// models.wrm - main file defining tree class structures
// This file is read only when starting a new database or when you select
// "Read Models" or "Add Update File" from the main menu.
//
// all tags must appear in tags.wrm or systags.wrm
//
// Magic tag2 construct, such as Inside xxx ?AA
// denotes a case where Inside and ?AA are read by the display code
// whereas the intermediate xxx is up to the schema designer
// @ is for Attach-Query
?Map No_cache // Don't cache segs for this map.
Type UNIQUE Global_map
Display Non_graphic // Prevents a graphic display!
Title UNIQUE ?Text
Flipped // Then coordinates go upwards
Unit UNIQUE Text
// e.g. kb, centiMorgan, MegaParsec
Centre UNIQUE Float UNIQUE Float
// default centre, width - else 0, 10
Extent UNIQUE Float UNIQUE Float
// min, max - else min, max gene/locus
Default_view UNIQUE ?View
Minimal_view UNIQUE ?View // use this when >1 map displayed
View ?View // Columns to display
Inherits From_map UNIQUE ?Map // To locally edit
Author Text // login name of who created it
Main_Marker Main_Locus ?Locus // XREF Main_Marker removed to
// allow tag2 system
// tag2 system for items shown left of locator
Map ?Map XREF Map_shown #Map_position
EMBL_chromosome UNIQUE Text
// Include all objects in these maps (must be mapped and have extents)
Includes ?Map
Contains Gene ?Gene XREF Map
Gene_i ?Gene XREF IntMap
Locus ?Locus XREF Map
Clone ?Clone XREF Map
Sequence ?Sequence XREF Map
Map_shown ?Map XREF Map
Section ?Section XREF Map
Transcribed_gene ?Transcribed_gene XREF Map
mRNA ?mRNA XREF Map
Product ?Product XREF Map
// OST_i ?OST XREF IntMap
// tag2 system for items shown in main region
#Map_position Position UNIQUE Float #Map_error
Ends Left UNIQUE Float #Map_error
Right UNIQUE Float #Map_error
Cyto_location Text
Multi_Position Float #Map_error
Multi_Ends Float UNIQUE Float
With UNIQUE With_locus UNIQUE ?Locus #Map_offset
With_clone UNIQUE ?Clone #Map_offset
// tag2 system for "burying"
#Map_error Error UNIQUE Float
?Map_offset Relative #Map_position
?MultiMap Map ?Map
Min Int // keep loci appearing on at least min maps. Default = 2
Anchor UNIQUE Text UNIQUE Text UNIQUE Text // Class tag1 tag2
// i.e Locus Homeology_group Homelogs
// class members on different maps with the
// same Anchor tag will be chained
?Primer Origin Text
Type UNIQUE Oligo Motif UNIQUE Text
Transposon
Vector_Primer UNIQUE T7
SP6
M13
Length UNIQUE Int
Clone UNIQUE ?Clone XREF Primer #Map_position
Read ?Sequence XREF Primer
Strand UNIQUE Forward
Reverse
RNAi ?RNAi XREF Primers
OST ?OST XREF Primers
Gene ?Gene XREF Primers
Hits ?Sequence XREF Primer_hit Int UNIQUE Int
?Section Map ?Map XREF Section #Map_position
Transcribed_gene ?Transcribed_gene XREF Section
Sequence ?Sequence XREF Section
?LocusId Title UNIQUE Text // we need to have this class around for the webquery system
?GeneId Gene ?Gene XREF GeneId // MUST be top line to simplify transfer of data
TT Title UNIQUE Text // human extracted from gene_info
Summary UNIQUE Text // human extracted from locus id
Proteome_summary UNIQUE Text // human extracted from locus id
ID NewName ?NewName XREF GeneId // same as Locustag
LocusLink ?LocusLink XREF GeneId
NM_id ?GenBank XREF GeneId
Related Locus ?Locus XREF GeneId
Synonym Text
Sequence ?Sequence XREF GeneId
Product Text
Predicted_gene ?Sequence XREF GeneId_pg
DbXref Text Text // URL description
Unigene ?Unigene XREF GeneId
Confirmation UNIQUE Confirmed
Not_confirmed
Status UNIQUE Provisional_ref_seq
Reviewed_ref_seq
Predicted_ref_seq
LocusLink_ref_seq
Validated_ref_seq
Inferred_ref_seq
Model_ref_seq
Position Map Text
Cytogenetic Text Text
IntMap ?Map UNIQUE Int UNIQUE Int // from NCBI gene2refseq file
Genetic Locus_Phenotype ?Text // Locus->phenotype but only [C.elegansII] if existing
Locus_description ?Text
Gene_RIF Text // goes to Gene->Locus_Phenotype
OMIM ?OMIM XREF GeneId
Go_b_ace ?GO_b Text Text
Molecular Descriptor ?Text // wormbase:locus->geneclass->phenotype //human: refseq +proteomesummary
Properties Text
Go_m_ace ?GO_m Text Text
Function EC_number ?Text
Gene_ontology Text Text Text Text
Expression Go_c_ace ?GO_c Text Text
Interacts with_gene ?GeneId XREF with_gene ?Text // 150 cases
with_geneBox ?Gene XREF with_geneId ?Text // 150 cases
with_protein ?GeneId XREF with_protein ?Text // 50 cases
Reference ?Paper XREF GeneId // locus->reference
?NewName Transcribed_gene ?Transcribed_gene XREF NewName
Gene ?Gene XREF NewName
GeneOld ?Gene XREF NewNameOld
GeneId ?GeneId XREF NewName
NM_id ?GenBank XREF NewName // to consolidate across gene renamings
Old_clone ?cDNA_clone XREF Old_newName
?Clone_group Contains ?cDNA_clone XREF Clone_group Text
Best_match ?Text
Transcribed_gene ?Transcribed_gene XREF Clone_group UNIQUE ?Sequence
Gene ?Gene XREF Clone_group UNIQUE ?Sequence
// tRNA UNIQUE Text
// rRNA UNIQUE Text
// snRNA UNIQUE Text
// scRNA UNIQUE Text
// misc_RNA UNIQUE Text
?cDNA_clone Read ?Sequence XREF cDNA_clone @"From_gene"
Fully_sequenced ?Transcribed_gene XREF Fully_sequenced_clone
Resequence r_gap // manual
s_gap ?mRNA XREF Gap_clone UNIQUE Int // automatic, estimated gap
Length Seq_length UNIQUE Int // bp
Insert_size UNIQUE Float Text // kb = pcr - vector (200bp for yk clones)
PCR_product_size UNIQUE Float Text REPEAT // text is kb
Library UNIQUE ?Library
WORF WORF1 Text Text // WS9 then WS100 pg-name
WORF3 Text // WS100 pg-name
MGC_ref
HINV_libs DKFZ
KIAA
FLJ
MGC MGC_r // MGC , MGC reference subset
No_NM
FLJ.1_1 // HRI+UT
FLJ.1_2 // KRDI
FLJ.2 // UT
FLJ.3 // ?? // FLJ.4 HRI
FLJ_HRIandIMS // 21791, filtered set june 20 2004
FLJ_KDRI // 397, filtered set june 20 2004
Primed_on_polyA // End of clone is the end of the full mRNA
RT_PCR // if set does not count in 5p_complete by clustering
Capped_5prime Confirmed CC_TSL
CC_other_SL
CC_stop // Begin of clone is the begin of the full mRNA
CC_blast
CC_cluster
From_gene ?Transcribed_gene XREF cDNA_clone @"Genetic_position"
Ignored_in_gene ?Transcribed_gene XREF Ignored_clone @"Genetic_position"
In_mRNA ?mRNA XREF cDNA_clone
In_gene ?Gene XREF Has_cDNA_clone
Best__of ?mRNA XREF Best_available_clone
Specific__of ?mRNA XREF Specific_clone
Complete_CDS_of ?Product XREF Complete_CDS_clone
Complete_CDS__of ?mRNA XREF Complete_CDS_clone // should be restricted to best product
R Representative
Redundant
Partial
Parent_clone ?cDNA_clone XREF Child_clone
Child_clone ?cDNA_clone XREF Parent_clone
Tracking_clone // for reconciliation, such clone will get assembled but not contribute to splicing
NM_id ?GenBank XREF GB_clone
Homolog_gene ?Transcribed_gene XREF Homolog_cDNA
Discarded_from ?Sequence XREF Discarded_cDNA Int UNIQUE Int
Clone_group UNIQUE ?Clone_group XREF Contains
Hit ?Sequence Int COORD UNIQUE Int COORD Int COORD UNIQUE Int COORD
Stage UNIQUE Mixed
Embryo
L1
L2
L3
Dauer
L4
Anomalous_clone Suspected_internal_deletion ?Sequence Int // will get assembled but disregard anomalous introns
Suspected_internal_deletion2 ?Sequence Int // to test cdna_flag
Manual_internal_deletion ?Sequence Int // done by hand
Manual_no_internal_deletion // done by hand
Suspected_genomic_contamination
VSim_Suspects_internal_deletion ?Sequence Int
VDel ?Sequence Int UNIQUE Int UNIQUE Int UNIQUE Int
Internal_priming // disregard 3p end
Internal_priming_on_A_rich // 12 A in genome in the 18 bp downstream of last aligned base
Internal_capping // disregard 5p end
Inverted
Mosaic // disregard length
Possible_mosaic // added automatically during clean_up (cDNA_31)
Partly_inverted // disregard length
Incomplete_5p_Match UNIQUE Int // disregard length
Incomplete_3p_Match UNIQUE Int // disregard length
Ignore_this_clone UNIQUE Text // disregard, for example non editable
Ignore_this_clone_automatic UNIQUE Text // disregard, for example non editable
Unspliced_non_coding
Possibly_unspliced Int // no intron et length = genome et ! in good transcript
Duplicate_clone // will get assembled but disregard anomalous introns
Length_anomaly UNIQUE Text UNIQUE Float UNIQUE Text UNIQUE Int UNIQUE Text
Double_fuzzy // automatically set in mrnaScore
Fuse_to_clone UNIQUE ?cDNA_clone
Comment ?Text
Hybridizes_to ?Clone XREF Positive_cDNA
Hybridizes_weakly_to ?Clone XREF Weak_Positive_cDNA
RNAi ?RNAi XREF cDNA_clone
Image ?Url XREF cDNA_clone
Previous_NewName Text Text // name in previous release, [pfam || (nothing == pseudo)]
Old_newName ?NewName XREF Old_clone Int Int Int Int Int // length begin ali error quality
?Clone Sequence ?Sequence XREF Clone
Main_Clone #Map_position // Contains main info on sequencing vector etc
Directed_sequencing Transposon Text UNIQUE Int // Int = Positition
Read ?Sequence XREF Subclone
Contig ?Sequence XREF Multiplet
Subclone ?Clone XREF Subclone_of
Subclone_of ?Clone XREF Subclone
Length Seq_length UNIQUE Int // bp
Gel_length UNIQUE Float // Kb
Insert_size UNIQUE Int UNIQUE Int
Subclone_Length UNIQUE Int // base pair, max direct/reverse distance
Gel ?Motif #Lane // Magic tag2 construct
Stolen_reads ?Sequence XREF Stolen // for neighbouring cosmids, not Main_clone
Vector Sequencing_Vector ?Vector UNIQUE Text // Text is the codage of the read names
Cloning_Vector ?Vector UNIQUE Text // CAF uses an Int here as the cloning site position (default 1)
Cutter ?Motif
Primer ?Primer XREF Clone
Clone_left_end ?Sequence XREF Clone_left_end
Clone_right_end ?Sequence XREF Clone_right_end
Map ?Map XREF Clone #Map_position
Positive_cDNA ?cDNA_clone XREF Hybridizes_to
Weak_Positive_cDNA ?cDNA_clone XREF Hybridizes_weakly_to
Strategy MainTitle UNIQUE Text // appears as main Window title
Species UNIQUE Text
Genome_release UNIQUE Text
Name_by UNIQUE Name_by_clone_group // default, YK clone groups
Name_by_section // geographic naming
Name_by_gene // phenotypic naming
Statistics Nb_RefSeq UNIQUE Int UNIQUE DateType
Nb_RefMrna UNIQUE Int UNIQUE DateType
Nb_EST UNIQUE Int UNIQUE DateType
PleaseNoGap // construct only gapless mRNAs
NoWeirdIntrons // keep only gt_ag gc_ag in (green) mRNAs
PleaseIntrons // construct mRNAs with at least one intron
MaxIntronSize UNIQUE Int // reject long introns
MinTranscriptSize UNIQUE Int // reject small mRNAs
MaskFrequentWords UNIQUE Text // Mask frequent genomic 15mers against seeding hits
SearchForTandemRepeats // slows the code by a factor 3
IgnoreWalls
IgnoreDiscard // incorporate discarded-clones as if normal
IgnorePolyAInProduct // do not search for a stop above a polyA, for anastasia
MarkDoubleFuzzy
StealFromPrediction
AddPolyA // autoamtically add a polyA if last 6bp == A
MultipleORF // look for several orfs
StealUpStream // allow to steal up to 18 bp if lib = yke/ykm
UseLeucine // authorization to start on ctg ttg
NoKantorInfo // do not attempt to add the kantor info
NoAbandon // do not abandon clones in very expressed genes
AcceptNegativeIntron // allow a gap on the genome
Kill_non_best_mRNA // kill non best_in_gene mrnas
// the way to use the vector description is as follows
// given a read, i will try to match its name against the Codage
// Text to identify the sequencing vector
// but you may also repeat in the read or the subclone just the
// short hand identifier.
// Note also the recursivity of the process: the sequencing vector
// of the complete clone is the cloning vector of its direct
// subclones.
?Vector Codage UNIQUE Text // may also be specified in main clone
// subclones whose name match use this vector
// if possible give the vector, cloning site and oligo used
// if i know the full vector, i will reconstruct from that the rest
Sequence UNIQUE ?Sequence // i.e. lawrist or M13, the full vector
Cloning_Site UNIQUE ?Motif UNIQUE ?Motif // i.e. bamhI ecoRV, (mind the roman I)
Oligo UNIQUE ?Oligo // the oligo used, if i have the vector sequence
// If these data are missing, you can directly give the clipping sites
// these are exactly the sequences you can read and want to clip on your abi traces
Left_Motif UNIQUE Text // 12 or more bases, left of insert
Followed_by_linker UNIQUE Text // linker
Followed_by_polyT // clip 6 or more T just downstream of this vector
Right_Motif UNIQUE Text // 12 or more bases, right of insert
Position UNIQUE Int // the approximate position of the vector in the read
// the approximate distance +- 20 bp facilitates the recognition of the vector site
Maximal_position UNIQUE Int // never clip a vector after this position
#Lane UNIQUE Bands UNIQUE Float REPEAT // In base pairs: if you prefer to minimise the ace format
Band_Lengths UNIQUE Float REPEAT // in mm: if you prefer to minimise the ace format
Band Float Text // if you wish to comment single band value
?Motif Site UNIQUE Text // AA or DNA or some more elaborate descriptor
Match_sequence UNIQUE Text // idem for ace4
Restriction_Enzyme Isoschizomer ?Motif XREF Isoschizomer
Offset UNIQUE Int
Cleavage UNIQUE Text // will show the cleavage points ex: G_ACGT'C
Overhang UNIQUE Int
Company UNIQUE Text
Redundant
Remark Text
Substrate UNIQUE DNA
Peptide
Homol DNA_homol ?Sequence XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Pep_homol ?Protein XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Motif_homol ?Motif XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Product_homol ?Product ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
?Pfam Accession ?Text
Definition UNIQUE ?Text
Interpro UNIQUE Text Text Text Text // not ?Text, so does not contribute to webquery
GO ?GO XREF Pfam
Reference Text UNIQUE Text UNIQUE Text
Paper ?Paper XREF Pfam
Comment UNIQUE Text
Pfam_comment UNIQUE Text
Interpro_comment UNIQUE Text
Manual_edition
Run_date UNIQUE DateType
Homol Gene ?Gene XREF Pfam
Product ?Product XREF Pfam @"Pfam"
CDS ?Sequence XREF Pfam_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
// Pfam data comes from http://pfam.wustl.edu, download the file
// Pfam-A.full.gz and load it into the database. After that, download
// the Interpro data and load it into the database. The Interpro data
// overwrites some of the WUSTL data, but is more complete.
//
// The name of the Pfam object is the pfam identifier from the Pfam-A.full file.
// Accession is the PF number.
// Definition is a short description.
// Interpro and GO come from the Interpro data.
// Reference is obsolete, but some databases may still contain this data.
// Paper is a list of pubmed Paper objects.
// Comment is the "GF CC" description in the Pfam file, or may be supersede by
// Interpro data
// Manual_edition is set manually when making manual changes to a Pfam record.
// After importing, "find pfam ; query manual_edition" and check all the
// resulting objects for correctness.
// Run_date is the date that the data was downloaded
// Homol is computed by the genome pipeline.
//
?Oligo Sequence UNIQUE Text // verbatim sequence
Length UNIQUE Int
In_sequence ?Sequence XREF Oligo
OSP Score UNIQUE Float
Tm UNIQUE Float
Pairwise_scores ?Oligo XREF Pairwise_scores UNIQUE Float Float // score and Tm
Status Temporary
Ordered UNIQUE DateType
//Received UNIQUE DateType
?Transcribed_gene T Transpliced_title UNIQUE Text
Operon_title UNIQUE Text
Antisens_title ?Transcribed_gene XREF Antisens_title // at least 100 bp
Gene ?Gene XREF Transcribed_gene
Locus ?Locus XREF Transcribed_gene
RNA_interference ?Text
Exactly_known mRNA_Length
Nb_codons
Total_intron_length UNIQUE Int
Composite
Transcribed_from Genomic_sequence UNIQUE ?Sequence XREF Transcribed_gene
Covers UNIQUE Int UNIQUE Text UNIQUE Int UNIQUE Int
Section UNIQUE ?Section XREF Transcribed_gene
NewName UNIQUE ?NewName XREF Transcribed_gene
DefinitiveName UNIQUE Text
Map ?Map XREF Transcribed_gene #Map_position
IntMap UNIQUE ?Map UNIQUE Int UNIQUE Int
mRNA ?mRNA XREF From_gene UNIQUE Int UNIQUE Int // coords of tr in tg
Product ?Product XREF From_gene
Comparison_to_genome Quality UNIQUE Int
Possible_SNP ?Sequence XREF Possible_SNP
Possible_genomic_error ?Sequence XREF Possible_genomic_error
Status Remark UNIQUE Text
To_do
To_be_done
Edited Date UNIQUE DateType Text
Submitted
HINV Method AceView
Bcembly
GBIRC
JBIRC
NEDO
Kent
EBI
FBI
NCBI
NCBH
Splign
Splign2
Unigene
Smith_Waterman_done
ORF UNIQUE Int Text // ORF_length "bp"
Rank G_strand G_forward
G_reverse
Masked // falls in a hyghly polymorphic region
Ali Score UNIQUE Int UNIQUE Int
No_score
Bad_score
Local_best
Best_in_method
Alternate UNIQUE Int
Repetition_5 UNIQUE Int
Genomic_contamination
ORF_bonus
Identical_exon UNIQUE Int
Exon_tested
M_score UNIQUE Int UNIQUE Int
M_range Best
Best5
Best50
Best500
Best5000
M_split M_Major
M_minor
Alibaba ?Sequence XREF Alibaba
Alibaba_old
AliName UNIQUE Text // Gold or Method_title
Identical_in_n UNIQUE Int
Gold Gold_score UNIQUE Int
Per_mille UNIQUE Int
Gold_rank Excellent Diamond
Good
Partial Partial1
Partial2
Dubious Dubious1
Dubious2
Dubious3
Dubious4
Bad_ignored
Bad Bad1
Bad2
Bad3
Bad4
Bad_short
Repetition UNIQUE Int
Rear Split Mosaic
Inversion UNIQUE Int
Transposition
Fuse_with
Pile_up UNIQUE Int
Genome_deletion UNIQUE Int
Variable_repeat UNIQUE Int
Multiple Major
Minor
Bug Twin // please always kill one of the twins
Ambiguous // aligned twice by same method
Duplicate_of_read Text
Bad_intron UNIQUE Int // number of non gt_ag gc_ag introns
ORF_malus Int // loses because of optimal ORF
Wrong_map // because an excellent gold is elsewhere
Wrong_strand
Dubious_strand
Dubious_map_B // because a very_good gold is elsewhere
Dubious_map_C // because a not_so_good gold is elsewhere
Too_long
More_exon UNIQUE Int
More_5p UNIQUE Int
More_central UNIQUE Int
More_3p UNIQUE Int
More_intron UNIQUE Int
More_micro_indel UNIQUE Int
PolyA_first_exon
PolyA_exon
Vector_exon
Too_short_first_exon UNIQUE Int
Wrong_exon
Missed_exon UNIQUE Int
Missed_5p UNIQUE Int
Missed_central UNIQUE Int
Missed_3p UNIQUE Int Text
Missed_intron UNIQUE Int
Missed_micro_indel UNIQUE Int
Structure Nb_possible_exons UNIQUE Int
Nb_alternative_exons UNIQUE Int
Nb_confirmed_introns UNIQUE Int
Nb_non_coding_introns UNIQUE Int
Nb_confirmed_alternative_introns UNIQUE Int
Total_gap_length UNIQUE Int
Transpliced_to ?Motif Int COORD UNIQUE Text
PolyA_after_base UNIQUE Int COORD
Initial_polyA UNIQUE Int COORD UNIQUE Int // start position number of A
No_5prime_read
No_3prime_read
Actual_gap Int Text ?cDNA_clone
Complete
Intron_boundaries gt_ag UNIQUE Int Int Int ?cDNA_clone // number x1 x2 support
ct_ac UNIQUE Int Int Int ?cDNA_clone
gc_ag UNIQUE Int Int Int ?cDNA_clone
at_ac UNIQUE Int Int Int ?cDNA_clone
Fuzzy UNIQUE Int Int Int ?cDNA_clone Text // type of fuzzy
Other Text UNIQUE Int Int Int ?cDNA_clone
V_repeat UNIQUE Int Int Int ?cDNA_clone // number x1 x2 supporting clone
Longest_cDNA_clone UNIQUE ?cDNA_clone UNIQUE Int
Longest_cDNA_product UNIQUE ?cDNA_clone UNIQUE Float UNIQUE Text
Fully_sequenced_clone ?cDNA_clone XREF Fully_sequenced
cDNA_clone ?cDNA_clone XREF From_gene @From_gene
Ignored_clone ?cDNA_clone XREF Ignored_in_gene
Image ?cDNA_clone @Image
Read ?Sequence XREF From_gene UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // length offset lengthmatch err quality
Homolog_cDNA ?cDNA_clone XREF Homolog_gene
Clone_group ?Clone_group XREF Transcribed_gene UNIQUE Int // number of clones of that group
Expression_profile Int REPEAT // sum of expression profile, each clone adds to 100
Matching_genefinder_gene ?Sequence XREF Matching_transcribed_gene
Identical_to_genefinder UNIQUE ?Sequence
Details Missing_read ?Sequence XREF Missing_from_gene @From_gene
LostRead ?Sequence
Overlaps ?Transcribed_gene XREF Overlaps
Antisens_to ?Transcribed_gene XREF Antisens_to UNIQUE Int
To_be_fused_with ?Transcribed_gene XREF Antisens_to UNIQUE Int
Shedded_from ?Transcribed_gene XREF Sheds
Sheds ?Transcribed_gene XREF Shedded_from
Possible_operon ?Transcribed_gene XREF Possible_operon UNIQUE Int
Next_gene_in_cis UNIQUE ?Transcribed_gene XREF Previous_gene_in_cis UNIQUE Int
Previous_gene_in_cis UNIQUE ?Transcribed_gene XREF Next_gene_in_cis UNIQUE Int
Splicing Int COORD Int COORD #Splicing_confirmation // do NOT say unique
Assembled_from Int Int ?Sequence UNIQUE Int UNIQUE Int UNIQUE Int // a1 a2 read x1 x2 nberr
?mRNA Title UNIQUE ?Text
Bad_quality Text
Fiche UNIQUE ?Fiche XREF mRNA
Genetic_code UNIQUE ?Genetic_code
From_gene ?Transcribed_gene XREF mRNA
NM_id ?GenBank XREF mRNA
NM_idexported ?GenBank XREF mRNAexported
NM_idaligned ?GenBank XREF mRNAaligned
Genefinder From_AM
From_prediction ?Sequence XREF Predicted_mRNA
Matching_genefinder ?Sequence XREF Matching_mRNA
Identical_to_genefinder ?Sequence XREF Identical_to_mRNA
RNAi ?RNAi XREF mRNA
SMAP S_Parent Genomic_sequence UNIQUE ?Sequence XREF mRNAs
Covers UNIQUE Int UNIQUE Text UNIQUE Int UNIQUE Text UNIQUE Int
DNA UNIQUE ?DNA UNIQUE Int Text // Int is the length
Constructed_from Int Int ?Sequence XREF In_mRNA Int Int
S_Child Product ?Product XREF mRNA UNIQUE Int UNIQUE Int Int UNIQUE Int @ID
Position IntMap UNIQUE ?Map UNIQUE Int UNIQUE Int
Map ?Map XREF mRNA #Map_position
Structure Longest_ORF UNIQUE Int UNIQUE Text UNIQUE Int UNIQUE Text // 600 bp 200 AA from end to end
Longest_CDS UNIQUE Int UNIQUE Text UNIQUE Int UNIQUE Text // 645 bp 215 AA from end to end
Length_5prime_UTR UNIQUE Int UNIQUE Text
Length_3prime_UTR UNIQUE Int UNIQUE Text
Splicing Int UNIQUE Int UNIQUE Int UNIQUE Int #Splicing_confirmation
Coding Int UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Text
Nb_exons UNIQUE Int
Nb_alternative_exons UNIQUE Int
Nb_stolen_exons UNIQUE Int
Nb_predicted_exons UNIQUE Int
Total_gap_length UNIQUE Int
Intron_boundaries gt_ag UNIQUE Int Int Int ?cDNA_clone
ct_ac UNIQUE Int Int Int ?cDNA_clone
gc_ag UNIQUE Int Int Int ?cDNA_clone
at_ac UNIQUE Int Int Int ?cDNA_clone
Fuzzy UNIQUE Int Int Int ?cDNA_clone Text // type of fuzzy
Other Text UNIQUE Int Int Int ?cDNA_clone
V_repeat UNIQUE Int Int Int ?cDNA_clone // number x1 x2 supporting clone
Quality Score UNIQUE Int // refsequisable mrna and score
Rating UNIQUE Text
RefSeq
Best_in_gene
Low_expression
Ambiguous_best_product
Well_supported // cds_covered_by == 1 && cds >= 100 AA || (cds >= 50 && tax != *sapiens*)
Mrna_covered_by ?Sequence // minimum covering set
CDS_covered_by ?Sequence // minimum covering set
RefSeqMaker UNIQUE ?Sequence XREF RefSeqMaker
Tiling Tiling_gap Int Int // in mrna, in cds
Tiling_error UNIQUE Int
Tiling_base_error UNIQUE Int
Tiling_path Int Int ?Sequence XREF mRNA_tiling Int Int
To_resequence ?cDNA_clone
Expression_profile Int REPEAT // sum of expression profile, each clone adds to 100
Coding_antisens_to ?mRNA XREF Coding_antisens_to Int
Signature SL0 SL0_m UNIQUE Int
SL0_e UNIQUE Int
SL0_d UNIQUE Int
SL0_L1 UNIQUE Int
SL0_L2 UNIQUE Int
SL0_L3 UNIQUE Int
SL0_L4 UNIQUE Int
SL1 SL1_m UNIQUE Int
SL1_e UNIQUE Int
SL1_d UNIQUE Int
SL1_L1 UNIQUE Int
SL1_L2 UNIQUE Int
SL1_L3 UNIQUE Int
SL1_L4 UNIQUE Int
SL2s SL2s_m UNIQUE Int
SL2s_e UNIQUE Int
SL2s_d UNIQUE Int
SL2s_L1 UNIQUE Int
SL2s_L2 UNIQUE Int
SL2s_L3 UNIQUE Int
SL2s_L4 UNIQUE Int
Completeness Complete // found5p && Found3p && convaincant
Found5p Transpliced_to ?Motif ?cDNA_clone
Aggregated_5p_clones UNIQUE Int
Submitted_as_5p_complete ?cDNA_clone
Found3p PolyA_primed_clone
PolyA_found Int ?cDNA_clone
PolyA_Signal AATAAA Int
Variant Text Int
Submitted_as_3p_complete ?cDNA_clone
Gap Gap_length UNIQUE Int
Gap_clone ?cDNA_clone XREF s_gap Int Int Int Int // gap unalignedLength 5pLength 3pLength
Clones Best_available_clone ?cDNA_clone XREF Best__of
Specific_clone ?cDNA_clone XREF Specific__of
Complete_CDS_clone ?cDNA_clone XREF Complete_CDS__of
cDNA_clone ?cDNA_clone XREF In_mRNA Int Text Int Text Float Text Int Text @Anomalous_clone // 1022 "bp measured" .9 "kb variation" -12 "%"
?Product ID Title UNIQUE ?Text // the title kernel we export to refseq
Kantor_title UNIQUE ?Text // copied from kantor->title or from kantor->Kantor_title
Short_kantor_title UNIQUE Text
uORF
Suggested_class Text // ufo nmt ... generated from kantor
Blastp_title UNIQUE Text // generated from kantor
Pfam_title ?Pfam REPEAT // liste des pfam
Motif_title UNIQUE Text // not text it would be too much XREF'd
Psort_title UNIQUE Text // not text it would be too much XREF'd
Tax_common_ancestor Text
Family_title UNIQUE Text
Molecular_weight UNIQUE Float UNIQUE Float
GeneBox ?Gene XREF Product
From_gene UNIQUE ?Transcribed_gene XREF Product
Genefinder From_prediction ?Sequence XREF Predicted_product
Matching_gene ?Sequence XREF Matching_product
Identical_to_gene ?Sequence XREF Identical_to_product
Expasy UNIQUE Float UNIQUE Float
Expasy_class A
B B1
B2
B3
Completeness Quality UNIQUE Int
Partial ?Product XREF Included_in_partial
Complete ?Product XREF Included_in_complete // NH2_Complete && COOH_Complete
NH2_Complete Up_stop UNIQUE Int REPEAT // negative numbers, if Met_at_position_1
Early_Met
Manual_Met
mRNA_5p_complete
Met at_position_1 // Only possible if NH2_Complete, if present: A of ATG defines base 1
First_Met UNIQUE Int // AA units, obsolete, kept for backwards compatibility
First_ATG UNIQUE Int // AA units
First_NTG UNIQUE Int UNIQUE Text // AA units
COOH_Complete Down_stop UNIQUE Int REPEAT
Best_product // longest CDS, or if none longest ORF
Good_product // has some kind of good annot or CDS >= 100 AA
Open_length UNIQUE Int UNIQUE Text UNIQUE Int UNIQUE Text // 645 bp 215 AA from end to end
Coding_gap UNIQUE Int UNIQUE Text UNIQUE Int UNIQUE Text // 201 bp 67 X
Length_5prime_UTR UNIQUE Int UNIQUE Text
Coding_length UNIQUE Int UNIQUE Text UNIQUE Int UNIQUE Text // from Met to Stop, and only if they exist
Length_3prime_UTR UNIQUE Int UNIQUE Text
Complete_CDS_clone ?cDNA_clone XREF Complete_CDS_of
Covered_by ?Sequence XREF Covers_product UNIQUE Text UNIQUE Int UNIQUE Text UNIQUE Int UNIQUE Text // delta # nV # type
Structure Introns Nb_introns_in_CDS UNIQUE Int
Nb_Introns_outside_CDS UNIQUE Int
Unicity Original // if complete not identical or partial not included and not identical
Identical_to ?Product
Included_in_complete ?Product XREF Complete
Included_in_partial ?Product XREF Partial
Homol AKG AceKogHuman Text UNIQUE Text // Gene NewName_or_GeneId Text, because this is an external reference
AceKogWorm Text UNIQUE Text // Text, because this is an external reference
AceKog Text Text Float Int UNIQUE Int Int UNIQUE Int ?Text
Pfam ?Pfam XREF Product ?Method Float Int UNIQUE Int Int UNIQUE Int Text Text
Blastp ?Protein ?Method Float Int UNIQUE Int Int UNIQUE Int Text // ?may be costly
Domain ?Motif ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Nucleic_acid_binding Leucine_zipper_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Zinc_finger_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
RNA_binding_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Psort_domain Transmembrane_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Cleavable_signal_peptide ?Method Float Int UNIQUE Int Int UNIQUE Int Text
N_terminal_signal_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
N_terminal_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Nuclear_localization_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
2nd_peroximal_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
actin_binding_1_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
actin_binding_2_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
ATP_binding_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Coiled_coil_region ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Coil_coil_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Coil_coil_4 ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Ribosomal_protein_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Dileucine_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
ER_membrane_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
ER_retention_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Golgi_transport_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
N_myristoylation_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
peroxisomal_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
prenylation_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
vacuolar_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Mitochondrial_cleavage_site_domain ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Tax_tree Archaea
Viruses
Bacteria Escherichia_coli
Eukaryota Plasmodium_falciparum
Mycetozoa Dictyostelium_discoideum
Viridiplantae Chlamydomonas_reinhardtii
Arabidopsis_thaliana
Zea_mays
Fungi_Metazoa_group Fungi Saccharomyces_cerevisiae
Schizosaccharomyces_pombe
Neurospora_crassa
Metazoa Bilateria Pseudocoelomata Caenorhabditis_elegans
Protostomia Mollusca
Panarthropoda Anopheles_gambiae_str_PEST
Drosophila_melanogaster
Deuterostomia Echinodermata
Chordata Vertebrata Teleostomi Teleostei Takifugu_rubripes
Danio_rerio
Amphibia Xenopus_laevis
Amniota Mammalia Eutheria Mus_musculus
Rattus_norvegicus
Homo_sapiens
Tax_count NArchaea UNIQUE Int
NViruses UNIQUE Int
NBacteria UNIQUE Int
NEscherichia_coli UNIQUE Int ?Method ?Protein Float
NEukaryota UNIQUE Int
NPlasmodium_falciparum UNIQUE Int ?Method ?Protein Float
NMycetozoa UNIQUE Int
NDictyostelium_discoideum UNIQUE Int ?Method ?Protein Float
NViridiplantae UNIQUE Int
NArabidopsis_thaliana UNIQUE Int ?Method ?Protein Float
NZea_mays UNIQUE Int ?Method ?Protein Float
NChlamydomonas_reinhardtii UNIQUE Int ?Method ?Protein Float
NFungi_Metazoa_group UNIQUE Int
NFungi UNIQUE Int
NSaccharomyces_cerevisiae UNIQUE Int ?Method ?Protein Float
NSchizosaccharomyces_pombe UNIQUE Int ?Method ?Protein Float
NNeurospora_crassa UNIQUE Int ?Method ?Protein Float
NMetazoa UNIQUE Int
NBilateria UNIQUE Int
NPseudocoelomata UNIQUE Int
NCaenorhabditis_elegans UNIQUE Int ?Method ?Protein Float
NProtostomia UNIQUE Int
NMollusca UNIQUE Int
NPanarthropoda UNIQUE Int
NAnopheles_gambiae_str_PEST UNIQUE Int ?Method ?Protein Float
NDrosophila_melanogaster UNIQUE Int ?Method ?Protein Float
NDeuterostomia UNIQUE Int
NEchinodermata UNIQUE Int
NChordata UNIQUE Int
NVertebrata UNIQUE Int
NTeleostomi UNIQUE Int
NTakifugu_rubripes UNIQUE Int ?Method ?Protein Float
NDanio_rerio UNIQUE Int ?Method ?Protein Float
NAmphibia UNIQUE Int
NXenopus_laevis UNIQUE Int ?Method ?Protein Float
NAmniota UNIQUE Int
NMammalia UNIQUE Int
NEutheria UNIQUE Int
NMus_musculus UNIQUE Int ?Method ?Protein Float
NRattus_norvegicus UNIQUE Int ?Method ?Protein Float
NHomo_sapiens UNIQUE Int ?Method ?Protein Float
Localisation Psort Cytoplasmic UNIQUE Float // was ?Psort XREF Product // localisation de la protein
Cytoskeletal UNIQUE Float
Endoplasmic_reticulum UNIQUE Float
Secreted UNIQUE Float // extracellular, including cell wall
Golgi UNIQUE Float
Mitochondrial UNIQUE Float
Membrane UNIQUE Float
Nuclear UNIQUE Float
Peroxisomal UNIQUE Float
Plasma_membrane UNIQUE Float
Vacuolar UNIQUE Float
Vesicles_of_secretory_system UNIQUE Float
Antibody
GFP_tag
Frame UNIQUE Int
Primers Text UNIQUE Text UNIQUE TEXT UNIQUE Float // ATGGATCAATTCCAAGCTTTGATT "(Met->24bp,T=55.1)" "osp_score" 70.0
SMAP S_Parent mRNA UNIQUE ?mRNA XREF Product
From_EST UNIQUE ?Sequence XREF EST_translation
Peptide UNIQUE ?Peptide UNIQUE Int UNIQUE Int // Int is the signature
Source_Exons Int COORD UNIQUE Int COORD #Protein_fragment // gene splicing in bp then AA
Position IntMap UNIQUE ?Map UNIQUE Int UNIQUE Int
Map ?Map XREF Product #Map_position
CDS Method UNIQUE ?Method // for display purposes
Kantor UNIQUE ?Kantor XREF Product @Title_hints
?Psort Title ?Text
// ClassK antor maintains exterior protein annotations maintained on the sole
// basis of its peptide sequence, it is named based on the peptide hash-value
// the searches (BLAST, PFAM etc) can be run 'in advance' of creating the Product
// object and are hooked to it on the basis of the peptide sequence hash value
// this is a secret class without any XREF originating from it
// ace -> michel peptide product Predicted_product Representative_product
// pfam -> pfam_date Pfam hit_info PFAM_title
// blastp -> blastp_date title_hints blastp Blastp_title Short_title
// taxblast-> taxblast_date Tax_count Tax_tree
// psort -> psort_date psort domain
// expasy -> expasy_date expasy
?Kantor Hand Title UNIQUE Text // hand edited out of kantor_title + GenBank Is_mrna ->Brief_identification
Short_title UNIQUE Text // hand edited
Auto ID Kantor_title UNIQUE Text // fully automatic
Short_kantor_title UNIQUE Text // fully automatic
mRNA_title UNIQUE Text
Suggested_class UNIQUE Text // ufo nmt ... generated from kantor
Family_title UNIQUE Text
Blastp_title UNIQUE Text
Taxblast_title UNIQUE Text
PFAM_title UNIQUE Text
Product ?Product // NO XREF
Representative_product UNIQUE ?Product // NO XREF
Peptide UNIQUE ?Peptide UNIQUE Int UNIQUE Int
Michel UNIQUE Float UNIQUE Float
Kantor_Date UNIQUE DateType
EXP Expasy_Date UNIQUE DateType
Expasy UNIQUE Float UNIQUE Float
PFM Pfam_Date UNIQUE DateType
Pfam ?Pfam ?Method Float Int UNIQUE Int Int UNIQUE Int Text Text // score,a1.a2.x1.x2,method,expect(out of range of floats)
Hit_Info Pfam_Significant_Hits UNIQUE Int
Pfam_Non_Significant_Hits UNIQUE Int
BLP Blastp_Date UNIQUE DateType
Blastp ?Protein ?Method Float Int UNIQUE Int Int UNIQUE Int Text
Title_hints Text
AKG AceKog_Date UNIQUE DateType
AceKog Text Text Float Int UNIQUE Int Int UNIQUE Int ?Text
AceKogHuman Text Text // Text, because this is an external reference
AceKogWorm Text Text // Text, because this is an external reference
PSR Psort_Date UNIQUE DateType
Psort Localization ?Psort UNIQUE Float
Domain ?Motif ?Method Float Int UNIQUE Int Int UNIQUE Int Text
TXB Taxblast_Date UNIQUE DateType
Tax_tree Archaea
Viruses
Bacteria Escherichia_coli
Eukaryota Plasmodium_falciparum
Mycetozoa Dictyostelium_discoideum
Viridiplantae Chlamydomonas_reinhardtii
Arabidopsis_thaliana
Zea_mays
Fungi_Metazoa_group Fungi Saccharomyces_cerevisiae
Schizosaccharomyces_pombe
Neurospora_crassa
Metazoa Bilateria Pseudocoelomata Caenorhabditis_elegans
Protostomia Mollusca
Panarthropoda Anopheles_gambiae_str_PEST
Drosophila_melanogaster
Deuterostomia Echinodermata
Chordata Vertebrata Teleostomi Teleostei Takifugu_rubripes
Danio_rerio
Amphibia Xenopus_laevis
Amniota Mammalia Eutheria Mus_musculus
Rattus_norvegicus
Homo_sapiens
Tax_count NArchaea UNIQUE Int
NViruses UNIQUE Int
NBacteria UNIQUE Int
NEscherichia_coli UNIQUE Int ?Method ?Protein Float
NEukaryota UNIQUE Int
NPlasmodium_falciparum UNIQUE Int ?Method ?Protein Float
NMycetozoa UNIQUE Int
NDictyostelium_discoideum UNIQUE Int ?Method ?Protein Float
NViridiplantae UNIQUE Int
NChlamydomonas_reinhardtii UNIQUE Int ?Method ?Protein Float
NArabidopsis_thaliana UNIQUE Int ?Method ?Protein Float
NZea_mays UNIQUE Int ?Method ?Protein Float
NFungi_Metazoa_group UNIQUE Int
NFungi UNIQUE Int
NSaccharomyces_cerevisiae UNIQUE Int ?Method ?Protein Float
NSchizosaccharomyces_pombe UNIQUE Int ?Method ?Protein Float
NNeurospora_crassa UNIQUE Int ?Method ?Protein Float
NMetazoa UNIQUE Int
NBilateria UNIQUE Int
NPseudocoelomata UNIQUE Int
NCaenorhabditis_elegans UNIQUE Int ?Method ?Protein Float
NProtostomia UNIQUE Int
NMollusca UNIQUE Int
NPanarthropoda UNIQUE Int
NAnopheles_gambiae_str_PEST UNIQUE Int ?Method ?Protein Float
NDrosophila_melanogaster UNIQUE Int ?Method ?Protein Float
NDeuterostomia UNIQUE Int
NEchinodermata UNIQUE Int
NChordata UNIQUE Int
NVertebrata UNIQUE Int
NTeleostomi UNIQUE Int
NTakifugu_rubripes UNIQUE Int ?Method ?Protein Float
NDanio_rerio UNIQUE Int ?Method ?Protein Float
NAmphibia UNIQUE Int
NXenopus_laevis UNIQUE Int ?Method ?Protein Float
NAmniota UNIQUE Int
NMammalia UNIQUE Int
NEutheria UNIQUE Int
NMus_musculus UNIQUE Int ?Method ?Protein Float
NRattus_norvegicus UNIQUE Int ?Method ?Protein Float
NHomo_sapiens UNIQUE Int ?Method ?Protein Float
?WbId Predicted_gene ?Sequence XREF WbId
Gene ?Gene XREF WbId
?Sequence Title UNIQUE Text // absolutelly NO ?Text here, 4M est have it
Product_title UNIQUE ?Text
mRNA_title UNIQUE ?Text
Full_name UNIQUE Text
OMIM ?OMIM XREF Sequence
GeneId_pg ?GeneId XREF Predicted_gene
GeneId ?GeneId XREF Sequence
WbId ?WbId XREF Predicted_gene
COG ?COG XREF Sequence @Info
GO ?GO
Has_EST has_exact_est
Homolog ?Text
Reference ?Paper XREF Sequence
DNA UNIQUE ?DNA UNIQUE Int Text // Int is the length
RNA // if this tag is set display AUGC
Type UNIQUE Is_read Difficult_to_align
Is_ignored_read
Is_contig
Is_assembly
Is_bac
Is_AM
Product
Genomic Is_Cosmid In_junction ?Sequence XREF Parts
Is_gene_tile // to cover large genes
// Is_Link // Parts ?Sequence
Junction Parts ?Sequence XREF In_junction
Is_Pair
Is_gap UNIQUE Int
Is_chain UNIQUE Int
YBR_contig
GS_tiling
Is_predicted_gene
Gene_predicted_by Genefinder
Vector Is_vector // double appelation fro compatibility
Structure From Source UNIQUE ?Sequence XREF Subsequence
Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int
Section UNIQUE ?Section XREF Sequence
Fragment ?Sequence XREF Compound
Compound ?Sequence XREF Fragment Int UNIQUE Int UNIQUE Int UNIQUE Int
Source_Exons Int COORD UNIQUE Int COORD #Splicing_confirmation // start at 1, to display gene splicing and translations
Transcribed_gene ?Transcribed_gene XREF Genomic_sequence UNIQUE Int UNIQUE Int
Gene_wall Int UNIQUE Int
Super_long
SMAP S_Child Genes ?Gene XREF Genomic_sequence UNIQUE Int UNIQUE Int #SMap_info
mRNAs ?mRNA XREF Genomic_sequence UNIQUE Int UNIQUE Int #SMap_info
RNAi ?RNAi XREF Genomic_sequence Int UNIQUE Int #SMap_info
OST ?OST XREF Genomic_sequence Int UNIQUE Int #SMap_info
Assembled_in In_mRNA ?mRNA
mRNA_tiling ?mRNA
Gene Gene_model ?Sequence XREF Model_of
Model_of UNIQUE ?Sequence XREF Gene_model
Model_of_gene ?Gene XREF Genefinder
Model_of_previous_gene ?Gene XREF Previous_genefinder
Identifies ?Sequence
Version UNIQUE Int
Primers Text UNIQUE Text
Confirmed_intron Int Int #Splice_confirmation
Map ?Map XREF Sequence #Map_position
IntMap UNIQUE ?Map UNIQUE Int UNIQUE Int
Tested_by Tested_by_AceView
Tested_by_JBIRC
Tested_by_GBIRC
Tested_by_NEDO
Tested_by_Kent
Tested_by_NCBI
Tested_by_NCBH
Tested_by_EBI
Tested_by_Splign
Alibaba ?Transcribed_gene XREF Alibaba
cDNA From_gene ?Transcribed_gene XREF Read UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Text // length offset lengthmatch nerors quality section
From_cosmid ?Sequence Int Int Int Int Int Int Int Int Text // cosmid a1 a2 x1 x2 lengthest ali nerr quality section
From_cosmid_jap34_oct13 ?Sequence Int Int Int Int Int Int Int Int Text // cosmid a1 a2 x1 x2 lengthest ali nerr quality section
From_cosmid_jap34_oct14 ?Sequence Int Int Int Int Int Int Int Int Text // cosmid a1 a2 x1 x2 lengthest ali nerr quality section
From_cosmid_ncbi34_oct14 ?Sequence Int Int Int Int Int Int Int Int Text // cosmid a1 a2 x1 x2 lengthest ali nerr quality section
From_cosmid_ncbi34_oct30 ?Sequence Int Int Int Int Int Int Int Int Text // cosmid a1 a2 x1 x2 lengthest ali nerr quality section
From_cosmid_jap34_oct30 ?Sequence Int Int Int Int Int Int Int Int Text // cosmid a1 a2 x1 x2 lengthest ali nerr quality section
Best_cosmid_alignment ?Sequence Int Int Int Int Int Int Int Int Text// cosmid a1 a2 x1 x2 lengthest ali nerr quality section
Best_gene_alignment ?Transcribed_gene Int Int Int Int Int Text// tg len offsett ali nerr quality section
Missing_from_gene ?Transcribed_gene XREF Missing_read
Assembly Colour #Colour // seen in trace editor
Is_Reference // Reference sequence, for acembly: align command
Assembled_from ?Sequence XREF Assembled_into UNIQUE Int COORD UNIQUE Int COORD UNIQUE Int UNIQUE Int
Assembled_into ?Sequence XREF Assembled_from
// these two are the binding relationships reads <-> contigs - they are loose
// the first two ints are the positions in the contig. The next two are the left and right clip points
// for the read with respect to this assembly.
Aligned ?Sequence XREF Aligned_into UNIQUE Int COORD UNIQUE Int COORD UNIQUE Int UNIQUE Int
Aligned_into ?Sequence XREF Aligned // for sequence comparisons in acembly
// historic of asssemblies
History Derived_from UNIQUE ?Sequence UNIQUE DateType
Previous_contig ?Sequence XREF Later_part_of UNIQUE Int COORD UNIQUE Int COORD UNIQUE Int UNIQUE Int
Later_part_of ?Sequence XREF Previous_contig
Golden_path ?Sequence UNIQUE Int COORD UNIQUE Int COORD
Phrap Tag // ?Tag_type Int COORD Int COORD Text
Template UNIQUE ?Clone XREF Read
Align_to_SCF Int COORD UNIQUE Int COORD UNIQUE Int UNIQUE Int
// tight alignment of current (edited) read to SCF file
Staden_id UNIQUE Int
Library ?Library UNIQUE Text UNIQUE Text // Texts are ID, Accession_number
// to be used for reads from EMBL etc.
Origin From_Library ?Library
Dev_stage Text // LOCK
Tissue ?Tissue // LOCK
Date Text
Genetic_Code unique ?Genetic_code @"name"
Japanese
HINV1
HINV2
Nb_cDNA_clone UNIQUE Int // includes shed clones
Species Text
Clone_structure Length UNIQUE Int
Nb_Exons UNIQUE Int
Exon_Length UNIQUE Int
Intron_Length UNIQUE Int
Gap_Length 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
Clone_left_end ?Clone XREF Clone_left_end UNIQUE Int
Clone_right_end ?Clone XREF Clone_right_end UNIQUE Int
Connected // no gap from here to origin of coordinates
Visible Remark ?Text // LOCK what people have put in their GenBank submission
Concise_description ?Text // used in wormbase elegans_cds
Long_remark ?LongText
Function ?Text // LOCK as imported from GenBank
Matching_Genomic ?Sequence XREF Matching_cDNA
Matching_cDNA ?Sequence XREF Matching_Genomic
Matching_transcribed_gene ?Transcribed_gene XREF Matching_genefinder_gene
Matching_mRNA ?mRNA XREF Matching_genefinder #Met_stop
Matching_product ?Product XREF Matching_gene #Met_stop
Identical_to_mRNA ?mRNA XREF Identical_to_genefinder
Predicted_mRNA ?mRNA XREF From_prediction
Predicted_product ?Product XREF From_prediction
Identical_to_product ?Product XREF Identical_to_gene
Corresponding_protein UNIQUE ?Protein XREF Corresponding_DNA
Related_protein ?Protein XREF Related_DNA
Spliced_cDNA ?Sequence XREF Component_of Int UNIQUE Int Int UNIQUE Int
Component_of ?Sequence XREF Spliced_cDNA
Rescued_gene ?Gene XREF Rescuing_cosmid
Locus ?Locus XREF Sequence
Locus_62 ?Locus XREF Sequence_62
Locus_81 ?Locus XREF Sequence_81
Locus_84 ?Locus XREF Sequence_84 // 84 o5 85
Locus_89 ?Locus XREF Sequence_89 //
Locus_102 ?Locus XREF Sequence_102 //
Locus_130 ?Locus XREF Sequence_130 //
Locus_GB ?Locus XREF Sequence_GB //LOCK GenBank names like unc-32
Locus_GB_dubious ?Locus XREF Sequence_GB_dubious // GB of bizare form
LocusLink ?LocusLink XREF Sequence
Locus_cgc ?Locus XREF Sequence_cgc
Allele ?Allele XREF Sequence
Brief_identification UNIQUE ?Text
Expr_pattern ?Expr_pattern XREF Sequence
Sage Text Int Int Float // catg #dauer #mixed score
Affymetrix Text // used on affymetrix chips
NCBI Ref_Seq Provisional_ref_seq
Reviewed_ref_seq
Predicted_ref_seq
LocusLink_ref_seq
Validated_ref_seq
Inferred_ref_seq
Model_ref_seq
RefSeqMaker UNIQUE ?mRNA XREF RefSeqMaker
Ref_id ?Locus XREF Ref_id
NM_id ?GenBank XREF Predicted_gene_NM
NM_idexported ?GenBank XREF Predicted_gene_NMexported
NM_idaligned ?GenBank XREF Predicted_gene_NMaligned
GenBank_id UNIQUE ?GenBank XREF Sequence
GeneCard_id UNIQUE Text
Ref_mRNA
Properties Pseudogene Text
Transposon Text // transposon type
Coding CDS UNIQUE Int COORD UNIQUE Int COORD
CDS_predicted_by ?Method Float // score of method
Precursor
Covers_product ?Product XREF Covered_by #Coverage
Status Received UNIQUE DateType
Library_construction UNIQUE DateType
Shotgun UNIQUE DateType
Shotgun_complete UNIQUE DateType
Contiguous UNIQUE DateType
Finished UNIQUE DateType
Submitted UNIQUE DateType
Archived UNIQUE DateType UNIQUE Text // Date Disk
ProcessStatus UNIQUE Text
Asped UNIQUE DateType
Is_mRNA
// is_mrna is more specific than it looks.. it
// means an mRNA that should be used to construct
// a reference sequence (an NM)
Is_partial
Is_EST
Is_mutant
Complete_mRNA // same as real_3prime AND Real_5prime
Complete_CDS // same has having an SL0, means find Met inside this read
Real_5prime // do not fuse upstream by hand
Real_3prime // do not fuse downstream by hand
Manual_real_5prime // do not fuse upstream by hand Danielle aug23
Manual_real_3prime // do not fuse downstream by hand Danielle aug23
Gold_repeat // repeat identified in Gold project
Start_not_found
End_not_found
GenBank_tag Text Text
AM Score UNIQUE Int
Rating UNIQUE Text
Transcript UNIQUE mRNA UNIQUE Processed_mRNA
Unprocessed_mRNA
tRNA UNIQUE Text
rRNA UNIQUE Text
ncRNA UNIQUE Text
snRNA UNIQUE Text
snoRNA UNIQUE Text
scRNA UNIQUE Text
stRNA UNIQUE Text // [010723 dl]
miRNA UNIQUE Text // [011129 dl]
misc_RNA UNIQUE Text
Anticodon UNIQUE Text
Oligo ?Oligo XREF In_sequence Int UNIQUE Int // for OSP
OligoRepeat UNIQUE ?OligoRepeat UNIQUE Int
cDNA_clone UNIQUE ?cDNA_clone XREF Read @From_gene
cDNA_clone_GB Text
EST_translation ?Product XREF From_EST UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // product_from to(excluding stop) .tg (met or leu) atg (met)
From_cDNA_clone UNIQUE ?cDNA_clone XREF Read @From_gene
Discarded_cDNA ?cDNA_clone XREF Discarded_from Int Int
Possible_error_at_base Int UNIQUE Text UNIQUE Text
Possible_genomic_error ?Transcribed_gene XREF Possible_genomic_error Int UNIQUE Text
Possible_SNP ?Transcribed_gene XREF Possible_SNP Int UNIQUE Text
Strand UNIQUE Forward
Reverse
Intron_boundaries gt_ag UNIQUE Int
ct_ac UNIQUE Int
gc_ag UNIQUE Int
at_ac UNIQUE Int
Fuzzy UNIQUE Int
other Text UNIQUE Int
V_repeat UNIQUE Int // number
Exon_coord Int UNIQUE Int Int UNIQUE Int // when mRNA is used as genome: a1 a2 x1 x2
Genbank_CDS UNIQUE Int UNIQUE Int // start stop of cds as seen in genbank
Bad_quality Text
Directed_sequencing Opposite ?Sequence XREF Opposite
Clone ?Clone
Subclone UNIQUE ?Clone XREF Read @Read
Duplicate_of_read ?Sequence // do not XREF Duplicate_of_read, do not label smallest
Insert_size UNIQUE Int UNIQUE Int // should really be in subclone
Seq_vec ?Vector Int Int Text
Clone_vec ?Vector Int Int Text
aPrioriStrand UNIQUE aForward
aReverse
manualStrand UNIQUE mForward
mReverse
RNA_editing Int ?Transcribed_gene Int
PolyA_after_base UNIQUE Int COORD
manual_polyA UNIQUE Int COORD
Number_of_N UNIQUE Int UNIQUE Int
Number_of_terminal_A UNIQUE Int
Initial_polyA UNIQUE Int COORD UNIQUE Int // start position number of A
Initial_polyT UNIQUE Int COORD UNIQUE Int // start position number of T
Transpliced_to ?Motif UNIQUE Int UNIQUE Text
Transpliced_to2 ?Motif UNIQUE Int UNIQUE Text
Transpliced_to3 ?Motif UNIQUE Int UNIQUE Text
Manual_transpliced_to ?Motif UNIQUE Int UNIQUE Text
Dye UNIQUE Dye_Primer
Dye_Terminator
Primer_Info UNIQUE Universal_primer
Custom UNIQUE Text // text may be the oligo - or should it be an object?
Primer UNIQUE ?Primer XREF Read
Contains Multiplet ?Clone XREF Contig UNIQUE Int // Dog mapping of contigs
// Clips is a tag 2 system, any sequence editor should update all numbers at once on a deletion
Clips Clipping UNIQUE Int COORD UNIQUE Int COORD // present clipping
Old_Clipping UNIQUE Int COORD UNIQUE Int COORD // as imported from Ted
CAF_Clipping UNIQUE Int COORD UNIQUE Int COORD // as imported from CAF
Vector_Clipping UNIQUE Int COORD UNIQUE Int COORD UNIQUE ?Vector Text// vector clipping, do not overpass, Text = OPen, meaning the est has its ORF open above the vector clipping
Contamination Int UNIQUE Int ?Vector // do not use to seed
Hand_Clipping UNIQUE Int COORD UNIQUE Int COORD // hand clip, can be restored
Excellent_upto UNIQUE Int COORD
Good_upto UNIQUE Int COORD
Fair_upto UNIQUE Int COORD
Best200 UNIQUE Int
Discarded By_hand
ABI ABI_Date Text
Run_Start Text
Run_Stop Text
BaseCall ?BaseCall UNIQUE Int
OriginalBaseCall ?BaseCall
SCF_Position ?BasePosition UNIQUE Int // CALF system
Quality ?BaseQuality UNIQUE Int // Int between 0 (bad) and 50 (excellent)
Base_caller Text // Phred, ABI, acembly
Significant_bases Int COORD UNIQUE Text
Otto Text REPEAT
Stolen ?Clone
ABI_Comment Text // comments no s for compatibility,
ABI_Comments Text // comments with s, using Text rather than expansive ?Text
ABI_Analysis Text
ABI_Machine Text
Sample Text
SCF_File UNIQUE Text
CTF_File UNIQUE Text
// for acembly: absolute file name, or relative to $SCF_DATA, or to $ACEDB/SCF
New_Read // Set by newScf, used by add new reads
Fragment_of UNIQUE ?Sequence
Padding UNIQUE Padded
Unpadded
DB_info Database ?Database Text Text Text // ID Accession.Version GI
AC_number Text
NI_number UNIQUE Text
Protein_id Text UNIQUE Int
DB_remark ?Text // EMBL/GenBank
SwissProt_DE ?Text // Swiss prot description
Keyword ?Keyword // // LOCK EMBL/GenBank
DB_annotation ?Database UNIQUE ?LongText
EMBL_dump_info #EMBL_dump_info
Imported DateType Text Text
// The date is the date that this sequence object
// was imported from some external database.
// The first text is the name of the importing
// program. The second text is the query
// identifier that the import program used to
// obtain the data.
Not_curated
Transfered
// This tag is set by the importing program
// to indicate that this record has not been
// examined and/or edited by a biologist. It is
// cleared when the record is manually curated.
Similarity Homol DNA_homol ?Sequence XREF DNA_homol ?Method Float Int COORD UNIQUE Int COORD 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
Sage_hit ?Sage XREF Hits ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Primer_hit ?Primer XREF Hits ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Pfam_homol ?Pfam XREF CDS ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Cel_homol ?Pfam XREF CDS ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Vector_homol ?Pfam XREF CDS ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
No_homol ?Pfam XREF CDS ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Other_homol ?Pfam XREF CDS ?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.
Hit ?Sequence XREF Hit Int COORD UNIQUE Int COORD Int COORD UNIQUE Int COORD
BlastHit ?Sequence XREF BlastHit Int COORD UNIQUE Int COORD Int COORD UNIQUE Int COORD
WordHit ?Sequence XREF WordHit UNIQUE Int
KentHit ?Sequence XREF KentHit Int COORD UNIQUE Int COORD
Method UNIQUE ?Method
Feature ?Method Int Int UNIQUE Float UNIQUE Text
// Float is score, Text is note
// note is shown on select, and same notes are neighbours
// again, each method has a column double-click shows the method.
// Absorb Assembly_tags?
#Coverage Gap Gap_length UNIQUE Int
nX UNIQUE Int
Length From Int
To Int
CDS_length UNIQUE Int Text // Length of corresponding CDS in Read
Delta UNIQUE Int Text // positive if Read CDS longer than Product CDS
Variation Nv UNIQUE Int Text // number of AA differences in Product zone, when delta >= 0
Score UNIQUE Float // use Blosom to measure the AA imporatance
Type UNIQUE Text // P236V V2423P (P236 exists and is AA 236 of Product)
#Splice_confirmation cDNA
EST
Homology
Spliced_cDNA
Begin_Not_Found
End_Not_Found
#Met_stop Predicted_Met UNIQUE mExact
mInexact
mNoInfo
mAbsent
Predicted_Stop UNIQUE sExact
sInexact
sNoInfo
sAbsent
Includes
Included
Identical
Different
Same_5p
Shorter_5p
Longer_5p
Identical_internal_exon UNIQUE Int
Different_internal_exon UNIQUE Int
Same_3p
Shorter_3p
Longer_3p
#Protein_fragment Exon UNIQUE Int UNIQUE Text // 23 56 aa
UTR_3prime
UTR_5prime
Gap
ORF_Gap
#Splicing_confirmation Intron UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // gt_ag, Length, %d , bp
Exon UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // exon number, length,%d, bp
Partial_Exon UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // exon number , length,, bp
First_Exon UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // exon number , length,, bp
Last_Exon UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // exon number , length,, bp
Stolen_Exon UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // exon number , length,, bp
Predicted_Exon UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // exon number , length,, bp
Gap UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // 'unspanned' length,, bp
ORF_Gap UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // 'open'exon number, length,, bp
Alternative_Intron UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // frame, gt_ag, Length,, bp
Stolen_Intron UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // frame, gt_ag, Length,, bp
Predicted_Intron UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // frame, gt_ag, Length,, bp
Alternative_Exon UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // exon number , length,, bp
Alternative_First_Exon UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // exon number , length,, bp
Alternative_Partial_Exon UNIQUE Text UNIQUE Text UNIQUE Int UNIQUE Text // exon number , length,, bp
3prime_UTR
5prime_UTR
UTR_3prime
UTR_5prime
?Protein Title UNIQUE ?Text
Other_name ?Text // for repeats
Description ?Text
Reference Text
Locus ?Locus XREF Protein
Peptide UNIQUE ?Peptide UNIQUE Int UNIQUE Int // Length + checksum
View ?View
Default_view UNIQUE ?View
DB_info Database ?Database Text Text // ID Accession_number
DB_remark ?Text // Swissprot CC entries
Keyword ?Keyword // Swissprot
DB_searched ?Database Text // Version
Origin From_Database ?Database UNIQUE Int // release number
Date DateType Text // Text for comments on operation
Species ?Species
Wormpep Replaces ?Protein XREF Replaced_by
Inactive Replaced_by ?Protein XREF Replaces
// inactive wormpep entries won't be output in standard wormpep dumps
Visible Corresponding_DNA ?Sequence XREF Corresponding_protein
Related_DNA ?Sequence XREF Related_protein
Related_protein ?Protein XREF Related_protein
// tag2 system. For now I have not populated this column. For C. elegans
// wormpep we want to get the information from the ?Corresponding_DNA
// object. Because those objects have long term continuity, while wormpep
// objects are one per protein sequence. At least that is the current
// plan.
Swiss_feature Text Int Int Text // feature name, start, stop, note
Match_table UNIQUE ?MatchTable
Homol DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Product_homol ?Product XREF Blastp ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
Feature ?Method Int Int UNIQUE Float // display according to method
// double-click shows the method
#Match Percent_identity UNIQUE Int
Score ?Method UNIQUE Float
N_gaps UNIQUE Int
Loop UNIQUE Int UNIQUE Int // rel start, stop
Unit_Length UNIQUE Int
// Method
?Method Remark ?Text
// the Display information controls how the column looks.
Display No_display
Colour #Colour
CDS_colour #Colour
Frame_sensitive
Strand_sensitive Show_up_strand #Colour
Score Score_by_offset // has priority over width, for Jean
Score_by_width
Score_by_histogram UNIQUE Float // baseline value
Score_bounds UNIQUE Float UNIQUE Float
// limits for squashing
Percent // '%' in text, + default bounds 25, 100
Overlap_mode UNIQUE Overlap // draw on top - default
Bumpable // bump to avoid overlap
Cluster // one column per homol target
Width UNIQUE Float
Symbol UNIQUE Text // first char only is used
Right_priority UNIQUE Float // the greater the more right
Web_right_priority UNIQUE Float // superseded web_priority on the web
Max_mag UNIQUE Float // don't show if more bases per line
Min_mag UNIQUE Float // don't show if fewer bases per line
Show_text // only put text in right-hand column if set
Blastn // can calculate percent from score if blastn
Blixem Blixem_X
Blixem_N
Blixem_P
Belvu
Gene_assemble Gene_assemble_method ?Method UNIQUE Float
// Float factor to multiply score by
Intron_min UNIQUE Int
Exon_min UNIQUE Int
Intron_cost UNIQUE Float UNIQUE Float UNIQUE Int
// base cost, cost per log bp beyond min
// Int is min for this if not Intron_min
Inter_gene_cost UNIQUE Float
GF_parameters GF_range UNIQUE Int
// +- range for genefinder feature calculation
GF_ATG_cutoff UNIQUE Float
GF_5_cutoff UNIQUE Float
GF_3_cutoff UNIQUE Float
EMBL_dump_info #EMBL_dump_info
EMBL_dump EMBL_feature UNIQUE Text // require this
EMBL_threshold UNIQUE Float // apply to score unless overridden
EMBL_qualifier Text UNIQUE Text
GFF GFF_source UNIQUE Text
GFF_feature UNIQUE Text
// if 1 Text, it is the entire qualifier including '/'
// if 2 Texts, 1st is an sprintf format and 2nd is
// an argument. If this is "score", "note", "y1", "y2" or "target"
// then use the corresponding field of the Feature or Homol line.
// multiple formats will be concatenated until one starts with '/'.
#EMBL_dump_info EMBL_dump_method UNIQUE ?Method
ID_template UNIQUE Text
ID_division UNIQUE Text
DE_format UNIQUE Text
OS_line UNIQUE Text
OC_line Text
RL_submission Text
// EMBL_reference ?Paper
CC_line Text
source_organism UNIQUE Text
#Homol_info Segs #Match_seg
Bury // do not show on the standard display
Score UNIQUE Float // remember the score and the expect are both mysterious but different
Expect UNIQUE Float // remember the score and the expect are both mysterious but different
Confidence Text // exemple in pfam a !! means we believe it !
#Match_seg UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int #Match_seg // Start, End of Aligment; Start, End of Subject
?Locus Map ?Map XREF Locus #Map_position
Gene ?Gene XREF Locus
Gene_class ?Gene_class XREF Loci
OMIM ?OMIM XREF Locus
LocusLink ?LocusLink XREF Locus
GeneId ?GeneId XREF Locus
Gene_information ?Text
Sequence ?Sequence XREF Locus
Sequence_62 ?Sequence XREF Locus_62
Sequence_81 ?Sequence XREF Locus_81
Sequence_84 ?Sequence XREF Locus_84
Sequence_89 ?Sequence XREF Locus_89
Sequence_102 ?Sequence XREF Locus_102
Sequence_130 ?Sequence XREF Locus_130
Sequence_GB ?Sequence XREF Locus_GB
Sequence_GB_dubious ?Sequence XREF Locus_GB_dubious
Sequence_cgc ?Sequence XREF Locus_cgc
SequenceTmp ?Sequence
Protein ?Protein XREF Locus
Transcribed_gene ?Transcribed_gene XREF Locus
Ref_id ?Sequence XREF Ref_id
Priority UNIQUE Int // for hierarchical display
Quality UNIQUE Int // for hierarchical display
Expr_pattern ?Expr_pattern XREF Locus
Reference ?Paper XREF Locus
?OMIM Gene ?Gene XREF OMIM
Locus ?Locus XREF OMIM
GeneId ?GeneId XREF OMIM
Sequence ?Sequence XREF OMIM
Description ?Locus_description XREF OMIM
//
// Views and Columns
//
?View Type UNIQUE Pepmap
Fmap Fmap_Header
Fmap_Locator
Fmap_Summary_bar
Fmap_scale Fmap_scale_coords
Fmap_DNA
Fmap_3_translation
Fmap_Clones
Fmap_Gene Fmap_Gene_Name
Fmap_Cloud_gene
Fmap_Gene_Up
Fmap_Gene_Down
Fmap_Pg Fmap_Pg_Up
Fmap_Pg_Down
Fmap_Tg Fmap_Tg_Up
Fmap_Tg__Down
Fmap_Tg_Just_Gold
Fmap_mRNA Fmap_mRNA_Up
Fmap_mRNA_Down
Fmap_mProduct Fmap_Down_Gene_Translation
Fmap_Spliced_cDNA Fmap_CDS_Tiling
Fmap_cDNA_Decorate
Fmap_Spliced_cDNA_Up
Fmap_Spliced_cDNA_Down
Fmap_RNAi Fmap_RNAi_Up
Fmap_RNAi_Down
Fmap_Oligo
Fmap_Allele
Fmap_Text_Features
Gmap
Grid Grid_map Int #View_tags // Int is priority
Grid_edit_default UNIQUE Text UNIQUE Text
Grid_edit_menu Text UNIQUE Text
Pmap Pmap_probes Pmap_probe_query Text
Pmap_probe_height Int
Pmap_YAC Pmap_YAC_query Text
Pmap_YAC_bold_query Text
Pmap_YAC_height Int
Pmap_cmid Pmap_cmid_query Text
Pmap_cmid_bold_query Text
Pmap_cmid_height Int
Pmap_locus Pmap_locus_query Text
Pmap_locus_height Int
Pmap_remark Pmap_remark_query Text
Pmap_remark_height Int
// 1st text tag name, 2nd text optional "Negative"
Display Submenus // BOOL for submenus on item boxes
Cambridge // Cambridge v. Montpellier behaviour
No_buttons // suppress header buttons for WWW
Hide_header // No headers and footers
Name UNIQUE Text
Columns Text UNIQUE Int #Column // Int is BOOL for Hidden/Visible
?Column UNIQUE Scale Scale_unit UNIQUE Float // minimum increment
Cursor Cursor_on
Cursor_unit UNIQUE Float
Scroller
Locator Magnification UNIQUE Float
Projection_lines_on
Marker_points
Marker_intervals
Contigs
Reversed_physical
Physical_genes
Two_point
Multi_point
Likelihood
Points Point_query UNIQUE Text
Point_yellow Text // To be made redundant.
Point_colour Text #Colour // to replace above
Point_width UNIQUE Int // max width if not at RHS
Point_error_scale UNIQUE Float
Point_segregate_ordered
Point_show_marginal
Point_pne #Colour // positive, no error
Point_pe #Colour // positive, error
Point_nne #Colour // negative, no error
Point_ne #Colour // negative, error
Point_symbol Text // can now have more than one of these
Interval_JTM #Interval_col_conf
Interval_RD #Interval_col_conf
Interval_SRK #Interval_col_conf
Derived_tags DT_query UNIQUE Text
DT_width UNIQUE Int
DT_no_duplicates
DT_neighbours
DT_parents
DT_follow_parent
DT_symbol_query
DT_tag Text Int
DT_hide
Spacer Spacer_colour #Colour
Spacer_width Float
RH_data RH_query UNIQUE Text
RH_spacing UNIQUE Float
RH_show_all
RH_positive #Colour
RH_negative #Colour
RH_contradictory #Colour
pepSequence PS_Highlight_residue // il all needed for colomn display of peptides
PS_Residues_per_wrap Int
PS_Colours Text #Colour
Hydrophobicity HP_Show_Zero_bar
HP_Fixed_Scaling
HP_Calculation_window Int
HP_Display_width Int
Homol HOM_bump
pepFeature FEA_bump
FEA_Query Text
Homol_Name HOM_NAME_bump
HOM_NAME_width Int
pepActiveZone
Submaps Loci_Query UNIQUE Text
Interval_Query UNIQUE Text
Show UNIQUE Int
Tolerance UNIQUE Int
Pos_By_Loci
?View_tags Colour #Colour
Surround_colour #Colour // colour when surround
Tag Text // could be many tags
?Interval_col_conf Query UNIQUE Text // Query
Names_on
No_neighbours
Show_multiple
Width UNIQUE Int
Symbol UNIQUE Text
Colours Text #Colour // Only for chrom_bands.
Pne #Colour // positive, no error
Pe #Colour // positive, error
Nne #Colour // negative, no error
Ne #Colour // negative, error
?Url Url UNIQUE Text // Simple, text of Url
Template UNIQUE ?Url // use this object as a generic template
Reference_tag UNIQUE Text // look for this tag in the reffing object for url
Remove_prefix UNIQUE Text // prefix to remove to make url
Remove_postfix UNIQUE Text // postfix to remove
Prepend UNIQUE Text // then add these.
Append UNIQUE Text
Use_name
Refers_to cDNA_clone ?cDNA_clone XREF Image
?Library Title UNIQUE ?Text
Symbol UNIQUE Text // One letter symbol, to be displayed under the Read arrow
Vector_length UNIQUE Int // (bp) length clone - length insert
Expression_profile Int REPEAT
Stage UNIQUE Mixed
Embryo
L1
L2
L3
Dauer
L4
Ovary
?Database Title UNIQUE ?Text
?Species Title UNIQUE ?Text
?Sage Origin Text
Motif UNIQUE Text
Length UNIQUE Int
Strand UNIQUE Forward
Reverse
RNAi ?RNAi XREF Primer
Hits ?Sequence XREF Sage_hit Int UNIQUE Int
?Fiche mRNA ?mRNA XREF Fiche
FichedDate UNIQUE Text
SubmittedDate UNIQUE Text
Title UNIQUE Text
FlatFile UNIQUE Text
Blast UNIQUE Text
Hints UNIQUE Text
Status UNIQUE Text
#SMap_info Method ?Method // methods used in child (optional)
Frame UNIQUE Int
Content Homol_only // useful for -nohomol gff option
Feature_only // useful for -nofeature gff option
Mapping Align Int UNIQUE Int UNIQUE Int
// not needed if full alignment is ungapped
// one row per ungapped alignment section
// first int is position in parent, second in child
// third int is length - only necessary when gaps in both sequences align
Mismatch Int
// Int give position(s) in parent of mismatches (technically in which they will
// not create an error if they occur
// if just the tag is set without values, then accept mismatches anywhere
Display Max_mag UNIQUE Float // don't show if more bases per line
Min_mag UNIQUE Float // don't show if fewer bases per line
// locus->Molecular_information->Product->Text should go in the title bar of the TGin some way
// the name of the phenotype is either unc-32 or 3B231 or zk637.4 if no info if associated with sjj-pair
?Chrom_band Gene ?Gene XREF Cytogenetic
?Unigene Gene ?Gene XREF Unigene
GeneId ?GeneId XREF Unigene
?LocusLink Gene ?Gene XREF LocusLink // MUST be top line to simplify transfer of data
Title UNIQUE Text // human extracted from locus id
Summary UNIQUE Text // human extracted from locus id
Proteome_summary UNIQUE Text // human extracted from locus id
GeneId ?GeneId XREF LocusLink
Locus ?Locus XREF LocusLink
Genetic Locus_Phenotype ?Text // Locus->phenotype but only [C.elegansII] if existing
Locus_description ?Text
Gene_RIF Text // goes to Gene->Locus_Phenotype
OMIM ?OMIM
Go_b_ace ?GO_b Text Text
Molecular Descriptor ?Text // wormbase:locus->geneclass->phenotype //human: refseq +proteomesummary
Properties Text
Go_m_ace ?GO_m Text Text
Function EC_number ?Text
Gene_ontology Text Text Text Text
Expression Go_c_ace ?GO_c Text Text
Sequence ?Sequence XREF LocusLink
Reference Text //?Paper XREF Gene // locus->reference
Position Map Text
Cytogenetic Text Text
?Allele Gene ?Gene XREF Allele
Strain ?Strain XREF Allele
Sequence ?Sequence XREF Allele
Remark ?Text
?Knock_out Gene ?Gene XREF Knock_out
Locus ?Locus
Cosmid UNIQUE ?Sequence UNIQUE Int UNIQUE Int // position according to ko consortium
Predicted_gene ?Sequence
Strain ?Strain
Description UNIQUE Text
?Locus_description Symbol Text // 3 letter symbol
Gene ?Gene XREF Locus_description
Gene_descriptor ?Gene XREF Descriptor
Genbank_product_descriptor ?Gene XREF Genbank_product_descriptor
Gene_class ?Gene_class XREF Description
OMIM ?OMIM XREF Description
?GenBank Gene_id ?Gene XREF GenBank_id
GeneId ?GeneId XREF NM_id
Gene_NM ?Gene XREF NM_id
NewName ?NewName XREF NM_id
Predicted_gene_NM ?Sequence XREF NM_id
Predicted_gene_NMexported ?Sequence XREF NM_idexported
Predicted_gene_NMaligned ?Sequence XREF NM_idaligned
mRNA ?mRNA XREF NM_id
mRNAexported ?mRNA XREF NM_idexported
mRNAaligned ?mRNA XREF NM_idaligned
GB_clone ?cDNA_clone XREF NM_id
Sequence ?Sequence XREF GenBank_id
Variant Text
NPtext Text // corresponding NP
Supporting_GB ?Sequence
Info Submission_date DateType
Title UNIQUE ?Text // hand edited at submission time
Product Product_Title UNIQUE ?Text // hand edited at submission time
mRNA_signature UNIQUE Int // establishes the signature of this submission
Fiche UNIQUE ?LongText // fiche as hand edited at submission time
Author ?Author REPEAT
Status UNIQUE RefSeq UNIQUE Predicted_refseq
Provisional_refseq
Validated_refseq
Inferred_ref_seq
LocusLink_refseq
Reviewed_refseq
Secondary_refseq
Supported UNIQUE mRNA_evidence
EST_evidence
mRNA_EST_evidence
Ab_initio with_EST_support
?Gene_id Gene ?Gene XREF Gene_id
?Gene_title Gene ?Gene XREF Title
?Gene Title UNIQUE ?Gene_title XREF Gene // hand edited
Title2 UNIQUE ?Text // hand edited tmp for debug
Summary ?Text // hand edited, rm UNIQUE jan 23, 2004
Proteome_summary UNIQUE ?Text // hand edited
Transcribed_gene ?Transcribed_gene XREF Gene @T
Product ?Product XREF GeneBox @ID // pfam_go a mettre sous ID
NewName UNIQUE ?NewName XREF Gene UNIQUE Text // NCBI Text = locuslink|pfam|pseudo|doublelocuslink newName
NewNameOld ?NewName XREF GeneOld UNIQUE Text // NCBI Text = locuslink|pfam|pseudo|doublelocuslink newName
Tmp Text // for temporary use such as while exporting to locuslink
WB_id ?Text // ->mocecular, avant old_product, herited from wormbase-51, then hand edited
WbId ?WbId XREF Gene
GenBank_id ?GenBank XREF Gene_id @Info // NCBI // GenBank submission, to be revamped
NM_id ?GenBank XREF Gene_NM Text // NCBI
Gene_id UNIQUE ?Gene_id XREF Gene // NCBI
GeneId ?GeneId XREF Gene // NCBI
LocusLink ?LocusLink XREF Gene // NCBI locuslink
GeneCard_id UNIQUE Text // GeneCard
Unigene ?Unigene XREF Gene
Clone_group ?Clone_group XREF Gene UNIQUE Int // NCBI //To be fixed in code, number of clones of that group
Error_in_genome
Bad_quality
Use_AM // use_am ->NCBI==ID, Error, to keep, detail de la soumission de l'error
Notes ?Text
Specialist ?Person XREF Specialist Text
Type Main
Putative
Cloud
Molecular Descriptor ?Locus_description XREF Gene_descriptor // wormbase:locus->geneclass->phenotype
Genbank_product_descriptor ?Locus_description XREF Genbank_product_descriptor
EC_number ?Text // a completer, now just let-70
Properties ?Text
Cloud_gene
Pseudogene // COUNT {>transcribed_gene;!gt_ag && !gc_ag;>mrna;COUNT cdna_clone>3 && tiling_error>10}>0
Non_protein_coding // non protein coding gene
COG ?COG XREF Gene @Info
GO_m_pfam ?GO_m XREF Gene Text // Text is the method IEAA etc
GO_m_ace ?GO_m XREF Genea Text Text // Text is the method IEAA etc
Gene_ontology Pfam_go Text Text Text // DELETE, in product, oxydase IP2001 GO:1234
Pfam ?Pfam XREF Gene
Old_product ?Text // 112 cases DELETE ??
Predicted Genefinder ?Sequence XREF Model_of_gene
Previous_genefinder ?Sequence XREF Model_of_previous_gene // tmp when moving
Homolog In_human Text // Text, because this is an external reference
In_Arabidopsis Text // Text, because this is an external reference
In_drosophila Text // Text, because this is an external reference
In_worm Text // Text, because this is an external reference
Genetic Locus ?Locus XREF Gene // all ?Locus of wormbase with Phenotype OR Allele
Locus_description ?Locus_description XREF Gene // locus->description, some locus->geneclass->phenotype
Locus_Phenotype ?Text // copy here LocusLink->Loc_pheno or in worm [C.elegansII] if existing
Gene_RIF ?Text // goes to Gene->Locus_Phenotype
GO_b_pfam ?GO_b XREF Gene Text // Text is the method IEAA etc
GO_b_ace ?GO_b XREF Genea Text Text // Text is the method IEAA etc
GO_locuslink Text Text Text// to import from locusLink in human case
OMIM ?OMIM XREF Gene @Description // human only
// Locus_remark ?Text // Locus->remark to verify
Allele ?Allele XREF Gene
Knock_out ?Knock_out XREF Gene
Knock_out_allele Text Text Text Text
Strain ?Strain XREF Gene @Remark // A reimporter en diff versus WS51
Rescued_by ?Text // 11 DELETE ?
Not_rescued_by Text // if !SMAP, 63 cases ???
Rescuing_cosmid ?Sequence XREF Rescued_gene Text REPEAT // if !SMAP, 1158 cases
RNAi ?RNAi XREF Gene @P // move away the OST from here
Transgenic ?Text // 86 cases
Expression Expression_title UNIQUE ?Text
Expression_profile @">Transcribed_gene ; Expression_profile"
Has_expression_profile UNIQUE Int REPEAT // a copy for the exported database
Pattern ?Text // hand curated resume of all expr_patterns
GO_c_psort ?GO_c XREF Geneps Text // Text is the method IEAA etc
GO_c_pfam ?GO_c XREF Gene Text // Text is the method IEAA etc
GO_c_ace ?GO_c XREF Genea Text Text// Text is the method IEAA etc
Expr_pattern ?Expr_pattern XREF Gene
Has_OST // == has amplified non ambiguous OST
OST ?OST XREF Gene
Has_cDNA_clone ?cDNA_clone XREF In_gene
Nb_cDNA_clone UNIQUE Int // includes shed clones
Regulation Promoter ?Text
Complex_locus
Operon Operon_title ?Text
Operon_with ?Gene XREF Operon_with
SL2_Blumenthal
SL2_Kohara
Other_tandem ?Text
Antisense ?Text
Antisens_to ?Gene XREF Antisens_to UNIQUE Int
Shedded_from ?Gene XREF Sheds
Sheds ?Gene XREF Shedded_from
Highly_mutable ?Text
RNA_editing ?Text
Translational_frameshift ?Text
Selenocysteine ?Text
Interacts with_gene ?Gene XREF with_gene ?Text // 150 cases
with_geneId ?GeneId XREF with_geneBox ?Text // 150 cases
with_protein ?Gene XREF with_protein ?Text // 50 cases
Reference ?Paper XREF Gene // locus->reference
WB_reference ?Paper XREF Gene_wb
GenBank_reference ?Paper XREF Gene_gb
DbXref Text UNIQUE Text
Method ?Method // a vider
Structure nExons UNIQUE Int
nIntrons UNIQUE Int
First_exon nPossiblePromotors UNIQUE Int
nAltFirstExons UNIQUE Int
nNonOverlappingAltFirstExons UNIQUE Int
nAltFirstCodingExons UNIQUE Int
Central_exon n5pSkippedCentralExons UNIQUE Int
nSkippedCentralExons UNIQUE Int
nsce nAnyCassettedExons UNIQUE Int
nCassettedExons UNIQUE Int
nCassettingIntrons UNIQUE Int
nMultiCassettedExons UNIQUE Int
nMultiCassettingIntrons UNIQUE Int
nMutExclusives UNIQUE Int
nCitroenIntrons UNIQUE Int
nOverlappingCentralExons UNIQUE Int
noce nInternalDonorSite UNIQUE Int
nInternalDonorSite369_18 UNIQUE Int REPEAT
nInternalAcceptorSite UNIQUE Int
nInternalAcceptorSite369_18 UNIQUE Int REPEAT
nRetainedIntrons UNIQUE Int
nOrfBreakingRetainedIntrons UNIQUE Int // break the ORF
Last_exon n3pSkippedCentralExons UNIQUE Int
nAltLastExons UNIQUE Int
nNonOverlappingAltLastExons UNIQUE Int
Position Balise // balise genes are shown to allow rapid motion on the maps
Map ?Map XREF Gene #Map_position
Map_priority UNIQUE Int
InterpolatedMap UNIQUE ?Map UNIQUE Float
IntMap UNIQUE ?Map XREF Gene_i UNIQUE Int UNIQUE Int
Cytogenetic ?Chrom_band XREF Gene Text // human
SMAP S_Parent Genomic_sequence UNIQUE ?Sequence XREF Genes
Primers ?Primer XREF Gene // Tracking, used when changing genome release
Ambiguous // Tracking, when positioned by primers used when changing genome release
Same_position // Tracking, used when changing genome release
Previous_cosmid UNIQUE ?Sequence UNIQUE Int UNIQUE Int // Tracking, used when changing genome release
?RNAi Gene ?Gene XREF RNAi
mRNA ?mRNA XREF RNAi #Met_stop
Experiment Reference Text // Paper as in medline
Author Text // ?Author
Date UNIQUE DateType
Injection
Feeding
Probe cDNA_clone ?cDNA_clone XREF RNAi
PCR_product Primer ?Sage XREF RNAi // ?PCR_product->Oligo
Primers ?Primer XREF RNAi // ?PCR_product->Oligo
Ambiguous
P Phenotype ?Text // ?RNAi ->Phenotype && ?RNAi->Phenotype->description %% ?Rnai ->Phenotype##Phenotype_info
Movie ?URL
Hyman DIC_Phenotype_Class ?Text
DIC_Phenotype_Definition ?Text
DIC_Phenotype_Description ?Text
DIC_Movie_available
Progeny_Phenotype_Class ?Text
Progeny_Phenotype_Definition ?Text
Progeny_Phenotype_Description ?Text
No_obvious_phenotype Text
Position IntMap UNIQUE ?Map Int UNIQUE Int
SMAP S_Parent Genomic_sequence ?Sequence XREF RNAi
Remark ?Text
Predicted_gene ?Sequence
?OST Gene ?Gene XREF OST
T Target UNIQUE Text // target accoding to vidal
Target_found // AceView analysis
R Amplified // experimental result
Not_amplified // experimental result
C Complete // exactly agrees with Tg
Partial // matches but too short relaive to Tg
Bad // not expected to amplify
Primers ?Primer XREF OST
P Amplified_not_ambiguous // result + alignment summary
Ambiguous // alignment summary
Position IntMap UNIQUE ?Map Int UNIQUE Int
SMAP S_Parent Genomic_sequence ?Sequence XREF OST
?Strain Genotype Text
Contains Gene ?Gene XREF Strain
Allele ?Allele XREF Strain
Expr_pattern ?Expr_pattern XREF Strain
Remark ?Text
?Expr_pattern Gene ?Gene XREF Expr_pattern
Locus ?Locus XREF Expr_pattern
Sequence ?Sequence XREF Expr_pattern
Protein_description Text // dl1 010307 from geneace
Expressed_in Cell ?Text
Cell_group ?Text
Life_stage Text
Subcellular_localization ?Text
Type Reporter_gene Text
In_situ Text
Antibody Text
Transgene Text
Western
Northern
RT_PCR Text
Pattern ?Text
Remark Text
Experiment Laboratory ?Laboratory
Author Text
Date UNIQUE DateType
Strain UNIQUE ?Strain XREF Expr_pattern
Picture
Reference ?Paper XREF Expr_pattern
Not_done
?Medline Paper ?Paper XREF Medline_acc
Paper_PMID ?Paper XREF PMID
Paper_CGCID ?Paper XREF CGCID
Paper_LeonID ?Paper XREF LeonID
?Journal Full_name ?Text
Paper ?Paper
?GO Nickname UNIQUE Text
Type Molecular_function ?GO_m XREF GO
Biological_process ?GO_b XREF GO
Cellular_component ?GO_c XREF GO
Synonym ?GO_s XREF GO
Pfam ?Pfam XREF GO
?GO_b GO ?GO XREF Biological_process
Gene ?Gene XREF GO_b_pfam
Genea ?Gene XREF GO_b_ace
?GO_c GO ?GO XREF Cellular_component
Geneps ?Gene XREF GO_c_psort
Gene ?Gene XREF GO_c_pfam
Genea ?Gene XREF GO_c_ace
?GO_m GO ?GO XREF Molecular_function
Gene ?Gene XREF GO_m_pfam
Genea ?Gene XREF GO_m_ace
?GO_s GO ?GO XREF Synonym
?COG Info Title ?Text
Information_storage_and_processing Translation_ribosomal_structure_and_biogenesis J ?Text
Transcription K ?Text
DNA_replication_recombination_and_repair L ?Text
Cellular_processes Cell_division_and_chromosome_partitioning D ?Text
Posttranslational_modification_protein_turnover_chaperones O ?Text
Cell_envelope_biogenesis_outer_membrane M ?Text
Cell_motility_and_secretion N ?Text
Inorganic_ion_transport_and_metabolism P ?Text
Signal_transduction_mechanisms T ?Text
Metabolism Energy_production_and_conversion C ?Text
Carbohydrate_transport_and_metabolism G ?Text
Amino_acid_transport_and_metabolism E ?Text
Nucleotide_transport_and_metabolism F ?Text
Coenzyme_metabolism H ?Text
Lipid_metabolism I ?Text
Secondary_metabolites_biosynthesis_transport_and_catabolism Q ?Text
Poorly_characterized General_function_prediction_only R ?Text
Function_unknown S ?Text
Gene ?Gene XREF COG
Sequence ?Sequence XREF COG
?Genetic_code Other_name ?Text
NCBI_id UNIQUE Int
Translation UNIQUE Text
Start UNIQUE Text
Base1 UNIQUE Text
Base2 UNIQUE Text
Base3 UNIQUE Text
?Paper Title ?Text
Author Text // ?Author // XREF Paper
Journal UNIQUE ?Journal
Year UNIQUE Int
Volume Text Text
Page UNIQUE Text UNIQUE Text
Medline_acc UNIQUE ?Medline XREF Paper
PMID UNIQUE Text // ?Medline XREF Paper_PMID
CGCID UNIQUE ?Medline XREF Paper_CGCID
LeonID UNIQUE ?Medline XREF Paper_LeonID
Sequence ?Sequence // XREF Reference
Gene ?Gene XREF Reference
Gene_class ?Gene_class XREF Reference
Locus ?Locus XREF Reference
Gene_symbol Text // ?Text
GeneId ?GeneId XREF Reference
EC_symbol Text
Pfam ?Pfam XREF Paper
Erratum_in Text
Retraction_in Text
Citation Text
Gene_wb ?Gene XREF WB_reference
Gene_gb ?Gene XREF GenBank_reference
Gene_mark ?Gene
Expr_pattern ?Expr_pattern XREF Reference
Not_done
Abstract ?LongText
//-----------------------------------------------------------------------------
// Paper is a description of a paper. Author is a reference to all the
// authors of the paper, but see author below.
?Author Full_name ?Text
Person ?Person XREF Author
Paper ?Paper // do NOT XREF, this would alter the author order
//-----------------------------------------------------------------------------
// Author is really just a name that is signed to a paper. It has a
// reference back to all the papers it was signed to, but we don't really
// know who it is. For example, Medline might list both John Smith and
// James Smith as "Smith J". We would then have an author named "Smith J"
// with the Who tag referencing both of them. A human reading the displayed
// data would be able to deal with the ambiguity even if a computer cannot.
//-----------------------------------------------------------------------------
?Laboratory Address Mail Text
Phone Text
E_mail Text
Fax Text
CGC Representative UNIQUE ?Person XREF Laboratory
Strain_designation Text
Allele_designation Text
Gene_classes ?Gene_class XREF Designating_laboratory
//-----------------------------------------------------------------------------
// Laboratory describes an institution. The Address tag refers to the
// organization, not a person at that organization. In particular, E_mail
// should be a general purpose address like "info" instead of the email
// address of the director.
// Contact is a person who expects to handle laboratory business.
// Who is a list of persons affiliated with that laboratory.
//
//-----------------------------------------------------------------------------
?Person Full_name ?Text UNIQUE Text UNIQUE Text UNIQUE Text // for gb submission: full, surname, first, initial
Author ?Author XREF Person @Paper
Address Mail Text
E_mail Text
Phone Text
Fax Text
Laboratory UNIQUE ?Laboratory XREF Representative
Gene_class ?Gene_class XREF Specialist
Specialist ?Gene XREF Specialist
Notes ?Text
//-----------------------------------------------------------------------------
// Person describes a real person.
// Names is a list of names that we know this person by.
// Author is a list of names that they have used to publish papers.
//
// For example, "Robert Smith" might have
//
// Names
// "Robert Smith"
// "Bob Smith"
// "Robert W Smith"
// Author
// "Smith R"
// "Smith RW"
//
// The address information is intended for a human to read, not for a
// computer to process. You can list multiple phone numbers with notes:
// Phone
// "+1 301 123 4567 (office)"
// "+1 240 765 4321 (cell)"
//
//-----------------------------------------------------------------------------
// Tags removed from Author:
//
// Details Surname UNIQUE Text
// Firstname UNIQUE Text
// Initial UNIQUE Text
// Laboratory UNIQUE ?Laboratory XREF Representative
// Address Mail Text
// E_mail Text
// Phone Text
// Fax Text
// Specialist ?Gene XREF Specialist
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
?Tissue Title Text
?Gene_class Main_name ?Gene_class XREF Other_name
Other_name ?Gene_class XREF Main_name
ID Description UNIQUE ?Locus_description XREF Gene_class
Specialist ?Person XREF Gene_class
Remark Text
Designating_laboratory UNIQUE ?Laboratory XREF Gene_classes
Type UNIQUE Genetic
Molecular
Loci ?Locus XREF Gene_class
Reference ?Paper XREF Gene_class
// comparison to wormbase WS85
// we throw away Allele ?Allele XREF Gene_class
// CGC_approved // added by krb 24/01/02
// CGC_unresolved Text // added by krb 28/01/02
// Phenotype we copy under description
// if phenotype != "", type = genetic
