positions [krb 030502]
Oligo ?Oligo XREF In_sequence Int UNIQUE Int // for OSP and human mapping mostly
Defines_feature ?Feature XREF Defined_by_sequence #Evidence // Feature data model [dl 030304]
Assembly_tags Text Int Int Text // type, start, stop, comment
Gene_regulation Cis_regulator ?Gene_regulation XREF Cis_regulator_seq // Wen
YH_bait ?YH XREF Sequence_bait ?Text// for yeast two hybrid data
YH_target ?YH XREF Sequence_target ?Text
Homol DNA_homol ?Sequence XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Pep_homol ?Protein XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Motif_homol ?Motif XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Homol_homol ?Homol_data XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
// We will generate a column for each distinct ?Method. So for
// distinct Worm_EST and Worm_genomic columns, use ?Method objects
// Worm_EST_Blastn and Worm_genomic_Blastn.
Method UNIQUE ?Method
Proposed Changes
Unused tags
AGP_parent
AGP_fragment
Source_exons
Flipped
Library - will probably use this when creating the ?Library objects for the original C_elegans sequencing.
Strain
Anatomy_term
Read_coverage
GO_term
Confidential_remark
Gene_count
Briggsae_canonical
EST_consensus
Processed_mRNA
Unprocessed_mRNA
tRNA Type
tRNA Anticodon
snoRNA
scRNA
Received
Library_construction
Shotgun_complete
Archived
Match_type
Match_with_function
Match_without_function
Predicted_5
Predicted_3
Cluster_information
Contains_reads
Contained_in_cluster
Gene_regulation
Cis_regulator
YH_bait
DNA_homol
Pep_homol
